@article {pmid31523509, year = {2019}, author = {Yeoman, CJ and Brutscher, LM and Esen, ÖC and Ibaoglu, F and Fowler, C and Eren, AM and Wanner, K and Weaver, DK}, title = {Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus).}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7548}, doi = {10.7717/peerj.7548}, pmid = {31523509}, issn = {2167-8359}, abstract = {Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.}, }
@article {pmid31522775, year = {2019}, author = {Requena, T and Velasco, M}, title = {The human microbiome in sickness and in health.}, journal = {Revista clinica espanola}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.rce.2019.07.004}, pmid = {31522775}, issn = {1578-1860}, abstract = {The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life. Human microbial colonization occurs in the skin, genitourinary system and, mainly, in the oral cavity and intestinal tract. In these locations, the human microbiota establishes a symbiotic relationship with the host and helps maintain the physiological homeostasis. Lifestyle, age, diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota. Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases. In addition to phylogenetic diversity studies, further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health.}, }
@article {pmid30787435, year = {2019}, author = {Whiteley, AT and Eaglesham, JB and de Oliveira Mann, CC and Morehouse, BR and Lowey, B and Nieminen, EA and Danilchanka, O and King, DS and Lee, ASY and Mekalanos, JJ and Kranzusch, PJ}, title = {Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.}, journal = {Nature}, volume = {567}, number = {7747}, pages = {194-199}, doi = {10.1038/s41586-019-0953-5}, pmid = {30787435}, issn = {1476-4687}, support = {S10 RR029205/RR/NCRR NIH HHS/United States ; R01 AI026289/AI/NIAID NIH HHS/United States ; R01 AI018045/AI/NIAID NIH HHS/United States ; S10 OD021527/OD/NIH HHS/United States ; S10 OD021832/OD/NIH HHS/United States ; P30 GM124165/GM/NIGMS NIH HHS/United States ; T32 CA207021/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Crystallography, X-Ray ; Dinucleoside Phosphates/biosynthesis/metabolism ; HEK293 Cells ; Humans ; Mice ; Nucleotides/*biosynthesis/chemistry/*metabolism ; Nucleotidyltransferases/*chemistry/genetics/*metabolism ; Operon/genetics ; Symbiosis ; }, abstract = {Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. A series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts.}, }
@article {pmid29963630, year = {2018}, author = {Kitada, Y and Muramatsu, K and Toju, H and Kibe, R and Benno, Y and Kurihara, S and Matsumoto, M}, title = {Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies.}, journal = {Science advances}, volume = {4}, number = {6}, pages = {eaat0062}, pmid = {29963630}, issn = {2375-2548}, mesh = {Agmatine/metabolism ; Animals ; Bacteria/metabolism ; Biosynthetic Pathways ; Escherichia coli/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; Polyamines/*metabolism ; Putrescine/biosynthesis ; Symbiosis ; Transcriptome ; }, abstract = {Metabolites of the intestinal microbiota are thought to be generated through metabolic pathways spanning multiple taxa of intestinal bacteria. We have previously shown that the level of putrescine, a polyamine found abundantly in the human intestinal lumen, is increased in the colonic lumen following administration of arginine and the probiotic Bifidobacterium sp.; however, the underlying mechanism remained poorly understood. We report a novel pathway for putrescine production from arginine through agmatine involving the collaboration of two bacterial groups, and triggered by environmental acidification (drop in pH to below 6.5 from neutral). This pathway comprises the acid tolerance system of Escherichia coli, representing bacteria that have an arginine-dependent acid resistance system; the energy production system of Enterococcus faecalis, representing bacteria that have an agmatine deiminase system; and the acid production system of the acid-producing bacteria, represented by Bifidobacterium spp. This pathway is unique in that it represents a relationship between the independent survival strategies of multiple bacteria.}, }
@article {pmid29476118, year = {2018}, author = {Stuhr, M and Blank-Landeshammer, B and Reymond, CE and Kollipara, L and Sickmann, A and Kucera, M and Westphal, H}, title = {Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3524}, pmid = {29476118}, issn = {2045-2322}, mesh = {Aquatic Organisms ; Calcification, Physiologic/genetics ; Coral Reefs ; Diatoms/*genetics/growth & development/metabolism ; Ecosystem ; Foraminifera/*genetics/growth & development/metabolism ; Gene Expression Regulation ; Gene Ontology ; Hot Temperature ; Molecular Sequence Annotation ; Oceans and Seas ; Photosynthesis/genetics ; Proteome/classification/*genetics/metabolism ; Proteomics/*methods ; *Stress, Physiological ; Symbiosis ; }, abstract = {The proliferation of key marine ecological engineers and carbonate producers often relies on their association with photosymbiotic algae. Evaluating stress responses of these organisms is important to predict their fate under future climate projections. Physiological approaches are limited in their ability to resolve the involved molecular mechanisms and attribute stress effects to the host or symbiont, while probing and partitioning of proteins cannot be applied in organisms where the host and symbiont are small and cannot be physically separated. Here we apply a label-free quantitative proteomics approach to detect changes of proteome composition in the diatom-bearing benthic foraminifera Amphistegina gibbosa experimentally exposed to three thermal-stress scenarios. We developed a workflow for protein extraction from less than ten specimens and simultaneously analysed host and symbiont proteomes. Despite little genomic data for the host, 1,618 proteins could be partially assembled and assigned. The proteomes revealed identical pattern of stress response among stress scenarios as that indicated by physiological measurements, but allowed identification of compartment-specific stress reactions. In the symbiont, stress-response and proteolysis-related proteins were up regulated while photosynthesis-related proteins declined. In contrast, host homeostasis was maintained through chaperone up-regulation associated with elevated proteosynthesis and proteolysis, and the host metabolism shifted to heterotrophy.}, }
@article {pmid31521732, year = {2019}, author = {Horiuchi, A and Kokubu, E and Warita, T and Ishihara, K}, title = {Synergistic biofilm formation by Parvimonas micra and Fusobacterium nucleatum.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102100}, doi = {10.1016/j.anaerobe.2019.102100}, pmid = {31521732}, issn = {1095-8274}, abstract = {Parvimonas micra is frequently isolated from lesions of apical periodontitis and is a major disease-related pathogen. One of the main causes of apical periodontitis is extraradicular biofilm. In this study, we investigated polymicrobial biofilm formation by P. micra and species associated with apical periodontitis. The coaggregation activity of P. micra with partner strains was investigated by visual assays. Synergistic biofilm formation was evaluated by cocultures of P. micra and partner strains. Growth of planktonic cells was measured by evaluating the absorbance at OD660, and biofilm formation was examined by staining with crystal violet. The effects of soluble components on synergistic biofilm formation and planktonic cell growth were examined after coculture of P. micra and other strains separated with a 0.4-μm pore-size porous membrane. P. micra coaggregated with Fusobacterium nucleatum, Porphyromonas gingivalis, or Capnoctyophaga ochracea. P. micra showed no coaggregation with Staphylococcus aureus, S. epidermidis, or Prevotella intermedia. In mixed cultures, biofilm formation by P. micra and F. nucleatum was greater than that by P. micra and P. gingivalis or C. ochracea. In separated cocultures, planktonic cell growth of P. micra was enhanced by each of the three species. Biofilm formation by P. micra was enhanced by F. nucleatum and C. ochracea; however, no significant enhancement was observed with P. gingivalis. These data indicated that P. micra and F. nucleatum had synergistic effects in biofilm formation and that these effects may be important for colonization by these two species in apical periodontitis lesions.}, }
@article {pmid31521050, year = {2019}, author = {Farci, D and Sanna, C and Medda, R and Pintus, F and Kalaji, HM and Kirkpatrick, J and Piano, D}, title = {Shedding light on the presymbiontic phase of C. arietinum.}, journal = {Plant physiology and biochemistry : PPB}, volume = {143}, number = {}, pages = {224-231}, doi = {10.1016/j.plaphy.2019.09.014}, pmid = {31521050}, issn = {1873-2690}, abstract = {A complex network of symbiotic events between plants and bacteria allows the biosphere to exploit the atmospheric reservoir of molecular nitrogen. In seeds, a series of presymbiotic steps are already identified during imbibition, while interactions between the host and its symbiont begin in the early stages of germination. In the present study, a detailed analysis of the substances' complex delivered by Cicer arietinum seeds during imbibition showed a relevant presence of proteins and amino acids, which, except for cysteine, occurred with the whole proteinogenic pool. The imbibing solution was found to provide essential probiotic properties able to sustain the growth of the specific chickpea symbiont Mesorhizobium ciceri. Moreover, the imbibing solution, behaving as a complete medium, was found to be critically important for the symbiont's attraction, a fact this that is strictly related to the presence of the amino acids glycine, serine, and threonine. Here, the presence of these amino acids is constantly supported by the presence of the enzymes serine hydroxymethyltransferase and formyltetrahydrofolate deformylase, which are both involved in their biosynthesis. The reported findings are discussed in the light of the pivotal role played by the imbibing solution in attracting and sustaining symbiosis between the host and its symbiont.}, }
@article {pmid31521032, year = {2019}, author = {Genc, O and van Capelleveen, G and Erdis, E and Yildiz, O and Yazan, DM}, title = {A socio-ecological approach to improve industrial zones towards eco-industrial parks.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109507}, doi = {10.1016/j.jenvman.2019.109507}, pmid = {31521032}, issn = {1095-8630}, abstract = {One of the concrete examples of industrial symbiosis development is eco-industrial parks, which improves resource efficiency and minimizes environmental impacts by adopting models for waste exchanges between industries. Despite past efforts, many industrial zones around the world are not yet considered as eco-industrial parks because of the low number (or total lack) of symbiotic relationships among industries. A promising strategy is to develop those existing industrial zones into eco-industrial parks. However, there is a lack of studies addressing how to assess environmental improvement in relation to network sustainability. This study demonstrates such an assessment approach using an integration of food web analysis and social network analysis. These two methods can assist in assessing differences in network configurations with respect to potential implementations of industrial symbiosis, and in analysing the resilience, redundancy, connectance, and cyclicity of eco-parks. The use of the methods is illustrated in a case study of an industrial zone in Turkey. Four potential future scenarios are proposed, including potential future co-location of companies in the industrial zone in order to foster industrial symbiotic network formation. These scenarios are compared with the current configuration. The results indicate the method's ability to assess the resilience of an industrial network. Moreover, the case shows an improvement of network sustainability and follows some sustainable properties of natural ecosystems as a result of implementing the industrial symbiosis.}, }
@article {pmid31520944, year = {2019}, author = {Noman, A and Aqeel, M and Qasim, M and Haider, I and Lou, Y}, title = {Plant-insect-microbe interaction: A love triangle between enemies in ecosystem.}, journal = {The Science of the total environment}, volume = {699}, number = {}, pages = {134181}, doi = {10.1016/j.scitotenv.2019.134181}, pmid = {31520944}, issn = {1879-1026}, abstract = {In natural ecosystems, plants interact with biotic components such as microbes, insects, animals and other plants as well. Generally, researchers have focused on each interaction separately, which condenses the significance of the interaction. This limited presentation of the facts masks the collective role of constantly interacting organisms in complex communities disturbing not only plant responses but also the response of organisms for each other in natural ecological settings. Beneficial microorganisms interact with insect herbivores, their predators and pollinators in a bidirectional way through the plant. Fascinatingly, insects employ diverse tactics to protect themselves from parasites or predators. Influences of microbial and insects attack on plants can bring changes in info-chemical frameworks and play a role in the food chain also. After insect herbivory and microbial pathogenesis, plants exhibit intense morpho-physiological and chemical reprogramming that leads to repellence/attraction of attacking organism or its natural enemy. The characterization of such interactions in different ecosystems is receiving due consideration, and underlying molecular and physiological mechanisms must be the point of concentration to unveil the evolution of multifaceted multitrophic interactions. Therefore, we have focused this phenomenon in a more realistic setting by integrating ecology and physiology to portray these multidimensional interfaces. We have shown, in this article, physiological trajectories in plant-microbe and insect relationship and their ecological relevance in nature. We focus and discuss microbial pathogenesis in plants, induced defense and the corresponding behavior of herbivore insects and vice-versa. It is hoped that this review will stimulate interest and zeal in microbes mediated plant-insect interactions along with their ecological consequences and encourage scientists to accept the challenges in this field.}, }
@article {pmid31518652, year = {2019}, author = {Carrillo, JD and Rugman-Jones, PF and Husein, D and Stajich, JE and Kasson, MT and Carrillo, D and Stouthamer, R and Eskalen, A}, title = {Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan.}, journal = {Fungal genetics and biology : FG & B}, volume = {}, number = {}, pages = {103269}, doi = {10.1016/j.fgb.2019.103269}, pmid = {31518652}, issn = {1096-0937}, abstract = {Carrillo, J.D., Rugman-Jones, PF., Husein, D., Stajich, J.E., Kasson, MT., Carrillo, D., Stouthamer, R., and Eskalen, A. 2019. Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan A number of ambrosia beetles have come to prominence in recent years because of the damage they inflict on a variety of trees within invaded habitats across the globe. Ambrosia beetles rely on symbiotic microorganisms, mainly fungi, as a dedicated food source and carry those microorganisms around with them within specialized organs termed mycangia. Investigation of members of the Euwallacea fornicatus species complex and their fungal symbionts in Taiwan revealed promiscuous symbioses with ambrosial Fusaria clade (AFC) members, Graphium spp., and Paracremonium spp. based on co-phylogenetic analyses. For AFC members, a novel diagnostic PCR assay targeting mating type genes MAT1-1-1 and MAT1-2-1 was developed and validated by amplicon size and sequencing. Mating types screening of AFC members revealed the isolates screened are all heterothallic (self-sterile), with both MAT types represented and recovered from fungi vectored by E. fornicatus, E. kuroshio, and E. whitfordiodendrus in Taiwan. Members of the Euwallacea fornicatus species complex and the variety of ambrosia fungi they utilize further confirms that their relationship with fungi are more likely promiscuous in native areas, as opposed to strictly obligate to a specific combination of fungi as observed in invaded areas.}, }
@article {pmid31515637, year = {2019}, author = {Liu, B and Liu, X and Liu, F and Ma, H and Ma, B and Zhang, W and Peng, L}, title = {Growth improvement of Lolium multiflorum Lam. induced by seed inoculation with fungus suspension of Xerocomus badius and Serendipita indica.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {145}, doi = {10.1186/s13568-019-0865-7}, pmid = {31515637}, issn = {2191-0855}, support = {2019LY009//Forestry Science and Technology Innovation Project of Shandong Province/ ; 31570614//National Natural Science Foundation of China/ ; }, abstract = {In this study, a pot experiment was carried out in greenhouse to investigate the potentials of Xerocomus badius and Serendipita indica to penetrate and colonize roots of ryegrass (Lolium multiflorum Lam.) and to induce beneficial effects on seed germination and seedling growth. The results showed that X. badius and S. indica successfully colonized in the root system of L. multiflorum seedlings and the root colonization rate was 72.65% and 88.42%, respectively. By microscopy, the hyphae, chlamydospores and spores produced by S. indica were observed in roots cortex of L. multiflorum seedlings. In comparison with the non-inoculated seedlings, seedlings inoculated with X. badius and S. indica showed significant increase in growth parameters with plant height, basal diameter, biomass accumulation, relative growth rate, leaf relative water content and chlorophyll content. Also, we found that seedlings inoculated with S. indica exhibited a greater growth-promotion as compared with X. badius-inoculated seedlings. No significant influence of the two fungus application has been observed with respect to seed germination. It suggested that well establishments of mutualistic symbiosis between L. multiflorum and X. badius or S. indica were not so essential to seed germination but contributed highly to the survival and growth of the seedlings.}, }
@article {pmid30936488, year = {2019}, author = {Spang, A and Stairs, CW and Dombrowski, N and Eme, L and Lombard, J and Caceres, EF and Greening, C and Baker, BJ and Ettema, TJG}, title = {Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1138-1148}, doi = {10.1038/s41564-019-0406-9}, pmid = {30936488}, issn = {2058-5276}, mesh = {Archaea/classification/*genetics/*metabolism ; Archaeal Proteins/genetics ; *Biological Evolution ; Eukaryotic Cells/metabolism/*physiology ; Genome, Archaeal/genetics ; Heterotrophic Processes ; Hydrogen/metabolism ; Metabolic Networks and Pathways ; *Models, Biological ; Oxidation-Reduction ; *Phylogeny ; Symbiosis ; }, abstract = {The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the 'reverse flow model', an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.}, }
@article {pmid30332582, year = {2018}, author = {Winbourne, JB and Harrison, MT and Sullivan, BW and Alvarez-Clare, S and Lins, SR and Martinelli, L and Nasto, M and Piotto, D and Rolim, S and Wong, M and Porder, S}, title = {A New Framework for Evaluating Estimates of Symbiotic Nitrogen Fixation in Forests.}, journal = {The American naturalist}, volume = {192}, number = {5}, pages = {618-629}, doi = {10.1086/699828}, pmid = {30332582}, issn = {1537-5323}, mesh = {Bacteria ; Brazil ; Computer Simulation ; Costa Rica ; *Nitrogen Fixation ; *Rainforest ; Root Nodules, Plant/*metabolism ; Soil/chemistry ; Symbiosis/physiology ; Tropical Climate ; }, abstract = {Symbiotic nitrogen fixation (SNF) makes atmospheric nitrogen biologically available and regulates carbon storage in many terrestrial ecosystems. Despite its global importance, estimates of SNF rates are highly uncertain, particularly in tropical forests where rates are assumed to be high. Here we provide a framework for evaluating the uncertainty of sample-based SNF estimates and discuss its implications for quantifying SNF and thus understanding of forest function. We apply this framework to field data sets from six lowland tropical rainforests (mature and secondary) in Brazil and Costa Rica. We use this data set to estimate parameters influencing SNF estimation error, notably the root nodule abundance and variation in SNF rates among soil cores containing root nodules. We then use simulations to gauge the relationship between sampling effort and SNF estimation accuracy for a combination of parameters. Field data illuminate a highly right-skewed lognormal distribution of SNF rates among soil cores containing root nodules that were rare and spanned five orders of magnitude. Consequently, simulations demonstrated that sample sizes of hundreds to even thousands of soil cores are needed to obtain estimates of SNF that are within, for example, a factor of 2 of the actual rate with 75% probability. This represents sample sizes that are larger than most studies to date. As a result of this previously undescribed uncertainty, we suggest that current estimates of SNF in tropical forests are not sufficiently constrained to elucidate forest stand-level controls of SNF, which hinders our understanding of the impact of SNF on tropical forest ecosystem processes.}, }
@article {pmid30109687, year = {2019}, author = {Pierart, A and Maes, AQ and Dumat, C and Sejalon-Delmas, N}, title = {Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {20}, pages = {20040-20051}, doi = {10.1007/s11356-018-2803-7}, pmid = {30109687}, issn = {1614-7499}, support = {ANR-12-0011-VBDU//Agence Nationale de la Recherche/ ; }, mesh = {Agriculture/methods ; *Composting ; Metals/*pharmacokinetics ; Mycobiome/genetics/*physiology ; Mycorrhizae ; Onions/*growth & development/microbiology ; Plant Roots/*microbiology ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*pharmacokinetics ; Symbiosis ; }, abstract = {In the context of urban agriculture, where soils are frequently contaminated with metal(loid)s (TM), we studied the influence of vermicompost amendments on symbiotic fungal communities associated with plants grown in two metal-rich soils. Leek (Allium porrum L.) plants were grown with or without vermicompost in two metal-rich soils characterized by either geogenic or anthropogenic TM sources, to assess the influence of pollutant origin on soil-plant transfer. Fungal communities associated with the leek roots were identified by high throughput Illumina MiSeq and TM contents were measured using mass spectrometry. Vermicompost addition led to a dramatic change in the fungal community with a loss of diversity in the two tested soils. This effect could partially explain the changes in metal transfer at the soil-AMF-plant interface. Our results suggest being careful while using composts when growing edibles in contaminated soils. More generally, this study highlights the need for further research in the field of fungal communities to refine practical recommendations to gardeners. Graphical abstract.}, }
@article {pmid29732407, year = {2018}, author = {Blažek, R and Polačik, M and Smith, C and Honza, M and Meyer, A and Reichard, M}, title = {Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaar4380}, pmid = {29732407}, issn = {2375-2548}, mesh = {Animals ; *Biological Evolution ; Catfishes/*physiology ; Cichlids/*physiology ; Reproduction ; Species Specificity ; *Symbiosis ; }, abstract = {Obligate brood parasites manipulate other species into raising their offspring. Avian and insect brood parasitic systems demonstrate how interacting species engage in reciprocal coevolutionary arms races through behavioral and morphological adaptations and counteradaptations. Mouthbrooding cichlid fishes are renowned for their remarkable evolutionary radiations and complex behaviors. In Lake Tanganyika, mouthbrooding cichlids are exploited by the only obligate nonavian vertebrate brood parasite, the cuckoo catfish Synodontis multipunctatus. We show that coevolutionary history and individual learning both have a major impact on the success of cuckoo catfish parasitism between coevolved sympatric and evolutionarily naïve allopatric cichlid species. The rate of cuckoo catfish parasitism in coevolved Tanganyikan hosts was 3 to 11 times lower than in evolutionarily naïve cichlids. Moreover, using experimental infections, we demonstrate that parasite egg rejection in sympatric hosts was much higher, leading to seven times greater parasite survival in evolutionarily naïve than sympatric hosts. However, a high rejection frequency of parasitic catfish eggs by coevolved sympatric hosts came at a cost of increased rejection of their own eggs. A significant cost of catfish parasitism was universal, except for coevolved sympatric cichlid species with previous experience of catfish parasitism, demonstrating that learning and individual experience both contribute to a successful host response.}, }
@article {pmid29462403, year = {2018}, author = {Lebreton, F and Valentino, MD and Schaufler, K and Earl, AM and Cattoir, V and Gilmore, MS}, title = {Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {6}, pages = {1479-1486}, pmid = {29462403}, issn = {1460-2091}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; P01 AI083214/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Cross Infection/microbiology ; Enterococcus faecium/drug effects/*genetics ; Feces/microbiology ; Genome, Bacterial ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Immunocompromised Host ; Microbial Sensitivity Tests ; Operon ; Phylogeny ; Plasmids/*genetics ; Symbiosis ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; Vancomycin-Resistant Enterococci/*genetics ; }, abstract = {Objectives: Vancomycin-resistant Enterococcus faecium is a leading cause of MDR hospital infection. Two genetically definable populations of E. faecium have been identified: hospital-adapted MDR isolates (clade A) and vancomycin-susceptible commensal strains (clade B). VanN-type vancomycin resistance was identified in two isolates of E. faecium recovered from blood and faeces of an immunocompromised patient. To understand the genomic context in which VanN occurred in the hospitalized patient, the risk it posed for transmission in the hospital and its origins, it was of interest to determine where these strains placed within the E. faecium population structure.<br><br>Methods: We obtained the genome sequence of the VanN isolates and performed comparative and functional genomics of the chromosome and plasmid content.<br><br>Results: We show that, in these strains, VanN occurs in a genetic background that clusters with clade B E. faecium, which is highly unusual. We characterized the chromosome and the conjugative plasmid that carries VanN resistance in these strains, pUV24. This plasmid exhibits signatures of in-host selection on the vanN operon regulatory system, which are associated with a constitutive expression of vancomycin resistance. VanN resistance in clade B strains may go undetected by current methods.<br><br>Conclusions: We report a case of vancomycin resistance in a commensal lineage of E. faecium responsible for an atypical bacteraemia in an immunocompromised patient. A reservoir of transferable glycopeptide resistance in the community could pose a concern for public health.}, }
@article {pmid29385453, year = {2018}, author = {Wang, Y and Staubach, F}, title = {Individual variation of natural D.melanogaster-associated bacterial communities.}, journal = {FEMS microbiology letters}, volume = {365}, number = {6}, pages = {}, doi = {10.1093/femsle/fny017}, pmid = {29385453}, issn = {1574-6968}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Drosophila melanogaster/*microbiology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Drosophila melanogaster has become an important model organism to study host-microbe interaction in the laboratory. However, the natural microbial communities that are associated with D. melanogaster have received less attention. Especially, information on inter-individual variation is still lacking, because most studies so far have used pooled material from several flies. Here, we collected bacterial 16S rRNA gene community profiles from a set of 32 individuals from a single population. We simulated pools from the individual data (i) to assess how well the microbiome of a host population is represented by pools, and (ii) to compare variation of Drosophila microbiomes within and between populations. Taxon richness was increased in simulated pools, suggesting that pools paint a more comprehensive picture of the taxa associated with a host population. Furthermore, microbiome composition varied less between pools than between individuals, indicating that differences even out in pools. Variation in microbiome composition was larger between populations than between simulated pools from a single population, adding to the notion that there are population-specific effects on the Drosophila microbiome. Surprisingly, samples from individuals clustered into two groups, suggesting that there are yet unknown factors that affect the composition of natural fly-associated microbial communities and need further research.}, }
@article {pmid29292829, year = {2018}, author = {Raven, JA and Lambers, H and Smith, SE and Westoby, M}, title = {Costs of acquiring phosphorus by vascular land plants: patterns and implications for plant coexistence.}, journal = {The New phytologist}, volume = {217}, number = {4}, pages = {1420-1427}, doi = {10.1111/nph.14967}, pmid = {29292829}, issn = {1469-8137}, mesh = {Adaptation, Physiological ; Embryophyta/*metabolism ; Phosphorus/*metabolism ; Plant Roots/physiology ; Soil/chemistry ; *Symbiosis ; }, abstract = {Content Summary 1420 I. Introduction 1421 II. Root adaptations that influence P acquisition 1422 III. Costs of P acquisition: general 1423 IV. Costs of P acquisition that are independent of soil P concentrations 1423 V. Costs of P acquisition that increase as soil P concentrations decline 1424 VI. Discussion and conclusions 1424 Acknowledgements 1425 References 1425 SUMMARY: We compare carbon (and hence energy) costs of the different modes of phosphorus (P) acquisition by vascular land plants. Phosphorus-acquisition modes are considered to be mechanisms of plants together with their root symbionts and structures such as cluster roots involved in mobilising or absorbing P. Phosphorus sources considered are soluble and insoluble inorganic and organic pools. Costs include operating the P-acquisition mechanisms, and resource requirements to construct and maintain them. For most modes, costs increase as the relevant soil P concentration declines. Costs can thus be divided into a component incurred irrespective of soil P concentration, and a component describing how quickly costs increase as the soil P concentration declines. Differences in sensitivity of costs to soil P concentration arise mainly from how economically mycorrhizal fungal hyphae or roots that explore the soil volume are constructed, and from costs of exudates that hydrolyse or mobilise insoluble P forms. In general, modes of acquisition requiring least carbon at high soil P concentrations experience a steeper increase in costs as soil P concentrations decline. The relationships between costs and concentrations suggest some reasons why different modes coexist, and why the mixture of acquisition modes differs between sites.}, }
@article {pmid29193223, year = {2018}, author = {Waller, LP and Felten, J and Hiiesalu, I and Vogt-Schilb, H}, title = {Sharing resources for mutual benefit: crosstalk between disciplines deepens the understanding of mycorrhizal symbioses across scales.}, journal = {The New phytologist}, volume = {217}, number = {1}, pages = {29-32}, doi = {10.1111/nph.14912}, pmid = {29193223}, issn = {1469-8137}, mesh = {Biological Evolution ; Mycorrhizae/*physiology ; Plants/microbiology ; Symbiosis/*physiology ; }, }
@article {pmid31512052, year = {2019}, author = {Gogoleva, OA and Shchuplova, EA}, title = {The influence of non-tuberculous mycobacteria on the interaction of opportunistic microorganisms with erythrocytes.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-019-00748-6}, pmid = {31512052}, issn = {1874-9356}, support = {№ 0420-2015-0005//The work wascarried out within the framework of the state task on the topic &quot;The role of the microbial factor in the functioning of the physiological systems of the human body&quot;/ ; }, abstract = {Getting into a weakened organism, non-tuberculosis mycobacteria (NTMB) contact not only with the cells of the microorganism but also with the microflora of the human body; however, these interactions are poorly understood. The purpose of this work was to study the effect of NTMB supernatants on the properties of conditionally pathogenic microorganisms in their interaction with red blood cells. We used strains of non-tuberculous mycobacteria Mycobacterium iranicum and M. rutilum, as well as strains of Staphylococcus epidermidis and Escherichia coli. Using the fluorescence in situ hybridisation (FISH) method, the processes of adhesion to the surface of erythrocytes and the intra-erythrocyte penetration of cells of S. epidermidis and E. coli under the influence of NTMB supernatants were studied. To study changes in the haemoglobin molecule under the action of the supernatants of NTMB, spectral analysis was performed. Statistical processing was performed using STATISTIKA 6.0. The results showed that the supernatants of M. iranicum and M. rutilum increased the adhesion of conditionally pathogenic bacteria with a low level of AntiHbA to the surface of erythrocytes by 3-4 times. It also increased the intra-erythrocyte penetration of cells of S. epidermidis and E. coli relative to the control values. As a result of studying the haemoglobin spectrum of erythrocytes under the influence of M. iranicum, a decrease in the optical density values of oxyhaemoglobin by a factor of 2 relative to the values in the control sample was noted. Thus, the supernatants of NTMB have a multidirectional effect on the interaction of opportunistic microorganisms with erythrocytes, increasing the adhesive activity and the penetration of cells into the erythrocytes, as well as reducing the optical density of oxyhaemoglobin.}, }
@article {pmid30777324, year = {2019}, author = {Mellal, H and Yacine, B and Boukaous, L and Khouni, S and Benguedouar, A and Castellano-Hinojosa, A and Bedmar, EJ}, title = {Phylogenetic diversity of Bradyrhizobium strains isolated from root nodules of Lupinus angustifolius grown wild in the North East of Algeria.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {3}, pages = {397-402}, doi = {10.1016/j.syapm.2019.01.003}, pmid = {30777324}, issn = {1618-0984}, mesh = {Algeria ; Bradyrhizobium/*classification/genetics/physiology ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Host Specificity ; Lupinus/*microbiology ; *Phylogeny ; Plant Root Nodulation ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {From a total of 80 bacterial strains isolated from root nodules of Lupinus angustifolius grown wild in the North-Eastern Algerian region of El Tarf, 64 plant host-nodulating strains clustered into 17 random amplified polymorphic DNA (RAPD) fingerprinting groups. The nearly complete 16S rRNA gene sequence from the representative strain of each group revealed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but their affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis, showed that 12 strains belong to B. lupini, other 2 strains affiliated with B. diazoefficiens and that 1 strain was closely related to B. japonicum. The remaining two strains showed similarity values ≤95% with B. cytisi and could represent new lineages within the genus Bradyrhizobium. Sequencing of the symbiotic nodC gene from 4 selected bradyrhizobial strains showed they were all similar to those of the species included in symbiovar genistearum.}, }
@article {pmid30487259, year = {2018}, author = {Harrison, TL and Simonsen, AK and Stinchcombe, JR and Frederickson, ME}, title = {More partners, more ranges: generalist legumes spread more easily around the globe.}, journal = {Biology letters}, volume = {14}, number = {11}, pages = {}, pmid = {30487259}, issn = {1744-957X}, mesh = {Fabaceae/microbiology/*physiology ; *Plant Dispersal ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rhizobium/genetics/*physiology ; *Symbiosis ; }, abstract = {How does mutualism affect range expansion? On the one hand, mutualists might thrive in new habitats thanks to the resources, stress tolerance or defence provided by their partners. On the other, specialized mutualists might fail to find compatible partners beyond their range margins, limiting further spread. A recent global analysis of legume ranges found that non-symbiotic legumes have been successfully introduced to more ranges than legumes that form symbioses with rhizobia, but there is still abundant unexplained variation in introduction success within symbiotic legumes. We test the hypothesis that generalist legumes have spread to more ranges than specialist legumes. We used published data and rhizobial 16S rRNA sequences from GenBank to quantify the number of rhizobia partners that associate with 159 legume species, spanning the legume phylogeny and the globe. We found that generalist legumes occur in more introduced ranges than specialist legumes, suggesting that among mutualists, specialization hinders range expansions.}, }
@article {pmid30381384, year = {2018}, author = {Palmer-Young, EC and Raffel, TR and McFrederick, QS}, title = {Temperature-mediated inhibition of a bumblebee parasite by an intestinal symbiont.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1890}, pages = {}, pmid = {30381384}, issn = {1471-2954}, support = {R01 GM122062/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bees/microbiology/parasitology ; Coculture Techniques ; Crithidia/drug effects/*growth &amp; development ; Lactobacillus/*growth &amp; development/metabolism ; Symbiosis/physiology ; *Temperature ; }, abstract = {Competition between organisms is often mediated by environmental factors, including temperature. In animal intestines, nonpathogenic symbionts compete physically and chemically against pathogens, with consequences for host infection. We used metabolic theory-based models to characterize differential responses to temperature of a bacterial symbiont and a co-occurring trypanosomatid parasite of bumblebees, which regulate body temperature during flight and incubation. We hypothesized that inhibition of parasites by bacterial symbionts would increase with temperature, due to symbionts having higher optimal growth temperatures than parasites. We found that a temperature increase over the range measured in bumblebee colonies would favour symbionts over parasites. As predicted by our hypothesis, symbionts reduced the optimal growth temperature for parasites, both in direct competition and when parasites were exposed to symbiont spent medium. Inhibitory effects of the symbiont increased with temperature, reflecting accelerated growth and acid production by symbionts. Our results indicate that high temperatures, whether due to host endothermy or environmental factors, can enhance the inhibitory effects of symbionts on parasites. Temperature-modulated manipulation of microbiota could be one explanation for fever- and heat-induced reductions of infection in animals, with consequences for diseases of medical and conservation concern.}, }
@article {pmid29034959, year = {2018}, author = {Helliwell, KE and Pandhal, J and Cooper, MB and Longworth, J and Kudahl, UJ and Russo, DA and Tomsett, EV and Bunbury, F and Salmon, DL and Smirnoff, N and Wright, PC and Smith, AG}, title = {Quantitative proteomics of a B12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism.}, journal = {The New phytologist}, volume = {217}, number = {2}, pages = {599-612}, pmid = {29034959}, issn = {1469-8137}, support = {BB/F011652/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I013164/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algal Proteins/metabolism ; Amino Acids/metabolism ; Chlorophyta/drug effects/genetics/*growth &amp; development/*metabolism ; Coculture Techniques ; Computational Biology ; Electron Transport/drug effects ; Gene Expression Regulation, Plant/drug effects ; Mesorhizobium/drug effects/*growth &amp; development ; Photosynthesis/drug effects ; *Proteomics ; RNA, Messenger/genetics/metabolism ; Symbiosis/*drug effects ; Vitamin B 12/*pharmacology ; }, abstract = {The unicellular green alga Lobomonas rostrata requires an external supply of vitamin B12 (cobalamin) for growth, which it can obtain in stable laboratory cultures from the soil bacterium Mesorhizobium loti in exchange for photosynthate. We investigated changes in protein expression in the alga that allow it to engage in this mutualism. We used quantitative isobaric tagging (iTRAQ) proteomics to determine the L. rostrata proteome grown axenically with B12 supplementation or in coculture with M. loti. Data are available via ProteomeXchange (PXD005046). Using the related Chlamydomonas reinhardtii as a reference genome, 588 algal proteins could be identified. Enzymes of amino acid biosynthesis were higher in coculture than in axenic culture, and this was reflected in increased amounts of total cellular protein and several free amino acids. A number of heat shock proteins were also elevated. Conversely, photosynthetic proteins and those of chloroplast protein synthesis were significantly lower in L. rostrata cells in coculture. These observations were confirmed by measurement of electron transfer rates in cells grown under the two conditions. The results indicate that, despite the stability of the mutualism, L. rostrata experiences stress in coculture with M. loti, and must adjust its metabolism accordingly.}, }
@article {pmid31509600, year = {2019}, author = {Radice, VZ and Brett, MT and Fry, B and Fox, MD and Hoegh-Guldberg, O and Dove, SG}, title = {Evaluating coral trophic strategies using fatty acid composition and indices.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0222327}, doi = {10.1371/journal.pone.0222327}, pmid = {31509600}, issn = {1932-6203}, abstract = {The ecological success of shallow water reef-building corals has been linked to the symbiosis between the coral host and its dinoflagellate symbionts (herein 'symbionts'). As mixotrophs, symbiotic corals depend on nutrients 1) transferred from their photosynthetic symbionts (autotrophy) and 2) acquired by host feeding on particulate organic resources (heterotrophy). However, coral species differ in the extent to which they depend on heterotrophy for nutrition and these differences are typically poorly defined. Here, a multi-tracer fatty acid approach was used to evaluate the trophic strategies of three species of common reef-building coral (Galaxea fascicularis, Pachyseris speciosa, and Pocillopora verrucosa) whose trophic strategies had previously been identified using carbon stable isotopes. The composition and various indices of fatty acids were compared to examine the relative contribution of symbiont autotrophy and host heterotrophy in coral energy acquisition. A linear discriminant analysis (LDA) was used to estimate the contribution of polyunsaturated fatty acids (PUFA) derived from various potential sources to the coral hosts. The total fatty acid composition and fatty acid indices revealed differences between the more heterotrophic (P. verrucosa) and more autotrophic (P. speciosa) coral hosts, with the coral host G. fascicularis showing overlap with the other two species and greater variability overall. For the more heterotrophic P. verrucosa, the fatty acid indices and LDA results both indicated a greater proportion of copepod-derived fatty acids compared to the other coral species. Overall, the LDA estimated that PUFA derived from particulate resources (e.g., copepods and diatoms) comprised a greater proportion of coral host PUFA in contrast to the lower proportion of symbiont-derived PUFA. These estimates provide insight into the importance of heterotrophy in coral nutrition, especially in productive reef systems. The study supports carbon stable isotope results and demonstrates the utility of fatty acid analyses for exploring the trophic strategies of reef-building corals.}, }
@article {pmid31508195, year = {2019}, author = {He, S and Grasis, JA and Nicotra, ML and Juliano, CE and Schnitzler, CE}, title = {Cnidofest 2018: the future is bright for cnidarian research.}, journal = {EvoDevo}, volume = {10}, number = {}, pages = {20}, doi = {10.1186/s13227-019-0134-5}, pmid = {31508195}, issn = {2041-9139}, abstract = {The 2018 Cnidarian Model Systems Meeting (Cnidofest) was held September 6-9th at the University of Florida Whitney Laboratory for Marine Bioscience in St. Augustine, FL. Cnidofest 2018, which built upon the momentum of Hydroidfest 2016, brought together research communities working on a broad spectrum of cnidarian organisms from North America and around the world. Meeting talks covered diverse aspects of cnidarian biology, with sessions focused on genomics, development, neurobiology, immunology, symbiosis, ecology, and evolution. In addition to interesting biology, Cnidofest also emphasized the advancement of modern research techniques. Invited technology speakers showcased the power of microfluidics and single-cell transcriptomics and demonstrated their application in cnidarian models. In this report, we provide an overview of the exciting research that was presented at the meeting and discuss opportunities for future research.}, }
@article {pmid31504077, year = {2017}, author = {Dupre, C and Grasis, JA and Steele, RE and Schnitzler, CE and Juliano, CE}, title = {Hydroidfest 2016: celebrating a renaissance in hydrozoan research.}, journal = {EvoDevo}, volume = {8}, number = {}, pages = {7}, doi = {10.1186/s13227-017-0070-1}, pmid = {31504077}, issn = {2041-9139}, abstract = {Hydroidfest 2016 took place on September 23-25 at the UC Davis Bodega Marine Laboratory in Bodega Bay, CA. The meeting brought together cnidarian researchers, with an emphasis on those studying hydrozoans, from North America and other parts of the world. The scientific topics discussed were diverse, including sessions focused on development, regeneration, aging, immunology, symbiosis, and neurobiology. Thanks to the application of modern biological technologies, hydrozoans and other cnidarians are now fertile ground for research in numerous disciplines. Moreover, their amenability to comparative approaches is a powerful asset that was repeatedly showcased during the meeting. Here, we give a brief account of the work that was presented and the opportunities that emerged from the ensuing discussions.}, }
@article {pmid31504533, year = {2019}, author = {Havird, JC and Weaver, RJ and Milani, L and Ghiselli, F and Greenway, R and Ramsey, AJ and Jimenez, AG and Dowling, DK and Hood, WR and Montooth, KL and Estes, S and Schulte, PM and Sokolova, IM and Hill, GE}, title = {Beyond the Powerhouse: Integrating Mitonuclear Evolution, Physiology, and Theory in Comparative Biology.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icz132}, pmid = {31504533}, issn = {1557-7023}, abstract = {Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this symposium volume, scientists working in diverse organismal systems spanning vast biological scales address emerging topics in integrative, comparative biology in light of mitonuclear interactions.}, }
@article {pmid31504465, year = {2019}, author = {Freed, LL and Easson, C and Baker, LJ and Fenolio, D and Sutton, TT and Khan, Y and Blackwelder, P and Hendry, TA and Lopez, JV}, title = {Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of mexico.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz146}, pmid = {31504465}, issn = {1574-6941}, abstract = {The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities ('microbiomes') and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission Electron Microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas genera. 16S rDNA sequencing results from adult fishes corroborate the previously published identity of ceratioid bioluminescent symbionts and support findings that these symbionts do not consistently exhibit host specificity at the host family level. Bioluminescent symbiont amplicon sequence variants (ASVs) were absent from larval ceratioid samples, but were found at all depths in the seawater, with a highest abundance found at mesopelagic depths. As adults spend the majority of their lives in the meso and bathypelagic, the trend in symbiont abundance is consistent with their life history. These findings support the hypothesis that bioluminescent symbionts are not present throughout host development, and that ceratioids acquire their bioluminescent symbionts from the environment.}, }
@article {pmid31504453, year = {2019}, author = {Barelli, L and Behie, SW and Bidochka, MJ}, title = {Availability of carbon and nitrogen in soil affects Metarhizium robertsii root colonization and transfer of insect-derived nitrogen.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz144}, pmid = {31504453}, issn = {1574-6941}, abstract = {The endophytic, insect pathogenic fungus, Metarhizium, exchanges insect-derived nitrogen for photosynthate as part of a symbiotic association similar to well-known mycorrhizal relationships. However, little is known about this nitrogen transfer in soils where there is an abundance of nitrogen and/or carbon. Here we applied D-glucose and ammonium nitrate to soil to examine the effect on root colonization and transfer of labelled nitrogen (15N) from an insect (injected with 15N-ammonium sulfate), to Metarhizium robertsii, into leaves of the common bean, Phaseolus vulgaris, over the course of 28 days. Application of exogenous carbon and/or nitrogen to soils significantly reduced detectable 15N in plant leaves. Metarhizium root colonization, quantified with real-time PCR, revealed colonization persisted under all conditions but was significantly greater on roots in soil supplemented with glucose and significantly lower in soil supplemented with ammonium nitrate. Fungal gene expression analysis revealed differential expression of sugar and nitrogen transporters (mrt, st3, nrr1, nit1, mep2) when Metarhizium was grown in pure broth culture or in co-culture with plant roots under various carbon and nitrogen conditions. The observation that Metarhizium maintained root colonization in the absence of nitrogen transfer, and without evidence of plant harm, is intriguing and indicates additional benefits with ecological importance.}, }
@article {pmid31500535, year = {2019}, author = {Foster, RA and Zehr, JP}, title = {Diversity, Genomics, and Distribution of Phytoplankton-Cyanobacterium Single-Cell Symbiotic Associations.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {435-456}, doi = {10.1146/annurev-micro-090817-062650}, pmid = {31500535}, issn = {1545-3251}, abstract = {Cyanobacteria are common in symbiotic relationships with diverse multicellular organisms (animals, plants, fungi) in terrestrial environments and with single-celled heterotrophic, mixotrophic, and autotrophic protists in aquatic environments. In the sunlit zones of aquatic environments, diverse cyanobacterial symbioses exist with autotrophic taxa in phytoplankton, including dinoflagellates, diatoms, and haptophytes (prymnesiophytes). Phototrophic unicellular cyanobacteria related to Synechococcus and Prochlorococcus are associated with a number of groups. N2-fixing cyanobacteria are symbiotic with diatoms and haptophytes. Extensive genome reduction is involved in the N2-fixing endosymbionts, most dramatically in the unicellular cyanobacteria associated with haptophytes, which have lost most of the photosynthetic apparatus, the ability to fix C, and the tricarboxylic acid cycle. The mechanisms involved in N2-fixing symbioses may involve more interactions beyond simple exchange of fixed C for N. N2-fixing cyanobacterial symbioses are widespread in the oceans, even more widely distributed than the best-known free-living N2-fixing cyanobacteria, suggesting they may be equally or more important in the global ocean biogeochemical cycle of N.Despite their ubiquitous nature and significance in biogeochemical cycles, cyanobacterium-phytoplankton symbioses remain understudied and poorly understood.}, }
@article {pmid31185402, year = {2019}, author = {Parvin, S and Van Geel, M and Yeasmin, T and Lievens, B and Honnay, O}, title = {Variation in arbuscular mycorrhizal fungal communities associated with lowland rice (Oryza sativa) along a gradient of soil salinity and arsenic contamination in Bangladesh.}, journal = {The Science of the total environment}, volume = {686}, number = {}, pages = {546-554}, doi = {10.1016/j.scitotenv.2019.05.450}, pmid = {31185402}, issn = {1879-1026}, mesh = {Arsenic/*analysis ; Bangladesh ; Environmental Monitoring ; Mycobiome ; Mycorrhizae/*growth &amp; development ; Oryza/*microbiology/physiology ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; Symbiosis ; }, abstract = {Rice is an essential food crop that nourishes >50% of the world population. In many regions of Bangladesh rice production is constrained by high soil salinity and heavy metal contamination due to irrigation practices. Plants may naturally overcome such stress through mutualistic interactions with arbuscular mycorrhizal fungi (AMF). Yet, little is known regarding the diversity and composition of AMF communities in rice fields with high saline and arsenic concentration. Here we used high throughput Illumina sequencing to characterize AMF communities in rice roots from 45 Bangladeshi rice fields, along a large geographical gradient of soil salinity and arsenic contamination. We obtained 77 operational taxonomic units (OTUs, based on a sequence similarity threshold of 97%) from eight AMF families, and showed that high soil salinity and arsenic concentration are significantly associated with low AMF diversity in rice roots. Soil salinity and arsenic concentration also explained a large part of the variation in AMF community composition, but also soil pH, moisture, organic matter content and plant available soil phosphorus played an important role. Overall, our study showed that even at very high salinity and arsenic levels, some AMF OTUs are present in rice roots. Their potential role in mediating a reduction of rice stress and arsenic uptake remains to be investigated.}, }
@article {pmid31101011, year = {2019}, author = {Zhang, Y and Chen, Q and Xie, JY and Yeung, YH and Xiao, B and Liao, B and Xu, J and Qiu, JW}, title = {Development of a transcriptomic database for 14 species of scleractinian corals.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {387}, doi = {10.1186/s12864-019-5744-8}, pmid = {31101011}, issn = {1471-2164}, support = {JCYJ20170307161326613//Shenzhen Science and Technology Innovation Committee (CN)/ ; 2017-03//Environment and Conservation Fund, Hong Kong/ ; 12102018//General Research Fund of Hong Kong/ ; }, mesh = {Animals ; Anthozoa/*classification/*genetics ; Computational Biology/*methods ; *Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Molecular Sequence Annotation ; Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea.<br><br>DESCRIPTION: We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface.<br><br>SHORT CONCLUSION: We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database (www.comp.hkbu.edu.hk/~db/CoralTBase). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.}, }
@article {pmid30857983, year = {2019}, author = {Wu, Y and Zhou, Z and Wang, J and Luo, J and Wang, L and Zhang, Y}, title = {Temperature regulates the recognition activities of a galectin to pathogen and symbiont in the scleractinian coral Pocillopora damicornis.}, journal = {Developmental and comparative immunology}, volume = {96}, number = {}, pages = {103-110}, doi = {10.1016/j.dci.2019.03.003}, pmid = {30857983}, issn = {1879-0089}, mesh = {Amino Acid Sequence ; Animals ; Anthozoa/*immunology/microbiology ; Cloning, Molecular ; Coral Reefs ; Escherichia coli/immunology ; Galectins/genetics/*immunology/metabolism ; Host Microbial Interactions/*immunology ; Recombinant Proteins/genetics/immunology/metabolism ; Sequence Homology, Amino Acid ; Streptococcus mutans/immunology ; Symbiosis/*immunology ; *Temperature ; Vibrio/immunology ; }, abstract = {Lectins serve as essential pattern recognition receptors, and play important roles in the recognition of non-self and mediation of innate immune response in metazoans. Scleractinian corals are vulnerable to pathogen infection and endosymbiosis disruption under heat stress that can finally lead to coral bleaching. In this study, a cDNA sequence encoding one galectin was cloned in scleractinian coral Pocillopora damicornis (PdGLT-1). The deduced PdGLT-1 protein shared highest amino acid sequence similarity (99%) with galectin from Stylophora pistillata (XP_022806650.1), and was composed of one signal peptide, one Collagen domain and one Gal-Lectin domain. PdGLT-1 recombinant protein (rPdGLT-1) was expressed and purified in vitro. Binding activities of rPdGLT-1 to bacteria and symbiont were determined using western blotting method. Results showed that rPdGLT-1 was able to bind to gram-positive bacterium Streptococcus mutans, gram-negative bacteria Vibrio coralliilyticus and Escherichia coli, with the highest activity for V. coralliilyticus, and further agglutinated them. The bound rPdGLT-1 to Symbiodinium (10-104 cells mL-1) was detectable, and its binding ability was concentration-dependent. Furthermore, dual binding activities were determined under different temperatures (20, 25, 30 and 35 °C), and the optimal temperatures were found to be 25 and 30 °C for V. coralliilyticus and Symbiodinium, respectively. Results suggested that PdGLT-1 could recognize pathogenic bacteria and symbiotic dinoflagellates Symbiodinium. However, their recognition activities were repressed under high temperature (>30 °C). This study provided insights into the underlying mechanism of lectin modulation to heat bleaching through its pathogen and Symbiodinium recognition in the scleractinian coral P. damicornis.}, }
@article {pmid30719426, year = {2018}, author = {Myles, IA and Moore, IN and Castillo, CR and Datta, SK}, title = {Differing Virulence of Healthy Skin Commensals in Mouse Models of Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {451}, doi = {10.3389/fcimb.2018.00451}, pmid = {30719426}, issn = {2235-2988}, mesh = {Animals ; Bacterial Infections/*microbiology/pathology ; Carrier State/microbiology ; Disease Models, Animal ; Methylobacteriaceae/*growth &amp; development/pathogenicity ; Mice ; Probiotics/administration &amp; dosage/*adverse effects ; Pseudomonas aeruginosa/*growth &amp; development/pathogenicity ; Staphylococcus/*growth &amp; development/pathogenicity ; *Symbiosis ; *Virulence ; }, abstract = {Introduction: As therapies for atopic dermatitis (AD) based on live biotherapeutic products (LBP) are developed, the potential displacement of biotherapeutic strains, and species to mucosal sites where they are not naturally found is of investigative interest. However, formal assessment of the toxicity potential of healthy skin commensal organisms has not been reported in the literature. Our previous research indicates that topical application of live Roseomonas mucosa to treat AD was associated with clinical benefit on the skin, but the effects of exposure via inhalation, eye inoculation, and ingestion were unknown. Methods: Herein we report our findings from mice inoculated with commensal strains of R. mucosa, coagulase negative Staphylococci (CNS), and Pseudomonas aeruginosa. Bacterial isolates were collected under clinical trial NCT03018275, however these results do not represent an interventional clinical trial. Results: Our tested R. mucosa isolates did not display significant infection or inflammation. However, neutropenic mice inoculated with CNS had infection without major inflammation in pulmonary models. In contrast, systemic infection generated hepatic and splenic pathology for P. aeruginosa and CNS, which was worsened by the presence of neutropenia. Discussion: Our results suggest that LBP derived from bacteria without significant infectivity histories, such as R. mucosa, may represent safer options than known pathobionts like P. aeruginosa and Staphylococcus spp. Overall, these results suggest that topically applied LBP from select skin commensals are likely to present safe therapeutic options and reinforce our prior clinical findings.}, }
@article {pmid31497392, year = {2019}, author = {Shtark, OY and Puzanskiy, RK and Avdeeva, GS and Yurkov, AP and Smolikova, GN and Yemelyanov, VV and Kliukova, MS and Shavarda, AL and Kirpichnikova, AA and Zhernakov, AI and Afonin, AM and Tikhonovich, IA and Zhukov, VA and Shishova, MF}, title = {Metabolic alterations in pea leaves during arbuscular mycorrhiza development.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7495}, doi = {10.7717/peerj.7495}, pmid = {31497392}, issn = {2167-8359}, abstract = {Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.}, }
@article {pmid31495588, year = {2019}, author = {Iwai, S and Fujita, K and Takanishi, Y and Fukushi, K}, title = {Photosynthetic Endosymbionts Benefit from Host's Phagotrophy, Including Predation on Potential Competitors.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.07.074}, pmid = {31495588}, issn = {1879-0445}, abstract = {In many endosymbioses, hosts have been shown to benefit from symbiosis, but it remains unclear whether intracellular endosymbionts benefit from their association with hosts [1, 2]. This makes it difficult to determine evolutionary mechanisms underlying cooperative behaviors between hosts and intracellular endosymbionts, such as mutual exchange of vital resources. Here, we investigate the fitness effects of symbiosis on the ciliate host Paramecium bursaria and on the algal endosymbiont Chlorella [3, 4], using experimental microcosms that include the free-living alga Chlamydomonas reinhardtii to mimic ecologically realistic conditions. We demonstrate that both host ciliate and the endosymbiotic algae gain fitness benefits from the symbiosis when another alga C. reinhardtii is present in the system. Specifically, the endosymbiotic Chlorella can grow as the host ciliate feeds and grows on C. reinhardtii, whereas the growth of free-living Chlorella is reduced by its competitor, C. reinhardtii. Thus, we propose that the endosymbiotic algae benefit from the host's phagotrophy, which allows the endosymbiont to access particulate nutrient sources and to indirectly prey on the potential competitors competing with its free-living counterparts. Even though the ecological contexts in which each partner receives its benefits differ, both partners would gain net fitness benefits in an ecological timescale. Thus, the cooperative behaviors can evolve through fitness feedback (partner fidelity feedback) between the host and the endosymbiont, without need for special partner control mechanisms. The proposed ecological and evolutionary mechanisms provide a basis for understanding cooperative resource exchanges in endosymbioses, including many photosynthetic endosymbioses widespread in aquatic ecosystems.}, }
@article {pmid31166161, year = {2019}, author = {Sazanova, AL and Safronova, VI and Kuznetsova, IG and Karlov, DS and Belimov, AA and Andronov, EE and Chirak, ER and Popova, JP and Verkhozina, AV and Willems, A and Tikhonovich, IA}, title = {Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {9}, pages = {2687-2695}, doi = {10.1099/ijsem.0.003509}, pmid = {31166161}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Bradyrhizobiaceae/*classification/isolation &amp; purification ; Caragana/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Mongolia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Two Gram-stain-negative strains, RCAM04680T and RCAM04685, were isolated from root nodules of the relict legume Caragana jubata (Pall.) Poir. originating from the south-western shore of Lake Khuvsgul (Mongolia). The 16S rRNA gene (rrs) sequencing data showed that these novel isolates belong to the genus Bosea and are phylogenetically closest to the type strains Bosea lathyri LMG 26379T, Bosea vaviloviae LMG 28367T, Bosea massiliensis LMG 26221T and Bosea lupini LMG 26383T (the rrs-similarity levels were 98.7-98.8 %). The recA gene of strain RCAM04680T showed the highest sequence similarity to the type strain B. lupini LMG 26383T (95.4 %), while its atpD gene was closest to that of B. lathyri LMG 26379T (94.4 %). The ITS, dnaK and gyrB sequences of this isolate were most similar to the B. vaviloviae LMG 28367T (86.8 % for ITS, 90.4 % for the other genes). The most abundant fatty acid was C18 : 1ω7c (40.8 %). The whole genomes of strains RCAM04680T and RCAM04685 were identical (100 % average nucleotide identity). The highest average nucleotide identity value (82.8 %) was found between the genome of strain RCAM04680T and B. vaviloviae LMG 28367T. The common nodABC genes required for legume nodulation were absent in both strains; however, some other symbiotic nol, nod, nif and fix genes were detected. Based on the genetic study, as well as analyses of the whole-cell fatty acid compositions and phenotypic properties, a new species, Boseacaraganae sp. nov. (type strain RCAM04680T (=LMG 31125T), is proposed.}, }
@article {pmid30904535, year = {2019}, author = {Javaheri-Kermani, M and Asoodeh, A}, title = {A novel beta-1,4 glucanase produced by symbiotic Bacillus sp. CF96 isolated from termite (Anacanthotermes).}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {752-759}, doi = {10.1016/j.ijbiomac.2019.03.124}, pmid = {30904535}, issn = {1879-0003}, mesh = {Animals ; Bacillus/classification/*enzymology/genetics/isolation &amp; purification ; Chemical Phenomena ; Chromatography, Thin Layer ; Enzyme Activation ; Enzyme Stability ; Glycoside Hydrolases/*chemistry/*isolation &amp; purification/metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; Isoptera/*microbiology ; Solvents ; Substrate Specificity ; Symbiosis ; Temperature ; }, abstract = {A novel beta-1,4-glucanase was purified and characterized from symbiotic Bacillus sp. CF96 of termite. The SDS-PAGE and zymogram analyses revealed a molecular mass of 35.6 kDa. Optimal activity was at 50 °C and pH 5.5, while the enzyme was active over a wide range of temperature 20-80 °C and pH 4-10 and interestingly more than 60% of the maximum activity remained up to pH 9. The enzyme activity increased in the presence of hexane, chloroform and methanol (20% v/v). while, the enzyme activity was inhibited by metal ions such as Mn2+, Hg2+, Cu2+, Zn2+, Mg2+, Fe2+. The isolated enzyme was able to degrade carboxymethyl cellulose (CMC), avicel and cellulose. Cellobiose was the hydrolytic product of enzymatic reaction based on thin layer chromatography (TLC) analysis. Regarding beta-1,4 endo/exoglucanase activity and high temperature, pH and solvent stability, the enzyme has potential for various industrial applications especially in designing pesticide for termite.}, }
@article {pmid30246365, year = {2018}, author = {Murakami, T and Segawa, T and Takeuchi, N and Barcaza Sepúlveda, G and Labarca, P and Kohshima, S and Hongoh, Y}, title = {Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {4170-4183}, doi = {10.1111/1462-2920.14420}, pmid = {30246365}, issn = {1462-2920}, support = {16H04840//Japan Society for the Promotion of Science/International ; 17K19423//Japan Society for the Promotion of Science/International ; 22241005//Japan Society for the Promotion of Science/International ; 23117003//Japan Society for the Promotion of Science/International ; 26241020//Japan Society for the Promotion of Science/International ; GS009//NEXT/International ; }, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Ice Cover/*parasitology ; In Situ Hybridization, Fluorescence ; Insecta/*microbiology/physiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {The glacier stonefly Andiperla willinki is the largest metazoan inhabiting the Patagonian glaciers. In this study, we analysed the gut microbiome of the aquatic nymphs by 16S rRNA gene amplicon and metagenomic sequencing. The bacterial gut community was consistently dominated by taxa typical of animal digestive tracts, such as Dysgonomonadaceae and Lachnospiraceae, as well as those generally indigenous to glacier environments, such as Polaromonas. Interestingly, the dominant Polaromonas phylotypes detected in the stonefly gut were almost never detected in the glacier surface habitat. Fluorescence in situ hybridization analysis revealed that the bacterial lineages typical of animal guts colonized the gut wall in a co-aggregated form, while Polaromonas cells were not included in the aggregates. Draft genomes of several dominant bacterial lineages were reconstructed from metagenomic datasets and indicated that the predominant Dysgonomonadaceae bacterium is capable of degrading various polysaccharides derived from host-ingested food, such as algae, and that other dominant bacterial lineages ferment saccharides liberated by the polysaccharide degradation. Our results suggest that the gut bacteria-host association in the glacier stonefly contributes to host nutrition as well as material cycles in the glacier environment.}, }
@article {pmid30062595, year = {2019}, author = {Kapitan, M and Niemiec, MJ and Steimle, A and Frick, JS and Jacobsen, ID}, title = {Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria.}, journal = {Current topics in microbiology and immunology}, volume = {422}, number = {}, pages = {265-301}, doi = {10.1007/82_2018_117}, pmid = {30062595}, issn = {0070-217X}, mesh = {*Bacteria ; Bacterial Infections/microbiology ; Candida albicans/pathogenicity/physiology ; Fungi/pathogenicity/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; *Microbial Interactions ; Symbiosis ; }, abstract = {The human microbiota consists of bacteria, archaea, viruses, and fungi that build a highly complex network of interactions between each other and the host. While there are many examples for commensal bacterial influence on host health and immune modulation, little is known about the role of commensal fungi inside the gut community. Up until now, fungal research was concentrating on opportunistic diseases caused by fungal species, leaving the possible role of fungi as part of the microbiota largely unclear. Interestingly, fungal and bacterial abundance in the gut appear to be negatively correlated and disruption of the bacterial microbiota is a prerequisite for fungal overgrowth. The mechanisms behind bacterial colonization resistance are likely diverse, including direct antagonism as well as bacterial stimulation of host defense mechanisms. In this work, we will review the current knowledge of the development of the intestinal bacterial and fungal community, the influence of the microbiota on human health and disease, and the role of the opportunistic yeast C. albicans. We will furthermore discuss the possible benefits of commensal fungal colonization. Finally, we will summarize the recent findings on bacterial-fungal interactions.}, }
@article {pmid29131106, year = {2018}, author = {Heiss, CN and Olofsson, LE}, title = {Gut Microbiota-Dependent Modulation of Energy Metabolism.}, journal = {Journal of innate immunity}, volume = {10}, number = {3}, pages = {163-171}, doi = {10.1159/000481519}, pmid = {29131106}, issn = {1662-8128}, mesh = {Animals ; *Energy Metabolism ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypothalamus/metabolism/physiology ; Leptin/metabolism ; Obesity/*metabolism/*microbiology ; Signal Transduction ; Symbiosis ; }, abstract = {The gut microbiota has emerged as an environmental factor that modulates the host's energy balance. It increases the host's ability to harvest energy from the digested food, and produces metabolites and microbial products such as short-chain fatty acids, secondary bile acids, and lipopolysaccharides. These metabolites and microbial products act as signaling molecules that modulate appetite, gut motility, energy uptake and storage, and energy expenditure. Several findings suggest that the gut microbiota can affect the development of obesity. Germ-free mice are leaner than conventionally raised mice and they are protected against diet-induced obesity. Furthermore, obese humans and rodents have an altered gut microbiota composition with less phylogeneic diversity compared to lean controls, and transplantation of the gut microbiota from obese subjects to germ-free mice can transfer the obese phenotype. Taken together, these findings indicate a role for the gut microbiota in obesity and suggest that the gut microbiota could be targeted to improve metabolic diseases like obesity. This review focuses on the role of the gut microbiota in energy balance regulation and its potential role in obesity.}, }
@article {pmid31493718, year = {2019}, author = {Hidalgo-Castellanos, J and Duque, AS and Burgueño, A and Herrera-Cervera, JA and Fevereiro, P and López-Gómez, M}, title = {Overexpression of the arginine decarboxylase gene promotes the symbiotic interaction Medicago truncatula-Sinorhizobium meliloti and induces the accumulation of proline and spermine in nodules under salt stress conditions.}, journal = {Journal of plant physiology}, volume = {241}, number = {}, pages = {153034}, doi = {10.1016/j.jplph.2019.153034}, pmid = {31493718}, issn = {1618-1328}, abstract = {Legumes have the capacity to fix nitrogen in symbiosis with soil bacteria known as rhizobia by the formation of root nodules. However, nitrogen fixation is highly sensitive to soil salinity with a concomitant reduction of the plant yield and soil fertilization. Polycationic aliphatic amines known as polyamines (PAs) have been shown to be involved in the response to a variety of stresses in plants including soil salinity. Therefore, the generation of transgenic plants overexpressing genes involved in PA biosynthesis have been proposed as a promising tool to improve salt stress tolerance in plants. In this work we tested whether the modulation of PAs in transgenic Medicago truncatula plants was advantageous for the symbiotic interaction with Sinorhizobium meliloti under salt stress conditions, when compared to wild type plants. Consequently, we characterized the symbiotic response to salt stress of the homozygous M. truncatula plant line L-108, constitutively expressing the oat adc gene, coding for the PA biosynthetic enzyme arginine decarboxylase, involved in PAs biosynthesis. In a nodulation kinetic assay, nodule number incremented in L-108 plants under salt stress. In addition, these plants at vegetative stage showed higher nitrogenase and nodule biomass and, under salt stress, accumulated proline (Pro) and spermine (Spm) in nodules, while in wt plants, the accumulation of glutamic acid (Glu), γ-amino butyric acid (GABA) and 1-aminocyclopropane carboxylic acid (ACC) (the ethylene (ET) precursor) were the metabolites involved in the salt stress response. Therefore, overexpression of oat adc gene favours the symbiotic interaction between plants of M. truncatula L-108 and S. meliloti under salt stress and the accumulation of Pro and Spm, seems to be the molecules involved in salt stress tolerance.}, }
@article {pmid31492935, year = {2019}, author = {Chagas, PMB and Caetano, AA and Tireli, AA and Cesar, PHS and Corrêa, AD and Guimarães, IDR}, title = {Use of an Environmental Pollutant From Hexavalent Chromium Removal as a Green Catalyst in The Fenton Process.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12819}, doi = {10.1038/s41598-019-49196-9}, pmid = {31492935}, issn = {2045-2322}, abstract = {The present study refers to the use of an environmental pollutant generated during the removal of hexavalent chromium from aqueous media. This pollutant is a material with catalytic properties suitable for application in the oxidative degradation of problematic organic compounds. The material, initially used as an adsorbent, is a composite prepared by modifying the crystalline phases of iron oxides together with the chitosan (CT-FeCr). Chemical and morphological characterizations of the materials were performed using SEM analysis coupled with EDS, XRD and DSC. The CT-FeCr beads were used in the degradation of methylene blue dye (MB) and showed excellent degradation potential (93.6%). The presence of Cr on the surface of the catalyst was responsible for the increase in catalytic activity compared to the CT-Fe and pure magnetite materials. The product of the effluent treatment and the presence of the catalyst itself in the environment do not pose toxic effects. In addition, the CT-FeCr beads showed catalytic stability for several consecutive reaction cycles with possible technical and economic viability. The concept of &quot;industrial symbiosis&quot; may be applied to this technology, with that term relating to the reuse of a byproduct generated in one particular industrial sector by another as a raw material.}, }
@article {pmid31492817, year = {2019}, author = {Treitli, SC and Kolisko, M and Husník, F and Keeling, PJ and Hampl, V}, title = {Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1910793116}, pmid = {31492817}, issn = {1091-6490}, abstract = {Lower termites harbor in their hindgut complex microbial communities that are involved in the digestion of cellulose. Among these are protists, which are usually associated with specific bacterial symbionts found on their surface or inside their cells. While these form the foundations of a classic system in symbiosis research, we still know little about the functional basis for most of these relationships. Here, we describe the complex functional relationship between one protist, the oxymonad Streblomastix strix, and its ectosymbiotic bacterial community using single-cell genomics. We generated partial assemblies of the host S. strix genome and Candidatus Ordinivivax streblomastigis, as well as a complex metagenome assembly of at least 8 other Bacteroidetes bacteria confirmed by ribosomal (r)RNA fluorescence in situ hybridization (FISH) to be associated with S. strix. Our data suggest that S. strix is probably not involved in the cellulose digestion, but the bacterial community on its surface secretes a complex array of glycosyl hydrolases, providing them with the ability to degrade cellulose to monomers and fueling the metabolism of S. strix In addition, some of the bacteria can fix nitrogen and can theoretically provide S. strix with essential amino acids and cofactors, which the protist cannot synthesize. On the contrary, most of the bacterial symbionts lack the essential glycolytic enzyme enolase, which may be overcome by the exchange of intermediates with S. strix This study demonstrates the value of the combined single-cell (meta)genomic and FISH approach for studies of complicated symbiotic systems.}, }
@article {pmid31492669, year = {2019}, author = {Zhou, K and Zhang, R and Sun, J and Zhang, W and Tian, RM and Chen, C and Kawagucci, S and Xu, Y}, title = {Potential SUP05-Phage Interactions in Hydrothermal Vent Sponges.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00992-19}, pmid = {31492669}, issn = {1098-5336}, abstract = {In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent-sponge-associated SUP05 and their phages have not been well documented. The current study analyzed the microbiome of Haplosclerida spp. sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially-symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05 and other symbiotic SUP05, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents, and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.Importance Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world,. SUP05 bacteria utilize the reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.}, }
@article {pmid31492667, year = {2019}, author = {Eckstein, S and Dominelli, N and Brachmann, A and Heermann, R}, title = {Phenotypic heterogeneity of insect pathogenic Photorhabdus luminescens - insights into the fate of secondary cells.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01910-19}, pmid = {31492667}, issn = {1098-5336}, abstract = {Photorhabdus luminescens are Gram-negative bacteria that live in symbiosis with soil nematodes and are simultaneously highly pathogenic towards insects. The bacteria exist in two phenotypically different forms, designated as primary (1°) and secondary (2°) cells. Yet unknown environmental stimuli as well as global stress conditions induce phenotypic switching of up to 50% of 1° to 2° cells. An important difference between the two phenotypic forms is that 2° cells are unable to live in symbiosis with nematodes and are therefore believed to remain in the soil after a successful infection cycle. In this work, we performed a transcriptomic analysis to highlight and better understand the role of 2° cells and their putative ability to adapt to a life in soil. We could confirm that the major phenotypic differences between the two cell forms are mediated at transcriptional level as the corresponding genes were down-regulated in 2° cells. Furthermore, 2° cells seem to be adapted to another environment as we found several differentially expressed genes involved in the cells' metabolism, motility and chemotaxis as well as stress resistance, which are either up- or down-regulated in 2° cells. As in contrast to 1° cells 2° cells chemotactically responded to different attractants including plant root exudates there is evidence for the rhizosphere as an alternative environment for the 2° cells. Since P. luminescens is biotechnologically used as bio-insecticide, investigation of a putative interaction of 2° cells with plants is also of great interest for agriculture.Importance The biological function and the fate of P. luminescens 2° cells was unclear. Here we performed comparative transcriptomics of P. luminescens 1° and 2° cultures and found several genes that are up- or down-regulated in 2° cells compared to 1° cells not only coding for known phenotypic differences of the two cell forms. Our results suggest that when 1° cells convert to 2° cells, they drastically change their way of life. Thus, 2° cells could easily adapt to an alternative environment such as a free live in the rhizosphere putatively utilizing plant derived compounds as nutrient source. Since 2° cells are not able to re-associate with the nematodes, an alternative lifestyle in the rhizosphere would be conceivable.}, }
@article {pmid31489370, year = {2019}, author = {Sakanaka, M and Hansen, ME and Gotoh, A and Katoh, T and Yoshida, K and Odamaki, T and Yachi, H and Sugiyama, Y and Kurihara, S and Hirose, J and Urashima, T and Xiao, JZ and Kitaoka, M and Fukiya, S and Yokota, A and Lo Leggio, L and Abou Hachem, M and Katayama, T}, title = {Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.}, journal = {Science advances}, volume = {5}, number = {8}, pages = {eaaw7696}, doi = {10.1126/sciadv.aaw7696}, pmid = {31489370}, issn = {2375-2548}, abstract = {The human gut microbiota established during infancy has persistent effects on health. In vitro studies have suggested that human milk oligosaccharides (HMOs) in breast milk promote the formation of a bifidobacteria-rich microbiota in infant guts; however, the underlying molecular mechanism remains elusive. Here, we characterized two functionally distinct but overlapping fucosyllactose transporters (FL transporter-1 and -2) from Bifidobacterium longum subspecies infantis. Fecal DNA and HMO consumption analyses, combined with deposited metagenome data mining, revealed that FL transporter-2 is primarily associated with the bifidobacteria-rich microbiota formation in breast-fed infant guts. Structural analyses of the solute-binding protein (SBP) of FL transporter-2 complexed with 2'-fucosyllactose and 3-fucosyllactose, together with phylogenetic analysis of SBP homologs of both FL transporters, highlight a unique adaptation strategy of Bifidobacterium to HMOs, in which the gain-of-function mutations enable FL transporter-2 to efficiently capture major fucosylated HMOs. Our results provide a molecular insight into HMO-mediated symbiosis and coevolution between bifidobacteria and humans.}, }
@article {pmid30249322, year = {2018}, author = {Chen, PW and Lin, YL and Huang, MS}, title = {Profiles of commensal and opportunistic bacteria in human milk from healthy donors in Taiwan.}, journal = {Journal of food and drug analysis}, volume = {26}, number = {4}, pages = {1235-1244}, doi = {10.1016/j.jfda.2018.03.004}, pmid = {30249322}, issn = {1021-9498}, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Humans ; *Microbiota ; Milk, Human/chemistry/*microbiology ; Phylogeny ; Symbiosis ; Taiwan ; Young Adult ; }, abstract = {Recent studies indicate that milk from healthy mothers may harbor potential probiotics. Nonetheless, the distribution of bacterial profiles in human milk samples in Taiwan is not fully understood. Therefore, with the aim to address this question, in this study, milk samples were collected from 33 healthy mothers (D1 to D33) visiting our hospital during a 6-month period. The milk microbiota was analyzed by a molecular approach (Illumina MiSeq sequencing). The results indicate that the milk samples have a unique profile and patterns of bacterial abundance levels. Moreover, in colostrum and transitional-milk samples, we detected 154 and 127 bacterial species, respectively, and these sets shared 42.6% of the bacterial species. The most common bacterial species among all milk samples were Staphylococcus epidermidis, Streptococcus lactarius, and Staphylococcus hominis, suggesting that the skin contamination route plays an important role in the composition of the milk microbiota. Nevertheless, four Lactobacillus species, Lactobacillus helveticus, Lactobacillus iners, Lactobacillus zeae, and Lactobacillus gasseri, were present in only 7 samples (21% prevalence), and bifidobacterial species were quite rare taxa among the present samples. The Staphylococcus aureus was detected in a total of 15 samples (45% prevalence), suggesting that this species may be commonly present in milk samples. In conclusion, each milk sample revealed a unique profile and patterns of bacterial abundance levels, and our data do not support the idea that lactobacilli and bifidobacteria are common and abundant in modern milk samples. Because none of the donors of the milk samples showed mastitis or any discomfort during the sampling process or at follow-up inspection, the microbiota of these milk samples is not likely to negatively affect its host. This study provides new information on the proportions of commensal bacteria in human milk in Taiwan.}, }
@article {pmid30165400, year = {2018}, author = {Gavelis, GS and Gile, GH}, title = {How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses.}, journal = {FEMS microbiology letters}, volume = {365}, number = {19}, pages = {}, doi = {10.1093/femsle/fny209}, pmid = {30165400}, issn = {1574-6968}, mesh = {*Biological Evolution ; Cyanobacteria/genetics/*physiology ; Directed Molecular Evolution ; Eukaryota/genetics/*physiology ; Genetic Engineering ; Humans ; Photosynthesis ; Plastids/*physiology ; *Symbiosis ; }, abstract = {Symbioses between phototrophs and heterotrophs (a.k.a 'photosymbioses') are extremely common, and range from loose and temporary associations to obligate and highly specialized forms. In the history of life, the most transformative was the 'primary endosymbiosis,' wherein a cyanobacterium was engulfed by a eukaryote and became genetically integrated as a heritable photosynthetic organelle, or plastid. By allowing the rise of algae and plants, this event dramatically altered the biosphere, but its remote origin over one billion years ago has obscured the sequence of events leading to its establishment. Here, we review the genetic, physiological and developmental hurdles involved in early primary endosymbiosis. Since we cannot travel back in time to witness these evolutionary junctures, we will draw on examples of unicellular eukaryotes (protists) spanning diverse modes of photosymbiosis. We also review experimental approaches that could be used to recreate aspects of early primary endosymbiosis on a human timescale.}, }
@article {pmid31485773, year = {2019}, author = {Feng, Z and Zhang, L and Wu, Y and Wang, L and Xu, M and Yang, M and Li, Y and Wei, G and Chou, M}, title = {The Rpf84 gene, encoding a ribosomal large subunit protein, RPL22, regulates symbiotic nodulation in Robinia pseudoacacia.}, journal = {Planta}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00425-019-03267-3}, pmid = {31485773}, issn = {1432-2048}, support = {2016YFD0800706//National Key Research and Development Program of China/ ; 31172252//National Natural Science Foundation of China (CN)/ ; 2016JM3004//Natural Science Foundation of Shaanxi Province/ ; }, abstract = {MAIN CONCLUSION: A homologue of the ribosomal protein L22e, Rpf84, regulates root nodule symbiosis by mediating the infection process of rhizobia and preventing bacteroids from degradation in Robinia pseudoacacia. Ribosomal proteins (RPs) are known to have extraribosomal functions, including developmental regulation and stress responses; however, the effects of RPs on symbiotic nodulation of legumes are still unclear. Ribosomal protein 22 of the large 60S subunit (RPL22), a non-typical RP that is only found in eukaryotes, has been shown to function as a tumour suppressor in animals. Here, a homologue of RPL22, Rpf84, was identified from the leguminous tree R. pseudoacacia. Subcellular localization assays showed that Rpf84 was expressed in the cytoplasm and nucleus. Knockdown of Rpf84 by RNA interference (RNAi) technology impaired the infection process and nodule development. Compared with the control, root and stem length, dry weight and nodule number per plant were drastically decreased in Rpf84-RNAi plants. The numbers of root hair curlings, infection threads and nodule primordia were also significantly reduced. Ultrastructure analyses showed that Rpf84-RNAi nodules contained fewer infected cells with fewer bacteria. In particular, remarkable deformation of bacteroids and fusion of multiple symbiosomes occurred in infected cells. By contrast, overexpression of Rpf84 promoted nodulation, and the overexpression nodules maintained a larger infection/differentiation region and had more infected cells filled with bacteroids than the control at 45 days post inoculation, suggesting a retarded ageing process in nodules. These results indicate for the first time that RP regulates the symbiotic nodulation of legumes and that RPL22 may function in initiating the invasion of rhizobia and preventing bacteroids from degradation in R. pseudoacacia.}, }
@article {pmid31484206, year = {2019}, author = {Huang, R and Li, Z and Mao, C and Zhang, H and Sun, Z and Li, H and Huang, C and Feng, Y and Shen, X and Bucher, M and Zhang, Z and Lin, Y and Cao, Y and Duanmu, D}, title = {Natural variation at OsCERK1 regulates arbuscular mycorrhizal symbiosis in rice.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.16158}, pmid = {31484206}, issn = {1469-8137}, abstract = {The symbiotic interaction between arbuscular mycorrhizal fungi (AMF) and land plants is essential for efficient nutrient acquisition and utilization. Our understanding of key processes controlling the AMF colonization in rice is still limited. Dongxiang wild rice (DY) exhibited a stronger colonization with Rhizophagus irregularis than the rice cultivar Zhongzao 35 (ZZ35). Chromosome-segment substitution lines were constructed and the OsCERK1 gene from DY was mapped. Transgenic plants in the japonica rice Zhonghua 11 (ZZ11) were constructed to compare root colonization by AMF. Chromosome single-segment substitution lines containing OsCERK1DY showed higher phosphorus content and grain yield relative to ZZ35. Four amino acids substitutions were identified among the OsCERK1 haplotypes of DY, ZZ35 and ZH11, and two of them were in the second lysin motif domain, which is essential for the differences of AMF colonization level among rice varieties. Heterologous expression of OsCERK1DY in ZH11 significantly enhanced AMF colonization and increased resistance against the pathogenic fungi Magnaporthe oryzae. Notably, the OsCERK1DY haplotype was absent from 4,660 cultivated rice varieties. We conclude that OsCERK1 is a key gene affecting the symbiotic interaction with AMF and OsCERK1DY has the biotechnological potential to increase rice phosphorus acquisition and utilization efficiency for sustainable agriculture. This article is protected by copyright. All rights reserved.}, }
@article {pmid31479939, year = {2019}, author = {Li, J and Wang, T and Yu, S and Bai, J and Qin, S}, title = {Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109459}, doi = {10.1016/j.jenvman.2019.109459}, pmid = {31479939}, issn = {1095-8630}, abstract = {Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.}, }
@article {pmid31479095, year = {2019}, author = {Azevedo, GPR and Paz, PHCD and Mattsson, HK and Moreira, APB and Leomil, L and Calegário, G and Appolinario, L and Vidal, L and Silva, BS and Tonon, LAC and Tschoeke, DA and Garcia, GD and Thompson, FL and Thompson, CC}, title = {[PROVISIONAL] Genome sequence of Shewanella corallii strain A687 isolated from pufferfish (Sphoeroides spengleri).}, journal = {Genetics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1590/1678-4685-GMB-2018-0314}, pmid = {31479095}, issn = {1415-4757}, abstract = {We present here the genome sequence of Shewanella corallii strain A687 isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae). The assembly consists of 5,215,037 bp and contains 284 contigs, with a G+C content of 50.3%. The genus Shewanella comprises 67 recognized species. These bacteria are Gram-negative, rod-shaped, facultatively anaerobic gammaproteobacteria and frequently isolated from marine environments (MacDonell &amp; Colwell, 1985, Sugimoto et al., 2018). Shewanella species are involved in the production of antimicrobial metabolites and tetrodotoxin, a strong neurotoxin (Simidu et al., 1990, Magarlamov et al., 2017, Matsui et al., 1989). Shewanella corallii was recorded from red sea coral (Shnit-Orland, 2010). The aim of the present study was to determine the genome sequence of Shewanella corallii strain A687. S. corallii A687 was isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae), in Arraial do Cabo (Brazil) in 2016. Genomic DNA was extracted using according to Pitcher's protocol (Pitcher et al., 1989) and used for 300-bp paired-end library preparation with Nextera XT DNA Sample Preparation Kit. The genome was sequenced using MiSeq (Illumina, San Diego, CA, USA) as previously described (Walter et al., 2016). Sequences obtained were pre-processed using PRINSEQ software to remove reads smaller than 35 bp and low-score sequences (Phred 30) (Schmieder &amp; Edwards, 2011). Sequence reads were assembled using A5-Miseq (Coil et al., 2015) and CAP3 software (Huang &amp; Madan, 1999). The gene prediction and functional annotation were performed using the RAST server (Overbeek et al., 2014). Secondary metabolism was analyzed by antiSMASH (Weber et al., 2015) and clustered regularly interspaced short palindromic repeat (CRISPR) arrays were determined with CRISPRFinder (Grissa et al., 2007). The sequencing generated a total of 4,557,272 reads and 768,079,097 bp that were assembled in 284 contigs (N50=298,540 bp). The estimated genome size is 5,215,037 bp with G+C of 50.3%, and a coverage of 146-fold. RAST predicted 4,555 coding sequences, and 175 RNA sequences (147 tRNAs, 11 16S rRNAs, 6 23S rRNAs, and 11 5S rRNAs). Analyzing the genes predicted by RAST, a total of 74 genes were involved in resistance to antibiotics and toxic compounds including copper homeostasis (N=8); bile hydrolysis (N=2); cobalt-zinc-cadmium resistance (N=20); resistance to fluoroquinolones (N=4); arsenic resistance (N=4); copper homeostasis: copper tolerance (N=6); tetracycline resistance, ribosome protection type II (N=2); beta-lactamase (N=5); multidrug resistance efflux pumps (N=22); resistance to chromium compounds (N=1); 24 genes for the metabolism of aromatic compounds, including salicylate ester, chloroaromatic and quinate degradation. Phage elements sequences (N=44) were found in this genome, and CRISPRs arrays candidates were predicted in four sequences. We searched through subsystems for genes associated to symbiosis. Genes encoding type I, (lapBCDE, lapL, lapP, RTX and TolC) and type II (TadA, TadB, TadC, VirB11, RcpC, CpaB and CpaF) secretion systems were detected. We also identified 16 genes related to vitamin B12 synthesis and four LuxR gene families (Bondarev et al., 2013).}, }
@article {pmid31478269, year = {2019}, author = {Breusing, C and Johnson, SB and Vrijenhoek, RC and Young, CR}, title = {Host hybridization as a potential mechanism of lateral symbiont transfer in deep-sea vesicomyid clams.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15224}, pmid = {31478269}, issn = {1365-294X}, abstract = {Deep-sea vesicomyid clams live in mutualistic symbiosis with chemosynthetic bacteria that are inherited through the maternal germ line. On evolutionary timescales, strictly vertical transmission should lead to co-speciation of host mitochondrial and symbiont lineages; nonetheless, examples of incongruent phylogenies have been reported, suggesting that symbionts are occasionally horizontally transmitted between host species. The current paradigm for vesicomyid clams holds that direct transfers cause host shifts or mixtures of symbionts. An alternative hypothesis suggests that hybridization between host species might explain symbiont transfers. Two clam species, Archivesica gigas and Phreagena soyoae, frequently co-occur at deep-sea hydrocarbon seeps in the eastern Pacific Ocean. Although the two species typically host gammaproteobacterial symbiont lineages marked by divergent 16S rRNA phylotypes, we identified a number of clams with the A. gigas mitotype that hosted symbionts with the P. soyoae phylotype. Demographic inference models based on genome-wide SNP data and three Sanger sequenced gene markers provided evidence that A. gigas and P. soyoae hybridized in the past, supporting the hypothesis that hybridization might be a viable mechanism of inter-specific symbiont transfer. These findings provide new perspectives on the evolution of vertically transmitted symbionts and their hosts in deep-sea chemosynthetic environments. This article is protected by copyright. All rights reserved.}, }
@article {pmid31477892, year = {2019}, author = {Müller, LM and Flokova, K and Schnabel, E and Sun, X and Fei, Z and Frugoli, J and Bouwmeester, HJ and Harrison, MJ}, title = {A CLE-SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41477-019-0501-1}, pmid = {31477892}, issn = {2055-0278}, abstract = {During arbuscular mycorrhizal symbiosis, colonization of the root is modulated in response to the physiological status of the plant, with regulation occurring locally and systemically. Here, we identify differentially expressed genes encoding CLAVATA3/ESR-related (CLE) peptides that negatively regulate colonization levels by modulating root strigolactone content. CLE function requires a receptor-like kinase, SUNN; thus, a CLE-SUNN-strigolactone feedback loop is one avenue through which the plant modulates colonization levels.}, }
@article {pmid31477738, year = {2019}, author = {Ibny, FYI and Jaiswal, SK and Mohammed, M and Dakora, FD}, title = {Symbiotic effectiveness and ecologically adaptive traits of native rhizobial symbionts of Bambara groundnut (Vigna subterranea L. Verdc.) in Africa and their relationship with phylogeny.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12666}, doi = {10.1038/s41598-019-48944-1}, pmid = {31477738}, issn = {2045-2322}, abstract = {Bambara groundnut (Vigna subterranea L. Verdc.) is an indigenous, drought-tolerant, underutilized African food legume, with the ability to fix atmospheric N2 in symbiosis with soil bacteria called rhizobia. The aim of this study was to assess the morpho-physiological, symbiotic and phylogenetic characteristics of rhizobia nodulating Bambara groundnut in Ghana, Mali and South Africa. The morpho-physiologically diverse isolates tested were also found to exhibit differences in functional efficiency and phylogenetic positions. Based on Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR banding patterns, the isolates were grouped into eight major clusters. The concentrations of Ca, Na and K in soils had a significant (p ≤ 0.01) effect on the distribution of rhizobia. Though many isolates were symbiotically very effective, the effectiveness index varied markedly (p ≤ 0.05) among them. Moreover, the isolates also exhibited tolerance to a wide range of NaCl (0.5-7%), streptomycin (50-500 µg.ml-1), and kanamycin (25-150 µg.ml-1) concentrations. Additionally, these isolates could produce 0.02 to 69.71 µg.ml-1 of indole-3-acetic acid (IAA) in tryptophan-supplemented medium, as well as solubilize tri-calcium phosphate. Phylogenetic analysis of these rhizobial isolates using 16S rRNA, atpD, glnII, gyrB, recA and symbiotic (nifH and nodC) gene sequences revealed distinct and novel evolutionary lineages related to the genus Bradyrhizobium, with some of them being very close to Bradyrhizobium vignae, B. kavangense, B. subterraneum, B. elkanii and B. pachyrhizi.}, }
@article {pmid31477173, year = {2019}, author = {Attardo, GM and Abd-Alla, AMM and Acosta-Serrano, A and Allen, JE and Bateta, R and Benoit, JB and Bourtzis, K and Caers, J and Caljon, G and Christensen, MB and Farrow, DW and Friedrich, M and Hua-Van, A and Jennings, EC and Larkin, DM and Lawson, D and Lehane, MJ and Lenis, VP and Lowy-Gallego, E and Macharia, RW and Malacrida, AR and Marco, HG and Masiga, D and Maslen, GL and Matetovici, I and Meisel, RP and Meki, I and Michalkova, V and Miller, WJ and Minx, P and Mireji, PO and Ometto, L and Parker, AG and Rio, R and Rose, C and Rosendale, AJ and Rota-Stabelli, O and Savini, G and Schoofs, L and Scolari, F and Swain, MT and Takáč, P and Tomlinson, C and Tsiamis, G and Van Den Abbeele, J and Vigneron, A and Wang, J and Warren, WC and Waterhouse, RM and Weirauch, MT and Weiss, BL and Wilson, RK and Zhao, X and Aksoy, S}, title = {Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {187}, doi = {10.1186/s13059-019-1768-2}, pmid = {31477173}, issn = {1474-760X}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; U01AI115648/NH/NIH HHS/United States ; R01AI051584/NH/NIH HHS/United States ; R03TW008413/NH/NIH HHS/United States ; R03TW009444/NH/NIH HHS/United States ; R21AI109263//National Institute of Allergy and Infectious Diseases/International ; U54HG003079/HG/NHGRI NIH HHS/United States ; }, abstract = {BACKGROUND: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.<br><br>RESULTS: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.<br><br>CONCLUSIONS: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.}, }
@article {pmid31475981, year = {2019}, author = {Wardhani, TAK and Roswanjaya, YP and Dupin, S and Li, H and Linders, S and Hartog, M and Geurts, R and van Zeijl, A}, title = {Transforming, Genome Editing and Phenotyping the Nitrogen-fixing Tropical Cannabaceae Tree Parasponia andersonii.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {150}, pages = {}, doi = {10.3791/59971}, pmid = {31475981}, issn = {1940-087X}, abstract = {Parasponia andersonii is a fast-growing tropical tree that belongs to the Cannabis family (Cannabaceae). Together with 4 additional species, it forms the only known non-legume lineage able to establish a nitrogen-fixing nodule symbiosis with rhizobium. Comparative studies between legumes and P. andersonii could provide valuable insight into the genetic networks underlying root nodule formation. To facilitate comparative studies, we recently sequenced the P. andersonii genome and established Agrobacterium tumefaciens-mediated stable transformation and CRISPR/Cas9-based genome editing. Here, we provide a detailed description of the transformation and genome editing procedures developed for P. andersonii. In addition, we describe procedures for the seed germination and characterization of symbiotic phenotypes. Using this protocol, stable transgenic mutant lines can be generated in a period of 2-3 months. Vegetative in vitro propagation of T0 transgenic lines allows phenotyping experiments to be initiated at 4 months after A. tumefaciens co-cultivation. Therefore, this protocol takes only marginally longer than the transient Agrobacterium rhizogenes-based root transformation method available for P. andersonii, though offers several clear advantages. Together, the procedures described here permit P. andersonii to be used as a research model for studies aimed at understanding symbiotic associations as well as potentially other aspects of the biology of this tropical tree.}, }
@article {pmid31475451, year = {2019}, author = {Hu, Y and Linz, DM and Parker, ES and Schwab, DB and Casasa, S and Macagno, ALM and Moczek, AP}, title = {Developmental bias in horned dung beetles and its contributions to innovation, adaptation, and resilience.}, journal = {Evolution &amp; development}, volume = {}, number = {}, pages = {}, doi = {10.1111/ede.12310}, pmid = {31475451}, issn = {1525-142X}, support = {//National Science Foundation/ ; //John Templeton Foundation/ ; }, abstract = {Developmental processes transduce diverse influences during phenotype formation, thereby biasing and structuring amount and type of phenotypic variation available for evolutionary processes to act on. The causes, extent, and consequences of this bias are subject to significant debate. Here we explore the role of developmental bias in contributing to organisms' ability to innovate, to adapt to novel or stressful conditions, and to generate well integrated, resilient phenotypes in the face of perturbations. We focus our inquiry on one taxon, the horned dung beetle genus Onthophagus, and review the role developmental bias might play across several levels of biological organization: (a) gene regulatory networks that pattern specific body regions; (b) plastic developmental mechanisms that coordinate body wide responses to changing environments and; (c) developmental symbioses and niche construction that enable organisms to build teams and to actively modify their own selective environments. We posit that across all these levels developmental bias shapes the way living systems innovate, adapt, and withstand stress, in ways that can alternately limit, bias, or facilitate developmental evolution. We conclude that the structuring contribution of developmental bias in evolution deserves further study to better understand why and how developmental evolution unfolds the way it does.}, }
@article {pmid31474965, year = {2019}, author = {Chang, ACG and Chen, T and Li, N and Duan, J}, title = {Perspectives on Endosymbiosis in Coralloid Roots: Association of Cycads and Cyanobacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1888}, doi = {10.3389/fmicb.2019.01888}, pmid = {31474965}, issn = {1664-302X}, abstract = {Past endosymbiotic events allowed photosynthetic organisms to flourish and evolve in terrestrial areas. The precursor of chloroplasts was an ancient photosynthetic cyanobacterium. Presently, cyanobacteria are still capable of establishing successful symbioses in a wide range of hosts. One particular host plant among the gymnosperms is cycads (Order Cycadales) in which a special type of root system, referred to as coralloid roots, develops to house symbiotic cyanobacteria. A number of studies have explained coralloid root formation and cyanobiont invasion but the questions on mechanisms of this host-microbe association remains vague. Most researches focus on diversity of symbionts in coralloid roots but equally important is to explore the underlying mechanisms of cycads-Nostoc symbiosis as well. Besides providing an overview of relevant areas presently known about this association and citing putative genes involved in cycad-cyanobacteria symbioses, this paper aims to identify the limitations that hamper attempts to get to the root of the matter and suggests future research directions that may prove useful.}, }
@article {pmid31474946, year = {2019}, author = {Beinart, RA and Luo, C and Konstantinidis, KT and Stewart, FJ and Girguis, PR}, title = {The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1818}, doi = {10.3389/fmicb.2019.01818}, pmid = {31474946}, issn = {1664-302X}, abstract = {Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.}, }
@article {pmid31474535, year = {2019}, author = {Weber, PM and Moessel, F and Paredes, GF and Viehboeck, T and Vischer, NOE and Bulgheresi, S}, title = {A Bidimensional Segregation Mode Maintains Symbiont Chromosome Orientation toward Its Host.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.07.064}, pmid = {31474535}, issn = {1879-0445}, abstract = {All living organisms require accurate segregation of their genetic material. However, in microbes, chromosome segregation is less understood than replication and cell division, which makes its decipherment a compelling research frontier. Furthermore, it has only been studied in free-living microbes so far. Here, we investigated this fundamental process in a rod-shaped symbiont, Candidatus Thiosymbion oneisti. This gammaproteobacterium divides longitudinally as to form a columnar epithelium ensheathing its nematode host. We hypothesized that uninterrupted host attachment would affect bacterial chromosome dynamics and set out to localize specific chromosomal loci and putative DNA-segregating proteins by fluorescence in situ hybridization and immunostaining, respectively. First, DNA replication origins (ori) number per cell demonstrated symbiont monoploidy. Second, we showed that sister ori segregate diagonally prior to septation onset. Moreover, the localization pattern of the centromere-binding protein ParB recapitulates that of ori, and consistently, we showed recombinant ParB to specifically bind an ori-proximal site (parS) in vitro. Third, chromosome replication ends prior to cell fission, and as the poles start to invaginate, termination of replication (ter) sites localize medially, at the leading edges of the growing septum. They then migrate to midcell, concomitantly with septation progression and until this is completed. In conclusion, we propose that symbiont ParB might drive chromosome segregation along the short axis and that tethering of sister ter regions to the growing septum mediates their migration along the long axis. Crucially, active bidimensional segregation of the chromosome allows transgenerational maintenance of its configuration, and therefore, it may represent an adaptation to symbiosis. VIDEO ABSTRACT.}, }
@article {pmid31471999, year = {2019}, author = {Khemaissia, H and Jelassi, R and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Evaluation of trace element contamination using Armadillo officinalis Duméril, 1816 (Crustacea, Isopoda) as a tool: An ultrastructural study.}, journal = {Microscopy research and technique}, volume = {}, number = {}, pages = {}, doi = {10.1002/jemt.23371}, pmid = {31471999}, issn = {1097-0029}, abstract = {To estimate trace element bioaccumulation in Armadillo officinalis, specimens were collected from Ghar El Melh lagoon then exposed for 3 weeks in contaminated sediments with copper, zinc, and cadmium. From the first week until the end of the experiment, a decrease in A. officinalis growth related to the increase of Cd concentration in the sediment was recorded. However, a mass gain was highlighted under Cu and Zn exposures. At the end of experiment, body metal concentrations were measured using flame atomic emission spectrometry. Results of the bioaccumulation factor showed that the species could be considered as a macroconcentrator of copper (BAF > 2) and a deconcentrator of zinc (BAF < 2). Microscopy observations of hepatopancreas cells showed morphological and histological changes even at the lowest concentration. They consisted in the microvillus border destruction, lipid droplets modifications, trace element accumulation, and the condensation of the majority of cellular organelles. The degree of these alterations was found to be dose-dependent. Through these results, the isopod A. officinalis could be used as relevant monitor organisms for soil metal contamination.}, }
@article {pmid31468195, year = {2019}, author = {Cui, Y and Gao, J and He, Y and Jiang, L}, title = {Plant extracellular vesicles.}, journal = {Protoplasma}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00709-019-01435-6}, pmid = {31468195}, issn = {1615-6102}, support = {AoE/M-05/12, CUHK14130716, 14102417, 14100818, 14104716, C4012-16E, C4002-17G, and RIF R4005-18//Chinese University of Hong Kong/ ; 31670179 and 91854201//National Natural Science Foundation of China/ ; }, abstract = {Exocytosis is a key mechanism for delivering materials into the extracellular space for cell function and communication. In plant cells, conventional protein secretion (CPS) is achieved via an ER (endoplasmic reticulum)-Golgi-TGN (trans-Golgi network)-PM (plasma membrane) pathway. Unconventional protein secretion (UPS) bypassing these secretory organelles is also in operation and can potentially lead to the formation of extracellular vesicles (EVs) in plant cells. Although multiple types of EVs have been identified and shown to play important roles in mediating intercellular communications in mammalian cells, there has been a long debate about the possible existence of EVs in plants because of the presence of the cell wall. However, increasing evidence suggests that plants also release EVs having various functions including unconventional protein secretion, RNA transport, and defense against pathogens. In this review, we present an update on the current knowledge about the nature, secretory mechanism, and function of various types of EVs in plants. The key regulators involved in EV secretion are also summarized and discussed. We pay special attention to the function of EVs in plant defense and symbiosis.}, }
@article {pmid31465455, year = {2019}, author = {Tikhonenkov, DV and Jhin, SH and Eglit, Y and Miller, K and Plotnikov, A and Simpson, AGB and Park, JS}, title = {Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0216188}, doi = {10.1371/journal.pone.0216188}, pmid = {31465455}, issn = {1932-6203}, abstract = {The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide, from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rRNA gene phylogenies, unlike most previous analyses based on two sequences.}, }
@article {pmid31464214, year = {2019}, author = {Shah, S and Darekar, B and Salvi, S and Kowale, A}, title = {Quadriceps strength in patients with chronic obstructive pulmonary disease.}, journal = {Lung India : official organ of Indian Chest Society}, volume = {36}, number = {5}, pages = {417-421}, doi = {10.4103/lungindia.lungindia_27_19}, pmid = {31464214}, issn = {0970-2113}, abstract = {Background: Skeletal muscle dysfunction is well known in chronic obstructive pulmonary disease (COPD). The muscle strength is altered in various muscles variedly. Lower-limb muscle strength is very important for walking distance. Reduced lower-limb strength can affect the physical quality of life.<br><br>Objectives: The aim of the study was to assess and compare the quadriceps strength in COPD patients and age-matched healthy controls and to study the correlation between lung function parameters and the quadriceps strength in patients with COPD.<br><br>Methodology: Thirty nonsmoker male patients; thirty nonsmoker female patients with COPD; and sixty age-, BMI-, and gender-matched healthy controls were studied. Quadriceps muscle strength was measured using a quadriceps dynamometer. Forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), FEF 25-75, and peak expiratory flow rate were measured using Helios 702 Spirometer. The quadriceps muscle strength between the two groups was compared using the unpaired Student's t-test. Correlations between FVC and FEV1with muscle strength were analyzed using the Pearson's coefficient.<br><br>Results: The mean unilateral and bilateral quadriceps strength in both male and female COPD patients was significantly lesser than the healthy controls (P < 0.05). There was a significant positive correlation between muscle strength and FVC and muscle strength and FEV1in patients with COPD.<br><br>Conclusion: The study shows that there is quadriceps weakness in COPD patients, and pulmonary functions have a direct impact on skeletal muscle strength. Identifying those patients who have reduced strength will allow early interventions targeted at improving the quality of life of the patient.}, }
@article {pmid31463869, year = {2019}, author = {Monteiro, PHR and Kaschuk, G and Winagraski, E and Auer, CG and Higa, AR}, title = {Rhizobial inoculation in black wattle plantation (Acacia mearnsii De Wild.) in production systems of southern Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00148-5}, pmid = {31463869}, issn = {1678-4405}, abstract = {Black wattle (Acacia mearnsii De Wild.) is a tree legume native to southeast Australia, but present in all continents. Today it covers about 142,400 ha in Brazil, with plantations concentrated in the southern region of the country. Black wattle may form nodules and establish rhizobial symbiosis capable of fixing N2, but rhizobial inoculation is not done in commercial plantations. About 40 kg ha-1 of urea is applied during seedling transplantation. In this review, evidences by which rhizobial inoculation affects monoculture, mixed cultivation, and agroforestry black wattle production systems were searched in literature. Previous measurements in cultivated forests have indicated that biological nitrogen fixation in black wattle may provide up to 200 kg of N ha-1 year-1 to the soil. Therefore, rhizobia inoculation may bring several opportunities to improve black wattle production systems. Black wattle is not a very selective partner in the rhizobial symbiosis, but the genus Bradyrhizobium dominates the rhizobial diversity of black wattle nodules. Investigation on rhizobial diversity in soils where the crop is cultivated may represent an opportunity to find more effective rhizobia strains for inoculants. The successful history of biological nitrogen fixation in grain legumes must inspire the history of tree legumes. Microbiology applied to forestry must overcome challenges on the lack of trained professionals and the development of new application technologies.}, }
@article {pmid31463006, year = {2019}, author = {Couret, J and Huynh-Griffin, L and Antolic-Soban, I and Acevedo-Gonzalez, TS and Gerardo, NM}, title = {Even obligate symbioses show signs of ecological contingency: Impacts of symbiosis for an invasive stinkbug are mediated by host plant context.}, journal = {Ecology and evolution}, volume = {9}, number = {16}, pages = {9087-9099}, doi = {10.1002/ece3.5454}, pmid = {31463006}, issn = {2045-7758}, abstract = {Abstract: Many species interactions are dependent on environmental context, yet the benefits of obligate, mutualistic microbial symbioses to their hosts are typically assumed to be universal across environments. We directly tested this assumption, focusing on the symbiosis between the sap-feeding insect Megacopta cribraria and its primary bacterial symbiont Candidatus Ishikawaella capsulata. We assessed host development time, survival, and body size in the presence and absence of the symbiont on two alternative host plants and in the insects' new invasive range. We found that association with the symbiont was critical for host survival to adulthood when reared on either host plant, with few individuals surviving in the absence of symbiosis. Developmental differences between hosts with and without microbial symbionts, however, were mediated by the host plants on which the insects were reared. Our results support the hypothesis that benefits associated with this host-microbe interaction are environmentally contingent, though given that few individuals survive to adulthood without their symbionts, this may have minimal impact on ecological dynamics and current evolutionary trajectories of these partners.<br><br>OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.kg4bc56.}, }
@article {pmid31461957, year = {2019}, author = {Bahadur, A and Batool, A and Nasir, F and Jiang, S and Mingsen, Q and Zhang, Q and Pan, J and Liu, Y and Feng, H}, title = {Mechanistic Insights into Arbuscular Mycorrhizal Fungi-Mediated Drought Stress Tolerance in Plants.}, journal = {International journal of molecular sciences}, volume = {20}, number = {17}, pages = {}, doi = {10.3390/ijms20174199}, pmid = {31461957}, issn = {1422-0067}, support = {41430749//National Natural Science Foundation of China/ ; 31670433//National Natural Science Foundation of China/ ; 31470524//National Natural Science Foundation of China/ ; 31500427//National Natural Science Foundation of China/ ; 31570512//National Natural Science Foundation of China/ ; 2014 T70949//China Postdoctoral Science Foundation/ ; 2015 M582735//China Postdoctoral Science Foundation/ ; SKLFSE200901//State Key Laboratory of Frozen Soil Engineering/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) establish symbiotic interaction with 80% of known land plants. It has a pronounced impact on plant growth, water absorption, mineral nutrition, and protection from abiotic stresses. Plants are very dynamic systems having great adaptability under continuously changing drying conditions. In this regard, the function of AMF as a biological tool for improving plant drought stress tolerance and phenotypic plasticity, in terms of establishing mutualistic associations, seems an innovative approach towards sustainable agriculture. However, a better understanding of these complex interconnected signaling pathways and AMF-mediated mechanisms that regulate the drought tolerance in plants will enhance its potential application as an innovative approach in environmentally friendly agriculture. This paper reviews the underlying mechanisms that are confidently linked with plant-AMF interaction in alleviating drought stress, constructing emphasis on phytohormones and signaling molecules and their interaction with biochemical, and physiological processes to maintain the homeostasis of nutrient and water cycling and plant growth performance. Likewise, the paper will analyze how the AMF symbiosis helps the plant to overcome the deleterious effects of stress is also evaluated. Finally, we review how interactions between various signaling mechanisms governed by AMF symbiosis modulate different physiological responses to improve drought tolerance. Understanding the AMF-mediated mechanisms that are important for regulating the establishment of the mycorrhizal association and the plant protective responses towards unfavorable conditions will open new approaches to exploit AMF as a bioprotective tool against drought.}, }
@article {pmid31456765, year = {2019}, author = {Balestrini, R and Rosso, LC and Veronico, P and Melillo, MT and De Luca, F and Fanelli, E and Colagiero, M and di Fossalunga, AS and Ciancio, A and Pentimone, I}, title = {Transcriptomic Responses to Water Deficit and Nematode Infection in Mycorrhizal Tomato Roots.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1807}, doi = {10.3389/fmicb.2019.01807}, pmid = {31456765}, issn = {1664-302X}, abstract = {Climate changes include the intensification of drought in many parts of the world, increasing its frequency, severity and duration. However, under natural conditions, environmental stresses do not occur alone, and, in addition, more stressed plants may become more susceptible to attacks by pests and pathogens. Studies on the impact of the arbuscular mycorrhizal (AM) symbiosis on tomato response to water deficit showed that several drought-responsive genes are differentially regulated in AM-colonized tomato plants (roots and leaves) during water deficit. To date, global changes in mycorrhizal tomato root transcripts under water stress conditions have not been yet investigated. Here, changes in root transcriptome in the presence of an AM fungus, with or without water stress (WS) application, have been evaluated in a commercial tomato cultivar already investigated for the water stress response during AM symbiosis. Since root-knot nematodes (RKNs, Meloidogyne incognita) are obligate endoparasites and cause severe yield losses in tomato, the impact of the AM fungal colonization on RKN infection at 7 days post-inoculation was also evaluated. Results offer new information about the response to AM symbiosis, highlighting a functional redundancy for several tomato gene families, as well as on the tomato and fungal genes involved in WS response during symbiosis, underlying the role of the AM fungus. Changes in the expression of tomato genes related to nematode infection during AM symbiosis highlight a role of AM colonization in triggering defense responses against RKN in tomato. Overall, new datasets on the tomato response to an abiotic and biotic stress during AM symbiosis have been obtained, providing useful data for further researches.}, }
@article {pmid31455640, year = {2019}, author = {Creekmore, BC and Gray, JH and Walton, WG and Biernat, KA and Little, MS and Xu, Y and Liu, J and Gharaibeh, RZ and Redinbo, MR}, title = {Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00452-19}, pmid = {31455640}, issn = {2379-5077}, abstract = {Gut microbial β-glucuronidase (GUS) enzymes play important roles in drug efficacy and toxicity, intestinal carcinogenesis, and mammalian-microbial symbiosis. Recently, the first catalog of human gut GUS proteins was provided for the Human Microbiome Project stool sample database and revealed 279 unique GUS enzymes organized into six categories based on active-site structural features. Because mice represent a model biomedical research organism, here we provide an analogous catalog of mouse intestinal microbial GUS proteins-a mouse gut GUSome. Using metagenome analysis guided by protein structure, we examined 2.5 million unique proteins from a comprehensive mouse gut metagenome created from several mouse strains, providers, housing conditions, and diets. We identified 444 unique GUS proteins and organized them into six categories based on active-site features, similarly to the human GUSome analysis. GUS enzymes were encoded by the major gut microbial phyla, including Firmicutes (60%) and Bacteroidetes (21%), and there were nearly 20% for which taxonomy could not be assigned. No differences in gut microbial gus gene composition were observed for mice based on sex. However, mice exhibited gus differences based on active-site features associated with provider, location, strain, and diet. Furthermore, diet yielded the largest differences in gus composition. Biochemical analysis of two low-fat-associated GUS enzymes revealed that they are variable with respect to their efficacy of processing both sulfated and nonsulfated heparan nonasaccharides containing terminal glucuronides.IMPORTANCE Mice are commonly employed as model organisms of mammalian disease; as such, our understanding of the compositions of their gut microbiomes is critical to appreciating how the mouse and human gastrointestinal tracts mirror one another. GUS enzymes, with importance in normal physiology and disease, are an attractive set of proteins to use for such analyses. Here we show that while the specific GUS enzymes differ at the sequence level, a core GUSome functionality appears conserved between mouse and human gastrointestinal bacteria. Mouse strain, provider, housing location, and diet exhibit distinct GUSomes and gus gene compositions, but sex seems not to affect the GUSome. These data provide a basis for understanding the gut microbial GUS enzymes present in commonly used laboratory mice. Further, they demonstrate the utility of metagenome analysis guided by protein structure to provide specific sets of functionally related proteins from whole-genome metagenome sequencing data.}, }
@article {pmid31455638, year = {2019}, author = {Lim, SJ and Alexander, L and Engel, AS and Paterson, AT and Anderson, LC and Campbell, BJ}, title = {Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00280-19}, pmid = {31455638}, issn = {2379-5077}, abstract = {Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data to resolve symbiont taxonomic, genetic, and functional diversity from Ctena orbiculata endosymbiont populations inhabiting carbonate-rich sediment at Sugarloaf Key, FL (USA). The sediment had mixed seagrass and calcareous green alga coverage and also was colonized by at least five other lucinid species. Four coexisting, thioautotrophic endosymbiont operational taxonomic units (OTUs), likely representing four strains from two different bacterial species, were identified from C. orbiculata Three of these OTUs also occurred at high relative abundances in the other sympatric lucinid species. Interspecies genetic differences averaged about 5% lower at both pairwise average nucleotide identity and amino acid identity than interstrain differences. Despite these genetic differences, C. orbiculata endosymbionts shared a high number of metabolic functions, including highly expressed thioautotrophy-related genes and a moderately to weakly expressed conserved one-carbon (C1) oxidation gene cluster previously undescribed in lucinid symbionts. Few symbiont- and host-related genes, including those encoding symbiotic sulfurtransferase, host respiratory functions, and host sulfide oxidation functions, were differentially expressed between seagrass- and alga-covered sediment locations. In contrast to previous studies, the identification of multiple endosymbiont taxa within and across C. orbiculata individuals, which were also shared with other sympatric lucinid species, suggests that neither host nor endosymbiont displays strict taxonomic specificity. This necessitates further investigations into the nature and extent of specificity of lucinid hosts and their symbionts.IMPORTANCE Symbiont diversity and host/symbiont functions have been comprehensively profiled for only a few lucinid species. In this work, unprecedented thioautotrophic gill endosymbiont taxonomic diversity was characterized within a Ctena orbiculata population associated with both seagrass- and alga-covered sediments. Endosymbiont metabolisms included known chemosynthetic functions and an additional conserved, previously uncharacterized C1 oxidation pathway. Lucinid-symbiont associations were not species specific because this C. orbiculata population hosted multiple endosymbiont strains and species, and other sympatric lucinid species shared overlapping symbiont 16S rRNA gene diversity profiles with C. orbiculata Our results suggest that lucinid-symbiont association patterns within some host species could be more taxonomically diverse than previously thought. As such, this study highlights the importance of holistic analyses, at the population, community, and even ecosystem levels, in understanding host-microbe association patterns.}, }
@article {pmid31450847, year = {2019}, author = {Wang, F and Sun, Y and Shi, Z}, title = {Arbuscular Mycorrhiza Enhances Biomass Production and Salt Tolerance of Sweet Sorghum.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090289}, pmid = {31450847}, issn = {2076-2607}, support = {41471395//National Natural Science Foundation of China/ ; 154100510010//Plan for Scientific Innovation Talent of Henan Province/ ; 0100229003//Doctoral Foundation of QUST/ ; Qian Jiao He KY Zi[2017]010//Education Department of Guizhou Province Key Laboratory of Soil Resources and Environment in Qianbei of Guizhou Province/ ; }, abstract = {Arbuscular mycorrhizal (AM) fungi (AMF) are widely known to form a symbiosis with most higher plants and enhance plant adaptation to a series of environmental stresses. Sweet sorghum (Sorghum bicolor (L.) Moench) is considered a promising alternative feedstock for bioalcohol production because of its sugar-rich stalk and high biomass. However, little is known of AMF benefit for biomass production and salt tolerance of sweet sorghum. Here, we investigated the effects of Acaulosporamellea ZZ on growth and salt tolerance in two sweet sorghum cultivars (Liaotian5 and Yajin2) under different NaCl addition levels (0, 0.5, 1, 2, and 3 g NaCl/kg soil). Results showed AMF colonized the two cultivars well under all NaCl addition levels. NaCl addition increased mycorrhizal colonization rates in Yajin2, but the effects on Liaotian5 ranged from stimulatory at 0.5 and 1 g/kg to insignificant at 2 g/kg, and even inhibitory at 3 g/kg. High NaCl addition levels produced negative effects on both AM and non-AM plants, leading to lower biomass production, poorer mineral nutrition (N, P, K), higher Na+ uptake, and lower soluble sugar content in leaves. Compared with non-AM plants, AM plants of both cultivars had improved plant biomass and mineral uptake, as well as higher K+/Na+ ratio, but only Yajin2 plants had a low shoot/root Na ratio. AM inoculation increased the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and soluble sugar content in leaves. Overall, both cultivars benefited from mycorrhization, and Yajin2 with less salt tolerance showed higher mycorrhizal response. In conclusion, AMF could help to alleviate the negative effects caused by salinity, and thus showed potential in biomass production of sweet sorghum in saline soil.}, }
@article {pmid31450827, year = {2019}, author = {Bi, Y and Wang, F and Zhang, W}, title = {Omics Analysis for Dinoflagellates Biology Research.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090288}, pmid = {31450827}, issn = {2076-2607}, support = {2018YFA0903000 and 2018YFA0903600//National Key R&amp;D Program of China/ ; 31770100, 91751102, 21621004, 31370115 and 31470217//National Natural Science Foundation of China/ ; }, abstract = {Dinoflagellates are important primary producers for marine ecosystems and are also responsible for certain essential components in human foods. However, they are also notorious for their ability to form harmful algal blooms, and cause shellfish poisoning. Although much work has been devoted to dinoflagellates in recent decades, our understanding of them at a molecular level is still limited owing to some of their challenging biological properties, such as large genome size, permanently condensed liquid-crystalline chromosomes, and the 10-fold lower ratio of protein to DNA than other eukaryotic species. In recent years, omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have been applied to the study of marine dinoflagellates and have uncovered many new physiological and metabolic characteristics of dinoflagellates. In this article, we review recent application of omics technologies in revealing some of the unusual features of dinoflagellate genomes and molecular mechanisms relevant to their biology, including the mechanism of harmful algal bloom formations, toxin biosynthesis, symbiosis, lipid biosynthesis, as well as species identification and evolution. We also discuss the challenges and provide prospective further study directions and applications of dinoflagellates.}, }
@article {pmid31450667, year = {2019}, author = {Chakraborty, S and Nguyen, B and Wasti, SD and Xu, G}, title = {Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK): Structure, Ligand Perception, and Activation Mechanism.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/molecules24173081}, pmid = {31450667}, issn = {1420-3049}, abstract = {In recent years, secreted peptides have been recognized as essential mediators of intercellular communication which governs plant growth, development, environmental interactions, and other mediated biological responses, such as stem cell homeostasis, cell proliferation, wound healing, hormone sensation, immune defense, and symbiosis, among others. Many of the known secreted peptide ligand receptors belong to the leucine-rich repeat receptor kinase (LRR-RK) family of membrane integral receptors, which contain more than 200 members within Arabidopsis making it the largest family of plant receptor kinases (RKs). Genetic and biochemical studies have provided valuable data regarding peptide ligands and LRR-RKs, however, visualization of ligand/LRR-RK complex structures at the atomic level is vital to understand the functions of LRR-RKs and their mediated biological processes. The structures of many plant LRR-RK receptors in complex with corresponding ligands have been solved by X-ray crystallography, revealing new mechanisms of ligand-induced receptor kinase activation. In this review, we briefly elaborate the peptide ligands, and aim to detail the structures and mechanisms of LRR-RK activation as induced by secreted peptide ligands within plants.}, }
@article {pmid31450061, year = {2019}, author = {Chen, X and Hu, Z and Qi, Y and Song, C and Chen, G}, title = {The interactions of algae-activated sludge symbiotic system and its effects on wastewater treatment and lipid accumulation.}, journal = {Bioresource technology}, volume = {292}, number = {}, pages = {122017}, doi = {10.1016/j.biortech.2019.122017}, pmid = {31450061}, issn = {1873-2976}, abstract = {The ability of Scenedesmus sp. 336, Chlorella sp. 1602 and activated sludge (AS) alone or in combination to remove nutrients and accumulate lipid in artificial municipal wastewater under light/dark conditions was studied. The symbiotic systems showed greater advantages than the sterile systems. Scenedesmus sp. 336 + AS system obtained the highest lipid productivity after seven days of cultivation in light, while the NO3--N and COD were completely absorbed and utilized, as well as the removal rate of PO43--P and NH4+-N were 99.82% and 87.13%, respectively. Total superoxide dismutase (SOD) activity was measured to demonstrate the relationship between oxidative stress and lipid accumulation. Besides, the results of microbial analysis showed that some dominant plant growth-promoting bacteria could secrete indole-3-acetic acid (IAA) to enhance the interaction between algae and bacteria, and the denitrifying bacteria that could coexist with microalgae also improved the efficiency of wastewater treatment in the symbiotic systems.}, }
@article {pmid31449853, year = {2019}, author = {Dorchin, N and Harris, KM and Stireman Iii, JO}, title = {Phylogeny of the gall midges (Diptera, Cecidomyiidae, Cecidomyiinae): systematics, evolution of feeding modes and diversification rates.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {106602}, doi = {10.1016/j.ympev.2019.106602}, pmid = {31449853}, issn = {1095-9513}, abstract = {Gall midges (Cecidomyiidae) constitute one of the largest and most diverse families of Diptera, with close to 6600 described species and thousands of undescribed species worldwide. The family is divided into six subfamilies, the five basal ones comprising only fungivorous taxa, whereas the largest, youngest and most diverse subfamily Cecidomyiinae includes fungivorous as well as herbivorous and predatory species. The currently accepted classification of the Cecidomyiinae is morphology-based, and the few phylogenetic inferences that have previously been suggested for it were based on fragmentary or limited datasets. In a first comprehensive phylogenetic analysis of the Cecidomyiinae we sampled 142 species representing 88 genera of 13 tribes from all feeding guilds and zoogeographic regions in order to test the validity of the systematic division of the subfamily and gain insight into patterns of diversification and the evolution of feeding modes. We used sequences from five mitochondrial and nuclear genes to reconstruct maximum likelihood and Bayesian, time-calibrated phylogenies and conducted ancestral state reconstruction of feeding modes. Our results corroborate to a great extent the morphology-based classification of the Cecidomyiinae, with strong support for all supertribes and tribes, all were apparently established in the Upper Cretaceous concordant with the major radiation of angiosperms. We infer that transitions from fungus-feeding to plant-feeding occurred only once or twice in the evolution of the subfamily and that predation evolved only once, contrary to previous hypotheses. All herbivorous clades in the subfamily are very species rich and have diversified at a significantly greater rate than expected, but we found no support for the assertion that herbivorous clades associated with symbiotic fungi in their galls diversify faster than clades that do not have such associations. Currently available data also do not support the hypothesis that symbiotic clades have broader host ranges than non-symbiotic clades.}, }
@article {pmid31448152, year = {2019}, author = {S, J and Kk, S}, title = {Multifunctional aspects of Piriformospora indica in plant endosymbiosis.}, journal = {Mycology}, volume = {10}, number = {3}, pages = {182-190}, doi = {10.1080/21501203.2019.1600063}, pmid = {31448152}, issn = {2150-1203}, abstract = {Piriformospora indica (Hymenomycetes, Basidiomycota) is an endophytic fungus that colonises plant roots, and was originally isolated from Rajasthan desert. It is comparable to Arbuscular Mycorrhizal (AM) fungi in terms of plant growth promotional effects. P. indica has been used as an ideal example to analyse the mechanisms of mutualistic symbiosis. Major benefit of P. indica over AM fungi is that it is axenically cultivable in different synthetic and complex media. A preliminary attempt was made to scrutinise the role of P. indica co-cultivation on seedling vigour of common vegetables like Cucumis sativus L., Abelmoschus esculentus (L.) Moench, Solanum melongena L. and Capsicum annuum L. The positive effect of P. indica co-culture on seedling performance was compared to the effects of growth hormones like indole acetic acid and benzyl amino purine when supplemented to the MS medium at a concentration of 0.1 mg ml-1. An exogenous supply of auxin resulted in enhanced production of roots and cytokinin supplement favoured shoot production, whereas P. indica co-culture favoured simultaneous production of shoot and root over the control. P. indica colonisation inside the roots of C. sativus L. was also successfully established. These preliminary results indicate the prospective role of P. indica in vegetable farming through its favourable effect on plant growth.}, }
@article {pmid31447821, year = {2019}, author = {Johansson, ON and Pinder, MIM and Ohlsson, F and Egardt, J and Töpel, M and Clarke, AK}, title = {Friends With Benefits: Exploring the Phycosphere of the Marine Diatom Skeletonema marinoi.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1828}, doi = {10.3389/fmicb.2019.01828}, pmid = {31447821}, issn = {1664-302X}, abstract = {Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a diverse array of bacterial species that closely interact within the diffusive boundary layer, or phycosphere, surrounding the diatom partner. Recently, we isolated seven distinct bacterial species from cultures of Skeletonema marinoi, a chain-forming, centric diatom that dominates the coastal regions of the temperate oceans. Genomes of all seven bacteria were sequenced revealing many unusual characteristics such as the existence of numerous plasmids of widely varying sizes. Here we have investigated the characteristics of the bacterial interactions with S. marinoi, demonstrating that several strains (Arenibacter algicola strain SMS7, Marinobacter salarius strain SMR5, Sphingorhabdus flavimaris strain SMR4y, Sulfitobacter pseudonitzschiae strain SMR1, Yoonia vestfoldensis strain SMR4r and Roseovarius mucosus strain SMR3) stimulate growth of the diatom partner. Testing of many different environmental factors including low iron concentration, high and low temperatures, and chemical signals showed variable effects on this growth enhancement by each bacterial species, with the most significant being light quality in which green and blue but not red light enhanced the stimulatory effect on S. marinoi growth by all bacteria. Several of the bacteria also inhibited growth of one or more of the other bacterial strains to different extents when mixed together. This study highlights the complex interactions between diatoms and their associated bacteria within the phycosphere, and that further studies are needed to resolve the underlying mechanisms for these relationships and how they might influence the global success of marine diatoms.}, }
@article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (CPR/Patescibacteria phylum) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential to co-metabolism interdependencies. Up to date, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from Acid Mine Drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotide, fatty acids, and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Taken together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome-reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives. This article is protected by copyright. All rights reserved.}, }
@article {pmid31445037, year = {2019}, author = {Fujimoto, K and Kawaguchi, Y and Shimohigoshi, M and Gotoh, Y and Nakano, Y and Usui, Y and Hayashi, T and Kimura, Y and Uematsu, M and Yamamoto, T and Akeda, Y and Rhee, JH and Yuki, Y and Ishii, KJ and Crowe, SE and Ernst, PB and Kiyono, H and Uematsu, S}, title = {Antigen-specific Mucosal Immunity Regulates Development of Intestinal Bacteria-mediated Diseases.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2019.08.021}, pmid = {31445037}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Dysregulation of the microbiome has been associated with development of complex diseases such as obesity and diabetes. However, no method has been developed to control disease-associated commensal microbes. We investigated whether immunization with microbial antigens, using CpG oligodeoxynucleotides (CpG-ODN) and/or curdlan as adjuvants, induces systemic antigen-specific immunoglobulin (Ig)A and IgG production and affects development of diseases in mice.<br><br>METHODS: C57BL/6 mice were given intramuscular injections of antigens (ovalbumin, cholera toxin (CT) B-subunit, or PspA) combined with CpG-ODN and/or curdlan. Blood and fecal samples were collected weekly and antigen-specific IgG and IgA titers were measured. Lymph nodes and spleens were collected and analyzed by ELISA for antigen-specific splenic T-helper (Th)1 cells, Th17 cells, and memory B cells. Six weeks after primary immunization, mice were given a oral, nasal, or vaginal boost of ovalbumin; intestinal lamina propria, bronchial lavage, and vaginal swab samples were collected and antibodies and cytokines were measured. Some mice were also given oral CT or intranasal Streptococcus pneumoniae and the severity of diarrhea or pneumonia was analyzed. Gnotobiotic mice were gavaged with fecal material from obese individuals, which had a high abundance of Clostridium ramosum (a commensal microbe associated with obesity and diabetes), and were placed on a high-fat diet 2 weeks after immunization with C. ramosum. Intestinal tissues were collected and analyzed by quantitative real-time PCR.<br><br>RESULTS: Serum and fecal samples from mice given injections of antigens in combination with CpG-ODN and curdlan for 3 weeks contained antigen-specific IgA and IgG, and splenocytes produced IFNG and IL17A. Lamina propria, bronchial, and vaginal samples contained antigen-specific IgA following the ovalbumin boost. This immunization regimen prevented development of diarrhea following injection of CT, and inhibited lung colonization by S. pneumoniae. In gnotobiotic mice colonized with C. ramosum and placed on a high-fat diet, the mice that had been immunized with C. ramosum became less obese than the non-immunized mice.<br><br>CONCLUSIONS: Injection of mice with microbial antigens and adjuvant induces antigen-specific mucosal and systemic immune responses. Immunization with S pneumoniae antigen prevented lung infection by this bacteria, and immunization with C ramosum reduced obesity in mice colonized with this microbe and placed on a high-fat diet. This immunization approach might be used to protect against microbe-associated disorders of intestine.}, }
@article {pmid31440828, year = {2019}, author = {Shimoda, Y and Imaizumi-Anraku, H and Hayashi, M}, title = {Kinase activity-dependent stability of calcium/calmodulin-dependent protein kinase of Lotus japonicus.}, journal = {Planta}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00425-019-03264-6}, pmid = {31440828}, issn = {1432-2048}, abstract = {MAIN CONCLUSION: Accumulation of calcium/calmodulin-dependent protein kinase (CCaMK) in root cell nucleus depends on its kinase activity but not on nuclear symbiotic components crucial for nodulation. Plant calcium/calmodulin-dependent protein kinase (CCaMK) is a key regulator of symbioses with rhizobia and arbuscular mycorrhizal fungi as it decodes symbiotic calcium signals induced by microsymbionts. CCaMK is expressed mainly in root cells and localizes to the nucleus, where microsymbiont-triggered calcium oscillations occur. The molecular mechanisms that control CCaMK localization are unknown. Here, we analyzed the expression and subcellular localization of mutated CCaMK in the roots of Lotus japonicus and found a clear relation between CCaMK kinase activity and its stability. Kinase-defective CCaMK variants showed lower protein levels than the variants with kinase activity. The levels of transcripts driven by the CaMV 35S promoter were similar among the variants, indicating that stability of CCaMK is regulated post-translationally. We also demonstrated that CCaMK localized to the root cell nucleus in several symbiotic mutants, including cyclops, an interaction partner and phosphorylation target of CCaMK. Our results suggest that kinase activity of CCaMK is required not only for the activation of downstream symbiotic components but also for its stability in root cells.}, }
@article {pmid31440434, year = {2019}, author = {Zhu, DT and Zou, C and Ban, FX and Wang, HL and Wang, XW and Liu, YQ}, title = {Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7477}, doi = {10.7717/peerj.7477}, pmid = {31440434}, issn = {2167-8359}, abstract = {Background: Bacterial symbiosis is widespread in arthropods, especially in insects. Some of the symbionts undergo a long-term co-evolution with the host, resulting in massive genome decay. One particular consequence of genome decay is thought to be the elimination of transcriptional elements within both the coding region and intergenic sequences. In the whitefly Bemisia tabaci species complex, the obligate symbiont Candidatus Portiera aleyrodidarum is of vital importance in nutrient provision, and yet little is known about the regulatory capacities of it.<br><br>Methods: Portiera genomes of two whitefly species in China were sequenced and assembled. Gene content of these two Portiera genomes was predicted, and then subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis. Together with two other Portiera genomes from whitefly species available previously, four Portiera genomes were utilized to investigate regulatory capacities of Portiera, focusing on transcriptional elements, including genes related with transcription and functional elements within the intergenic spacers.<br><br>Results: Comparative analyses of the four Portiera genomes of whitefly B. tabaci indicate that the obligate symbionts Portiera is similar in different species of whiteflies, in terms of general genome features and possible functions in the biosynthesis of essential amino acids. The screening of transcriptional factors suggests compromised ability of Portiera to regulate the essential amino acid biosynthesis pathways. Meanwhile, thermal tolerance ability of Portiera is indicated with the detection of a σ32 factor, as well as two predicted σ32 binding sites. Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs.}, }
@article {pmid31440229, year = {2019}, author = {Li, Y and Zhang, K and Liu, Y and Li, K and Hu, D and Wronski, T}, title = {Community Composition and Diversity of Intestinal Microbiota in Captive and Reintroduced Przewalski's Horse (Equus ferus przewalskii).}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1821}, doi = {10.3389/fmicb.2019.01821}, pmid = {31440229}, issn = {1664-302X}, abstract = {Large and complex intestinal microbiota communities in hosts have profound effects on digestion and metabolism. To better understand the community structure of intestinal microbiota in Przewalski's horse (Equus ferus przewalskii) under different feeding regimes, we compared bacterial diversity and composition between captive and reintroduced Przewalski's horses, using high-throughput 16S-rRNA gene sequencing for identification. Reintroduced Przewalski's horses were sampled in two Chinese nature reserves, i.e., Dunhuang Xihu Nature Reserve (DXNR; n = 8) in Gansu Province and Kalamaili Nature Reserve (KNR; n = 12) in Xinjiang Province, and compared to a captive population at the Przewalski's Horse Breeding Center in Xinjiang (PHBC; n = 11). The composition of intestinal microbiota in Przewalski's horses was significantly different at the three study sites. Observed species was lowest in DXNR, but highest in KNR. Lowest Shannon diversity was observed in DXNR, while in KNR and PHBC had a moderately high diversity; Simpson diversity showed an opposite trend compared with the Shannon index. Linear Discriminant Analysis effect size was used to determine differentially distributed bacterial taxa at each study site. The most dominant phyla of intestinal microbiota were similar in all feeding regimes, including mainly Firmicutes, Bacteroidetes, Verrucomicrobia, and Spirochaetes. Differing abundances of intestinal microbiota in Przewalski's horses may be related to different food types at each study site, differences in diversity may be attributed to low quality food in DXNR. Results indicated that diet is one of the important factors that can influence the structure of intestinal microbiota communities in Przewalski's horse. These findings combined with a detailed knowledge of the available and consumed food plant species could provide guidelines for the selection of potential future reintroduction sites.}, }
@article {pmid31439018, year = {2019}, author = {Li, C and Chng, KR and Kwah, JS and Av-Shalom, TV and Tucker-Kellogg, L and Nagarajan, N}, title = {An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {118}, doi = {10.1186/s40168-019-0729-z}, pmid = {31439018}, issn = {2049-2618}, abstract = {BACKGROUND: The dynamics of microbial communities is driven by a range of interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood. With the increasing availability of high-throughput microbiome taxonomic profiling data, it is now conceivable to directly learn the ecological models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is severely limited by the lack of accurate absolute cell density measurements (biomass).<br><br>METHODS: We present a new computational approach that resolves this key limitation in the inference of generalized Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference with an expectation-maximization algorithm (BEEM).<br><br>RESULTS: BEEM outperforms the state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM's application to previously inaccessible public datasets (due to the lack of biomass data) allowed us to construct ecological models of microbial communities in the human gut on a per-individual basis, revealing personalized dynamics and keystone species.<br><br>CONCLUSIONS: BEEM addresses a key bottleneck in &quot;systems analysis&quot; of microbiomes by enabling accurate inference of ecological models from high throughput sequencing data without the need for experimental biomass measurements.}, }
@article {pmid31438811, year = {2019}, author = {Hammer, TJ and Moran, NA}, title = {Links between metamorphosis and symbiosis in holometabolous insects.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1783}, pages = {20190068}, doi = {10.1098/rstb.2019.0068}, pmid = {31438811}, issn = {1471-2970}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; }, abstract = {Many animals depend on microbial symbionts to provide nutrition, defence or other services. Holometabolous insects, as well as other animals that undergo metamorphosis, face unique constraints on symbiont maintenance. Microbes present in larvae encounter a radical transformation of their habitat and may also need to withstand chemical and immunological challenges. Metamorphosis also provides an opportunity, in that symbiotic associations can be decoupled over development. For example, some holometabolous insects maintain the same symbiont as larvae and adults, but house it in different tissues; in other species, larvae and adults may harbour entirely different types or numbers of microbes, in accordance with shifts in host diet or habitat. Such flexibility may provide an advantage over hemimetabolous insects, in which selection on adult-stage microbial associations may be constrained by its negative effects on immature stages, and vice versa. Additionally, metamorphosis itself can be directly influenced by symbionts. Across disparate insect taxa, microbes protect hosts from pathogen infection, supply nutrients essential for rebuilding the adult body and provide cues regulating pupation. However, microbial associations remain completely unstudied for many families and even orders of Holometabola, and future research will undoubtedly reveal more links between metamorphosis and microbiota, two widespread features of animal life. This article is part of the theme issue 'The evolution of complete metamorphosis'.}, }
@article {pmid31437925, year = {2019}, author = {Mei, J and Xia, E}, title = {Knowledge Learning Symbiosis for Developing Risk Prediction Models from Regional EHR Repositories.}, journal = {Studies in health technology and informatics}, volume = {264}, number = {}, pages = {258-262}, doi = {10.3233/SHTI190223}, pmid = {31437925}, issn = {1879-8365}, abstract = {Secondary use of regional EHR data suffers several problems, including data selection bias and limited data size caused by data incompleteness. Here, we propose knowledge learning symbiosis (KLS) as a framework to incorporate domain knowledge to address the problems and make better secondary use of EHR data. Under the framework, we introduce three main categories of methods: knowledge injection to input features, objective functions, and output labels, where knowledge-enhanced neural network (KENN) was first introduced to inject knowledge into objective functions. A case study was conducted to build a cardiovascular disease risk prediction model on the type 2 diabetes patient cohort using regional EHR repositories. By incorporating a well-established knowledge risk model as domain knowledge under our KLS framework, we increased risk prediction performance both on small and biased data, where KENN showed the best performance among all methods.}, }
@article {pmid31437324, year = {2019}, author = {Teotia, D and Gaid, M and Saini, SS and Verma, A and Yennamalli, RM and Khare, SP and Ambatipudi, K and Mir, JI and Beuerle, T and Hänsch, R and Roy, P and Agrawal, PK and Beerhues, L and Sircar, D}, title = {Cinnamate:CoA-ligase is involved in benzoate-derived biphenyl phytoalexin biosynthesis in Malus × domestica 'Golden Delicious' cell cultures.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.14506}, pmid = {31437324}, issn = {1365-313X}, abstract = {Apple (Malus sp.) and other genera belonging to the sub-tribe Malinae of the Rosaceous family produce unique benzoic acid-derived biphenyl phytoalexins. Cell cultures of Malus domestica cv. 'Golden Delicious' accumulate two biphenyl phytoalexins, aucuparin and noraucuparin, in response to the addition of Venturia inaequalis elicitor (VIE). In this study, we isolated and expressed a cinnamate-CoA ligase-encoding sequence in VIE-treated cell cultures of cv. 'Golden Delicious' (M. domestica CNL; MdCNL). MdCNL catalyzes the conversion of cinnamic acid into cinnamoyl-CoA, which is subsequently converted to biphenyls. MdCNL failed to accept benzoic acid as a substrate. When scab-resistant (cv. 'Shireen') and moderately scab-susceptible (cv. 'Golden Delicious') apple cultivars were challenged with the V. inaequalis scab fungus, an increase in MdCNL transcript levels was observed in internodal regions. The increase in MdCNL transcript levels could conceivably correlate with the accumulation pattern of biphenyls. C-terminal signal in the MdCNL protein directed its N-terminal reporter fusion to peroxisomes in Nicotiana benthamiana leaves. Thus, this report records the cloning and characterization of a cinnamoyl-CoA-forming enzyme from apple via a series of in vivo and in vitro studies. Defining the key step of phytoalexin formation in apple provides a biotechnological tool for engineering elite cultivars with improved resistance. This article is protected by copyright. All rights reserved.}, }
@article {pmid31437265, year = {2019}, author = {Watanabe, D and Takagi, H}, title = {Yeast prion-based metabolic reprogramming induced by bacteria in fermented foods.}, journal = {FEMS yeast research}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsyr/foz061}, pmid = {31437265}, issn = {1567-1364}, abstract = {Microbial communities of yeast and bacterial cells are often observed in the manufacturing processes of fermented foods and drinks, such as sourdough bread, cheese, kefir, wine, and sake. Community interactions and dynamics among microorganisms, as well as their significance during the manufacturing processes, are central issues in modern food microbiology. Recent studies demonstrated that emergence of a yeast prion termed [GAR+] in Saccharomyces cerevisiae is induced by coculturing with bacterial cells, resulting in switching of the carbon metabolism. In order to facilitate mutualistic symbiosis among microorganisms, this mode of microbial interaction is induced between yeasts and lactic acid bacteria species used in traditional sake making. Thus, yeast prions have attracted much attention as novel platforms that govern the metabolic adaptation of cross-kingdom ecosystems. Our mini-review focuses on the plausible linkage between fermented-food microbial communication and yeast prion-mediated metabolic reprogramming.}, }
@article {pmid31430416, year = {2019}, author = {Reiter, S and Cahn, JKB and Wiebach, V and Ueoka, R and Piel, J}, title = {Characterization of an orphan type III polyketide synthase conserved in uncultivated 'Entotheonella' sponge symbionts.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cbic.201900352}, pmid = {31430416}, issn = {1439-7633}, abstract = {Uncultivated bacterial symbionts from the candidate genus 'Entotheonella' have been shown to produce diverse natural products previously attributed to their sponge hosts. In addition to these known compounds, 'Entotheonella' genomes contain rich sets of biosynthetic gene clusters lacking identified natural products. Among these is a small type III polyketide synthase (PKS) cluster, one of only three clusters present in all known 'Entotheonella' genomes. This c onserved ' E ntotheonella' P KS (cep) cluster encodes the type III PKS CepA and the putative methyltransferase CepB. Here we report the characterization of CepA as an enzyme involved in phenolic lipid biosynthesis. In vitro analysis showed a specificity for alkyl starter substrates and the production of tri- and tetraketide pyrones and tetraketide resorcinols. The conserved distribution of the cep cluster suggests an important role for the phenolic lipid polyketides produced in 'Entotheonella' variants.}, }
@article {pmid31428118, year = {2019}, author = {Nadzieja, M and Stougaard, J and Reid, D}, title = {A Toolkit for High Resolution Imaging of Cell Division and Phytohormone Signaling in Legume Roots and Root Nodules.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1000}, doi = {10.3389/fpls.2019.01000}, pmid = {31428118}, issn = {1664-462X}, abstract = {Legume plants benefit from a nitrogen-fixing symbiosis in association with rhizobia hosted in specialized root nodules. Formation of root nodules is initiated by de novo organogenesis and coordinated infection of these developing lateral root organs by rhizobia. Both bacterial infection and nodule organogenesis involve cell cycle activation and regulation by auxin and cytokinin is tightly integrated in the process. To characterize the hormone dynamics and cell division patterns with cellular resolution during nodulation, sensitive and specific sensors suited for imaging of multicellular tissues are required. Here we report a modular toolkit, optimized in the model legume Lotus japonicus, for use in legume roots and root nodules. This toolkit includes synthetic transcriptional reporters for auxin and cytokinin, auxin accumulation sensors and cell cycle progression markers optimized for fluorescent and bright field microscopy. The developed vectors allow for efficient one-step assembly of multiple units using the GoldenGate cloning system. Applied together with a fluorescence-compatible clearing approach, these reporters improve imaging depth and facilitate fluorescence examination in legume roots. We additionally evaluate the utility of the dynamic gravitropic root response in altering the timing and location of auxin accumulation and nodule emergence. We show that alteration of auxin distribution in roots allows for preferential nodule emergence at the outer side of the bend corresponding to a region of high auxin signaling capacity. The presented tools and procedures open new possibilities for comparative mutant studies and for developing a more comprehensive understanding of legume-rhizobia interactions.}, }
@article {pmid31426312, year = {2019}, author = {Cherif-Silini, H and Thissera, B and Bouket, AC and Saadaoui, N and Silini, A and Eshelli, M and Alenezi, FN and Vallat, A and Luptakova, L and Yahiaoui, B and Cherrad, S and Vacher, S and Rateb, ME and Belbahri, L}, title = {Durum Wheat Stress Tolerance Induced by Endophyte Pantoea agglomerans with Genes Contributing to Plant Functions and Secondary Metabolite Arsenal.}, journal = {International journal of molecular sciences}, volume = {20}, number = {16}, pages = {}, doi = {10.3390/ijms20163989}, pmid = {31426312}, issn = {1422-0067}, abstract = {In the arid region Bou-Saâda at the South of Algeria, durum wheat Triticum durum L. cv Waha production is severely threatened by abiotic stresses, mainly drought and salinity. Plant growth-promoting rhizobacteria (PGPR) hold promising prospects towards sustainable and environmentally-friendly agriculture. Using habitat-adapted symbiosis strategy, the PGPR Pantoea agglomerans strain Pa was recovered from wheat roots sampled in Bou-Saâda, conferred alleviation of salt stress in durum wheat plants and allowed considerable growth in this unhostile environment. Strain Pa showed growth up to 35 °C temperature, 5-10 pH range, and up to 30% polyethylene glycol (PEG), as well as 1 M salt concentration tolerance. Pa strain displayed pertinent plant growth promotion (PGP) features (direct and indirect) such as hormone auxin biosynthesis, production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia and phosphate solubilization. PGPR features were stable over wide salt concentrations (0-400 mM). Pa strain was also able to survive in seeds, in the non-sterile and sterile wheat rhizosphere, and was shown to have an endophytic life style. Phylogenomic analysis of strain Pa indicated that Pantoea genus suffers taxonomic imprecision which blurs species delimitation and may have impacted their practical use as biofertilizers. When applied to plants, strain Pa promoted considerable growth of wheat seedlings, high chlorophyll content, lower accumulation of proline, and favored K+ accumulation in the inoculated plants when compared to Na+ in control non-inoculated plants. Metabolomic profiling of strain Pa under one strain many compounds (OSMAC) conditions revealed a wide diversity of secondary metabolites (SM) with interesting salt stress alleviation and PGP activities. All these findings strongly promote the implementation of Pantoea agglomerans strain Pa as an efficient biofertilizer in wheat plants culture in arid and salinity-impacted regions.}, }
@article {pmid31425566, year = {2019}, author = {Doremus, MR and Kelly, SE and Hunter, MS}, title = {Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility.}, journal = {PLoS pathogens}, volume = {15}, number = {8}, pages = {e1008022}, doi = {10.1371/journal.ppat.1008022}, pmid = {31425566}, issn = {1553-7374}, abstract = {Terrestrial arthropods, including insects, commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny. These symbionts may be especially vulnerable to thermal stress, potentially leading to destabilization of the symbiosis and imposing costs to the host. For example, increased temperatures can reduce the density of a common reproductive manipulator, Wolbachia, and the strength of its crossing incompatibility (cytoplasmic incompatibility, or CI) phenotype. Another manipulative symbiont, Cardinium hertigii, infects ~ 6-10% of Arthropods, and also can induce CI, but there is little homology between the molecular mechanisms of CI induced by Cardinium and Wolbachia. Here we investigated whether temperature disrupts the CI phenotype of Cardinium in a parasitic wasp host, Encarsia suzannae. We examined the effects of both warm (32°C day/ 29°C night) and cool (20°C day/ 17°C night) temperatures on Cardinium CI and found that both types of temperature stress modified aspects of this symbiosis. Warm temperatures reduced symbiont density, pupal developmental time, vertical transmission rate, and the strength of both CI modification and rescue. Cool temperatures also reduced symbiont density, however this resulted in stronger CI, likely due to cool temperatures prolonging the host pupal stage. The opposing effects of cool and warm-mediated reductions in symbiont density on the resulting CI phenotype indicates that CI strength may be independent of density in this system. Temperature stress also modified the CI phenotype only if it occurred during the pupal stage, highlighting the likely importance of this stage for CI induction in this symbiosis.}, }
@article {pmid31419535, year = {2019}, author = {Ikuta, T and Tame, A and Saito, M and Aoki, Y and Nagai, Y and Sugimura, M and Inoue, K and Fujikura, K and Ohishi, K and Maruyama, T and Yoshida, T}, title = {Identification of cells expressing two peptidoglycan recognition proteins in the gill of the vent mussel, Bathymodiolus septemdierum.}, journal = {Fish &amp; shellfish immunology}, volume = {93}, number = {}, pages = {815-822}, doi = {10.1016/j.fsi.2019.08.022}, pmid = {31419535}, issn = {1095-9947}, abstract = {In symbiotic systems in which symbionts are transmitted horizontally, hosts must accept symbionts from the environment while defending themselves against invading pathogenic microorganisms. How they distinguish pathogens from symbionts and how the latter evade host immune defences are not clearly understood. Recognition of foreign materials is one of the most critical steps in stimulating immune responses, and pattern recognition receptors (PRRs) play vital roles in this process. In this study, we focused on a group of highly conserved PRRs, peptidoglycan recognition proteins (PGRPs), in the deep-sea mussel, Bathymodiolus septemdierum, which harbours chemosynthetic bacteria in their gill epithelial cells. We isolated B. septemdierum PGRP genes BsPGRP-S and BsPGRP-L, which encode a short- and a long-type PGRP, respectively. The short-type PGRP has a signal peptide and was expressed in the asymbiotic goblet mucous cells in the gill epithelium, whereas the long-type PGRP was predicted to include a transmembrane domain and was expressed in gill bacteriocytes. Based on these findings, we hypothesize that the secreted and transmembrane PGRPs are engaged in host defence against pathogenic bacteria and/or in the regulation of symbiosis via different cellular localizations and mechanisms.}, }
@article {pmid31418995, year = {2019}, author = {Liu, X and Tang, K and Zhang, D and Li, Y and Liu, Z and Yao, J and Wood, TK and Wang, X}, title = {Symbiosis of a P2-family phage and deep-sea Shewanella putrefaciens.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14781}, pmid = {31418995}, issn = {1462-2920}, support = {2017YFC0506303//National Key Research and Development Program of China/ ; 2018YFC1406500//National Key Research and Development Program of China/ ; 31400162//National Natural Science Foundation of China/ ; 31625001//National Natural Science Foundation of China/ ; 41706172//National Natural Science Foundation of China/ ; 2017A030313193//Natural Science Foundation of Guangdong Province, China/ ; }, abstract = {Almost all bacterial genomes harbour prophages, yet it remains unknown why prophages integrate into tRNA-related genes. Approximately 1/3 of Shewanella isolates harbour a prophage at the tmRNA (ssrA) gene. Here, we discovered a P2-family prophage integrated at the 3'-end of ssrA in the deep-sea bacterium S. putrefaciens. We found that ~0.1% of host cells are lysed to release P2 constitutively during host growth. P2 phage production is induced by a prophage-encoded Rep protein and its excision is induced by the Cox protein. We also found that P2 genome excision leads to the disruption of wobble base pairing of SsrA due to site-specific recombination, thus disrupting the trans-translation function of SsrA. We further demonstrated that P2 excision greatly hinders growth in seawater medium and inhibits biofilm formation. Complementation with a functional SsrA in the P2-excised strain completely restores the growth defects in seawater medium and partially restores biofilm formation. Additionally, we found that products of the P2 genes also increase biofilm formation. Taken together, this study illustrates a symbiotic relationship between P2 and its marine host, thus providing multiple benefits for both sides when a phage is integrated but suffers from reduced fitness when the prophage is excised.}, }
@article {pmid31418981, year = {2019}, author = {Chen, Q and Wu, WW and Qi, SS and Cheng, H and Li, Q and Ran, Q and Dai, ZC and Du, DL and Egan, S and Thomas, T}, title = {Arbuscular mycorrhizal fungi improve the growth and disease resistance of the invasive plant Wedelia trilobata.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14415}, pmid = {31418981}, issn = {1365-2672}, abstract = {AIMS: Arbuscular mycorrhizal fungi (AMF) are symbiotic partners of many invasive plants, however it is still unclear how AMF contribute to traits that are important for the successful invasion of their host and how environmental factors, such as nutrient conditions, influence this. This study was to explore the effects of Glomus versiforme (GV) and Glomus mosseae (GM) on the growth and disease resistance of the invasive plant Wedelia trilobata under different nutrient conditions.<br><br>METHODS AND RESULTS: We found that GV and GM had higher root colonization rates resulting in faster W. trilobata growth under both low-N and low-P nutrient conditions compared to the normal condition. Also, the colonization of W. trilobata by GV significantly reduced the infection area of the pathogenic fungus Rhizoctonia solani under low-N conditions.<br><br>CONCLUSIONS: These results demonstrated that AMF can promote the growth and pathogenic defense of W. trilobata in a nutrient-poor environment, which might contribute to their successful invasion into certain type of habitats.<br><br>In this study, we report for the first time that AMF can promote growth and disease resistance of W. trilobata under nutrient-poor environment, which contribute to a better understanding of plant invasion. This article is protected by copyright. All rights reserved.}, }
@article {pmid31416861, year = {2019}, author = {Andryuschenko, SV and Ivanova, EV and Perunova, NB and Bukharin, OV}, title = {Genome Sequence and Biochemical Properties of Bifidobacterium longum Strain ICIS-505, Isolated from the Intestine of a Healthy Woman.}, journal = {Microbiology resource announcements}, volume = {8}, number = {33}, pages = {}, doi = {10.1128/MRA.00491-19}, pmid = {31416861}, issn = {2576-098X}, abstract = {This report describes the genome sequence of Bifidobacterium longum strain ICIS-505, isolated from human feces. The size of the genome was 2,448,844 bp (59.71% G+C content), including 3,751 bp of the crypto-plasmid pBL505. Annotation revealed 2,241 gene sequences, including 2,033 proteins, 7 rRNA genes, 76 tRNA genes, and 4 noncoding RNA genes.}, }
@article {pmid31416823, year = {2019}, author = {Cope, KR and Bascaules, A and Irving, TB and Venkateshwaran, M and Maeda, J and Garcia, K and Rush, T and Ma, C and Labbe, JJ and Jawdy, S and Steigerwald, E and Setzke, J and Fung, E and Schnell, KG and Wang, Y and Schlief, N and Bücking, H and Strauss, SH and Maillet, F and Jargeat, P and Bécard, G and Puech-Pagès, V and Ane, JM}, title = {The Ectomycorrhizal Fungus Laccaria bicolor Produces Lipochitooligosaccharides and Uses the Common Symbiosis Pathway to Colonize Populus Roots.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1105/tpc.18.00676}, pmid = {31416823}, issn = {1532-298X}, abstract = {Mycorrhizal fungi form mutualistic associations with the roots of most land plants and provide them with mineral nutrients from the soil in exchange for fixed carbon derived from photosynthesis. The common symbiosis pathway (CSP) is a conserved molecular signaling pathway in all plants capable of associating with arbuscular mycorrhizal fungi . It is required not only for arbuscular mycorrhizal symbiosis but also for rhizobia-legume and actinorhizal symbioses. Given its role in such diverse symbiotic associations, we hypothesized that the CSP also plays a role in ectomycorrhizal associations. We showed that the ectomycorrhizal fungus Laccaria bicolor produces an array of lipochitooligosaccharides (LCOs) that can trigger both root hair branching in legumes and, most importantly, calcium spiking in the host plant Populus in a CASTOR/POLLUX-dependent manner. Nonsulfated LCOs enhanced lateral root development in Populus in a CCaMK-dependent manner, and sulfated LCOs enhanced the colonization of Populus by L. bicolor. Compared to wild-type Populus, the colonization of CASTOR/POLLUX and CCaMK RNA interference lines by L. bicolor was reduced. Our work demonstrates that similar to other root symbioses, L. bicolor uses the CSP for the full establishment of its mutualistic association with Populus.}, }
@article {pmid31416582, year = {2019}, author = {Černajová, I and Škaloud, P}, title = {The first survey of Cystobasidiomycete yeasts in the lichen genus Cladonia; with the description of Lichenozyma pisutiana gen. nov., sp. nov.}, journal = {Fungal biology}, volume = {123}, number = {9}, pages = {625-637}, doi = {10.1016/j.funbio.2019.05.006}, pmid = {31416582}, issn = {1878-6146}, abstract = {The view of lichens as a symbiosis only between a mycobiont and a photobiont has been challenged by discoveries of diverse associated organisms. Specific basidiomycete yeasts in the cortex of a range of macrolichens were hypothesized to influence the lichens' phenotype. The present study explores the occurrence and diversity of cystobasidiomycete yeasts in the lichen genus Cladonia. We obtained seven cultures and 56 additional sequences using specific primers from 27 Cladonia species from all over Europe and performed phylogenetic analyses based on ITS, LSU and SSU rDNA loci. We revealed yeast diversity distinct from any previously reported. Representatives of Cyphobasidiales, Microsporomycetaceae and of an unknown group related to Symmetrospora have been found. We present evidence that the Microsporomycetaceae contains mainly lichen-associated yeasts. Lichenozyma pisutiana is circumscribed here as a new genus and species. We report the first known associations between cystobasidiomycete yeasts and Cladonia (both corticate and ecorticate), and find that the association is geographically widespread in various habitats. Our results also suggest that a great diversity of lichen associated yeasts remains to be discovered.}, }
@article {pmid31416417, year = {2019}, author = {Yang, QS and Dong, JD and Ahmad, M and Ling, J and Zhou, WG and Tan, YH and Zhang, YZ and Shen, DD and Zhang, YY}, title = {Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {188}, doi = {10.1186/s12866-019-1565-9}, pmid = {31416417}, issn = {1471-2180}, support = {XDA13020300;XDA11020202//Chinese Academy of Sciences/ ; 41676107, 41276114, and 41676163//National Natural Science Foundation of China/ ; 2017B030314052//Science and Technology Planning Project of Guangdong Province/ ; }, abstract = {BACKGROUND: Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea.<br><br>RESULTS: The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high.<br><br>CONCLUSIONS: The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.}, }
@article {pmid31416010, year = {2019}, author = {Ruszkiewicz, JA and Tinkov, AA and Skalny, AV and Siokas, V and Dardiotis, E and Tsatsakis, A and Bowman, AB and da Rocha, JBT and Aschner, M}, title = {Brain diseases in changing climate.}, journal = {Environmental research}, volume = {177}, number = {}, pages = {108637}, doi = {10.1016/j.envres.2019.108637}, pmid = {31416010}, issn = {1096-0953}, support = {R01 ES007331/ES/NIEHS NIH HHS/United States ; R01 ES010563/ES/NIEHS NIH HHS/United States ; R01 ES020852/ES/NIEHS NIH HHS/United States ; }, abstract = {Climate change is one of the biggest and most urgent challenges for the 21st century. Rising average temperatures and ocean levels, altered precipitation patterns and increased occurrence of extreme weather events affect not only the global landscape and ecosystem, but also human health. Multiple environmental factors influence the onset and severity of human diseases and changing climate may have a great impact on these factors. Climate shifts disrupt the quantity and quality of water, increase environmental pollution, change the distribution of pathogens and severely impacts food production - all of which are important regarding public health. This paper focuses on brain health and provides an overview of climate change impacts on risk factors specific to brain diseases and disorders. We also discuss emerging hazards in brain health due to mitigation and adaptation strategies in response to climate changes.}, }
@article {pmid31415751, year = {2019}, author = {Cheng, YT and Zhang, L and He, SY}, title = {Plant-Microbe Interactions Facing Environmental Challenge.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {183-192}, doi = {10.1016/j.chom.2019.07.009}, pmid = {31415751}, issn = {1934-6069}, support = {R01 GM109928/GM/NIGMS NIH HHS/United States ; }, abstract = {In the past four decades, tremendous progress has been made in understanding how plants respond to microbial colonization and how microbial pathogens and symbionts reprogram plant cellular processes. In contrast, our knowledge of how environmental conditions impact plant-microbe interactions is less understood at the mechanistic level, as most molecular studies are performed under simple and static laboratory conditions. In this review, we highlight research that begins to shed light on the mechanisms by which environmental conditions influence diverse plant-pathogen, plant-symbiont, and plant-microbiota interactions. There is a great need to increase efforts in this important area of research in order to reach a systems-level understanding of plant-microbe interactions that are more reflective of what occurs in nature.}, }
@article {pmid31415746, year = {2019}, author = {Fleming, BA and Mulvey, MA}, title = {Commensal Strains of Neisseria Use DNA to Poison Their Pathogenic Rivals.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {156-158}, doi = {10.1016/j.chom.2019.07.014}, pmid = {31415746}, issn = {1934-6069}, mesh = {DNA ; *Neisseria ; Neisseria gonorrhoeae ; *Poisons ; Symbiosis ; }, abstract = {Commensal bacteria can interfere with colonization of the host by infiltrating pathogens. In this issue of Cell Host &amp; Microbe, Kim et al. (2019) describe an intriguing mechanism of colonization resistance driven by the mismatching of methylation patterns following uptake of commensal-derived DNA by pathogenic strains of Neisseria.}, }
@article {pmid31413521, year = {2019}, author = {Boem, F and Amedei, A}, title = {Healthy axis: Towards an integrated view of the gut-brain health.}, journal = {World journal of gastroenterology}, volume = {25}, number = {29}, pages = {3838-3841}, doi = {10.3748/wjg.v25.i29.3838}, pmid = {31413521}, issn = {2219-2840}, abstract = {Despite the lack of precise mechanisms of action, a growing number of studies suggests that gut microbiota is involved in a great number of physiological functions of the human organism. In fact, the composition and the relations of intestinal microbial populations play a role, either directly or indirectly, to both the onset and development of various pathologies. In particular, the gastrointestinal tract and nervous system are closely connected by the so-called gut-brain axis, a complex bidirectional system in which the central and enteric nervous system interact with each other, also engaging endocrine, immune and neuronal circuits. This allows us to put forward new working hypotheses on the origin of some multifactorial diseases: from eating to neuropsychiatric disorders (such as autism spectrum disorders and depression) up to diabetes and tumors (such as colorectal cancer). This scenario reinforces the idea that the microbiota and its composition represent a factor, which is no longer negligible, not only in preserving what we call &quot;health&quot; but also in defining and thus determining it. Therefore, we propose to consider the gut-brain axis as the focus of new scientific and clinical investigation as long as the locus of possible systemic therapeutic interventions.}, }
@article {pmid31412166, year = {2019}, author = {McIntire, PJ}, title = {Mankind and the machine: A relationship of symbiosis or conflict?.}, journal = {Cancer cytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncy.22175}, pmid = {31412166}, issn = {1934-6638}, }
@article {pmid31410554, year = {2019}, author = {Salloum, MS and Insani, M and Monteoliva, MI and Menduni, MF and Silvente, S and Carrari, F and Luna, C}, title = {Metabolic responses to arbuscular mycorrhizal fungi are shifted in roots of contrasting soybean genotypes.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00909-y}, pmid = {31410554}, issn = {1432-1890}, abstract = {Modern breeding programs have reduced genetic variability and might have caused a reduction in plant colonization by arbuscular mycorrhizal fungi (AM). In our previous studies, mycorrhizal colonization was affected in improved soybean genotypes, mainly arbuscule formation. Despite substantial knowledge of the symbiosis-related changes of the transcriptome and proteome, only sparse clues regarding metabolite alterations are available. Here, we evaluated metabolite changes between improved (I-1) and unimproved (UI-4) soybean genotypes and also compare their metabolic responses after AM root colonization. Soybean genotypes inoculated or not with AM were grown in a chamber under controlled light and temperature conditions. At 20 days after inoculation, we evaluated soluble metabolites of each genotype and treatment measured by GC-MS. In this analysis, when comparing non-AM roots between genotypes, I-1 had a lower amount of 31 and higher amount of only 4 metabolites than the UI-4 genotype. When comparing AM roots, I-1 had a lower amount of 36 and higher amount of 4 metabolites than UI-4 (different to those found altered in non-AM treated plants). Lastly, comparing the AM vs non-AM treatments, I-1 had increased levels of three and reduced levels of 24 metabolites, while UI-4 only had levels of 12 metabolites reduced by the effect of mycorrhizas. We found the major changes in sugars, polyols, amino acids, and carboxylic acids. In a targeted analysis, we found lower levels of isoflavonoids and alpha-tocopherol and higher levels of malondialdehyde in the I-1 genotype that can affect soybean-AM symbiosis. Our studies have the potential to support improving soybean with a greater capacity to be colonized and responsive to AM interaction.}, }
@article {pmid31409660, year = {2019}, author = {Zhang, S and Song, W and Wemheuer, B and Reveillaud, J and Webster, N and Thomas, T}, title = {Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00288-19}, pmid = {31409660}, issn = {2379-5077}, abstract = {Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names &quot;CandidatusUNitrosopumilus hexadellus,&quot; &quot;CandidatusUNitrosopumilus detritiferus,&quot; and &quot;CandidatusUCenporiarchaeum stylissum&quot; (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that &quot;CaUCenporiarchaeum stylissum&quot; has been exclusively detected in sponges and can hence be classified as a specialist, while &quot;CaUNitrosopumilus detritiferus&quot; and &quot;CaUNitrosopumilus hexadellus&quot; are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.}, }
@article {pmid31409658, year = {2019}, author = {Gorman, R}, title = {What's in it for the animals? Symbiotically considering 'therapeutic' human-animal relations within spaces and practices of care farming.}, journal = {Medical humanities}, volume = {45}, number = {3}, pages = {313-325}, doi = {10.1136/medhum-2018-011627}, pmid = {31409658}, issn = {1473-4265}, abstract = {Human-animal relations are increasingly imbricated, encountered and experienced in the production of medicine and health. Drawing on an empirical study of care farms in the UK, this article uses the language of symbiosis to develop a framework for critically considering the relationships enrolled within interspecies therapeutic practices. Care farming is an emerging paradigm that aims to deploy farming practices as a form of therapeutic intervention, with human-animal relations framed as providing important opportunities for human health. This article moves to attend to multispecies therapeutic interventions and relationships from a more-than-human perspective, drawing attention to the often-troubling anthropocentrism in which such practices are framed and performed. Attempting to perform and realise human imaginations of 'therapeutic' affects, spaces and relationships can rely on processes that reduce animals' own opportunities for flourishing. Yet, the therapeutic use of other species does not have to be forever anthropocentric or utilitarian. The article explores whether relations between humans and animals might result in a level of mutual proliferation of affective capacities, reciprocally beneficial. These human-animal entanglements highlight opportunities to think more critically about how to practice interspecies relationships and practices in ways that are less parasitic, and instead framed more by attempts at producing opportunities for mutualistic flourishing.}, }
@article {pmid31409030, year = {2019}, author = {Dalit, M and Keren, ML and Eviatar, W and Hiba, WB and Gal, E and Ehud, B and Yossi, L and Oren, L}, title = {The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa During Heat Stress.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, doi = {10.3390/microorganisms7080256}, pmid = {31409030}, issn = {2076-2607}, abstract = {The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship-coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphylliaparadivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of &quot;symbiosis differentially expressed genes&quot; and &quot;coral heat-stress genes&quot; in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E.paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.}, }
@article {pmid31408529, year = {2019}, author = {Mestre, A and Poulin, R and Holt, RD and Barfield, M and Clamp, JC and Fernandez-Leborans, G and Mesquita-Joanes, F}, title = {The interplay of nested biotic interactions and the abiotic environment regulates populations of a hypersymbiont.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.13091}, pmid = {31408529}, issn = {1365-2656}, abstract = {1.The role of biotic interactions in shaping the distribution and abundance of species should be particularly pronounced in symbionts. Indeed, symbionts have a dual niche composed of traits of their individual hosts and the abiotic environment external to the host, and often combine active dispersal at finer scales with host-mediated dispersal at broader scales. The biotic complexity in the determinants of species distribution and abundance should be even more pronounced for hypersymbionts (symbionts of other symbionts). 2.We use a chain of symbiosis to explore the relative influence of nested biotic interactions and the abiotic environment on occupancy and abundance of a hypersymbiont. 3.Our empirical system is the epibiont ciliate Lagenophrys discoidea, which attaches to an ostracod that is itself ectosymbiotic on crayfish (the basal host). We applied multimodel selection and variance partitioning for GLMM to assess the relative importance of: 1) traits of symbiotic hosts (ostracod sex and abundance), 2) traits of basal hosts (crayfish body weight, abundance and intermoult stage), 3) the abiotic environment (water chemistry and climate), and 4) geospatial autocorrelation patterns (capturing potential effects of crayfish dispersal among localities). 4.Our models explained about half of the variation in prevalence and abundance of the hypersymbiont. Variation in prevalence was partly explained, in decreasing order of importance (18-4%) by shared effects of symbiotic host traits and the abiotic environment, pure fixed effects of symbiotic hosts, abiotic environment and geospatial patterns (traits of basal hosts were not relevant). Hypersymbiont abundance was most strongly explained by random effects of host traits (mainly the symbiotic host), in addition to weaker fixed effects (mostly abiotic environment). 5.Our results highlight the major role of the interplay between abundance of symbiotic hosts and water physico-chemistry in regulating populations of a hypersymbiotic ciliate, which is likely critical for dispersal dynamics, availability of attachment resources and suitability of on-host living conditions for the ciliate. We also found moderate signal of regulation by the basal host, for which we propose three mechanisms: 1) modulation of microhabitat suitability (crayfish-created water currents); 2) concentration of symbiotic hosts within crayfish; and 3) dispersal mediated by crayfish. This article is protected by copyright. All rights reserved.}, }
@article {pmid31407021, year = {2019}, author = {Bockoven, AA and Bondy, EC and Flores, MJ and Kelly, SE and Ravenscraft, AM and Hunter, MS}, title = {What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01417-4}, pmid = {31407021}, issn = {1432-184X}, support = {DEB-1020460//Division of Environmental Biology/ ; IOS-1256905//Division of Integrative Organismal Systems/ ; }, abstract = {Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.}, }
@article {pmid31406945, year = {2019}, author = {Cecchi, G and Di Piazza, S and Marescotti, P and Zotti, M}, title = {Evidence of pyrite dissolution by Telephora terrestris Ehrh in the Libiola mine (Sestri Levante, Liguria, Italy).}, journal = {Heliyon}, volume = {5}, number = {8}, pages = {e02210}, doi = {10.1016/j.heliyon.2019.e02210}, pmid = {31406945}, issn = {2405-8440}, abstract = {Evidence of pyrite dissolution by Telephora terrestris Ehrh were observed for the first time in the abandoned sulphide Libiola mine in May 2017 (Sestri Levante, Liguria, Italy). This fungus is an ectomycorrhizal species able to colonize this extreme environment and bioaccumulate metals such as copper and silver in its fruiting bodies, and it is known to establish symbiosis with maritime pines present in the area, thus favouring their recolonization of the site. This paper presents evidence of T. terrestris promoted dissolution of sulphide minerals. This species can remove from soil not only metals possibly toxic to the pine trees, but it can also contribute to the ions bioaccumulation through the bioweathering of sulphide mineral grains (especially pyrite).}, }
@article {pmid31405380, year = {2019}, author = {Dang, X and Xie, Z and Liu, W and Sun, Y and Liu, X and Zhu, Y and Staehelin, C}, title = {The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {643}, doi = {10.1186/s12864-019-6004-7}, pmid = {31405380}, issn = {1471-2164}, support = {U1806206//NSFC-Shandong Joint Fund Key Projects/ ; 31570063 and 31870020//National Natural Science Foundation of China/ ; KFZD-SW-112//Key Deployment Project of Chinese Academy of Sciences/ ; 2017GSF17129//Shandong Key Research and Development Program/ ; 2017CXGC0303//Shandong Key Scientific and Technological Innovation Program/ ; }, abstract = {BACKGROUND: Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a narrow-host-range strain that establishes a symbiotic relationship with S. cannabina. The complete genome of this strain was sequenced to better understand the genetic basis of host specificity and adaptation to saline-alkaline soils.<br><br>RESULTS: E. alkalisoli YIC4027 was found to possess a 6.1-Mb genome consisting of three circular replicons: one chromosome (3.7 Mb), a chromid (1.9 Mb) and a plasmid (0.46 Mb). Genome comparisons showed that strain YIC4027 is phylogenetically related to broad-host-range Ensifer fredii strains. Synteny analysis revealed a strong collinearity between chromosomes of E. alkalisoli YIC4027 and those of the E. fredii NGR234 (3.9 Mb), HH103 (4.3 Mb) and USDA257 (6.48 Mb) strains. Notable differences were found for genes required for biosynthesis of nodulation factors and protein secretion systems, suggesting a role of these genes in host-specific nodulation. In addition, the genome analysis led to the identification of YIC4027 genes that are presumably related to adaptation to saline-alkaline soils, rhizosphere colonization and nodulation competitiveness. Analysis of chemotaxis cluster genes and nodulation tests with constructed che gene mutants indicated a role of chemotaxis and flagella-mediated motility in the symbiotic association between YIC4027 and S. cannabina.<br><br>CONCLUSIONS: This study provides a basis for a better understanding of host specific nodulation and of adaptation to a saline-alkaline rhizosphere. This information offers the perspective to prepare optimal E. alkalisoli inocula for agriculture use and soil remediation.}, }
@article {pmid31405202, year = {2019}, author = {Miura, C and Saisho, M and Yagame, T and Yamato, M and Kaminaka, H}, title = {Bletilla striata (Orchidaceae) Seed Coat Restricts the Invasion of Fungal Hyphae at the Initial Stage of Fungal Colonization.}, journal = {Plants (Basel, Switzerland)}, volume = {8}, number = {8}, pages = {}, doi = {10.3390/plants8080280}, pmid = {31405202}, issn = {2223-7747}, support = {15K14550//Japan Society for the Promotion of Science/ ; 201801755//Japan Society for the Promotion of Science/ ; 18J01755//Japan Society for the Promotion of Science/ ; n/a//Tottori Prefecture Research Fund for the Promotion of Environmental Academic Research/ ; }, abstract = {Orchids produce minute seeds that contain limited or no endosperm, and they must form an association with symbiotic fungi to obtain nutrients during germination and subsequent seedling growth under natural conditions. Orchids need to select an appropriate fungus among diverse soil fungi at the germination stage. However, there is limited understanding of the process by which orchids recruit fungal associates and initiate the symbiotic interaction. This study aimed to better understand this process by focusing on the seed coat, the first point of fungal attachment. Bletilla striata seeds, some with the seed coat removed, were prepared and sown with symbiotic fungi or with pathogenic fungi. The seed coat-stripped seeds inoculated with the symbiotic fungi showed a lower germination rate than the intact seeds, and proliferated fungal hyphae were observed inside and around the stripped seeds. Inoculation with the pathogenic fungi increased the infection rate in the seed coat-stripped seeds. The pathogenic fungal hyphae were arrested at the suspensor side of the intact seeds, whereas the seed coat-stripped seeds were subjected to severe infestation. These results suggest that the seed coat restricts the invasion of fungal hyphae and protects the embryo against the attack of non-symbiotic fungi.}, }
@article {pmid31404343, year = {2019}, author = {Wilker, J and Navabi, A and Rajcan, I and Marsolais, F and Hill, B and Torkamaneh, D and Pauls, KP}, title = {Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {952}, doi = {10.3389/fpls.2019.00952}, pmid = {31404343}, issn = {1664-462X}, abstract = {Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation of SNF. High-yielding, conventionally bred bean varieties are developed using conventional production practices and selection criteria, typically not including SNF efficiency, and may have lost this trait over decades of modern breeding. In contrast, heirloom bean genotypes were developed before the advent of modern production practices and may represent an underutilized pool of genetics which could be used to improve SNF. This study compared the SNF capacity under low-N field conditions, of collections of heirloom varieties with and conventionally bred dry bean varieties. The heirloom-conventional panel (HCP) consisted of 42 genotypes from various online seed retailers or from the University of Guelph Bean Breeding program seedbank. The HCP was genotyped using a single nucleotide polymorphism (SNP) array to investigate genetic relatedness within the panel. Field trials were conducted at three locations in ON, Canada from 2014 to 2015 and various agronomic and seed composition traits were measured, including capacity for nitrogen fixation (using the natural abundance method to measure seed N isotope ratios). Significant variation for SNF was found in the panel. However, on average, heirloom genotypes did not fix significantly more nitrogen than conventionally bred varieties. However, five heirloom genotypes fixed >60% of their nitrogen from the atmosphere. Yield (kg ha-1) was not significantly different between heirloom and conventional genotypes, suggesting that incorporating heirloom genotypes into a modern breeding program would not negatively impact yield. Nitrogen fixation was significantly higher among Middle American genotypes than among Andean genotypes, confirming previous findings. The best nitrogen fixing line was Coco Sophie, a European heirloom white bean whose genetic makeup is admixed between the Andean and Middle American genepools. Heirloom genotypes represent a useful source of genetics to improve SNF in modern bean breeding.}, }
@article {pmid31400717, year = {2019}, author = {Irshad, S and Xie, Z and Wang, J and Nawaz, A and Luo, Y and Wang, Y and Mehmood, S and Faheem, }, title = {Indigenous strain Bacillus XZM assisted phytoremediation and detoxification of arsenic in Vallisneria denseserrulata.}, journal = {Journal of hazardous materials}, volume = {381}, number = {}, pages = {120903}, doi = {10.1016/j.jhazmat.2019.120903}, pmid = {31400717}, issn = {1873-3336}, abstract = {The symbiosis between Vallisneria denseserrulata and indigenous Bacillus sp. XZM was investigated for arsenic removal for the first time. It was found that the native bacterium was able to reduce arsenic toxicity to the plant by producing higher amount of extra cellular polymeric substances (EPS), indole-3-acetic acid (IAA) and siderosphore. Interestingly, V. denseserrulata-Bacillus sp. XZM partnership showed significantly higher arsenic uptake and removal efficiency. The shift in FT-IR spectra indicated the involvement of amide, carboxyl, hydroxyl and thiol groups in detoxification of arsenic, and the existence of an arsenic metabolizing process in V. denseserrulata leaves. The scanning electron microscopy (SEM) images further confirmed that the bacterium colonized on plant roots and facilitated arsenic uptake by plant under inoculation condition. In plant, most of the arsenic existed as As(III) (85%) and was massively (>77%) found in vacuole of particularly leaves cells. Thus, these findings are highly suggested for arsenic remediation in the constructed wetlands.}, }
@article {pmid31400692, year = {2019}, author = {Xiang, N and Jiang, C and Huang, W and Nordhaus, I and Zhou, H and Drews, M and Diao, X}, title = {The impact of acute benzo(a)pyrene on antioxidant enzyme and stress-related genes in tropical stony corals (Acropora spp.).}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133474}, doi = {10.1016/j.scitotenv.2019.07.280}, pmid = {31400692}, issn = {1879-1026}, abstract = {Coral reefs have extremely high ecological value in tropical and subtropical waters worldwide. However, they have been subjected to the most extensive and prolonged damage in recent decades. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous hazardous pollutants and are highly resistant to degradation in marine environments. Among these compounds, benzo(a)pyrene (BaP) has exerted pressure on corals due to water discharges, oil spills and coastal tourism. In the present study, the physiological response, oxidative stress and stress-related genetic expressions of two Acropora spp. (Acropora formosa and Acropora nasuta) were analysed. These two coral species were exposed to 10 and 40 μg·L-1 BaP for 24 hand 72 h, respectively. The results show that (1) BaP affects the health of the zooxanthellae in coral symbiosis after BaP exposure for 72 h due to a significant decline in chlorophyll a concentrations in Acropora spp. during this period. (2) An exposure of 10 μg·L-1 BaP for 24 h induced serious oxidative damage to Acropora spp., with a significant decline and increase in superoxide dismutase (SOD) activities in A. formosa and A. nasuta. (3) The P-gp gene is more sensitive in A. formosa, while the Hsp70 gene is more sensitive in A. nasuta. (4) A. formosa showed a lower ability to resist organic pollutants in coral reefs. Overall, further ecotoxicological studies are needed to investigate the impact of chemical pollutants on corals and to compare their different response mechanisms.}, }
@article {pmid31400167, year = {2019}, author = {Schwartzman, JA and Lynch, JB and Flores Ramos, S and Zhou, L and Apicella, MA and Yew, JY and Ruby, EG}, title = {Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria-animal mutualism.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14365}, pmid = {31400167}, issn = {1365-2958}, support = {GM008505/GM/NIGMS NIH HHS/United States ; GM119238/GM/NIGMS NIH HHS/United States ; GM135254/GM/NIGMS NIH HHS/United States ; AI055397//National Institute of Allergy and Infectious Diseases/ ; AI50661//National Institute of Allergy and Infectious Diseases/ ; //Division of Integrative Organismal Systems/ ; OD11024//NIH Office of the Director/ ; P20 GM103449/GM/NIGMS NIH HHS/United States ; R01 AI050661/AI/NIAID NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, abstract = {Environmental pH can be an important cue for symbiotic bacteria as they colonize their eukaryotic hosts. Using the model mutualism between the marine bacterium Vibrio fischeri and the Hawaiian bobtail squid, we characterized the bacterial transcriptional response to acidic pH experienced during the shift from planktonic to host-associated lifestyles. We found several genes involved in outer membrane structure were differentially expressed based on pH, indicating alterations in membrane physiology as V. fischeri initiates its symbiotic program. Exposure to host-like pH increased the resistance of V. fischeri to the cationic antimicrobial peptide polymixin B, which resembles antibacterial molecules that are produced by the squid to select V. fischeri from the ocean microbiota. Using a forward genetic screen, we identified a homolog of eptA, a predicted phosphoethanolamine transferase, as critical for antimicrobial defense. We used MALDI-MS to verify eptA as an ethanolamine transferase for the lipid-A portion of V. fischeri lipopolysaccharide. We then used a DNA pulldown approach to discover that eptA transcription is activated by the global regulator H-NS. Finally, we revealed that eptA promotes successful squid colonization by V. fischeri, supporting its potential role in initiation of this highly specific symbiosis.}, }
@article {pmid31397886, year = {2019}, author = {Cohen, ML and Mashanova, EV and Rosen, NM and Soto, W}, title = {Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes).}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13819}, pmid = {31397886}, issn = {1558-5646}, support = {120084//College of William and Mary/ ; 120819//College of William and Mary/ ; }, abstract = {For microorganisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether adaptation to stress during the free-living stage can impact microbial fitness in the host. To address this topic, the mutualism between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bioluminescent bacterium Vibrio fischeri was utilized. Using microbial experimental evolution, V. fischeri was selected to low (8°C), high (34°C), and fluctuating temperature stress (8°C/34°C) for 2000 generations. The temperatures 8°C and 34°C were the lower and upper growth limits, respectively. V. fischeri was also selected to benign temperatures (21°C and 28°C) for 2000 generations, which served as controls. V. fischeri demonstrated significant adaptation to low, high, and fluctuating temperature stress. V. fischeri did not display significant adaptation to the benign temperatures. Adaptation to stressful temperatures facilitated V. fischeri's ability to colonize the squid host relative to the ancestral lines. Bioluminescence levels also increased. Evolution to benign temperatures did not manifest these results. In summary, microbial adaptation to stress during the free-living stage can promote coevolution between hosts and microorganisms.}, }
@article {pmid31396616, year = {2019}, author = {Lallemand, F and Logacheva, M and Le Clainche, I and Bérard, A and Zheleznaia, E and May, M and Jakalski, M and Delannoy, É and Le Paslier, MC and Selosse, MA}, title = {Thirteen new plastid genomes from mixotrophic and autotrophic species provide insights into heterotrophy evolution in Neottieae orchids.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz170}, pmid = {31396616}, issn = {1759-6653}, abstract = {Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including nine mixotrophic species and covering all six Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared to autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.}, }
@article {pmid31396562, year = {2019}, author = {Weizman, E and Levy, O}, title = {The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {282}, doi = {10.1038/s42003-019-0543-y}, pmid = {31396562}, issn = {2399-3642}, abstract = {Extreme weather events frequency and scale are altered due to climate change. Symbiosis between corals and their endosymbiotic-dinoflagellates (Symbiodinium) is susceptible to these events and can lead to what is known as bleaching. However, there is evidence for coral adaptive plasticity in the role of epigenetic that have acclimated to high-temperature environments. We have implemented ATAC-seq and RNA-seq to study the cnidarian-dinoflagellate model Exaptasia pallida (Aiptasia) and expose the role of chromatin-dynamics in response to thermal-stress. We have identified 1309 genomic sites that change their accessibility in response to thermal changes. Moreover, apo-symbiotic Aiptasia accessible sites were enriched with NFAT, ATF4, GATA3, SOX14, and PAX3 motifs and expressed genes related to immunological pathways. Symbiotic Aiptasia accessible sites were enriched with NKx3-1, HNF4A, IRF4 motifs and expressed genes related to oxidative-stress pathways. Our work opens a new path towards understanding thermal-stress gene regulation in association with gene activity and chromatin-dynamics.}, }
@article {pmid31396243, year = {2019}, author = {Romero-Munar, A and Baraza, E and Gulías, J and Cabot, C}, title = {Arbuscular Mycorrhizal Fungi Confer Salt Tolerance in Giant Reed (Arundo donax L.) Plants Grown Under Low Phosphorus by Reducing Leaf Na+ Concentration and Improving Phosphorus Use Efficiency.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {843}, doi = {10.3389/fpls.2019.00843}, pmid = {31396243}, issn = {1664-462X}, abstract = {Salinization is one of the major causes of agricultural soil degradation worldwide. In arid and semi-arid regions with calcareous soils, phosphorus (P) deficiency further worsens the quality of salinized soils. Nonetheless, nutrient poor soils could be suitable of producing second-generation energy crops. Due to its high biomass production, Arundo donax L. (giant reed) is one of the most promising species for energy and second-generation biofuel production. A. donax can be propagated by micropropagation, an in vitro technique that produces high number of homogeneous plantlets. However, crop establishment is often compromised due to poor plantlet acclimatization to the soil environment. Arbuscular mycorrhizal fungi (AM) are components of soil-plant systems able to increase root phosphorus uptake and to confer the plant an increase tolerance to salinity with a consequent enhancement effect of plant growth and yield. In the present study, the relative importance of the early symbiosis establishment between AM fungi and A. donax micropropagated plantlets in the response to salt stress under low phosphorus availability was determined. A commercial inoculum which contained two different AM fungi species: Rhizophagus intraradices and Funneliformis mosseae was used. AM-symbionts (AM) and non-symbionts plants were grown at two phosphorus [2.5 μM (C) and 0.5 mM (P)] and three NaCl (1, 75 and 150 mM) concentrations in a room chamber under controlled conditions. After 5 weeks, AM root colonization was 60, 26 and 15% in 1, 75 and 150 mM NaCl-treated plants, respectively. At 1 and 75 mM NaCl, AM plants showed increased growth. In all saline treatments, AM plants had decreased Na+ uptake, Na+ root-to-shoot translocation, Na+/K+ ratio and increased P and K use efficiencies with respect to C and P plants. AM improved the nutritional status of A. donax plants by enhancing nutrient use efficiency rather than nutrient uptake. Increased phosphorus use efficiency in AM plants could have benefited ion (Na+ and K+) uptake and/or allocation and ultimately ameliorate the plant's response to saline conditions.}, }
@article {pmid31396178, year = {2019}, author = {Trappeniers, K and Matetovici, I and Van Den Abbeele, J and De Vooght, L}, title = {The Tsetse Fly Displays an Attenuated Immune Response to Its Secondary Symbiont, Sodalis glossinidius.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1650}, doi = {10.3389/fmicb.2019.01650}, pmid = {31396178}, issn = {1664-302X}, abstract = {Sodalis glossinidius, a vertically transmitted facultative symbiont of the tsetse fly, is a bacterium in the early/intermediate state of its transition toward symbiosis, representing an important model for investigating how the insect host immune defense response is regulated to allow endosymbionts to establish a chronic infection within their hosts without being eliminated. In this study, we report on the establishment of a tsetse fly line devoid of S. glossinidius only, allowing us to experimentally investigate (i) the complex immunological interactions between a single bacterial species and its host, (ii) how the symbiont population is kept under control, and (iii) the impact of the symbiont on the vector competence of the tsetse fly to transmit the sleeping sickness parasite. Comparative transcriptome analysis showed no difference in the expression of genes involved in innate immune processes between symbiont-harboring (GmmSod+) and S. glossinidius-free (GmmSod-) flies. Re-exposure of (GmmSod-) flies to the endosymbiotic bacterium resulted in a moderate immune response, whereas exposure to pathogenic E. coli or to a close non-insect associated relative of S. glossinidius, i.e., S. praecaptivus, resulted in full immune activation. We also showed that S. glossinidius densities are not affected by experimental activation or suppression of the host immune system, indicating that S. glossinidius is resistant to mounted immune attacks and that the host immune system does not play a major role in controlling S. glossinidius proliferation. Finally, we demonstrate that the absence or presence of S. glossinidius in the tsetse fly does not alter its capacity to mount an immune response to pathogens nor does it affect the fly's susceptibility toward trypanosome infection.}, }
@article {pmid31395953, year = {2019}, author = {Cardini, U and Bartoli, M and Lücker, S and Mooshammer, M and Polzin, J and Lee, RW and Micić, V and Hofmann, T and Weber, M and Petersen, JM}, title = {Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0486-9}, pmid = {31395953}, issn = {1751-7370}, support = {VRG14-021//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; VRG14-021//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; 09.3.3-LMT-K-712-01-0069//Lietuvos Mokslo Taryba (Research Council of Lithuania)/ ; 09.3.3-LMT-K-712-01-0069//Lietuvos Mokslo Taryba (Research Council of Lithuania)/ ; }, abstract = {In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.}, }
@article {pmid31395464, year = {2019}, author = {Payen, VL and Mina, E and Van Hée, VF and Porporato, PE and Sonveaux, P}, title = {Monocarboxylate transporters in cancer.}, journal = {Molecular metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmet.2019.07.006}, pmid = {31395464}, issn = {2212-8778}, abstract = {BACKGROUND: Tumors are highly plastic metabolic entities composed of cancer and host cells that can adopt different metabolic phenotypes. For energy production, cancer cells may use 4 main fuels that are shuttled in 5 different metabolic pathways. Glucose fuels glycolysis that can be coupled to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) in oxidative cancer cells or to lactic fermentation in proliferating and in hypoxic cancer cells. Lipids fuel lipolysis, glutamine fuels glutaminolysis, and lactate fuels the oxidative pathway of lactate, all of which are coupled to the TCA cycle and OXPHOS for energy production. This review focuses on the latter metabolic pathway.<br><br>SCOPE OF REVIEW: Lactate, which is prominently produced by glycolytic cells in tumors, was only recently recognized as a major fuel for oxidative cancer cells and as a signaling agent. Its exchanges across membranes are gated by monocarboxylate transporters MCT1-4. This review summarizes the current knowledge about MCT structure, regulation and functions in cancer, with a specific focus on lactate metabolism, lactate-induced angiogenesis and MCT-dependent cancer metastasis. It also describes lactate signaling via cell surface lactate receptor GPR81.<br><br>MAJOR CONCLUSIONS: Lactate and MCTs, especially MCT1 and MCT4, are important contributors to tumor aggressiveness. Analyses of MCT-deficient (MCT+/- and MCT-/-) animals and (MCT-mutated) humans indicate that they are druggable, with MCT1 inhibitors being in advanced development phase and MCT4 inhibitors still in the discovery phase. Imaging lactate fluxes non-invasively using a lactate tracer for positron emission tomography would further help to identify responders to the treatments.}, }
@article {pmid31393956, year = {2019}, author = {Kokkoris, V and Hamel, C and Hart, MM}, title = {Mycorrhizal response in crop versus wild plants.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221037}, doi = {10.1371/journal.pone.0221037}, pmid = {31393956}, issn = {1932-6203}, abstract = {We proposed a theoretical framework predicting mutualistic outcomes for the arbuscular mycorrhizal (AM) symbiosis based on host provenance (crop versus wild). To test the framework, we grew two isolates of Rhizoglomus irregulare (commercial versus an isolate locally isolated), with five crop plants and five wild plants endemic to the region that co-occur with the locally sourced fungus. While inoculation with either isolate had no effect on plant biomass, it decreased leaf P content, particularly for wild plants. All plants associating with the commercial fungus had lower leaf P. Overall, our data shows that wild plants may be more sensitive to differences in mutualistic quality among fungal isolates.}, }
@article {pmid31392918, year = {2019}, author = {Buendia, L and Ribeyre, C and Bensmihen, S and Lefebvre, B}, title = {Brachypodium distachyon tar2lhypo mutant shows reduced root developmental response to symbiotic signal but increased arbuscular mycorrhiza.}, journal = {Plant signaling &amp; behavior}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/15592324.2019.1651608}, pmid = {31392918}, issn = {1559-2324}, abstract = {Auxin is a major phytohormone that controls root development. A role for auxin is also emerging in the control of plant-microbe interactions, including for the establishment of root endosymbiosis between plants and arbuscular mycorrhizal fungi (AMF). Auxin perception is important both for root colonization by AMF and for arbuscule formation. AMF produce symbiotic signals called lipo-chitooligosaccharides (LCOs) that can modify auxin homeostasis and promote lateral root formation (LRF). Since Brachypodium distachyon (Brachypodium) has a different auxin sensitivity compared to other plant species, we wondered whether this would interfere with the effect of auxin in arbuscular mycorrhizal (AM) symbiosis. Here we tested whether tar2lhypo a Brachypodium mutant with an increase in endogenous auxin content is affected in LRF stimulation by LCOs and in AM symbiosis. We found that, in contrast to control plants, LCO treatment inhibited LRF of the tar2lhypo mutant. However, the level of AMF colonization and the abundance of arbuscules were increased in tar2lhypo compared to control plants, suggesting that auxin also plays a positive role in both AMF colonization and arbuscule formation in Brachypodium.}, }
@article {pmid31389400, year = {2019}, author = {Kavadi, SN}, title = {The founding of the Tata Memorial Hospital, 1932-1941.}, journal = {Indian journal of cancer}, volume = {56}, number = {3}, pages = {282-284}, doi = {10.4103/ijc.IJC_13_19}, pmid = {31389400}, issn = {1998-4774}, abstract = {This article presents a brief account of the founding of the Tata Memorial Hospital. It draws upon archival material to show that this was not a mere philanthropic act but a scheme carefully thought-out by the Trustees of the Sir Dorabji Tata Trust. It discusses the major concerns of the Trustees as they deliberated upon establishing the Hospital.}, }
@article {pmid31388025, year = {2019}, author = {Lanzoni, O and Plotnikov, A and Khlopko, Y and Munz, G and Petroni, G and Potekhin, A}, title = {The core microbiome of sessile ciliate Stentor coeruleus is not shaped by the environment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11356}, doi = {10.1038/s41598-019-47701-8}, pmid = {31388025}, issn = {2045-2322}, support = {295176//EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme &amp;quot;People&amp;quot; Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 16-14-10157//Russian Science Foundation (RSF)/ ; }, abstract = {Microbiomes of multicellular organisms are one of the hottest topics in microbiology and physiology, while only few studies addressed bacterial communities associated with protists. Protists are widespread in all environments and can be colonized by plethora of different bacteria, including also human pathogens. The aim of this study was to characterize the prokaryotic community associated with the sessile ciliate Stentor coeruleus. 16S rRNA gene metabarcoding was performed on single cells of S. coeruleus and on their environment, water from the sewage stream. Our results showed that the prokaryotic community composition differed significantly between Stentor cells and their environment. The core microbiome common for all ciliate specimens analyzed could be defined, and it was composed mainly by representatives of bacterial genera which include also potential human pathogens and commensals, such as Neisseria, Streptococcus, Capnocytophaga, Porphyromonas. Numerous 16S rRNA gene contigs belonged to endosymbiont &quot;Candidatus Megaira polyxenophila&quot;. Our data suggest that each ciliate cell can be considered as an ecological microniche harboring diverse prokaryotic organisms. Possible benefits for persistence and transmission in nature for bacteria associated with protists are discussed. Our results support the hypothesis that ciliates attract potentially pathogenic bacteria and play the role of natural reservoirs for them.}, }
@article {pmid31386172, year = {2019}, author = {David, AS and Bell-Dereske, LP and Emery, SM and McCormick, BM and Seabloom, EW and Rudgers, JA}, title = {Testing for loss of Epichloë and non-epichloid symbionts under altered rainfall regimes.}, journal = {American journal of botany}, volume = {106}, number = {8}, pages = {1081-1089}, doi = {10.1002/ajb2.1340}, pmid = {31386172}, issn = {1537-2197}, support = {DEB 0918267//NSF/ ; DEB 1145588//NSF/ ; NSF 0940902//NSF/ ; DGE-0653827//NSF/ ; NSF 00039202//NSF/ ; }, abstract = {PREMISE: Microbial symbionts can buffer plant hosts from environmental change. Therefore, understanding how global change factors alter the associations between hosts and their microbial symbionts may improve predictions of future changes in host population dynamics and microbial diversity. Here, we investigated how one global change factor, precipitation, affected the maintenance or loss of symbiotic fungal endophytes in a C3 grass host. Specifically, we examined the distinct responses of Epichloë (vertically transmitted and systemic) and non-epichloid endophytes (typically horizontally transmitted and localized) by considering (1) how precipitation altered associations with Epichloë and non-epichloid endophytic taxa across host ontogeny, and (2) interactive effects of water availability and Epichloë on early seedling life history stages.<br><br>METHODS: We manipulated the presence of Epichloë amarillans in American beachgrass (Ammophila breviligulata) in a multiyear field experiment that imposed three precipitation regimes (ambient or ±30% rainfall). In laboratory assays, we investigated the interactive effects of water availability and Epichloë on seed viability and germination.<br><br>RESULTS: Reduced precipitation decreased the incidence of Epichloë in leaves in the final sampling period, but had no effect on associations with non-epichloid taxa. Epichloë reduced the incidence of non-epichloid endophytes, including systemic p-endophytes, in seeds. Laboratory assays suggested that association with Epichloë is likely maintained, in part, due to increased seed viability and germination regardless of water availability.<br><br>CONCLUSIONS: Our study empirically demonstrates several pathways for plant symbionts to be lost or maintained across host ontogeny and suggests that reductions in precipitation can drive the loss of a plant's microbial symbionts.}, }
@article {pmid31382604, year = {2019}, author = {Nobre, T}, title = {Symbiosis in Sustainable Agriculture: Can Olive Fruit Fly Bacterial Microbiome Be Useful in Pest Management?.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, doi = {10.3390/microorganisms7080238}, pmid = {31382604}, issn = {2076-2607}, support = {PTDC/ASP-PLA/30650/2017//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {The applied importance of symbiosis has been gaining recognition. The relevance of symbiosis has been increasing in agriculture, in developing sustainable practices, including pest management. Insect symbiotic microorganisms' taxonomical and functional diversity is high, and so is the potential of manipulation of these microbial partners in suppressing pest populations. These strategies, which rely on functional organisms inhabiting the insect, are intrinsically less susceptible to external environmental variations and hence likely to overcome some of the challenges posed by climate change. Rates of climate change in the Mediterranean Basin are expected to exceed global trends for most variables, and this warming will also affect olive production and impact the interactions of olives and their main pest, the obligate olive fruit fly (Bactroceraoleae). This work summarizes the current knowledge on olive fly symbiotic bacteria towards the potential development of symbiosis-based strategies for olive fruit fly control. Particular emphasis is given to Candidatus Erwinia dacicola, an obligate, vertically transmitted endosymbiont that allows the insect to cope with the olive-plant produced defensive compound oleuropein, as a most promising target for a symbiosis disruption approach.}, }
@article {pmid31380084, year = {2019}, author = {Yoshida, K and Sanada-Morimura, S and Huang, SH and Tokuda, M}, title = {Influences of two coexisting endosymbionts, CI-inducing Wolbachia and male-killing Spiroplasma, on the performance of their host Laodelphax striatellus (Hemiptera: Delphacidae).}, journal = {Ecology and evolution}, volume = {9}, number = {14}, pages = {8214-8224}, doi = {10.1002/ece3.5392}, pmid = {31380084}, issn = {2045-7758}, abstract = {The small brown planthopper Laodelphax striatellus (Hemiptera: Delphacidae) is reported to have the endosymbiont Wolbachia, which shows a strong cytoplasmic incompatibility (CI) between infected males and uninfected females. In the 2000s, female-biased L. striatellus populations were found in Taiwan, and this sex ratio distortion was the result of male-killing induced by the infection of another endosymbiont, Spiroplasma. Spiroplasma infection is considered to negatively affect both L. striatellus and Wolbachia because the male-killing halves the offspring of L. striatellus and hinders the spread of Wolbachia infection via CI. Spiroplasma could have traits that increase the fitness of infected L. striatellus and/or coexisting organisms because the coinfection rates of Wolbachia and Spiroplasma were rather high in some areas. In this study, we investigated the influences of the infection of these two endosymbionts on the development, reproduction, and insecticide resistance of L. striatellus in the laboratory. Our results show that the single-infection state of Spiroplasma had a negative influence on the fertility of L. striatellus, while the double-infection state had no significant influence. At late nymphal and adult stages, the abundance of Spiroplasma was lower in the double-infection state than in the single-infection state. In the double-infection state, the reduction of Spiroplasma density may be caused by competition between the two endosymbionts, and the negative influence of Spiroplasma on the fertility of host may be relieved. The resistance of L. striatellus to four insecticides was compared among different infection states of endosymbionts, but Spiroplasma infection did not contribute to increase insecticide resistance. Because positive influences of Spiroplasma infection were not found in terms of the development, reproduction, and insecticide resistance of L. striatellus, other factors improving the fitness of Spiroplasma-infected L. striatellus may be related to the high frequency of double infection in some L. striatellus populations.}, }
@article {pmid31380028, year = {2019}, author = {Bromfield, ESP and Cloutier, S and Robidas, C and Tran Thi, TV and Darbyshire, SJ}, title = {Invasive Galega officinalis (Goat's rue) plants in Canada form a symbiotic association with strains of Neorhizobium galegae sv. officinalis originating from the Old World.}, journal = {Ecology and evolution}, volume = {9}, number = {12}, pages = {6999-7004}, doi = {10.1002/ece3.5266}, pmid = {31380028}, issn = {2045-7758}, abstract = {The toxic legume plant, Galega officinalis, is native to the Eastern Mediterranean and Black Sea regions. This legume is considered to be a noxious weed, and its establishment in Canada may have resulted from ornamental planting and/or field trials. In its native range, a highly specific nitrogen-fixing symbiosis with the bacterium, Neorhizobium galegae symbiovar (sv.) officinalis, is required for normal growth. In North America, nothing is known about the bacterial symbionts of G. officinalis. Our purpose was to determine the species and symbiovar identity of symbiotic bacteria associated with invasive plants of G. officinalis at five sites in the province of Ontario, Canada. Sequence analysis of four housekeeping (16S rRNA, atpD, glnII, and recA) and two symbiosis (nodC and nifH) genes showed that all 50 bacterial isolates from root nodules of G. officinalis at the five Canadian sites were identical to strains of N. galegae sv. officinalis originating either from Europe or the Caucasus. Plant tests indicated that soils collected from four Canadian sites without a history of agriculture or presence of G. officinalis were deficient in symbiotic bacteria capable of eliciting nodules on this plant. Collectively our data support the hypothesis of anthropogenic co-introduction of G. officinalis and its specific symbiotic bacterium into Canada from the Old World. Factors that may limit the spread of G. officinalis in new environments are discussed.}, }
@article {pmid31377982, year = {2019}, author = {González, CT and Saltonstall, K and Fernández-Marín, H}, title = {Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae).}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12275-019-8639-0}, pmid = {31377982}, issn = {1976-3794}, abstract = {Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllo-bacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enter-obacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.}, }
@article {pmid31377102, year = {2019}, author = {Bailey, GF and Bilsky, AM and Rowland, MB and Poole, AZ}, title = {Characterization and expression of tyrosinase-like genes in the anemone Exaiptasia pallida as a function of health and symbiotic state.}, journal = {Developmental and comparative immunology}, volume = {101}, number = {}, pages = {103459}, doi = {10.1016/j.dci.2019.103459}, pmid = {31377102}, issn = {1879-0089}, abstract = {Coral disease is a major threat to reef ecosystems and therefore, understanding the cellular pathways underlying disease progression and resistance is critical to mitigating future outbreaks. This study focused on tyrosinase-like proteins in cnidarians, which contribute to melanin synthesis, an invertebrate innate immune defense. Specifically, characterization and phylogenetic analysis of cnidarian tyrosinases were performed, and their role in symbiosis and a &quot;mystery disease&quot; in the anemone Exaiptasia pallida was investigated using qPCR. The results reveal a diversity of tyrosinase-like proteins in cnidarians that separate into two major clades on a phylogenetic tree, suggesting functional divergence. Two E. pallida sequences, Ep_Tyr1 and Ep_Tyr2, were further investigated, and qPCR results revealed no gene expression differences as a function of symbiotic state, but decreased expression in late disease stages. Overall this work provides evidence for the participation of tyrosinases in the cnidarian immune response.}, }
@article {pmid31375484, year = {2019}, author = {Sun, YW and Li, Y and Hu, Y and Chen, WX and Tian, CF}, title = {Coordinated regulation of size and number of PHB granules by core and accessory phasins in the facultative microsymbiont Sinorhizobium fredii NGR234.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00717-19}, pmid = {31375484}, issn = {1098-5336}, abstract = {The exact roles of various granule-associated proteins (GAPs) of polyhydroxybutyrate (PHB) are poorly investigated particularly in bacteria associated with plants. Here, four structural GAPs, named as phasins PhaP1-PhaP4, were identified and demonstrated as true phasins colocalized with PHB granules in Sinorhizobium fredii NGR234, a facultative microsymbiont of Vigna unguiculata and many other legumes. The conserved PhaP2 dominated in regulation of granule size under both free-living and symbiotic conditions. PhaP1, another conserved phasin, made a higher contribution than accessory PhaP4 and PhaP3 to PHB biosynthesis at stationary phase. PhaP3, with limited phyletic distribution on the symbiosis plasmid of Sinorhizobium, was more important than PhaP1 in regulating PHB biosynthesis in V. unguiculata nodules. In the test conditions, no significant symbiotic defects were observed for mutants lacking individual or multiple phaP genes. The mutant lacking two PHB synthases showed impaired symbiotic performance while mutations in individual PHB synthases or a PHB depolymerase had no symbiotic defects. This phenomenon is not related to either the number or size of PHB granules in test mutants within nodules. Distinct metabolic profiles and cocktail pools of GAPs of different phaP(s) mutants imply that core and accessory phasins can be differentially involved in regulating other cellular process in the facultative microsymbiont S. fredii NGR234.Importance Polyhydroxybutyrate (PHB) granules are a store of carbon and energy in bacteria and archaea, and play an important role in stress adaptation. Recent studies have highlighted distinct roles of several granule-associated proteins (GAPs) in regulating the size, number and localization of PHB granules in free-living bacteria, though our knowledge on the role of GAPs in bacteria associated with plants is still limited. Here we report distinct roles of core and accessory phasins associated with PHB granules of Sinorhizobium fredii NGR234, a broad host range microsymbiont of diverse legumes. Core phasins PhaP2 and PhaP1 are conserved major phasins in free living cells. PhaP2 and an accessory phasin PhaP3 encoded by an auxiliary gene on the symbiosis plasmid are major phasins in nitrogen fixing bacteroids in cowpea nodules. GAPs and metabolic profiles can vary in different phaP mutants. Contrasting symbiotic performance between mutants lacking PHB synthases, depolymerase or phasins were revealed.}, }
@article {pmid31373013, year = {2019}, author = {Zhang, W and Yuan, J and Cheng, T and Tang, MJ and Sun, K and Song, SL and Xu, FJ and Dai, CC}, title = {Flowering-mediated root-fungus symbiosis loss is related to jasmonate-dependent root soluble sugar deprivation.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13636}, pmid = {31373013}, issn = {1365-3040}, support = {NSFC 31870478//National Natural Science Foundation of China/ ; //Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions of China/ ; 1812000006317//Doctor Breeding Project of Nanjing Normal University/ ; }, abstract = {The role of flowering in root-fungal symbiosis is not well understood. Because flowering and fungal symbionts are supported by carbohydrates, we hypothesized that flowering modulates root-beneficial fungal associations through alterations in carbohydrate metabolism and transport. We monitored fungal colonization and soluble sugars in the roots of Arabidopsis thaliana following inoculation with a mutualistic fungus Phomopsis liquidambari across different plant developmental stages. Jasmonate signalling of wild-type plants, sugar transport, and root invertase of wild-type and jasmonate-insensitive plants were exploited to assess whether and how jasmonate-dependent sugar dynamics are involved in flowering-mediated fungal colonization alterations. We found that flowering restricts root-fungal colonization and activates root jasmonate signalling upon fungal inoculation. Jasmonates reduce the constitutive and fungus-induced accumulation of root glucose and fructose at the flowering stage. Further experiments with sugar transport and metabolism mutant lines revealed that root glucose and fructose positively influence fungal colonization. Diurnal, jasmonate-dependent inhibitions of sugar transport and soluble invertase activity were identified as likely mechanisms for flowering-mediated root sugar depletion upon fungal inoculation. Collectively, our results reveal that flowering drives root-fungus cooperation loss, which is related to jasmonate-dependent root soluble sugar depletion. Limiting the spread of root-fungal colonization may direct more resources to flower development.}, }
@article {pmid31372335, year = {2019}, author = {McElwain, A and Warren, MB and Pereira, FB and Ksepka, SP and Bullard, SA}, title = {Pathobiology and first report of larval nematodes (Ascaridomorpha sp.) infecting freshwater mussels (Villosa nebulosa, Unionidae), including an inventory of nematode infections in freshwater and marine bivalves.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {10}, number = {}, pages = {41-58}, doi = {10.1016/j.ijppaw.2019.05.006}, pmid = {31372335}, issn = {2213-2244}, abstract = {Little information is available on host-parasite relationships between bivalves and larval nematodes. Herein, we describe nematode larvae (likely stage 2) in the infraorder Ascaridomorpha infecting the foot, intestine, and mantle of a freshwater mussel (Alabama rainbow, Villosa nebulosa [Conrad, 1834]) and detail histopathological changes to infected tissues. A total of 43 live mussels from the South Fork of Terrapin Creek, Alabama, were collected between 2010 and 2014, with 14 sectioned for histopathology and 29 dissected. Of the 14 sectioned mussels, 5 appeared to be uninfected, and 7, 1, and 1 had histozoic infections observed in the foot and intestine, intestine only, and mantle edge and foot, respectively. Twenty-three of 29 (79%) of the mussels dissected were infected by live nematodes, and mean nematode abundance was 8.3 (CL = 5.23-13), with 2 mussels infected with >100 nematodes each. Thus, with a total of 32 of the 43 collected mussels observed with nematodes, overall infection prevalence was 74.4% (CL = 0.594-0.855). The 18S rDNA of this nematode was 99% similar to that of several ascaridids (species of Kathlaniidae Lane, 1914 and Quimperiidae Baylis, 1930) that mature in aquatic/semi-aquatic vertebrates; the recovered 18S phylogenetic tree indicated this nematode from V. nebulosa shares a recent common ancestor with Ichthyobronema hamulatum (Ascaridomorpha: Quimperiidae; GenBank Accession Number KY476351). Pathological changes to tissue associated with these infections comprised focal tissue damage, but a cellular response was not evident. The Alabama rainbow possibly represents an intermediate or paratenic host. Given these results, the nematode is likely not pathogenic under normal stream conditions; however, high intensity infections in the foot could inhibit pedal extension and retraction; which would have demonstrable health consequences to a freshwater mussel. Based on our review of the bivalve mollusc parasite literature, a collective biodiversity of 61 nematodes reportedly exhibit some degree of symbiosis (from commensal to parasitic) with 21 bivalves (28 nematode spp. from 17 marine bivalve spp.; 33 nematode spp. from 4 freshwater bivalve spp.); only four records exist of putatively parasitic nematodes from Unionida. The present study represents the first description of a nematode species that invades the tissues of a Unionidae species.}, }
@article {pmid31371739, year = {2019}, author = {Ullah, I and Magdy, M and Wang, L and Liu, M and Li, X}, title = {Genome-wide identification and evolutionary analysis of TGA transcription factors in soybean.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11186}, doi = {10.1038/s41598-019-47316-z}, pmid = {31371739}, issn = {2045-2322}, support = {31730066//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The gain of function in genes and gene families is a continuous process and is a key factor in understanding gene and genome evolution in plants. TGACG-Binding (TGA) transcription factors (TFs) have long been known for their essential roles in plant defence in Arabidopsis, but their roles in legume symbiosis are yet to be explored. Here, we identified a total of 25 TGA (named GmTGA1-GmTGA25) genes in soybean. Through phylogenetic analysis, we discovered a clade of GmTGA proteins that appear to be legume-specific. Among them, two GmTGAs were unique by possessing the autophagy sequence in their proteins, while the third one was an orphan gene in soybean. GmTGAs were structurally different from AtTGAs, and their expression patterns also differed with the dominant expression of AtTGAs and GmTGAs in aerial and underground parts, respectively. Moreover, twenty-five GmTGAs showed a strong correlation among the gene expression in roots, nodules, and root hairs. The qRT-PCR analysis results revealed that among 15 tested GmTGAs, six were induced and four were suppressed by rhizobia inoculation, while 11 of these GmTGAs were induced by high nitrate. Our findings suggested the important roles of GmTGAs in symbiotic nodulation and in response to nitrogen availability in soybean.}, }
@article {pmid31368540, year = {2019}, author = {Pereira, J and Simões, M and Silva, JL}, title = {Microalgal assimilation of vitamin B12 toward the production of a superfood.}, journal = {Journal of food biochemistry}, volume = {43}, number = {8}, pages = {e12911}, doi = {10.1111/jfbc.12911}, pmid = {31368540}, issn = {1745-4514}, abstract = {A network of components from different metabolic pathways is the building scaffold of an indispensable compound in the human organism-vitamin B12 . The biosynthesis of this compound is restricted to a limited number of representatives of bacteria and archaea, while vitamin B12 -dependent enzymes are spread through several domains of life. Different attempts have been performed to increase vitamin B12 levels in dietary products, particularly in vegetarian and vegan dietary regimes. The integration of vitamin B12 in microalgae through symbiosis with microorganisms generally recognized as safe, for example the probiotic Lactobacillus reuteri, can even increase the nutritional value of the microalgal biomass. This study reviews the microbial production of vitamin B12 based on genetic analyses and chemical studies. Recent genetic approaches are focused, particularly potential metabolic engineering targets to increase vitamin B12 production. The bioincorporation of vitamin B12 in microalgae as an attempt to provide a superfood is also reviewed. PRACTICAL APPLICATIONS: Novel food habits (i.e., vegan lifestyle) may lack relevant nutrients, including vitamin B12 . Therefore, there is an increased demand for dietary products rich in vitamin B12 . Of potential interest is the provision of microbial-based superfood rich in numerous nutrients, including this vitamin. This manuscript provides an in-depth and timely overview on vitamin B12 biosynthesis and the major advances on metabolic engineering for improved vitamin B12 production by probiotic bacteria and other microorganisms generally recognized as safe. A relevant advance would result from the bioincorporation of vitamin B12 in alternative microorganisms (non-vitamin B12 producers) increasingly recognized as superfood, that is microalgae.}, }
@article {pmid31359038, year = {2019}, author = {Kashkouli, M and Fathipour, Y and Mehrabadi, M}, title = {Heritable Gammaproteobacterial Symbiont Improves the Fitness of Brachynema germari Kolenati (Hemiptera: Pentatomidae).}, journal = {Environmental entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ee/nvz089}, pmid = {31359038}, issn = {1938-2936}, abstract = {The pistachio green stink bug, Brachynema germari Kolenati, is an abundant and economic insect pest in most pistachio-growing regions. Some physiological and ecological features of this pest have been studied, but the microbiological nature of symbiotic bacteria and biological aspects of this host-symbiont interaction have been poorly understood. In the present study, we explored the host-associated environment, phylogeny, and acquisition features of the bacterial symbiont of the insect. Furthermore, the importance of the symbiont on the biological (i.e., lifespan, stage composition, and body weight) and behavioral characteristics (i.e., resting/wandering behaviors of the newborn nymphs) of the host were investigated. We found that a rod-shaped gammaproteobacterium was persistently colonized the fourth midgut region of the insect. Molecular phylogenetic and fluorescence in situ hybridization analyses strongly suggest that this symbiont should be placed in the genus Pantoea of the Enterobacteriales. Egg surface sterilization resulted in the aposymbiotic insects suggesting the vertical transmission of symbiont via egg surface smearing upon oviposition. Symbiotic and aposymbiotic B. germari showed no significant differences in the wandering behaviors of the first nymphal stages, whereas the symbiont-free insects exhibited retarded growth, lower longevity, and adult body weight. Taken together, these data provide a better understanding of the relationship between the bacterial symbiont and B. germari and demonstrate that the insect is heavily affected by the deprival of its gut symbionts.}, }
@article {pmid31354772, year = {2019}, author = {Li, X and He, XL and Zhou, Y and Hou, YT and Zuo, YL}, title = {Effects of Dark Septate Endophytes on the Performance of Hedysarum scoparium Under Water Deficit Stress.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {903}, doi = {10.3389/fpls.2019.00903}, pmid = {31354772}, issn = {1664-462X}, abstract = {Hedysarum scoparium, a species characterized by rapid growth and high drought resistance, has been used widely for vegetative restoration of arid regions in Northwest China that are prone to desertification. Desert soil is typically deficient in available water and the alleviation of drought stress to host plants by endophytes could be an efficient strategy to increase the success of desert restoration. With the objective to seek more beneficial symbionts that can be used in the revegetation strategies, we addressed the question whether H. scoparium can benefit from inoculation by dark septate endophytes (DSEs) isolated from other desert plants. We investigated the influences of four non-host DSE strains (Phialophora sp., Knufia sp., Leptosphaeria sp., and Embellisia chlamydospora) isolated from other desert plants on the performance of H. scoparium under different soil water conditions. Differences in plant performance, such as plant growth, antioxidant enzyme activities, carbon, nitrogen, and phosphorous concentration under all the treatments, were examined. Four DSE strains could colonize the roots of H. scoparium successfully, and they established a positive symbiosis with the host plants depending on DSE species and water availability. The greatest benefits of DSE inoculation occurred in water stress treatment. Specifically, Phialophora sp. and Leptosphaeria sp. improved the root biomass, total biomass, nutrient concentration, and antioxidant enzyme activities of host plants under water deficit conditions. These data contribute to the understanding of the ecological function of DSE fungi in drylands.}, }
@article {pmid31354767, year = {2019}, author = {Wilkinson, TDJ and Miranda, JP and Ferrari, J and Hartley, SE and Hodge, A}, title = {Aphids Influence Soil Fungal Communities in Conventional Agricultural Systems.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {895}, doi = {10.3389/fpls.2019.00895}, pmid = {31354767}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi (AMF) form symbioses with the roots of most plant species, including cereals. AMF can increase the uptake of nutrients including nitrogen (N) and phosphorus (P), and of silicon (Si) as well as increase host resistance to various stresses. Plants can simultaneously interact with above-ground insect herbivores such as aphids, which can alter the proportion of plant roots colonized by AMF. However, it is unknown if aphids impact the structure of AMF communities colonizing plants or the extent of the extraradical mycelium produced in the soil, both of which can influence the defensive and nutritional benefit a plant derives from the symbiosis. This study investigated the effect of aphids on the plant-AMF interaction in a conventionally managed agricultural system. As plants also interact with other soil fungi, the non-AMF fungal community was also investigated. We hypothesized that aphids would depress plant growth, and reduce intraradical AMF colonization, soil fungal hyphal density and the diversity of AM and non-AM fungal communities. To test the effects of aphids, field plots of barley enclosed with insect proof cages were inoculated with Sitobion avenae or remained uninoculated. AMF specific and total fungal amplicon sequencing assessed root fungal communities 46 days after aphid addition. Aphids did not impact above-ground plant biomass, but did increase the grain N:P ratio. Whilst aphid presence had no impact on AMF intraradical colonization, soil fungal hyphal length density, or AMF community characteristics, there was a trend for the aphid treatment to increase vesicle numbers and the relative abundance of the AMF family Gigasporaceae. Contrary to expectations, the aphid treatment also increased the evenness of the total fungal community. This suggests that aphids can influence soil communities in conventional arable systems, a result that could have implications for multitrophic feedback loops between crop pests and soil organisms across the above-below-ground interface.}, }
@article {pmid31352211, year = {2019}, author = {Xu, H and Shao, H and Lu, Y}, title = {Arbuscular mycorrhiza fungi and related soil microbial activity drive carbon mineralization in the maize rhizosphere.}, journal = {Ecotoxicology and environmental safety}, volume = {182}, number = {}, pages = {109476}, doi = {10.1016/j.ecoenv.2019.109476}, pmid = {31352211}, issn = {1090-2414}, abstract = {This research is aimed to investigate the effect of arbuscular mycorrhiza (AM) fungi on soil microbial activity and carbon mineralization in the maize rhizosphere under potted condition. Glomus etunicatum was used for our experiment. Results showed that AM symbiosis increased the levels of microorganism in the maize rhizosphere soil, and enhanced activity of soil microbial enzymes. After inoculating AM fungi, the contents of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and readily oxidizable carbon (ROC) in the rhizosphere soil of maize increased with varying degrees. We obtained strong evidence that higher contents of MBC, DOC, ROC, superior number of microbes and stronger soil enzyme activities could be responsible for the higher rate of carbon mineralization in AM fungi treatment. AM fungi inoculation was confirmed to be effective to improve the soil quality for larger-scale ecoengineering.}, }
@article {pmid31351601, year = {2019}, author = {Antoniou, NA and Zorpas, AA}, title = {Quality protocol and procedure development to define end-of-waste criteria for tire pyrolysis oil in the framework of circular economy strategy.}, journal = {Waste management (New York, N.Y.)}, volume = {95}, number = {}, pages = {161-170}, doi = {10.1016/j.wasman.2019.05.035}, pmid = {31351601}, issn = {1879-2456}, abstract = {The requirements to define End-of-Waste Criteria (EWC) were set in the Waste Framework Directive (WFD), Article 6 and the detailed data collected are considered to be the baseline for the elaboration of the operational EWC through several steps. Such waste stream (which is produced from End of Life Tires-ELT) could be a valuable source for energy recovery and can be used on a pan-European basis as an alternative fuel, for co-incineration in cement plants or furthermore in internal compunctions engines. The exploration for sustainable energy is one of the most dynamic areas of research currently. This study aims to investigate the ability to manage and exploit the energy content of Tire Pyrolysis Oil (TPO), through pyrolysis technology as incineration/co-incineration technology for ELTs presents significant environmental issues. However, TPO, must be declassified from waste in order to be able to be use as an alternative fuel in internal combustion engines for power generation participating in the loop of circular economy and industrial symbiosis. This paper focus on the development of a Quality Protocol (QP) and the procedure how to develop EWC for the declassification of TPO in order to replace Light Fuel Oil (LFO).}, }
@article {pmid31347943, year = {2019}, author = {Sarsaiya, S and Shi, J and Chen, J}, title = {A comprehensive review on fungal endophytes and its dynamics on Orchidaceae plants: current research, challenges, and future possibilities.}, journal = {Bioengineered}, volume = {10}, number = {1}, pages = {316-334}, doi = {10.1080/21655979.2019.1644854}, pmid = {31347943}, issn = {2165-5987}, mesh = {Biological Products/*chemistry/isolation &amp; purification ; Endophytes/classification/genetics/*metabolism ; Fungi/classification/genetics/*metabolism ; Metabolic Networks and Pathways/physiology ; Orchidaceae/*microbiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Secondary Metabolism/physiology ; Symbiosis/*physiology ; }, abstract = {In the development of medicinally important Orchidaceae, the extent of fungal endophytes specificity is not presently very clear. Limited study has been available on natural products formed and its role on plant growth, defence mechanism by endophytes, and to characterize the chief treasure of bioactive molecules. Therefore, this review article presents an evaluation of the endophytes associated with Orchidaceae for physiology, metabolism, and genomics which have prominently contributed to the resurgence of novel metabolite research increasing our considerate of multifaceted mechanisms regulatory appearance of biosynthetic gene groups encoding diverse metabolites. Additionally, we presented the comprehensive recent development of bio-strategies for the cultivation of endophytes from Orchidaceae and integration of bioengineered 'Genomics with metabolism' approaches with emphases collective omics as powerful approach to discover novel metabolite compounds. The Orchidaceae-fungal endophytes' biodynamics for sustainable development of bioproducts and its applications are supported in large-scale biosynthesis of industrially and pharmaceutical important biomolecules.}, }
@article {pmid31346602, year = {2019}, author = {Petersen, G and Darby, H and Lam, VKY and Pedersen, HÆ and Merckx, VSFT and Zervas, A and Seberg, O and Graham, SW}, title = {Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz114}, pmid = {31346602}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared to green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after photosynthesis loss.<br><br>METHODS: We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes to those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared to autotrophic relatives.<br><br>KEY RESULTS: Plastomes of two species of Epirixanthes have become substantially degraded compared to that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes.<br><br>CONCLUSIONS: Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.}, }
@article {pmid31345767, year = {2019}, author = {Rueckert, S and Betts, EL and Tsaousis, AD}, title = {The Symbiotic Spectrum: Where Do the Gregarines Fit?.}, journal = {Trends in parasitology}, volume = {35}, number = {9}, pages = {687-694}, doi = {10.1016/j.pt.2019.06.013}, pmid = {31345767}, issn = {1471-5007}, abstract = {Gregarine apicomplexans are closely related to parasites such as Plasmodium, Toxoplasma, and Cryptosporidium, which are causing severe health and economic burdens. Colonizing only invertebrates and having no obvious medical relevance, they are mostly ignored in 'omics' studies, although gregarines are the most basal apicomplexans and therefore key players in the understanding of the evolution of parasitism in the Apicomplexa from free-living ancestors. They belong to the largest exclusively parasitic phylum, but is this perception actually true? The effects of gregarines on their hosts seem to cover the whole spectrum of symbiosis from mutualistic to parasitic. We suggest future research directions to understand the evolutionary role of gregarines, by elucidating their biology and interaction with their hosts and the hosts' microbiota.}, }
@article {pmid31342139, year = {2019}, author = {Ogawa, W and Takeda, Y and Endo, N and Yamashita, S and Takayama, T and Fukuda, M and Yamada, A}, title = {Repeated fruiting of Japanese golden chanterelle in pot culture with host seedlings.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00908-z}, pmid = {31342139}, issn = {1432-1890}, support = {KAKENHI 15H01751//Japan Society for the Promotion of Science ()/ ; general research grant//Institute for Fermentation, Osaka/ ; }, abstract = {Yellow chanterelles are among the most popular wild edible ectomycorrhizal mushrooms worldwide. The representative European golden chanterelle, Cantharellus cibarius, has only once been reported to fruit under greenhouse conditions, due to the difficulty of establishing pure culture. Recently, we developed a new technique for establishing a pure culture of a Japanese golden chanterelle (Cantharellus anzutake), and conducted in vitro ectomycorrhizal synthesis using established strains and Pinus densiflora. Acclimated pine mycorrhizal seedlings colonized with C. anzutake in a pot system under laboratory conditions produced small but distinct basidiomata with developed basidiospores. C. anzutake mycorrhizae were established on Quercus serrata seedlings by inoculation of mycorrhizal root tips of the fungus synthesized on P. densiflora. A scaled-up C. anzutake-host system in larger pots (4 L soil volume) exhibited repeated fruiting at 20-24 °C under continuous light illumination at 150 μmol m-2 s-1 during a 2-year incubation period. Therefore, a C. anzutake cultivation trial is practical under controlled environmental conditions.}, }
@article {pmid31338082, year = {2019}, author = {Bernasconi, R and Stat, M and Koenders, A and Paparini, A and Bunce, M and Huggett, MJ}, title = {Establishment of Coral-Bacteria Symbioses Reveal Changes in the Core Bacterial Community With Host Ontogeny.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1529}, doi = {10.3389/fmicb.2019.01529}, pmid = {31338082}, issn = {1664-302X}, abstract = {Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral Acropora digitifera from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to egg-sperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.}, }
@article {pmid31337682, year = {2019}, author = {Feng, H and Edwards, N and Anderson, CMH and Althaus, M and Duncan, RP and Hsu, YC and Luetje, CW and Price, DRG and Wilson, ACC and Thwaites, DT}, title = {Trading amino acids at the aphid-Buchnera symbiotic interface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {32}, pages = {16003-16011}, doi = {10.1073/pnas.1906223116}, pmid = {31337682}, issn = {1091-6490}, abstract = {Plant sap-feeding insects are widespread, having evolved to occupy diverse environmental niches despite exclusive feeding on an impoverished diet lacking in essential amino acids and vitamins. Success depends exquisitely on their symbiotic relationships with microbial symbionts housed within specialized eukaryotic bacteriocyte cells. Each bacteriocyte is packed with symbionts that are individually surrounded by a host-derived symbiosomal membrane representing the absolute host-symbiont interface. The symbiosomal membrane must be a dynamic and selectively permeable structure to enable bidirectional and differential movement of essential nutrients, metabolites, and biosynthetic intermediates, vital for growth and survival of host and symbiont. However, despite this crucial role, the molecular basis of membrane transport across the symbiosomal membrane remains unresolved in all bacteriocyte-containing insects. A transport protein was immunolocalized to the symbiosomal membrane separating the pea aphid Acyrthosiphon pisum from its intracellular symbiont Buchnera aphidicola The transporter, A. pisum nonessential amino acid transporter 1, or ApNEAAT1 (gene: ACYPI008971), was characterized functionally following heterologous expression in Xenopus oocytes, and mediates both inward and outward transport of small dipolar amino acids (serine, proline, cysteine, alanine, glycine). Electroneutral ApNEAAT1 transport is driven by amino acid concentration gradients and is not coupled to transmembrane ion gradients. Previous metabolite profiling of hemolymph and bacteriocyte, alongside metabolic pathway analysis in host and symbiont, enable prediction of a physiological role for ApNEAAT1 in bidirectional host-symbiont amino acid transfer, supplying both host and symbiont with indispensable nutrients and biosynthetic precursors to facilitate metabolic complementarity.}, }
@article {pmid31337355, year = {2019}, author = {Armaleo, D and Müller, O and Lutzoni, F and Andrésson, ÓS and Blanc, G and Bode, HB and Collart, FR and Dal Grande, F and Dietrich, F and Grigoriev, IV and Joneson, S and Kuo, A and Larsen, PE and Logsdon, JM and Lopez, D and Martin, F and May, SP and McDonald, TR and Merchant, SS and Miao, V and Morin, E and Oono, R and Pellegrini, M and Rubinstein, N and Sanchez-Puerta, MV and Savelkoul, E and Schmitt, I and Slot, JC and Soanes, D and Szövényi, P and Talbot, NJ and Veneault-Fourrey, C and Xavier, BB}, title = {The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {605}, doi = {10.1186/s12864-019-5629-x}, pmid = {31337355}, issn = {1471-2164}, support = {IGSP 2008001//Duke Institute for Genomic Sciences and Policy/ ; FWP 61327//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-FC02-02ER63421//U.S. Department of Energy/ ; 112442//U.S. Department of Energy/ ; 1011101//National Science Foundation/ ; }, abstract = {BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.<br><br>RESULTS: A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.<br><br>CONCLUSIONS: The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.}, }
@article {pmid31333627, year = {2019}, author = {Ruiz, B and Le Scornet, A and Sauviac, L and Rémy, A and Bruand, C and Meilhoc, E}, title = {The Nitrate Assimilatory Pathway in Sinorhizobium meliloti: Contribution to NO Production.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1526}, doi = {10.3389/fmicb.2019.01526}, pmid = {31333627}, issn = {1664-302X}, abstract = {The interaction between rhizobia and their legume host plants culminates in the formation of specialized root organs called nodules in which differentiated endosymbiotic bacteria (bacteroids) fix atmospheric nitrogen to the benefit of the plant. Interestingly, nitric oxide (NO) has been detected at various steps of the rhizobium-legume symbiosis where it has been shown to play multifaceted roles. It is recognized that both bacterial and plant partners of the Sinorhizobium meliloti-Medicago truncatula symbiosis are involved in NO synthesis in nodules. S. meliloti can also produce NO from nitrate when living as free cells in the soil. S. meliloti does not possess any NO synthase gene in its genome. Instead, the denitrification pathway is often described as the main driver of NO production with nitrate as substrate. This pathway includes the periplasmic nitrate reductase (Nap) which reduces nitrate into nitrite, and the nitrite reductase (Nir) which reduces nitrite into NO. However, additional genes encoding putative nitrate and nitrite reductases (called narB and nirB, respectively) have been identified in the S. meliloti genome. Here we examined the conditions where these genes are expressed, investigated their involvement in nitrate assimilation and NO synthesis in culture and their potential role in planta. We found that narB and nirB are expressed under aerobic conditions in absence of ammonium in the medium and most likely belong to the nitrate assimilatory pathway. Even though these genes are clearly expressed in the fixation zone of legume root nodule, they do not play a crucial role in symbiosis. Our results support the hypothesis that in S. meliloti, denitrification remains the main enzymatic way to produce NO while the assimilatory pathway involving NarB and NirB participates indirectly to NO synthesis by cooperating with the denitrification pathway.}, }
@article {pmid31333602, year = {2019}, author = {Nouioui, I and Cortés-Albayay, C and Carro, L and Castro, JF and Gtari, M and Ghodhbane-Gtari, F and Klenk, HP and Tisa, LS and Sangal, V and Goodfellow, M}, title = {Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1457}, doi = {10.3389/fmicb.2019.01457}, pmid = {31333602}, issn = {1664-302X}, abstract = {This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.}, }
@article {pmid31332951, year = {2019}, author = {Gilbert, SF}, title = {Developmental symbiosis facilitates the multiple origins of herbivory.}, journal = {Evolution &amp; development}, volume = {}, number = {}, pages = {e12291}, doi = {10.1111/ede.12291}, pmid = {31332951}, issn = {1525-142X}, support = {IOS-145177//National Science Foundation/ ; }, abstract = {Developmental bias toward particular evolutionary trajectories can be facilitated through symbiosis. Organisms are holobionts, consisting of zygote-derived cells and a consortia of microbes, and the development, physiology, and immunity of animals are properties of complex interactions between the zygote-derived cells and microbial symbionts. Such symbionts can be agents of developmental plasticity, allowing an organism to develop in particular directions. This plasticity can lead to genetic assimilation either through the incorporation of microbial genes into host genomes or through the direct maternal transmission of the microbes. Such plasticity can lead to niche construction, enabling the microbes to remodel host anatomy and/or physiology. In this article, I will focus on the ability of symbionts to bias development toward the evolution of herbivory. I will posit that the behavioral and morphological manifestations of herbivorous phenotypes must be preceded by the successful establishment of a community of symbiotic microbes that can digest cell walls and detoxify plant poisons. The ability of holobionts to digest plant materials can range from being a plastic trait, dependent on the transient incorporation of environmental microbes, to becoming a heritable trait of the holobiont organism, transmitted through the maternal propagation of symbionts or their genes.}, }
@article {pmid31332487, year = {2019}, author = {Singh, RP}, title = {Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {18}, pages = {7287-7315}, doi = {10.1007/s00253-019-10012-z}, pmid = {31332487}, issn = {1432-0614}, abstract = {Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.}, }
@article {pmid31331977, year = {2019}, author = {Guckes, KR and Cecere, AG and Wasilko, NP and Williams, AL and Bultman, KM and Mandel, MJ and Miyashiro, T}, title = {Incompatibility of Vibrio fischeri strains during symbiosis establishment depends on two functionally redundant hcp genes.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00221-19}, pmid = {31331977}, issn = {1098-5530}, support = {R01 GM129133/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria that have the capacity to fill the same niche will compete with one another for space and resources available within an ecosystem. Such competition is heightened among different strains of the same bacterial species. Nevertheless, different strains often inhabit the same host. The molecular mechanisms that impact competition between different strains within the same host are poorly understood. To address this knowledge gap, the type VI secretion system (T6SS), which is a mechanism for bacteria to kill neighboring cells, was examined in the marine bacterium Vibrio fischeri Different strains of V. fischeri naturally colonize the light organ of the bobtail squid Euprymna scolopes The genome of FQ-A001, which is a T6SS-positive strain, features two hcp genes that are predicted to encode identical subunits of the T6SS. Co-incubation assays showed that either hcp gene is sufficient for FQ-A001 to kill another strain via T6SS in vitro Additionally, induction of hcp expression is sufficient to induce killing activity in an Hcp- mutant of FQ-A001. Squid colonization assays involving inoculums of FQ-A001-derived strains mixed with ES114 revealed that both hcp genes must be deleted for FQ-A001 and ES114 to occupy the same space within the light organ. These experimental results provide insight into the genetic factors necessary for the T6SS of V. fischeri to function in vivo, thereby increasing understanding of the molecular mechanisms that impact strain diversity within a host.IMPORTANCE Different bacterial strains compete to occupy the same niche. The outcome from such competition can be affected by the type VI secretion system (T6SS), which is an intercellular killing mechanism of bacteria. Here, an animal-bacterial symbiosis is used as a platform to study the genetic factors that promote T6SS-mediated killing of one strain by another strain. Identification of the molecular determinants of T6SS function in vivo contributes to the understanding of how different strains interact within a host.}, }
@article {pmid31331976, year = {2019}, author = {Lynch, JB and Schwartzman, JA and Bennett, BD and McAnulty, SJ and Knop, M and Nyholm, SV and Ruby, EG}, title = {Ambient pH alters protein content of outer membrane vesicles, driving host development in a beneficial symbiosis.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00319-19}, pmid = {31331976}, issn = {1098-5530}, abstract = {Outer membrane vesicles (OMVs) are continuously produced by Gram-negative bacteria, and are increasingly recognized as ubiquitous mediators of bacterial physiology. In particular, OMVs are powerful effectors in inter-organismal interactions, driven largely by their molecular contents. These impacts have been studied extensively in bacterial pathogenesis, but have not been well documented within the context of mutualism. Here, we examined the proteomic composition of OMVs from the marine bacterium Vibrio fischeri, which forms a specific mutualism with the Hawaiian bobtail squid, Euprymna scolopes We found that V. fischeri upregulates transcription of its major outer membrane protein, OmpU, during growth at an acidic pH, which V. fischeri experiences when it transitions from its environmental reservoir to host tissues. We used comparative genomics and DNA pull-down analyses to search for regulators of ompU, and found that differential expression of ompU is governed by the OmpR, H-NS, and ToxR proteins. This transcriptional control combines with nutritional conditions to govern OmpU levels in OMVs. Under a host-encountered acidic pH, V. fischeri OMVs become more potent stimulators of symbiotic host development in an OmpU-dependent manner. Finally, we found that symbiotic development could be stimulated by OMVs containing a homolog of OmpU from the pathogenic species Vibrio cholerae, connecting the role of a well-described virulence factor with a mutualistic element. This work explores the symbiotic effects of OMV variation, identifies shared regulatory machinery between pathogenic and mutualistic bacteria, and provides evidence of the role that OMVs play in animal-bacteria mutualism.Importance Beneficial bacteria communicate with their hosts through a variety of means. These communications are often carried out by a combination of molecules that stimulate responses from the host and are necessary for development of the relationship between these organisms. Naturally produced bacterial outer membrane vesicles (OMVs) contain many of those molecules and can stimulate a wide range of responses from recipient organisms. Here, we describe how a marine bacterium, Vibrio fischeri, changes the makeup of its OMVs under conditions that it experiences as it goes from its free-living lifestyle to associating with its natural host, the Hawaiian bobtail squid. This work improves our understanding of how bacteria change their signaling profile as they begin to associate with their beneficial partner animals.}, }
@article {pmid31330021, year = {2019}, author = {Ji, J and Luo, CL and Zou, X and Lv, XH and Xu, YB and Shu, DM and Qu, H}, title = {Association of host genetics with intestinal microbial relevant to body weight in a chicken F2 resource population.}, journal = {Poultry science}, volume = {98}, number = {9}, pages = {4084-4093}, doi = {10.3382/ps/pez199}, pmid = {31330021}, issn = {1525-3171}, abstract = {Host-microbiota interactions describe a co-evolution and mutualistic symbiosis. Gut microbial communities are important for diverse host functions. However, in birds, the relationship between the composition of the intestinal microbiota and the genetic variation of the host is not clearly understood. To dissect these interactions, a Chinese yellow broiler line (genetically selected for a high growth rate) and Huiyang Beard chickens (low growth rate) were crossed, generating an F2 population. The population structures of the gut microbes in the phenotypically high and low 91-d body weight individuals of both sexes in the F2 population were studied. Interestingly, a non-metric multidimensional scaling analysis revealed that the microbiota of the high-weight and low-weight females was clearly separated into 2 clusters. A β-diversity analysis showed that the locus rs16775833 within the doublesex and mab-3-related transcription factor (DMRT) gene cluster accounted for approximately 21% of the variation in the population structure of the gut microbiota. Furthermore, the 2 genetic loci rs15142709 and rs15142674 were significantly associated with specific species of Methanobacterium. These loci are located in the pleiomorphic adenoma gene 1 (PLAG1) and lck/yes-related novel tyrosine kinase (LYN) genes, which are involved in cell differentiation and growth. This finding suggests evidence for the influence of the host genetics on the composition of the gut microbiota in birds and the importance and utility of the host-microbe status to better understand its effect on the potential growth of birds.}, }
@article {pmid31329832, year = {2019}, author = {Cardós, JLH and Prieto, M and Jylhä, M and Aragón, G and Molina, MC and Martínez, I and Rikkinen, J}, title = {A case study on the re-establishment of the cyanolichen symbiosis: where do the compatible photobionts come from?.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz052}, pmid = {31329832}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: In order to re-establish lichen symbiosis, fungal spores must first germinate and then associate with a compatible photobiont. To detect possible establishment limitations in a sexually reproducing cyanolichen species, we studied ascospore germination, photobiont growth and photobiont association patterns in Pectenia plumbea.<br><br>METHODS: Germination tests were made with ascospores from 500 apothecia under different treatments, and photobiont growth was analysed in 192 isolates obtained from 24 thalli. We determined the genotype identity [tRNALeu (UAA) intron] of the Nostoc cyanobionts from 30 P. plumbea thalli from one population. We also sequenced cyanobionts of 41 specimens of other cyanolichen species and 58 Nostoc free-living colonies cultured from the bark substrate.<br><br>KEY RESULTS: Not a single fungal ascospore germinated and none of the photobiont isolates produced motile hormogonia. Genetic analyses revealed that P. plumbea shares Nostoc genotypes with two other cyanolichen species of the same habitat, but these photobionts were hardly present in the bark substrate.<br><br>CONCLUSIONS: Due to the inability of both symbionts to thrive independently, the establishment of P. plumbea seems to depend on Dendriscocaulon umhausense, the only cyanolichen species in the same habitat that reproduces asexually and acts as a source of appropriate cyanobionts. This provides support to the hypothesis about facilitation among lichens.}, }
@article {pmid31328784, year = {2019}, author = {Muñoz-Gómez, SA and Durnin, K and Eme, L and Paight, C and Lane, CE and Saffo, MB and Slamovits, CH}, title = {Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz155}, pmid = {31328784}, issn = {1759-6653}, abstract = {A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.}, }
@article {pmid31328352, year = {2019}, author = {Khemaissia, H and Jelassi, R and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Effects of trace metal elements on ultrastructural features of hepatopancreas of Armadillidium granulatum Brandt, 1833 (Crustacea, Isopoda).}, journal = {Microscopy research and technique}, volume = {}, number = {}, pages = {}, doi = {10.1002/jemt.23349}, pmid = {31328352}, issn = {1097-0029}, support = {LR18ES06//Laboratory of Diversity, Management and Conservation of Biological Systems/ ; }, abstract = {This study was conducted to compare metals bioaccumulation in the terrestrial isopod Armadillidium granulatum collected from Ghar El Melh lagoon. We focused on recognizing the effects of trace elements on hepatopancreas functional role. To this end, isopod specimens were exposed for 3 weeks to sediments contaminated with cadmium, copper, zinc, mercury, and nickel. Three concentrations were used in duplicate for each experimental condition. At the end of the experiment, metal body burdens were determined using flame atomic absorption spectrometry. Results of the bioaccumulation factor (BAF) showed that the species A. granulatum was classified as a Cu macroconcentrator (BAF > 2) and a Zn deconcentrator (BAF < 2). Dose dependent morphological and histological changes were observed in the hepatopancreas cells using transmission electron microscopy. The predominant features were: microvillus border disruption, condensation of the cytoplasm with increasing endoplasmic reticulum, mitochondria, lysosomes and granules that accumulated metals in B and S cells. The number of lipid droplets decreased especially after Cd, Zn, Hg, and Ni treatments. This study demonstrated that the terrestrial isopod A. gramulatum could be a good indicator of soil metal contamination.}, }
@article {pmid31327928, year = {2019}, author = {Xie, L and Chen, YL and Long, YY and Zhang, Y and Liao, ST and Liu, B and Qin, LP and Nong, Q and Zhang, WL}, title = {Three new species of Conlarium from sugarcane rhizosphere in southern China.}, journal = {MycoKeys}, volume = {56}, number = {}, pages = {1-11}, doi = {10.3897/mycokeys.56.35857}, pmid = {31327928}, issn = {1314-4049}, abstract = {Three new species isolated from sugarcane rhizosphere in China, namely Conlariumbaiseensesp. nov., C.nanningensesp. nov., and C.saccharisp. nov., are described and illustrated. Molecular evidence (phylogenetic analysis of combined LSU, SSU, ITS and RPB2 sequence data) and phenotypical characters support their independent status from related and similar species. The new species, as dark spetate endophytes, inhabit sugarcane rhizosphere and can form a symbiosis with sugarcane.}, }
@article {pmid31327121, year = {2019}, author = {Fileccia, V and Ingraffia, R and Amato, G and Giambalvo, D and Martinelli, F}, title = {Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat.}, journal = {Molecular biology reports}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11033-019-04974-6}, pmid = {31327121}, issn = {1573-4978}, abstract = {Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal treatment while six were regulated in presence of it. The most represented miRNA family was miR167 that was regulated by water deficit in both leaf and root tissues. Interestingly, miR827-5p was differentially regulated in leaves in the absence of mycorrhizal treatment while it was water deficit-modulated in roots irrespective of AMF treatment. In roots, water deficit repressed miR827-5p, miR394, miR6187, miR167e-3p, and miR9666b-3p affecting transcription, RNA synthesis, protein synthesis, and protein modifications. In leaves, mycorrhizae modulated miR5384-3p and miR156e-3p affecting trafficking and cell redox homeostasis. DNA replication and transcription regulation should be targeted by the repression of miR1432-5p and miR166h-3p. This work provided interesting insights into the post-transcriptional mechanisms of wheat responses to water deficit in relation to mycorrhizal symbiosis.}, }
@article {pmid31325057, year = {2019}, author = {Zhang, S and Kondorosi, É and Kereszt, A}, title = {An anthocyanin marker for direct visualization of plant transformation and its use to study nitrogen-fixing nodule development.}, journal = {Journal of plant research}, volume = {132}, number = {5}, pages = {695-703}, doi = {10.1007/s10265-019-01126-6}, pmid = {31325057}, issn = {1618-0860}, support = {OTKA 120120/119652//Hungarian National Office for Research, Development and Innovation/ ; GINOP 2.3.2-15-2016-00014//Hungarian National Office for Research, Development and Innovation/ ; GINOP 2.3.2-15-2016-00015//Hungarian National Office for Research, Development and Innovation/ ; }, abstract = {The development and functioning of the nitrogen fixing symbiosis between legume plants and soil bacteria collectively called rhizobia requires continuous chemical dialogue between the partners using different molecules such as flavonoids, lipo-chitooligosaccharides, polysaccharides and peptides. Agrobacterium rhizogenes mediated hairy root transformation of legumes is widely used to study the function of plant genes involved in the process. The identification of transgenic plant tissues is based on antibiotics/herbicide selection and/or the detection of different reporter genes that usually require special equipment such as fluorescent microscopes or destructive techniques and chemicals to visualize enzymatic activity. Here, we developed and efficiently used in hairy root experiments binary vectors containing the MtLAP1 gene driven by constitutive and tissue-specific promoters that facilitate the production of purple colored anthocyanins in transgenic tissues and thus allowing the identification of transformed roots by naked eye. Anthocyanin producing roots were able to establish effective symbiosis with rhizobia. Moreover, it was shown that species-specific allelic variations and a mutation preventing posttranslational acetyl modification of an essential nodule-specific cysteine-rich peptide, NCR169, do not affect the symbiotic interaction of Medicago truncatula cv. Jemalong with Sinorhizobium medicae strain WSM419. Based on the experiments, it could be concluded that it is preferable to use the vectors with tissue-specific promoters that restrict anthocyanin production to the root vasculature for studying biotic interactions of the roots such as symbiotic nitrogen fixation or mycorrhizal symbiosis.}, }
@article {pmid31323808, year = {2019}, author = {Faluaburu, MS and Nakai, R and Imura, S and Naganuma, T}, title = {Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica.}, journal = {Microorganisms}, volume = {7}, number = {7}, pages = {}, doi = {10.3390/microorganisms7070203}, pmid = {31323808}, issn = {2076-2607}, support = {JP16H05765//Japan Society for the Promotion of Science/ ; }, abstract = {Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.}, }
@article {pmid31323069, year = {2019}, author = {Morishima, SY and Yamashita, H and O-Hara, S and Nakamura, Y and Quek, VZ and Yamauchi, M and Koike, K}, title = {Study on expelled but viable zooxanthellae from giant clams, with an emphasis on their potential as subsequent symbiont sources.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0220141}, doi = {10.1371/journal.pone.0220141}, pmid = {31323069}, issn = {1932-6203}, abstract = {Unlike most bivalve shellfishes, giant clams (tridacnines) harbor symbiotic microalgae (zooxanthellae) in their fleshy bodies. Zooxanthellae are not maternally inherited by tridacnine offspring, hence, the larvae must acquire zooxanthellae from external sources, although such algal populations or sources in the environment are currently unknown. It is well known that giant clams expel fecal pellets that contain viable zooxanthellae cells, but whether these cells are infectious or just an expelled overpopulation from the giant clams has not been investigated. In this study, we observed the ultrastructural and photosynthetic competencies of zooxanthellae in the fecal pellets of Tridacna crocea and further tested the ability of these cells to infect T. squamosa juveniles. The ultrastructure of the zooxanthellae cells showed that the cells were intact and had not undergone digestion. Additionally, these zooxanthellae cells showed a maximum quantum yield of photosystem II (Fv/Fm) as high as those retained in the mantle of the giant clam. Under the assumption that feces might provide symbionts to the larvae of other giant clams, fecal pellets from Tridacna squamosa and T. crocea were given to artificially hatched 1-day-old T. squamosa larvae. On the 9th day, 15-34% of the larvae provided with the fecal pellets took up zooxanthellae in their stomach, and on the 14th day, zooxanthellae cells reached the larval margin, indicating the establishment of symbiosis. The rate reaching this stage was highest, ca. 5.3%, in the larvae given whole (nonhomogenized) pellets from T. crocea. The composition of zooxanthellae genera contained in the larvae were similar to those in the fecal pellets, although the abundance ratios were significantly different. This study is the first to demonstrate the potential of giant clam fecal pellets as symbiont vectors to giant clam larvae. These results also demonstrate the possibility that fecal pellets are a source of zooxanthellae in coral reefs.}, }
@article {pmid31319203, year = {2019}, author = {Ingavle, G and Shabrani, N and Vaidya, A and Kale, V}, title = {Mimicking megakaryopoiesis in vitro using biomaterials: Recent advances and future opportunities.}, journal = {Acta biomaterialia}, volume = {96}, number = {}, pages = {99-110}, doi = {10.1016/j.actbio.2019.07.025}, pmid = {31319203}, issn = {1878-7568}, abstract = {Presently donor-derived platelets used in the clinic are associated with concerns about adequate availability, expense, risk of bacterial contamination and complications due to immunological reaction. To prevail over our dependence on transfusion of donor-derived platelets, efforts are being made to generate them in vitro. Development of biomaterials that support or mimic bone marrow niche micro-environmental cues could improve the in vitro production of platelets from megakaryocytes (MKs) derived from various stem cell sources. In spite of significant advances in the production of MKs from various stem cell sources using 2D as well as 3D culture approaches in vitro and the development of biomaterials-based platelet systems, yield and quality of these platelets remains unsuitable for clinical use. Thus, in vitro production of clinically useful platelets on a large scale remains an unmet target to date. This review summarizes the most frequently used 2D and 3D approaches to generate MKs and platelets in vitro, emphasizing the importance of mimicking in vivo micro-environment. Further, this review proposes the use of interpenetrating network (IPN) biomaterial-based approach as a promising strategy for improving the generation of MK and platelets in sufficient numbers in vitro. STATEMENT OF SIGNIFICANCE: Thrombocytopenia is one of the major global health and socio-economic problems. Transfusion with donor-derived platelets (PLTs) is the only effective treatment for this condition. However, this approach is limited by factors like short shelf-life of PLTs, PLT activation, alloimmunization, risk of bacterial contamination, infection etc. In vitro generated MKs and PLTs derived from non-donor-dependent sources may help to overcome the platelet transfusion concerns. Here we have reviewed various 2D and 3D strategies used for in vitro generation of MKs and PLTs, with special emphasis on various biomaterial platforms and different physico/chemical cues being used for the purpose. We have also proposed a biomaterial-based approach of using interpenetrating network (IPN) for generating clinically relevant numbers of MKs and PLTs.}, }
@article {pmid31317283, year = {2019}, author = {Ali, HRK and Hemeda, NF and Abdelaliem, YF}, title = {Symbiotic cellulolytic bacteria from the gut of the subterranean termite Psammotermes hypostoma Desneux and their role in cellulose digestion.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {111}, doi = {10.1186/s13568-019-0830-5}, pmid = {31317283}, issn = {2191-0855}, abstract = {The subterranean termite Psammotermes hypostoma Desneux is considered as an important pest that could cause severe damage to buildings, furniture, silos of grain and crops or any material containing cellulose. This species of termites is widespread in Egypt and Africa. The lower termite's ability to digest cellulose depends on the association of symbiotic organisms gut that digest cellulose (flagellates and bacteria). In this study, 33 different bacterial isolates were obtained from the gut of the termite P. hypostoma which were collected using cellulose traps. Strains were grown on carboxymethylcellulose (CMC) as a sole source of carbon. Cellulolytic strains were isolated in two different cellulose medium (mineral salt medium containing carboxymethylcellulose as the sole carbon source and agar cellulose medium). Five isolates showed significant cellulolytic activity identified by a Congo red assay which gives clear zone. Based on biochemical tests and sequencing of 16s rRNA genes these isolates were identified as Paenibacillus lactis, Lysinibacillus macrolides, Stenotrophomonas maltophilia, Lysinibacillus fusiformis and Bacillus cereus, that deposited in GenBank with accession numbers MG991563, MG991564, MG991565, MG991566 and MG991567, respectively.}, }
@article {pmid31314793, year = {2019}, author = {Hoe, C and Adhikari, B and Glandon, D and Das, A and Kaur, N and Gupta, S}, title = {Using social network analysis to plan, promote and monitor intersectoral collaboration for health in rural India.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219786}, doi = {10.1371/journal.pone.0219786}, pmid = {31314793}, issn = {1932-6203}, abstract = {BACKGROUND: As population health and well-being are influenced by multiple factors that cut across sectoral boundaries, an intersectoral approach that acknowledges and leverages the multiple determinants, actors and sectors at play is increasingly seen as critical for achieving meaningful and lasting improvements. In this study, we utilize social network analysis (SNA) to characterize the intersectoral collaboration between the organizations working on maternal &amp; child health (MCH) and water &amp; sanitation (WASH) before and immediately after the implementation of HCL Foundation (HCLF)-funded HCL Samuday Project (2015-2017) in a rural block of Uttar Pradesh state, India. While SNA has been used to examine public health issues, few have used it monitor stakeholder relationships, intervene, improve and facilitate project implementation involving intersectoral partnerships, particularly in the context of a low-and middle-income countries.<br><br>METHOD: An organization-level SNA was conducted with 31 key informants from 24 organizations working on MCH and/or WASH in Kachhauna, Uttar Pradesh, India. Data were collected using face-to-face, semi-structured interviews between June and September 2017. Density, centrality and homophily were calculated to describe the network and a qualitative analysis was also conducted to identify the strengths and weaknesses of collaboration between organizations working on MCH and WASH.<br><br>RESULTS: Overall, our findings showed that the network of organizations working on MCH and WASH in Kachhauna grew in number since the implementation of Samuday. HCLF rapidly achieved centrality, thus positioning the organization to serve as a gatekeeper of information and enabling it to play a coordinator role within the network. Direct collaboration between other organizations working on MCH and WASH was low at both time points. Interviews with key informants indicated widespread interest in increasing interorganizational interactions and engagement throughout the network.<br><br>CONCLUSION: This study demonstrates the feasibility and practical application of SNA for projects like Samuday that involve intersectoral collaboration. It also provides lessons about the use of SNA with organizations as the unit of analysis and in the context of rural India, including challenges, practical considerations, and limitations.}, }
@article {pmid31314666, year = {2019}, author = {Martínez-Medina, A and Fernández, I and Pescador, L and Romero-Puertas, MC and Pozo, MJ}, title = {Trichoderma harzianum triggers an early and transient burst of nitric oxide and the upregulation of PHYTOGB1 in tomato roots.}, journal = {Plant signaling &amp; behavior}, volume = {14}, number = {9}, pages = {1640564}, doi = {10.1080/15592324.2019.1640564}, pmid = {31314666}, issn = {1559-2324}, abstract = {We recently demonstrated that nitric oxide (NO) accumulation and PHYTOGB1 transcriptional regulation are early components of the regulatory pathway that is activated in tomato roots during the onset of the mycorrhizal symbiosis between Rhizophagus irregularis and tomato roots. We further showed that the mycorrhizal interaction was associated with a specific NO-related signature, different from that triggered by the pathogen Fusarium oxysporum. Here, we extend our investigation by exploring the NO- and PHYTOGB1-related root responses elicited by another root mutualistic endosymbiotic fungus: Trichoderma harzianum T-78. By using T-78 in vitro-grown cultures, we found that T-78 triggered an early and transient burst of NO in tomato roots during the first hours after the interaction. T-78 also elicited the early upregulation of PHYTOGB1, which was maintained during the analyzed timespan. By using glass-house bioassays, we found that in a well-established tomato-T-78 symbiosis, NO root levels were maintained at basal level while PHYTOGB1 expression remained upregulated. Our results demonstrate that the T-78 symbiosis is associated with a rapid and transient burst of NO in the host roots and the transcriptional activation of PHYTOGB1 from early stages of the interaction until the establishment of the symbiosis, most likely to control NO levels and favor the mutualistic symbiosis.}, }
@article {pmid31313020, year = {2019}, author = {Liu, M and Soyano, T and Yano, K and Hayashi, M and Kawaguchi, M}, title = {ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus.}, journal = {Journal of plant research}, volume = {132}, number = {5}, pages = {641-653}, doi = {10.1007/s10265-019-01122-w}, pmid = {31313020}, issn = {1618-0860}, support = {22128006//Ministry of Education, Culture, Sports, Science and Technology/ ; 17H03702//Ministry of Education, Culture, Sports, Science and Technology/ ; 150574//Sumitomo Foundation/ ; }, abstract = {Legumes engage in symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia, under nitrogen-limited conditions. In many legumes, the root invasion of rhizobia is mediated by infection threads (ITs), tubular invaginations of the host cell wall and plasma membrane, developed from infection foci of deformed root hairs. IT formation is regulated by a series of signal transduction in host root. Nodulation signals activate the host transcription factor (TF), CYCLOPS, which directly induces expression of two TF genes, ERF REQUIRED FOR NODULATION1 (ERN1) and NODULE INCEPTION (NIN), essential for IT development. Here, we explored the relationship among these three symbiotic TF genes in the model legume Lotus japonicus and examined how their interplay contributes to IT formation. qRT-PCR analysis showed that NIN expression induced by rhizobial infection was attenuated in ern1-1, and further declined in cyclops-3 ern1-1. ERN1 overexpression led to induction of NIN expression in cyclops-3 ern1-1 in the presence of rhizobia. Thus, in addition to CYCLOPS, ERN1 is able to increase the NIN expression level depending on infection. Furthermore, consistent with this transcriptional hierarchy, ectopic expression of ERN1 as well as NIN suppressed the IT-deficient cyclops-3 phenotype, but ERN1 failed to confer ITs in the nin-2 root. However, the ern1-1 symbiotic epidermal phenotype was not suppressed by the NIN ectopic expression. The cyclops-3 ern1-1 double mutant was less sensitive to rhizobial infection than the single mutants and defective in the symbiotic root hair response at earlier stages. This more severe phenotype of the double mutant suggests a role for ERN1 that independent of the CYCLOPS-mediated transcriptional regulation. We conclude that ERN1 is involved in regulating NIN expression in addition to CYCLOPS, and these TFs coordinately promote the symbiotic root hair response and IT development. Our data help to reveal the extensive role of ERN1 in root nodule symbiosis signaling.}, }
@article {pmid31311876, year = {2019}, author = {Xie, XG and Zhang, FM and Yang, T and Chen, Y and Li, XG and Dai, CC}, title = {Endophytic Fungus Drives Nodulation and N2 Fixation Attributable to Specific Root Exudates.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, doi = {10.1128/mBio.00728-19}, pmid = {31311876}, issn = {2150-7511}, abstract = {Endophytic fungi play important roles in the modification of ecosystem productivity; however, the underlying mechanisms are only partly understood. A 2-year field plot experiment verified that the endophytic fungus Phomopsis liquidambaris increased peanut (Arachis hypogaea L.) yields and significantly increased nodulation and N2 fixation regardless of whether N fertilizers were added. Root exudates collected from P. liquidambaris-colonized plants significantly improved nodulation and N2 fixation. Rhizosphere stimulation experiments further showed that colonized root exudates had significantly decreased soil nitrate (NO3-) concentrations, with decreased abundance and diversity of ammonia oxidizing archaea (AOA). In contrast, the abundance and diversity of diazotrophs significantly increased, and most diazotrophs identified were peanut nodulation-related strains (Bradyrhizobium sp.). P. liquidambaris symbiosis increased the expression of phenolic and flavonoid synthesis-related genes, and the derived phenolics and flavonoids could effectively increase the chemotaxis, biofilm formation, and nodC gene expression (nodulation-related biological processes) of the Bradyrhizobium strain. Metabolic pattern analysis showed that phenolics and flavonoids are more likely to accumulate to higher levels in the rhizosphere soil of peanuts colonized with P. liquidambaris Finally, a synthetic root exudate experiment further confirmed the underlying mechanisms for the P. liquidambaris-induced improvement in nodulation and N2 fixation, i.e., that the specific root exudates derived from P. liquidambaris colonization decrease nitrate concentration and increase the population and biological activities of peanut nodulation-related Bradyrhizobium species, which beneficially enhance peanut-Bradyrhizobium interactions. Therefore, this study is the first to provide new insight into a positive relationship between an exotic endophytic fungus, crop nodulation, and N2 fixation increase.IMPORTANCE Endophytic fungi play an important role in balancing the ecosystem and boosting host growth; however, the underpinning mechanisms remain poorly understood. Here, we found that endophytic fungal colonization with P. liquidambaris significantly increased the productivity, nodulation, and N2 fixation of peanuts through the secretion of specific root exudates. We provide a reasonable mechanism explaining how P. liquidambaris promotes peanut nodulation and N2 fixation, whereby the specific root exudates produced by P. liquidambaris colonization decrease rhizosphere soil nitrate (NO3-) and increase the population and biological activities of peanut-nodulating-related Bradyrhizobium strains, which is beneficial to enhancing the peanut-Bradyrhizobium symbiotic interaction. Our study provides reliable empirical evidence to show the mechanism of how an exotic endophytic fungus drives an increase in nodulation and N2 fixation, which will be helpful in erecting a resource-efficient and sustainable agricultural system.}, }
@article {pmid31310638, year = {2019}, author = {Sinnesael, A and Leroux, O and Janssens, SB and Smets, E and Panis, B and Verstraete, B}, title = {Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219863}, doi = {10.1371/journal.pone.0219863}, pmid = {31310638}, issn = {1932-6203}, abstract = {BACKGROUND &amp; AIMS: The bacterial leaf nodule symbiosis is an interaction where bacteria are housed in specialised structures in the leaves of their plant host. In the Rubiaceae plant family, host plants interact with Burkholderia bacteria. This interaction might play a role in the host plant defence system. It is unique due to its high specificity; the vertical transmission of the endophyte to the next generation of the host plant; and its supposedly obligatory character. Although previous attempts have been made to investigate this obligatory character by developing Burkholderia-free plants, none have succeeded and nodulating plants were still produced. In order to investigate the obligatory character of this endosymbiosis, our aims were to develop Burkholderia-free Psychotria umbellata plants and to investigate the effect of the absence of the endophytes on the host in a controlled environment.<br><br>METHODS: The Burkholderia-free plants were obtained via embryo culture, a plant cultivation technique. In order to analyse the endophyte-free status, we screened the plants morphologically, microscopically and molecularly over a period of three years. To characterise the phenotype and growth of the in vitro aposymbiotic plants, we compared the growth of the Burkholderia-free plants to the nodulating plants under the same in vitro conditions.<br><br>KEY RESULTS: All the developed plants were Burkholderia-free and survived in a sterile in vitro environment. The growth analysis showed that plants without endophytes had a slower development.<br><br>CONCLUSIONS: Embryo culture is a cultivation technique with a high success rate for the development of Burkholderia-free plants of P. umbellata. The increased growth rate in vitro when the specific endophyte is present cannot be explained by possible benefits put forward in previous studies. This might indicate that the benefits of the endosymbiosis are not yet completely understood.}, }
@article {pmid31307572, year = {2019}, author = {Bonfante, P}, title = {Algae and fungi move from the past to the future.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.49448}, pmid = {31307572}, issn = {2050-084X}, abstract = {The ability of photosynthetic algae to enter the hyphae of a soil fungus could tell us more about the evolution of these species and their potential for applications in the production of biofuel.}, }
@article {pmid31307571, year = {2019}, author = {Du, ZY and Zienkiewicz, K and Vande Pol, N and Ostrom, NE and Benning, C and Bonito, GM}, title = {Algal-fungal symbiosis leads to photosynthetic mycelium.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.47815}, pmid = {31307571}, issn = {2050-084X}, support = {DE-FG02-91ER20021//U.S. Department of Energy/International ; DE-SC0018409//U.S. Department of Energy/International ; DE-FC02-07ER64494//U.S. Department of Energy/International ; FP7/2007-2013 n° [627266]//European Union Seventh Framework Programme/International ; DEB 1737898//National Science Foundation/International ; }, abstract = {Mutualistic interactions between free-living algae and fungi are widespread in nature and are hypothesized to have facilitated the evolution of land plants and lichens. In all known algal-fungal mutualisms, including lichens, algal cells remain external to fungal cells. Here, we report on an algal-fungal interaction in which Nannochloropsis oceanica algal cells become internalized within the hyphae of the fungus Mortierella elongata. This apparent symbiosis begins with close physical contact and nutrient exchange, including carbon and nitrogen transfer between fungal and algal cells as demonstrated by isotope tracer experiments. This mutualism appears to be stable, as both partners remain physiologically active over months of co-cultivation, leading to the eventual internalization of photosynthetic algal cells, which persist to function, grow and divide within fungal hyphae. Nannochloropsis and Mortierella are biotechnologically important species for lipids and biofuel production, with available genomes and molecular tool kits. Based on the current observations, they provide unique opportunities for studying fungal-algal mutualisms including mechanisms leading to endosymbiosis.}, }
@article {pmid31306759, year = {2019}, author = {Chen, H and Wang, M and Zhang, H and Wang, H and Lv, Z and Zhou, L and Zhong, Z and Lian, C and Cao, L and Li, C}, title = {An LRR-domain containing protein identified in Bathymodiolus platifrons serves as intracellular recognition receptor for the endosymbiotic methane-oxidation bacteria.}, journal = {Fish &amp; shellfish immunology}, volume = {93}, number = {}, pages = {354-360}, doi = {10.1016/j.fsi.2019.07.032}, pmid = {31306759}, issn = {1095-9947}, abstract = {As domain species in seep and vent ecosystem, Bathymodioline mussels has been regarded as a model organism in investigating deep sea chemosymbiosis. However, mechanisms underlying their symbiosis with chemosynthetic bacteria, especially how the host recognizes symbionts, have remained largely unsolved. In the present study, a modified pull-down assay was conducted using enriched symbiotic methane-oxidation bacteria as bait and gill proteins of Bathymodiolus platifrons as a target to isolate pattern recognition receptors involved in the immune recognition of symbionts. As a result, a total of 47 proteins including BpLRR-1 were identified from the pull-down assay. It was found that complete cDNA sequence of BpLRR-1 contained an open reading frame of 1479 bp and could encode a protein of 492 amino acid residues with no signal peptide or transmembrane region but eight LRR motif and two EFh motif. The binding patterns of BpLRR-1 against microbial associated molecular patterns were subsequently investigated by surface plasmon resonance analysis and LPS pull-down assay. Consequently, BpLRR-1 was found with high binding affinity with LPS and suggested as a key molecule in recognizing symbionts. Besides, transcripts of BpLRR-1 were found decreased significantly during symbiont depletion assay yet increased rigorously during symbionts or nonsymbiotic Vibrio alginolyticus challenge, further demonstrating its participation in the chemosynthetic symbiosis. Collectively, these results suggest that BpLRR-1 could serve as an intracellular recognition receptor for the endosymbionts, providing new hints for understanding the immune recognition in symbiosis of B. platifrons.}, }
@article {pmid31306482, year = {2019}, author = {Ntoukakis, V and Gifford, ML}, title = {Plant-microbe interactions: tipping the balance.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz321}, pmid = {31306482}, issn = {1460-2431}, }
@article {pmid31304965, year = {2019}, author = {Tian, H and Wang, R and Li, M and Dang, H and Solaiman, ZM}, title = {Molecular signal communication during arbuscular mycorrhizal formation induces significant transcriptional reprogramming of wheat (Triticum aestivum L.) roots.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz119}, pmid = {31304965}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Arbuscular mycorrhizal (AM) symbiosis initiates with molecular signal communication (MSC) between AM fungi and the roots of the host plant. We aimed to test the hypothesis that the transcriptional profiles of wheat roots can be changed significantly by AM symbiotic signals, without direct contact.<br><br>METHODS: Non-mycorrhizal (NM) and MSC treatments involved burying filter membrane bags containing sterilized and un-sterilized inoculum of the AM fungus Rhizophagus irregularis, respectively. The bags physically separated roots and AM structures but allowed molecular signals to pass through. Extracted RNA from wheat roots was sequenced by high-throughput sequencing.<br><br>RESULTS: Shoot total nitrogen and phosphorus content of wheat plants was decreased by the MSC treatment. A total of 2,360 differentially expressed genes (DEGs), including 1,888 up-regulated DEGs and 472 down-regulated DEGs were found dominantly distributed on the 2A, 2B, 2D, 3B, 5B and 5D chromosomes. The expression of 59 and 121 genes was greatly up- and down-regulated, respectively. Only a portion of DEGs could be enriched into known terms during gene ontology analysis, and were mostly annotated to 'catalytic activity', 'protein metabolic process' and 'membrane' in the molecular function, biological process and cellular component ontology, respectively. More than 120 genes that may be involved in key processes during AM symbiosis development were regulated at the pre-physical contact stages.<br><br>CONCLUSIONS: The transcriptional profiles of wheat roots can be changed dramatically by MSC. Much of the information provided by our study is of great importance for understanding the mechanisms underlying the development of AM symbiosis.}, }
@article {pmid31302359, year = {2019}, author = {Oliva, G and Ángeles, R and Rodríguez, E and Turiel, S and Naddeo, V and Zarra, T and Belgiorno, V and Muñoz, R and Lebrero, R}, title = {Comparative evaluation of a biotrickling filter and a tubular photobioreactor for the continuous abatement of toluene.}, journal = {Journal of hazardous materials}, volume = {380}, number = {}, pages = {120860}, doi = {10.1016/j.jhazmat.2019.120860}, pmid = {31302359}, issn = {1873-3336}, abstract = {The negative effects of volatile organic compounds (VOCs) on humans' health and the environment have boosted the enforcement of regulations, resulting in the need of effective and environmentally friendly off-gas treatment technologies. In this work, the synergism between microalgae and bacteria was investigated as a sustainable platform to enhance the biological degradation of toluene, herein selected as a model VOC. An innovative algal-bacterial tubular photobioreactor (TPBR) was systematically compared with a conventional biotrickling filter (BTF). The BTF supported average removal efficiencies close to those obtained in the TPBR (86 ± 9% and 88 ± 4%, respectively) at the highest inlet load (∼23 g m3 h-1) and lowest gas residence time (0.75 min). However, the BTF was more sensitive towards the accumulation of secondary metabolites. In this regard, photosynthetic O2 supplementation (resulting in dissolved oxygen concentrations of ∼7.3 mg O2 L-1) and CO2 consumption by microalgae (which reduced the impact of acidification) enhanced toluene abatement performance and process stability.}, }
@article {pmid31296160, year = {2019}, author = {Richards, S and Rose, LE}, title = {The evolutionary history of LysM-RLKs (LYKs/LYRs) in wild tomatoes.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {141}, doi = {10.1186/s12862-019-1467-3}, pmid = {31296160}, issn = {1471-2148}, abstract = {BACKGROUND: The LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1-5 exons per gene, lacking conserved kinase residues), and LysM-III (two exons per gene, with a kinase unlike other LysM-RLK kinases and restricted to legumes). LysM-II gene products are presumably not functional as conventional receptor kinases, but several are known to operate in complexes with other LysM-RLKs. One aim of our study was to take advantage of recently mapped wild tomato transcriptomes to evaluate the evolutionary history of LysM-RLKs within and between species. The second aim was to place these results into a broader phylogenetic context by integrating them into a sequence analysis of LysM-RLKs from other functionally well-characterized model plant species. Furthermore, we sought to assess whether the Group III LysM-RLKs were restricted to the legumes or found more broadly across Angiosperms.<br><br>RESULTS: Purifying selection was found to be the prevailing form of natural selection within species at LysM-RLKs. No signatures of balancing selection were found in species-wide samples of two wild tomato species. Most genes showed a greater extent of purifying selection in their intracellular domains, with the exception of SlLYK3 which showed strong purifying selection in both the extracellular and intracellular domains in wild tomato species. The phylogenetic analysis did not reveal a clustering of microbe/functional specificity to groups of closely related proteins. We also discovered new putative LysM-III genes in a range of Rosid species, including Eucalyptus grandis.<br><br>CONCLUSIONS: The LysM-III genes likely originated before the divergence of E. grandis from other Rosids via a fusion of a Group II LysM triplet and a kinase from another RLK family. SlLYK3 emerges as an especially interesting candidate for further study due to the high protein sequence conservation within species, its position in a clade of LysM-RLKs with distinct LysM domains, and its close evolutionary relationship with LYK3 from Arabidopsis thaliana.}, }
@article {pmid31295658, year = {2019}, author = {Amirikhah, R and Etemadi, N and Sabzalian, MR and Nikbakht, A and Eskandari, A}, title = {Physiological consequences of gamma ray irradiation in tall fescue with elimination potential of Epichloë fungal endophyte.}, journal = {Ecotoxicology and environmental safety}, volume = {182}, number = {}, pages = {109412}, doi = {10.1016/j.ecoenv.2019.109412}, pmid = {31295658}, issn = {1090-2414}, abstract = {Perennial plants and their associated microorganisms grow in the areas that may be contaminated with long-lived gamma-emitting radionuclides. This will induce gamma stress response in plants and their accompanying microorganisms. The present work investigated the growth and physiological responses of Epichloe endophyte infected tall fescue to gamma radiation, as well as whether the endophyte could persist and infect the host plant once exposed to gamma radiation. Seeds of Iranian native genotype of 75B+ of tall fescue were exposed to different doses, including 5.0, 10.0, 15.0, 20.0, 30.0 and 40.0 krad of gamma ray from a 60Co source. Irradiated and unirradiated seeds were sown in pots and grown under controlled conditions in the greenhouse. The growth and physiological parameters associated with plant tolerance to oxidative stress of host plants, as well as endophytic infection frequency (% of plants infected) and intensity (mean number of endophytic hyphae per the field of view), were examined in 3 months-old seedlings. The results indicated that all gamma radiation doses (except 5.0 kr) significantly reduced the height and survival percentage of the host plant. Days to the emergence of seedling increased gradually as gamma doses rose. A dose-rate dependent induction was seen for photosynthetic pigments and proline content. Malondialdehyde (MDA) content grew with elevation of irradiation doses. Depending on the dose and time, the activities of antioxidant enzymes in the host plant responded differently to gamma radiation. Gamma radiation altered the enzyme activities with sever decline in SOD and CAT activities. However, it had barely any effect on in APX and POD activities. The results also revealed that the persistence and intensity of endophyte were affected after gamma-ray irradiation. The initial percentage of tall fescue seeds infected with the endophyte was 91% in un-irradiated seeds. Presence of the viable endophyte started to decline significantly (23%) at 5.0 kr of gamma radiation. A dramatic reduction in the presence and intensity of endophyte occurred at 10.0 to 40.0 kr intensities. Gamma radiation × trait (GT)-biplot analysis indicated positive correlations between the endophyte symbiosis and antioxidant enzyme activities. Also, negative correlations were observed between the endophyte and MDA content in the host plant. Our results suggest that radiation stress (doses over 5.0 kr) caused reduction in the growth and antioxidant enzyme activities of the host plant that accompanied by a dramatic reduction in the persistence and intensity of endophyte fungi. Our findings have provided the basic information for future studies on the effect of gamma irradiation on the interaction between endophytic fungi and its host plant.}, }
@article {pmid31292767, year = {2019}, author = {Ogura-Tsujita, Y and Yamamoto, K and Hirayama, Y and Ebihara, A and Morita, N and Imaichi, R}, title = {Fern gametophytes of Angiopteris lygodiifolia and Osmunda japonica harbor diverse Mucoromycotina fungi.}, journal = {Journal of plant research}, volume = {132}, number = {5}, pages = {581-588}, doi = {10.1007/s10265-019-01121-x}, pmid = {31292767}, issn = {1618-0860}, support = {17K07536//Japan Society for the Promotion of Science/ ; 18K06391//Japan Society for the Promotion of Science/ ; }, abstract = {Mycorrhizal symbiosis between plants and fungi is ubiquitous, and has been played key roles in plant terrestrialization and diversification. Although arbuscular mycorrhizal (AM) symbioses with Glomeromycotina fungi have long been recognized as both ancient and widespread symbionts, recent studies showed that Mucoromycotina fungi were also ancestral symbionts and would thus be expected to co-exist with many land plants. To explore whether Mucoromycotina colonize fern gametophytes, we subjected fungal associations with gametophytes of two distantly related ferns, Angiopteris lygodiifolia (Marattiales) and Osmunda japonica (Osmundales), to molecular analysis. Direct PCR amplification from intracellular hyphal coils was also performed. We detected Mucoromycotina sequences in the gametophytes of A. lygodiifolia and O. japonica at rates of 41% (7/17) and 50% (49/98) of gametophytes, respectively, and assigned them to 10 operational taxonomic units of Endogonales lineages. In addition, we used AM fungal-specific primers and detected Glomeromycotina sequences in all individuals examined. The results suggest that Glomeromycotina and Mucoromycotina colonized fern gametophytes simultaneously. We found that Mucoromycotina were present in fern gametophytes of Marratiales and Osmundales, which implies that a variety of fern taxa have Mucoromycotina associations.}, }
@article {pmid31291473, year = {2019}, author = {Montesinos-Navarro, A and Valiente-Banuet, A and Verdú, M}, title = {Plant facilitation through mycorrhizal symbiosis is stronger between distantly related plant species.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.16051}, pmid = {31291473}, issn = {1469-8137}, support = {FPDI-2013-16266//Consejo Superior de Investigaciones Científicas/ ; IJCI-2015-23498//Consejo Superior de Investigaciones Científicas/ ; RTI2018-099672-J-I00//Consejo Superior de Investigaciones Científicas/ ; GV/2016/187//Generalitat Valenciana/ ; PROMETEO/2016/021//Generalitat Valenciana/ ; CGL2016-81706-REDT//Ecometas excellence network/ ; P417RT0228//CYTED Ciencia y Tecnología para el Desarrollo/ ; 3975-4849//British Ecological Society/ ; IN-210117//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; IN-213414-3//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, abstract = {The tendency of closely related plant species to share natural enemies has been suggested to limit their co-occurrence and performance, but we lack a deep understanding on how mutualistic interactions such as the mycorrhizal symbiosis affect plant-plant interactions depending on the phylogenetic relatedness of the interacting plants. We hypothesise that the effect of the mycorrhizal symbiosis on plant-plant facilitative interactions depends on the phylogenetic distance between the nurse and facilitated plants. A recently published meta-analysis compiled the strength of plant facilitative interactions in the presence or absence (or reduced abundance) of mycorrhizal fungi. We use phylogenetically informed Bayesian linear models to test whether the effect size is influenced by the phylogenetic distance between the plant species involved in each plant facilitative interaction. Conspecific facilitative interactions are more strongly enhanced by mycorrhizal fungi than interactions between closely related species. In heterospecific interactions, the effect of the mycorrhizal symbiosis on plant facilitation increases with the phylogenetic distance between the nurse and facilitated plant species. Our result showing that the effect of mycorrhizal symbiosis on the facilitation interactions between plants depends on their phylogenetic relatedness provides new mechanisms to understand how facilitation is assembling ecological communities.}, }
@article {pmid31291312, year = {2019}, author = {Marqués-Gálvez, JE and Morte, A and Navarro-Ródenas, A and García-Carmona, F and Pérez-Gilabert, M}, title = {Purification and characterization of Terfezia claveryi TcCAT-1, a desert truffle catalase upregulated in mycorrhizal symbiosis.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219300}, doi = {10.1371/journal.pone.0219300}, pmid = {31291312}, issn = {1932-6203}, abstract = {Terfezia claveryi Chatin is a mycorrhizal fungus that forms ectendomycorrhizal associations with plants of Helianthemum genus. Its appreciated edibility and drought resistance make this fungus a potential alternative crop in arid and semiarid areas of the Mediterranean region. In order to increase the knowledge about the biology of this fungus in terms of mycorrhiza formation and response to drought stress, a catalase from T. claveryi (TcCAT-1) has been purified to apparent homogeneity and biochemically characterized; in addition, the expression pattern of this enzyme during different stages of T. claveryi biological cycle and under drought stress conditions are reported. The results obtained, together with the phylogenetic analysis and homology modeling, indicate that TcCAT-1 is a homotetramer large subunit size monofunctional-heme catalase belonging to Clade 2. The highest expression of this enzyme occurs in mature mycorrhiza, revealing a possible role in mycorrhiza colonization, but it is not upregulated under drought stress. However, the H2O2 content of mycorrhizal plants submitted to drought stress is lower than in well watered treatments, suggesting that mycorrhization improves the plant's oxidative stress response, although not via TcCAT-1 upregulation.}, }
@article {pmid31288964, year = {2019}, author = {Uroz, S and Courty, PE and Oger, P}, title = {Plant Symbionts Are Engineers of the Plant-Associated Microbiome.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2019.06.008}, pmid = {31288964}, issn = {1878-4372}, abstract = {Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.}, }
@article {pmid31287538, year = {2019}, author = {Suzuki, N}, title = {Glycan diversity in the course of vertebrate evolution.}, journal = {Glycobiology}, volume = {29}, number = {9}, pages = {625-644}, doi = {10.1093/glycob/cwz038}, pmid = {31287538}, issn = {1460-2423}, abstract = {Vertebrates are estimated to have arisen over 500 million years ago in the Cambrian Period. Species that survived the Big Five extinction events at a global scale underwent repeated adaptive radiations along with habitat expansions from the sea to the land and sky. The development of the endoskeleton and neural tube enabled more complex body shapes. At the same time, vertebrates became suitable for the invasion and proliferation of foreign organisms. Adaptive immune systems were acquired for responses to a wide variety of pathogens, and more sophisticated systems developed during the evolution of mammals and birds. Vertebrate glycans consist of common core structures and various elongated structures, such as Neu5Gc, Galα1-3Gal, Galα1-4Gal, and Galβ1-4Gal epitopes, depending on the species. During species diversification, complex glycan structures were generated, maintained or lost. Whole-genome sequencing has revealed that vertebrates harbor numerous and even redundant glycosyltransferase genes. The production of various glycan structures is controlled at the genetic level in a species-specific manner. Because cell surface glycans are often targets of bacterial and viral infections, glycan structural diversity is presumed to be protective against infections. However, the maintenance of apparently redundant glycosyltransferase genes and investment in species-specific glycan structures, even in higher vertebrates with highly developed immune systems, are not well explained. This fact suggests that glycans play important roles in unknown biological processes.}, }
@article {pmid31287368, year = {2019}, author = {Liu, X and Xie, Z and Zhang, H}, title = {Inactivation of the phosphatase CheZ alters cell-surface properties of Azorhizobium caulinodans ORS571 and symbiotic association with Sesbania rostrata.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-05-19-0143-R}, pmid = {31287368}, issn = {0894-0282}, abstract = {Azorhizobium caulinodans can form root and stem nodules with the host plant Sesbania rostrata. The role of the CheZ phosphatase in the A. caulinodans chemotaxis pathway was previously explored using the non-chemotactic cheZ mutant strain (AC601). This mutant displayed stronger attachment to the root surface, enhancing early colonization but this did not result into increased nodulation efficiency. In this study, we further investigated the role of CheZ in the interaction between ORS571 and the roots of its host plant. By tracking long-term colonization dynamic of cheZ mutant marked with LacZ, we found a decrease of colonization of the cheZ mutant during this process. Furthermore, cheZ mutant could not spread on root surface freely and was gradually outcompeted by the wild type in original colonization sites. Quantitative reverse transcription-PCR analyses showed that exp genes encoding exopolysaccharides synthesis, including oac3, were highly expressed in cheZ mutant. Construction of a strain carrying a deletion of both cheZ and oac3 resulted in a mutant strain defective in the colonization process to the same extent as found with the oac3 single mutant strain. This result suggested that the enhanced colonization of the cheZ mutant may be achieved through regulating the formation of EPS. This shows the importance of the chemotactic proteins in the interaction between rhizobia and host plant, and expands our understanding about the symbiosis interaction between rhizobium and host plant.}, }
@article {pmid31285778, year = {2019}, author = {Viennois, E and Chassaing, B and Tahsin, A and Pujada, A and Wang, L and Gewirtz, AT and Merlin, D}, title = {Host-derived fecal microRNAs can indicate gut microbiota healthiness and ability to induce inflammation.}, journal = {Theranostics}, volume = {9}, number = {15}, pages = {4542-4557}, doi = {10.7150/thno.35282}, pmid = {31285778}, issn = {1838-7640}, support = {R01 DK099071/DK/NIDDK NIH HHS/United States ; I01 BX002526/BX/BLRD VA/United States ; R01 DK107739/DK/NIDDK NIH HHS/United States ; R01 DK071594/DK/NIDDK NIH HHS/United States ; IK6 BX004476/BX/BLRD VA/United States ; R01 DK116306/DK/NIDDK NIH HHS/United States ; }, abstract = {Disruption of intestine-microbiota symbiosis can result in chronic gut inflammation. We hypothesize that assessing the initial inflammatory potential of the microbiota in patients is essential and that host-derived miRNAs, which can be found in feces, could fulfill this function. We investigated whether the gut microbiota composition impacts the fecal miRNA profile and thereby indicates its ability to influence intestinal inflammation. Methods: We used high-throughput qPCR to compare fecal miRNA profile between germ-free and conventional mice. Conventionalization of germfree mice by various colitogenic and non-colitogenic microbiotas (IL10-/- and TLR5-/- associated microbiota) was performed. Results: We identified 12 fecal miRNAs impacted by the presence of a microbiota. Conventionalization of germfree mice by various colitogenic and non-colitogenic microbiotas associated with the development of intestinal inflammation (IL10-/- and TLR5-/- associated microbiota) yielded distinctively altered fecal miRNA profiles compared to that of mice receiving a &quot;healthy&quot; microbiota. Correlation analysis revealed the existence of interactions between the 12 abovementioned miRNAs and specific microbiota members. Conclusion: These results showed that fecal miRNA profile can be differentially and specifically impacted by microbiota composition, and that miRNA could importantly serve as markers of the colitogenic potential of the microbiota. This is particularly relevant to assess individual state of the microbiota in patients with dysbiosis-related disorders, such as IBD and potentially determine their ability to respond to therapeutics.}, }
@article {pmid31285337, year = {2019}, author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR}, title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15200-15209}, doi = {10.1073/pnas.1900056116}, pmid = {31285337}, issn = {1091-6490}, abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.}, }
@article {pmid31285273, year = {2019}, author = {Pederson, ERA and Warshan, D and Rasmussen, U}, title = {Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {9}, pages = {2791-2797}, doi = {10.1534/g3.119.400279}, pmid = {31285273}, issn = {2160-1836}, abstract = {The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N2)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, Pschreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.}, }
@article {pmid31283433, year = {2019}, author = {Thapa, SP and Davis, EW and Lyu, Q and Weisberg, AJ and Stevens, DM and Clarke, CR and Coaker, G and Chang, JH}, title = {The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria.}, journal = {Annual review of phytopathology}, volume = {57}, number = {}, pages = {341-365}, doi = {10.1146/annurev-phyto-082718-100124}, pmid = {31283433}, issn = {1545-2107}, abstract = {Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.}, }
@article {pmid31283425, year = {2019}, author = {Apprill, A}, title = {The Role of Symbioses in the Adaptation and Stress Responses of Marine Organisms.}, journal = {Annual review of marine science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-marine-010419-010641}, pmid = {31283425}, issn = {1941-0611}, abstract = {Ocean ecosystems are experiencing unprecedented rates of climate and anthropogenic change, which can often initiate stress in marine organisms. Symbioses, or associations between different organisms, are plentiful in the ocean and could play a significant role in facilitating organismal adaptations to stressful ocean conditions. This article reviews current knowledge about the role of symbiosis in marine organismal acclimation and adaptation. It discusses stress and adaptations in symbioses from coral reef ecosystems, which are among the most affected environments in the ocean, including the relationships between corals and microalgae, corals and bacteria, anemones and clownfish, and cleaner fish and client fish. Despite the importance of this subject, knowledge of how marine organisms adapt to stress is still limited, and there are vast opportunities for research and technological development in this area. Attention to this subject will enhance our understanding of the capacity of symbioses to alleviate organismal stress in the oceans. Expected final online publication date for the Annual Review of Marine Science Volume 12 is January 3, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31283172, year = {2019}, author = {Niehs, SP and Dose, B and Scherlach, K and Pidot, SJ and Stinear, TP and Hertweck, C}, title = {Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis.}, journal = {ACS chemical biology}, volume = {14}, number = {8}, pages = {1811-1818}, doi = {10.1021/acschembio.9b00406}, pmid = {31283172}, issn = {1554-8937}, abstract = {The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.}, }
@article {pmid31281920, year = {2019}, author = {de Oliveira, ISR and Jesus, EDC and Ribeiro, TG and Santos Reis de Andrade da Silva, M and Tenorio, JO and Martins, LMV and de Faria, SM}, title = {Mimosa caesalpiniifolia Benth. adapts to rhizobia populations with differential taxonomy and symbiotic effectiveness outside of its location of origin.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz109}, pmid = {31281920}, issn = {1574-6941}, abstract = {Mimosa caesalpiniifolia Benth. is a legume native to the semi-arid region of Brazil, in the Northeast. Its successful adaptation to other locations, such as the Atlantic Forest in the Southeast region, may be related to its ability to establish symbiosis with nitrogen-fixing bacteria, especially β-rhizobia of the genus Paraburkholderia. The objective of this work was to determine whether M. caesalpiniifolia adapted to bacterial symbionts in locals where it was introduced. Bacteria were recovered from nodules of M. caesalpiniifolia and characterized at the genetic level by BOX-PCR and sequencing of the 16S rRNA, recA, nifH, and nodC genes. Their symbiotic effectiveness was assessed under axenic conditions. M. caesalpiniifolia nodulated mainly with Paraburkholderia sabiae and a few strains of Rhizobium in the Southeast. On the other hand, the symbionts found in the Northeast were, predominantly, Paraburkholderia diazotrophica. Regardless of its origin, P. diazotrophica promoted a superior accumulation of plant biomass than other bacterial species. The results presented here demonstrate the ability of M. caesalpiniifolia to adapt to bacterial populations outside its location of origin, and indicate that, in this case, the symbiotic effectiveness was associated with the taxonomical classification of the strains.}, }
@article {pmid31279967, year = {2019}, author = {Wang, Y and White, MM and Moncalvo, JM}, title = {Diversification of the gut fungi Smittium and allies (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera).}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106550}, doi = {10.1016/j.ympev.2019.106550}, pmid = {31279967}, issn = {1095-9513}, abstract = {Smittium (Harpellales, Kickxellomycotina) includes fungal symbionts associated with the digestive tracts of immature aquatic stages of various Diptera, including Chironomidae, Culicidae, Dixidae, Simuliidae, Thaumaleidae, and Tipulidae. With 84 species and the largest collection of cultured strains, Smittium has served as a model to understand the biology of these enigmatic trichomycetes gut fungi, from aspects of biodiversity, evolution, genomics, immunology, and physiology. However, evolutionary histories between Smittium species and their hosts are still not firmly established. Robust phylogenies of both Smittium sensu lato (s.l.) and their lower Diptera hosts have been reconstructed separately, facilitating comparative evolutionary studies between the two. The divergence time of the Smittium s.l. clade was estimated for the first time and compared with the evolutionary history of the insect hosts. The insect gut fungi diversified around 272 Ma (204-342 Ma), which co-occurred with the origin of complete metamorphosis of the insect hosts, presumably between 280 Ma and 355 Ma (~270 Ma for Diptera). A co-phylogenetic pattern was recovered for the insects and their symbiotic gut fungi using the statistical method ParaFit. Ancestral state reconstructions of the symbiotic relationship suggest that the ancestor of the Chironomidae may have contributed to the initiation of these insect-fungus symbiotic interactions. Further sampling and sequencing of Smittium and allies as well as their hosts are needed to uncover more patterns and interactions that may occur in this type of symbiosis.}, }
@article {pmid31277471, year = {2019}, author = {Fukudome, M and Watanabe, E and Osuki, KI and Uchi, N and Uchiumi, T}, title = {Ectopic or Over-Expression of Class 1 Phytoglobin Genes Confers Flooding Tolerance to the Root Nodules of Lotus japonicus by Scavenging Nitric Oxide.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {8}, number = {7}, pages = {}, doi = {10.3390/antiox8070206}, pmid = {31277471}, issn = {2076-3921}, support = {16-305, 17-309, and 18-312//National Institute of Basic Biology (NIBB)/ ; JP18J11872//JSPS KAKENHI Research Fellowship/ ; }, abstract = {Flooding limits biomass production in agriculture. Leguminous plants, important agricultural crops, use atmospheric dinitrogen gas as nitrogen nutrition by symbiotic nitrogen fixation with rhizobia, but this root-nodule symbiosis is sometimes broken down by flooding of the root system. In this study, we analyzed the effect of flooding on the symbiotic system of transgenic Lotus japonicus lines which overexpressed class 1 phytoglobin (Glb1) of L. japonicus (LjGlb1-1) or ectopically expressed that of Alnus firma (AfGlb1). In the roots of wild-type plants, flooding increased nitric oxide (NO) level and expression of senescence-related genes and decreased nitrogenase activity; in the roots of transgenic lines, these effects were absent or less pronounced. The decrease of chlorophyll content in leaves and the increase of reactive oxygen species (ROS) in roots and leaves caused by flooding were also suppressed in these lines. These results suggest that increased levels of Glb1 help maintain nodule symbiosis under flooding by scavenging NO and controlling ROS.}, }
@article {pmid31276218, year = {2019}, author = {Burghardt, LT}, title = {Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.16045}, pmid = {31276218}, issn = {1469-8137}, support = {IOS-1237993//Division of Integrative Organismal Systems/ ; IOS-1724993//Division of Integrative Organismal Systems/ ; //National Science Foundation/ ; }, abstract = {Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.}, }
@article {pmid31275282, year = {2019}, author = {He, C and Wang, W and Hou, J}, title = {Characterization of Dark Septate Endophytic Fungi and Improve the Performance of Liquorice Under Organic Residue Treatment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1364}, doi = {10.3389/fmicb.2019.01364}, pmid = {31275282}, issn = {1664-302X}, abstract = {Dark septate endophytic (DSE) fungi is a diverse group of Ascomycetes fungi that colonize the plants roots, and may facilitate plant growth and fitness, however, their ecological roles need further clarification. This study aimed to evaluate the growth promoting effects of DSE fungi in a medicinal plant, liquorice (Glycyrrhiza uralensis), under additional organic residues. First, we isolated, identified and characterized, two DSE fungal species (Acrocalymma vagum and Paraboeremia putaminum) harboring inside the roots of liquorice growing in arid areas of China. Second, we examined the performance and rhizosphere soil parameters of liquorice plants inoculated with these fungi under additional sterilized organic residues and unsterilized organic residue (containing Trichoderma viride population) in a growth chamber. The results showed that two DSE strains could effectively colonize plant roots and formed a strain-dependent symbiosis with liquorice. DSE inoculation alone increased the plant biomass, and glycyrrhizic acid and glycyrrhizin content. It also improved the root system and N and P absorption by plants, consequently depleting these macronutrients in the soil. Residues alone increased soil organic matter, available phosphorus (P), and available nitrogen (N) content, and plant biomass, N, P, glycyrrhizic acid, and glycyrrhizin content. Mantel test and structural equation model (SEM) analysis demonstrated that DSE associated with residues significantly positively influenced soil organic matter, available P and available N, and plant biomass, glycyrrhizin, N, P, and root surface area. Variation in plant growth and glycyrrhizic acid and glycyrrhizin accumulation can be attributed to the effects of DSE inoculation. DSE associated with residues exhibited a general synergistic effect on the growth and accumulation of glycyrrhizic acid and glycyrrhizin of liquorice. We demonstrate for the first time, two DSE fungi in the liquorice roots that have potential use as promoter for the cultivation of medicinal plant.}, }
@article {pmid31275256, year = {2019}, author = {Chen, B and Yu, K and Liang, J and Huang, W and Wang, G and Su, H and Qin, Z and Huang, X and Pan, Z and Luo, W and Luo, Y and Wang, Y}, title = {Latitudinal Variation in the Molecular Diversity and Community Composition of Symbiodiniaceae in Coral From the South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1278}, doi = {10.3389/fmicb.2019.01278}, pmid = {31275256}, issn = {1664-302X}, abstract = {Coral reefs are continuing to decline worldwide due to anthropogenic climate change. The study of the molecular diversity and biogeographical patterns of Symbiodiniaceae, is essential to understand the adaptive potential and resilience of coral-algal symbiosis. Next generation sequencing was used to analyze the Symbiodiniaceae rDNA internal transcribed spacer 2 marker genes from 178 reef-building coral samples in eight coral habitats across approximately 13° of latitude in the South China Sea (SCS). A total of three Symbiodiniaceae genera, Cladocopium, Durusdinium, and Gerakladium, as well as 31 dominant Symbiodiniaceae types, were identified. Symbiodiniaceae richness, diversity, and community composition varied according to latitude; intermediate and low latitude coral reefs (IR and LR) have higher Symbiodiniaceae richness and diversity than high latitude coral habitats (HC and HR). A PERMANOVA analysis found significant differences in the Symbiodiniaceae community composition in the SCS (F = 14.75, R2 = 0.20, p = 0.001 < 0.01). The major dominant Symbiodiniaceae types were C1 in the HC and the HR, C1/Cspc/C50/C15 and D1 in the IR, and C3u and C15 in the LR. Canonical correspondence analysis showed that the relative abundance of different Symbiodiniaceae types is affected by multiple environmental factors. Phylogenetic analysis indicated that the Symbiodiniaceae type Cladocopium, which shared common ancestors, shows similar environmental adaptability. Based on these results, we suggest that coral host species played a relatively small role in the identity of the dominant Symbiodiniaceae type. Therefore, the biogeographical patterns of Symbiodiniaceae may be mainly affected by environmental factors. Our research provides a comprehensive overview of the biogeography of Symbiodiniaceae in the SCS, where coral communities and reefs are widely distributed across different latitude regions and have variable environmental conditions. Our data will provide support for further study of the regional diversification of Symbiodiniaceae and the ecological resilience of the coral-Symbiodiniaceae symbioses.}, }
@article {pmid31274160, year = {2019}, author = {Wang, X and Huo, H and Luo, Y and Liu, D and Zhao, L and Zong, L and Chou, M and Chen, J and Wei, G}, title = {Type III secretion systems impact Mesorhizobium amorphae CCNWGS0123 compatibility with Robinia pseudoacacia.}, journal = {Tree physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/treephys/tpz077}, pmid = {31274160}, issn = {1758-4469}, abstract = {Rhizobia and legume plants are famous mutualistic symbiosis partners who provide nitrogen nutrition to natural environment. Rhizobial type III secretion systems (T3SSs) deliver effectors that manipulate the metabolism of eukaryotic host cells. Mesorhizobium amorphae CCNWGS0123 (GS0123) contains two T3SS gene clusters, T3SS-I and T3SS-II. T3SS-I contains all the basal components for an integrated T3SS, and the expression of T3SS-I genes is up-regulated in the presence of flavonoids. In contrast, T3SS-II lacks the primary extracellular elements of T3SSs, and the expression of T3SS-II genes is down-regulated in the presence of flavonoids. Inoculation tests on Robinia pseudoacacia displayed considerable differences in gene expression patterns and levels among roots inoculated with GS0123 and T3SS-deficient mutant (GS0123ΔT1, GS0123ΔT2 or GS0123ΔS). Compared with the GS0123-inoculated plants, GS0123ΔT1-inoculated roots formed very few infection threads and effective nodules, while GS0123ΔT2-inoculated roots formed a little fewer infection threads and effective nodules with increased numbers of bacteroids enclosed in one symbiosome. Moreover, almost no infection threads or effective nodules were observed in GS0123ΔS-inoculated roots. In addition to evaluations of plant immunity signals, we observed that the coexistence of T3SS-I and T3SS-II promoted infection by suppressing host defense response in ROS defense response pathway. Future studies should focus on identifying rhizobial T3SS effectors and their host target proteins.}, }
@article {pmid31273746, year = {2019}, author = {Vadakke-Madathil, S and Limaye, LS and Kale, VP and Chaudhry, HW}, title = {Flow Cytometry and Cell Sorting Using Hematopoietic Progenitor Cells.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2029}, number = {}, pages = {235-246}, doi = {10.1007/978-1-4939-9631-5_18}, pmid = {31273746}, issn = {1940-6029}, abstract = {Flow cytometry is a widely used laser-based technology for rapid analysis of the expression of cell surface antigens and intracellular molecules in various cell types including hematopoietic stem/progenitor cells (HSPCs). Multiparametric analysis of individual cells within a short time frame makes this tool attractive and indispensable in the field of stem cell research. This is accomplished by harnessing the specific light scattering ability of the cell type, which determines its size and internal complexity. In addition, use of fluorescently conjugated antibodies allows the detection of a specific surface or intracellular antigen present at that particular stage. Fluorescent Activated Cell Sorting (FACS) is used to separate a subset of cells from a heterogeneous cell population based on fluorescent labeling. Here we describe the general principles of flow cytometry and detailed methods for the isolation of HSPCs using flow cytometry as a tool.}, }
@article {pmid31272899, year = {2019}, author = {Plassard, C and Becquer, A and Garcia, K}, title = {Phosphorus Transport in Mycorrhiza: How Far Are We?.}, journal = {Trends in plant science}, volume = {24}, number = {9}, pages = {794-801}, doi = {10.1016/j.tplants.2019.06.004}, pmid = {31272899}, issn = {1878-4372}, abstract = {Mycorrhizal fungi considerably improve plant nutrition and help them to cope with changing environments. Particularly, these fungi express proteins to transfer inorganic phosphate (Pi) from the soil to colonized roots through symbiotic interfaces. The mechanisms involved in Pi transfer from fungal to plant cells are still largely unknown. Here, we discuss the recent progress made on the description of these mechanisms and we propose the most promising hypotheses and alternative mechanisms for this process. Specifically, we present a phylogenetic survey of candidate Pi transporters of mycorrhizal fungi that might ensure Pi unload into the symbiotic interfaces. Gathering additional knowledge on mycorrhizal Pi transport will improve the Pi-useefficiency in agroecological systems and will guide towards addressing future research challenges.}, }
@article {pmid31271695, year = {2019}, author = {Harman, GE and Doni, F and Khadka, RB and Uphoff, N}, title = {Endophytic strains of Trichoderma increase plants' photosynthetic capability.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14368}, pmid = {31271695}, issn = {1365-2672}, abstract = {The world faces two enormous challenges that can be met, at least in part and at low cost, by making certain changes in agricultural practices. There is need to produce enough food and fibre for a growing population in the face of adverse climatic trends, and to remove greenhouse gases to avert the worst consequences of global climate change. Improving photosynthetic efficiency of crop plants can help meet both challenges. Fortuitously, when crop plants' roots are colonized by certain root endophytic fungi in the genus Trichoderma, this induces up-regulation of genes and pigments that improve the plants' photosynthesis. Plants under physiological or environmental stress suffer losses in their photosynthetic capability through damage to photosystems and other cellular processes caused by reactive oxygen species (ROS). But certain Trichoderma strains activate biochemical pathways that reduce ROS to less harmful molecules. This and other mechanisms described here make plants more resistant to biotic and abiotic stresses. The net effect of these fungi's residence in plants is to induce greater shoot and root growth, increasing crop yields, which will raise future food production. Furthermore, if photosynthesis rates are increased, more CO2 will be extracted from the atmosphere, and enhanced plant root growth means that more sequestered C will be transferred to roots and stored in the soil. Reductions in global greenhouse gas levels can be accelerated by giving incentives for climate-friendly carbon farming and carbon cap-and-trade programmes that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production.}, }
@article {pmid31271473, year = {2019}, author = {Leeks, A and Dos Santos, M and West, SA}, title = {Transmission, relatedness, and the evolution of cooperative symbionts.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeb.13505}, pmid = {31271473}, issn = {1420-9101}, support = {P2LAP3-158669//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; BB/M011224/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Cooperative interactions between species, termed mutualisms, play a key role in shaping natural ecosystems, economically important agricultural systems, and in influencing human health. Across different mutualisms, there is significant variation in the benefit that hosts receive from their symbionts. Empirical data suggest that transmission mode can help explain this variation: vertical transmission, where symbionts infect their host's offspring, leads to symbionts that provide greater benefits to their hosts than horizontal transmission, where symbionts leave their host and infect other hosts in the population. However, two different theoretical explanations have been given for this pattern: firstly, vertical transmission aligns the fitness interests of hosts and their symbionts; secondly, vertical transmission leads to increased relatedness between symbionts sharing a host, favouring cooperation between symbionts. We used a combination of analytical models and dynamic simulations to tease these factors apart, in order to compare their separate influences and see how they interact. We found that relatedness between symbionts sharing a host, rather than transmission mode per se, was the most important factor driving symbiont cooperation. Transmission mode mattered mainly because it determined relatedness. We also found evolutionary branching throughout much of our simulation, suggesting that a combination of transmission mode and multiplicity of infections could lead to the stable coexistence of different symbiont strategies.}, }
@article {pmid31271421, year = {2019}, author = {Sørensen, MES and Lowe, CD and Minter, EJA and Wood, AJ and Cameron, DD and Brockhurst, MA}, title = {The role of exploitation in the establishment of mutualistic microbial symbioses.}, journal = {FEMS microbiology letters}, volume = {366}, number = {12}, pages = {}, doi = {10.1093/femsle/fnz148}, pmid = {31271421}, issn = {1574-6968}, abstract = {Evolutionary theory suggests that the conditions required for the establishment of mutualistic symbioses through mutualism alone are highly restrictive, often requiring the evolution of complex stabilising mechanisms. Exploitation, whereby initially the host benefits at the expense of its symbiotic partner and mutual benefits evolve subsequently through trade-offs, offers an arguably simpler route to the establishment of mutualistic symbiosis. In this review, we discuss the theoretical and experimental evidence supporting a role for host exploitation in the establishment and evolution of mutualistic microbial symbioses, including data from both extant and experimentally evolved symbioses. We conclude that exploitation rather than mutualism may often explain the origin of mutualistic microbial symbioses.}, }
@article {pmid31271364, year = {2019}, author = {Kavadi, S}, title = {John B Grant and public health in India.}, journal = {Indian journal of medical ethics}, volume = {4}, number = {2}, pages = {123-128}, doi = {10.20529/IJME.2019.010}, pmid = {31271364}, issn = {0975-5691}, abstract = {From 1939 to 1945, John Black Grant a Rockefeller Foundation officer and former Professor of Public Health at the Peking Union Medical College served as the Director of the All Institute of Hygiene and Public Health, Calcutta. Grant's India tenure is important for his efforts to ameliorate the condition of public health in India. Much has been written about Grant's contribution to transforming public health in China but his work in India has not received sufficient attention. This article acquaints readers with some of his more noteworthy ideas and endeavours to remodel the colonial public health and medical system. His views on Indian public health may also be viewed as a critique of the colonial health system.}, }
@article {pmid31269590, year = {2019}, author = {Wen, ZL and Chen, DC}, title = {[Clinical significance of intestinal micro-ecological symbiosis disruption in critically ill patients].}, journal = {Zhonghua yi xue za zhi}, volume = {99}, number = {25}, pages = {1921-1924}, doi = {10.3760/cma.j.issn.0376-2491.2019.25.001}, pmid = {31269590}, issn = {0376-2491}, mesh = {*Critical Illness ; Humans ; Intestines ; *Symbiosis ; }, }
@article {pmid31268231, year = {2019}, author = {Xu, XR and Li, NN and Bao, XY and Douglas, AE and Luan, JB}, title = {Patterns of host cell inheritance in the bacterial symbiosis of whiteflies.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.12708}, pmid = {31268231}, issn = {1744-7917}, support = {31871967//National Natural Science Foundation of China/ ; 2018B0078//Liaoning and Shenyang High-Level Talent Support Foundation/ ; RC18001//Liaoning and Shenyang High-Level Talent Support Foundation/ ; OPP1058938//The Bill &amp; Melinda Gates foundation/ ; }, abstract = {Whiteflies possess bacterial symbionts Candidatus Portiera aleyrodidium that are housed in specialized cells called bacteriocytes and are faithfully transmitted via the ovary to insect offspring. In one whitefly species studied previously, Bemisia tabaci MEAM1, transmission is mediated by somatic inheritance of bacteriocytes, with a single bacteriocyte transferred to each oocyte and persisting through embryogenesis to the next generation. Here, we investigate the mode of bacteriocyte transmission in two whitefly species, B. tabaci MED, the sister species of MEAM1, and the phylogenetically distant species Trialeurodes vaporariorum. Microsatellite analysis supported by microscopical studies demonstrates that B. tabaci MED bacteriocytes are genetically different from other somatic cells and persist through embryogenesis, as for MEAM1, but T. vaporariorum bacteriocytes are genetically identical to other somatic cells of the insect, likely mediated by the degradation of maternal bacteriocytes in the embryo. These two alternative modes of transmission provide a first demonstration among insect symbioses that the cellular processes underlying vertical transmission of bacterial symbionts can diversify among related host species associated with a single lineage of symbiotic bacteria.}, }
@article {pmid31268133, year = {2019}, author = {Elkrief, A and Derosa, L and Kroemer, G and Zitvogel, L and Routy, B}, title = {The negative impact of antibiotics on outcomes in cancer patients treated with immunotherapy: a new independent prognostic factor?.}, journal = {Annals of oncology : official journal of the European Society for Medical Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1093/annonc/mdz206}, pmid = {31268133}, issn = {1569-8041}, abstract = {Immune checkpoint inhibitors (ICI) now represent the standard of care for several cancer types. In pre-clinical models, absence of an intact gut microbiome negatively impacted ICI efficacy and these findings permitted to unravel the importance of the commensal microbiota in immuno-oncology. Recently, multiple clinical studies including more than 1800 patients in aggregate demonstrated the negative predictive impact of treatments with broad-spectrum antibiotics (ATB) on cancer patients receiving ICI. Altogether, these results have led to the hypothesis that ATB-induced symbiosis might influence the clinical response through the modulation of the gut microbiome. Controversy still remains, as ATB treatment might simply constitute a surrogate marker of unfit or immunodeficient patients. In this review, we summarize recent publications addressing the impact of the gut microbiome on ICI efficacy, discuss currently available data on the effect of ATB administered in different time-frames respect to ICI initiation, and finally evoke the therapeutic implications of these findings.}, }
@article {pmid31267680, year = {2019}, author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC}, title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14728}, pmid = {31267680}, issn = {1462-2920}, support = {GBMF3303//Gordon and Betty Moore Foundation/ ; ECF2016-626//Leverhulme Trust/ ; }, abstract = {The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.}, }
@article {pmid31266522, year = {2019}, author = {Cappelli, A and Valzano, M and Cecarini, V and Bozic, J and Rossi, P and Mensah, P and Amantini, C and Favia, G and Ricci, I}, title = {Killer yeasts exert anti-plasmodial activities against the malaria parasite Plasmodium berghei in the vector mosquito Anopheles stephensi and in mice.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {329}, doi = {10.1186/s13071-019-3587-4}, pmid = {31266522}, issn = {1756-3305}, support = {842429//European Research Council/International ; 842429//Horizon 2020- ERC POC 2018/ ; }, mesh = {Animals ; Anopheles/*microbiology/parasitology ; Antimalarials/*pharmacology ; Female ; Malaria/parasitology/*prevention &amp; control/transmission ; Mice ; Mosquito Vectors/*microbiology/parasitology ; Mycotoxins/*pharmacology ; Plasmodium berghei/*drug effects ; Saccharomycetales/*physiology ; Symbiosis ; }, abstract = {BACKGROUND: Wickerhamomyces anomalus is a yeast associated with different insects including mosquitoes, where it is proposed to be involved in symbiotic relationships with hosts. Different symbiotic strains of W. anomalus display a killer phenotype mediated by protein toxins with broad-spectrum antimicrobial activities. In particular, a killer toxin purified from a W. anomalus strain (WaF17.12), previously isolated from the malaria vector mosquito Anopheles stephensi, has shown strong in vitro anti-plasmodial activity against early sporogonic stages of the murine malaria parasite Plasmodium berghei.<br><br>RESULTS: Here, we provide evidence that WaF17.12 cultures, properly stimulated to induce the expression of the killer toxin, can directly affect in vitro P. berghei early sporogonic stages, causing membrane damage and parasite death. Moreover, we demonstrated by in vivo studies that mosquito dietary supplementation with activated WaF17.12 cells interfere with ookinete development in the midgut of An. stephensi. Besides the anti-sporogonic action of WaF17.12, an inhibitory effect of purified WaF17.12-killer toxin was observed on erythrocytic stages of P. berghei, with a consequent reduction of parasitaemia in mice. The preliminary safety tests on murine cell lines showed no side effects.<br><br>CONCLUSIONS: Our findings demonstrate the anti-plasmodial activity of WaF17.12 against different developmental stages of P. berghei. New studies on P. falciparum are needed to evaluate the use of killer yeasts as innovative tools in the symbiotic control of malaria.}, }
@article {pmid31262532, year = {2019}, author = {Biedermann, PHW and Müller, J and Grégoire, JC and Gruppe, A and Hagge, J and Hammerbacher, A and Hofstetter, RW and Kandasamy, D and Kolarik, M and Kostovcik, M and Krokene, P and Sallé, A and Six, DL and Turrini, T and Vanderpool, D and Wingfield, MJ and Bässler, C}, title = {Bark Beetle Population Dynamics in the Anthropocene: Challenges and Solutions.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2019.06.002}, pmid = {31262532}, issn = {1872-8383}, abstract = {Tree-killing bark beetles are the most economically important insects in conifer forests worldwide. However, despite >200 years of research, the drivers of population eruptions and crashes are still not fully understood and the existing knowledge is thus insufficient to face the challenges posed by the Anthropocene. We critically analyze potential biotic and abiotic drivers of population dynamics of an exemplary species, the European spruce bark beetle (ESBB) (Ips typographus) and present a multivariate approach that integrates the many drivers governing this bark beetle system. We call for hypothesis-driven, large-scale collaborative research efforts to improve our understanding of the population dynamics of this and other bark beetle pests. Our approach can serve as a blueprint for tackling other eruptive forest insects.}, }
@article {pmid31262007, year = {2019}, author = {Pilon-Smits, EAH}, title = {On the Ecology of Selenium Accumulation in Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {8}, number = {7}, pages = {}, doi = {10.3390/plants8070197}, pmid = {31262007}, issn = {2223-7747}, abstract = {Plants accumulate and tolerate Se to varying degrees, up to 15,000 mg Se/kg dry weight for Se hyperaccumulators. Plant Se accumulation may exert positive or negative effects on other species in the community. The movement of plant Se into ecological partners may benefit them at low concentrations, but cause toxicity at high concentrations. Thus, Se accumulation can protect plants against Se-sensitive herbivores and pathogens (elemental defense) and reduce surrounding vegetation cover via high-Se litter deposition (elemental allelopathy). While hyperaccumulators negatively impact Se-sensitive ecological partners, they offer a niche for Se-tolerant partners, including beneficial microbial and pollinator symbionts as well as detrimental herbivores, pathogens, and competing plant species. These ecological effects of plant Se accumulation may facilitate the evolution of Se resistance in symbionts. Conversely, Se hyperaccumulation may evolve driven by increasing Se resistance in herbivores, pathogens, or plant neighbors; Se resistance also evolves in mutualist symbionts, minimizing the plant's ecological cost. Interesting topics to address in future research are whether the ecological impacts of plant Se accumulation may affect species composition across trophic levels (favoring Se resistant taxa), and to what extent Se hyperaccumulators form a portal for Se into the local food chain and are important for Se cycling in the local ecosystem.}, }
@article {pmid31261721, year = {2019}, author = {Haro, R and Benito, B}, title = {The Role of Soil Fungi in K+ Plant Nutrition.}, journal = {International journal of molecular sciences}, volume = {20}, number = {13}, pages = {}, doi = {10.3390/ijms20133169}, pmid = {31261721}, issn = {1422-0067}, support = {AGL2016-80593-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {K+ is an essential cation and the most abundant in plant cells. After N, its corresponding element, K, is the nutrient required in the largest amounts by plants. Despite the numerous roles of K in crop production, improvements in the uptake and efficiency of use of K have not been major focuses in conventional or transgenic breeding studies in the past. In research on the mineral nutrition of plants in general, and K in particular, this nutrient has been shown to be essential to soil-dwelling-microorganisms (fungi, bacteria, protozoa, nematodes, etc.) that form mutualistic associations and that can influence the availability of mineral nutrients for plants. Therefore, this article aims to provide an overview of the role of soil microorganisms in supplying K+ to plants, considering both the potassium-solubilizing microorganisms and the potassium-facilitating microorganisms that are in close contact with the roots of plants. These microorganisms can influence the active transporter-mediated transfer of K+. Regarding the latter group of microorganisms, special focus is placed on the role of endophytic fungus. This review also includes a discussion on productivity through sustainable agriculture.}, }
@article {pmid31260142, year = {2019}, author = {Pellegrin, C and Daguerre, Y and Ruytinx, J and Guinet, F and Kemppainen, M and Frey, NFD and Puech-Pagès, V and Hecker, A and Pardo, AG and Martin, FM and Veneault-Fourrey, C}, title = {Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14727}, pmid = {31260142}, issn = {1462-2920}, support = {//European Fund for Regional Development/ ; Plant-Microbe Interfaces Scientific Focus Area//Genomic Science Program, US Department of Energy, Office of Science, Biological and Environmental Research/ ; ANR-11-LABX-0002_ARBRE//Laboratory of Excellence ARBRE/ ; //Région Lorraine Research council/ ; }, abstract = {The ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems sustaining tree growth and health. Its establishment and functioning implies a long-term and intimate relationship between the soil-borne fungi and the roots of trees. Mycorrhiza-induced Small-Secreted Proteins (MiSSPs) are hypothesized as keystone symbiotic proteins, required to set up the symbiosis by modifying the host metabolism and/or building the symbiotic interfaces. L. bicolor MiSSP8 is the third most highly induced MiSSPs in symbiotic tissues and it is also expressed in fruiting bodies. The MiSSP8-RNAi knockdown mutants are strongly impaired in their mycorrhization ability with Populus, with the lack of fungal mantle and Hartig net development due to the lack of hyphal aggregation. MiSSP8 C-terminus displays a repetitive motif containing a kexin cleavage site, recognized by KEX2 in vitro. This suggests MiSSP8 protein might be cleaved into small peptides. Moreover, the MiSSP8 repetitive motif is found in other proteins predicted secreted by both saprotrophic and ectomycorrhizal fungi. Thus, our data indicate that MiSSP8 is a small-secreted protein involved at early stages of ectomycorrhizal symbiosis, likely by regulating hyphal aggregation and pseudoparenchyma formation.}, }
@article {pmid31260050, year = {2019}, author = {Carrier, TJ and Dupont, S and Reitzel, AM}, title = {Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz103}, pmid = {31260050}, issn = {1574-6941}, abstract = {Determining the factors underlying the assembly, structure, and diversity of symbiont communities remains a focal point of animal-microbiome research. Much of these efforts focus on taxonomic variation of microbiota within or between animal populations, but rarely test the proportional impacts of ecological components that may affect animal-associated microbiota. Using larvae from the sea urchin Strongylocentrotus droebachiensis from the Atlantic and Pacific Oceans, we test the hypothesis that, under natural conditions, inter-population differences in the composition of larval-associated bacterial communities are larger than intra-population variation due to a heterogeneous feeding environment. Despite significant differences in bacterial community structure within each S. droebachiensis larval population based on food availability, development, phenotype, and time, variation in OTU membership and community composition correlated more strongly with geographic location. Moreover, 20-30% of OTUs associated with larvae were specific to a single location while less than 10% were shared. Taken together, these results suggest that inter-populational variation in symbiont communities may be more pronounced than intra-populational variation, and that this difference may suggest that broad-scale ecological variables (e.g., across ocean basins) may mask smaller scale ecological variables (e.g., food availability).}, }
@article {pmid31257129, year = {2019}, author = {Wein, T and Romero Picazo, D and Blow, F and Woehle, C and Jami, E and Reusch, TBH and Martin, WF and Dagan, T}, title = {Currency, Exchange, and Inheritance in the Evolution of Symbiosis.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2019.05.010}, pmid = {31257129}, issn = {1878-4380}, abstract = {Symbiotic interactions between eukaryotes and prokaryotes are widespread in nature. Here we offer a conceptual framework to study the evolutionary origins and ecological circumstances of species in beneficial symbiosis. We posit that mutual symbiotic interactions are well described by three elements: a currency, the mechanism of currency exchange, and mechanisms of symbiont inheritance. Each of these elements may be at the origin of symbiosis, with the other elements developing with time. The identity of currency in symbiosis depends on the ecological context of the symbiosis, while the specificity of the exchange mechanism underlies molecular adaptations for the symbiosis. The inheritance regime determines the degree of partner dependency and the symbiosis evolutionary trajectory. Focusing on these three elements, we review examples and open questions in the research on symbiosis.}, }
@article {pmid31254821, year = {2019}, author = {Yang, XC and Han, ZZ and Ruan, XY and Chai, J and Jiang, SW and Zheng, R}, title = {Composting swine carcasses with nitrogen transformation microbial strains: Succession of microbial community and nitrogen functional genes.}, journal = {The Science of the total environment}, volume = {688}, number = {}, pages = {555-566}, doi = {10.1016/j.scitotenv.2019.06.283}, pmid = {31254821}, issn = {1879-1026}, abstract = {In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p < 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p < 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p < 0.05) strengthened nitrogen fixation and remarkably (p < 0.01) weakened nitrification and denitrification, which, however, were notably (p < 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.}, }
@article {pmid31254637, year = {2019}, author = {Bouletreau, P and Makaremi, M and Ibrahim, B and Louvrier, A and Sigaux, N}, title = {Artificial Intelligence: Applications in orthognathic surgery.}, journal = {Journal of stomatology, oral and maxillofacial surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jormas.2019.06.001}, pmid = {31254637}, issn = {2468-7855}, abstract = {Artificial Intelligence (AI) applications have already invaded our everyday life, and the last 10 years have seen the emergence of very promising applications in the field of medicine. However, the literature dealing with the potential applications of IA in Orthognathic Surgery is remarkably poor to date. Yet, it is very likely that due to its amazing power in image recognition AI will find tremendous applications in dento-facial deformities recognition in a near future. In this article, we point out the state-of-the-art AI applications in medicine and its potential applications in the field of orthognathic surgery. AI is a very powerful tool and it is the responsibility of the entire medical profession to achieve a positive symbiosis between clinical sense and AI.}, }
@article {pmid31253759, year = {2019}, author = {Liu, CW and Breakspear, A and Stacey, N and Findlay, K and Nakashima, J and Ramakrishnan, K and Liu, M and Xie, F and Endre, G and de Carvalho-Niebel, F and Oldroyd, GED and Udvardi, MK and Fournier, J and Murray, JD}, title = {A protein complex required for polar growth of rhizobial infection threads.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2848}, doi = {10.1038/s41467-019-10029-y}, pmid = {31253759}, issn = {2041-1723}, support = {TULIP ANR-10-LABX-41 (TULIP)/COME-IN ANR-14-CE35-0007-01//Agence Nationale de la Recherche (French National Research Agency)/International ; BB/L010305/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; BB/L010305/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; }, mesh = {Agrobacterium ; Gene Expression Regulation, Plant ; Medicago truncatula/*genetics/*microbiology ; Plant Proteins/genetics/*metabolism ; Plant Root Nodulation/genetics/physiology ; Plant Roots ; Sinorhizobium meliloti/*physiology ; Symbiosis/physiology ; Two-Hybrid System Techniques ; }, abstract = {During root nodule symbiosis, intracellular accommodation of rhizobia by legumes is a prerequisite for nitrogen fixation. For many legumes, rhizobial colonization initiates in root hairs through transcellular infection threads. In Medicago truncatula, VAPYRIN (VPY) and a putative E3 ligase LUMPY INFECTIONS (LIN) are required for infection thread development but their cellular and molecular roles are obscure. Here we show that LIN and its homolog LIN-LIKE interact with VPY and VPY-LIKE in a subcellular complex localized to puncta both at the tip of the growing infection thread and at the nuclear periphery in root hairs and that the punctate accumulation of VPY is positively regulated by LIN. We also show that an otherwise nuclear and cytoplasmic exocyst subunit, EXO70H4, systematically co-localizes with VPY and LIN during rhizobial infection. Genetic analysis shows that defective rhizobial infection in exo70h4 is similar to that in vpy and lin. Our results indicate that VPY, LIN and EXO70H4 are part of the symbiosis-specific machinery required for polar growth of infection threads.}, }
@article {pmid31251718, year = {2019}, author = {Bromfield, ESP and Cloutier, S and Nguyen, HDT}, title = {Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {9}, pages = {2841-2848}, doi = {10.1099/ijsem.0.003569}, pmid = {31251718}, issn = {1466-5034}, abstract = {A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.}, }
@article {pmid31249389, year = {2019}, author = {Meunier, V and Bonnet, S and Pernice, M and Benavides, M and Lorrain, A and Grosso, O and Lambert, C and Houlbrèque, F}, title = {Bleaching forces coral's heterotrophy on diazotrophs and Synechococcus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0456-2}, pmid = {31249389}, issn = {1751-7370}, abstract = {Coral reefs are threatened by global warming, which disrupts the symbiosis between corals and their photosynthetic symbionts (Symbiodiniaceae), leading to mass coral bleaching. Planktonic diazotrophs or dinitrogen (N2)-fixing prokaryotes are abundant in coral lagoon waters and could be an alternative nutrient source for corals. Here we incubated untreated and bleached coral colonies of Stylophora pistillata with a 15N2-pre-labelled natural plankton assemblage containing diazotrophs. 15N2 assimilation rates in Symbiodiniaceae cells and tissues of bleached corals were 5- and 30-fold higher, respectively, than those measured in untreated corals, demonstrating that corals incorporate more nitrogen derived from planktonic diazotrophs under bleaching conditions. Bleached corals also preferentially fed on Synechococcus, nitrogen-rich picophytoplanktonic cells, instead of Prochlorococcus and picoeukaryotes, which have a lower cellular nitrogen content. By providing an alternative source of bioavailable nitrogen, both the incorporation of nitrogen derived from planktonic diazotrophs and the ingestion of Synechococcus may have profound consequences for coral bleaching recovery, especially for the many coral reef ecosystems characterized by high abundance and activity of planktonic diazotrophs.}, }
@article {pmid31245768, year = {2019}, author = {Kramer, EM and Statter, SA and Yi, HJ and Carlson, JW and McClelland, DHR}, title = {Flowering plant immune repertoires expand under mycorrhizal symbiosis.}, journal = {Plant direct}, volume = {3}, number = {3}, pages = {e00125}, doi = {10.1002/pld3.125}, pmid = {31245768}, issn = {2475-4455}, abstract = {Immune perception in flowering plants is mediated by a repertoire of cytoplasmic and cell-surface receptors that detect invading microbes and their effects on cells. Here, we show that several large families of immune receptors exhibit size variations related to a plant's competence to host symbiotic root fungi (mycorrhiza). Plants that do not participate in mycorrhizal associations have significantly smaller immune repertoires, while the most promiscuous symbiotic hosts (ectomycorrhizal plant species) have significantly larger immune repertoires. By contrast, we find no significant increase in immune repertoire size among legumes competent to form a symbiosis with nitrogen-fixing bacteria (rhizobia). To explain these observations, we hypothesize that plant immune repertoire size expands with symbiote species diversity.}, }
@article {pmid31244787, year = {2019}, author = {Heise, P and Liu, Y and Degenkolb, T and Vogel, H and Schäberle, TF and Vilcinskas, A}, title = {Antibiotic-Producing Beneficial Bacteria in the Gut of the Burying Beetle Nicrophorus vespilloides.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1178}, doi = {10.3389/fmicb.2019.01178}, pmid = {31244787}, issn = {1664-302X}, abstract = {The increasing prevalence of antibiotic-resistant human pathogens is a growing public concern and there is intense pressure to identify new antibacterial compounds that can be developed into antibiotics with novel mode of action. Evolutionary theory predicts that insects that have evolved to occupy sophisticated ecological niches by feeding and reproducing on carcasses will depend on their gut microbiome to prevent colonization by invading pathogens taken up with the diet. This inspired our hypothesis that the complex interactions between the core microbiome and the more flexible microbial communities dependent on the environment may promote the outsourcing of antibiotic synthesis to beneficial microbes. We tested this hypothesis by cultivating and characterizing bacteria isolated from the gut of the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses buried in the soil to avoid competitors such as fly maggots. The extracts of isolated bacteria were screened for activity against human pathogens such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans. More than 400 strains were isolated, among which the crude extract of Serratia marcescens 2MH3-2 displayed promising activity against Staphylococcus aureus. Bioactivity-guided fractionation enabled purification of the primary antimicrobial compound of the extract. By LC-MS and NMR experiments, it was identified as serrawettin W2 (C38H61N5O9), the antibacterial and nematostatic activity of which was corroborated in our study. We postulate that this antibiotic could contribute to the control of both bacteria and phoretic nematodes in the gut, which compete for food when transferred to the carcass. Our study shows that the gut microbiome of N. vespilloides is a promising resource for the screening of antibiotic-producing bacteria.}, }
@article {pmid31243442, year = {2019}, author = {Vuong, HQ and McFrederick, QS}, title = {Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2151-2161}, doi = {10.1093/gbe/evz136}, pmid = {31243442}, issn = {1759-6653}, abstract = {Symbiosis with bacteria is common across insects, resulting in adaptive host phenotypes. The recently described bacterial symbionts Lactobacillus micheneri, Lactobacillus timberlakei, and Lactobacillus quenuiae are found in wild bee pollen provisions, bee guts, and flowers but have small genomes in comparison to other lactobacilli. We sequenced, assembled, and analyzed 27 new L. micheneri clade genomes to identify their possible ecological functions in flower and bee hosts. We determined possible key functions for the L. micheneri clade by identifying genes under positive selection, balancing selection, genes gained or lost, and population structure. A host adherence factor shows signatures of positive selection, whereas other orthologous copies are variable within the L. micheneri clade. The host adherence factors serve as strong evidence that these lactobacilli are adapted to animal hosts as their targets are found in the digestive tract of insects. Next, the L. micheneri clade is adapted toward a nutrient-rich environment, corroborating observations of where L. micheneri is most abundant. Additionally, genes involved in osmotolerance, pH tolerance, temperature resistance, detoxification, and oxidative stress response show signatures of selection that allow these bacteria to thrive in pollen and nectar masses in bee nests and in the bee gut. Altogether, these findings not only suggest that the L. micheneri clade is primarily adapted to the wild bee gut but also exhibit genomic features that would be beneficial to survival in flowers.}, }
@article {pmid31239506, year = {2019}, author = {Van Treuren, W and Brower, KK and Labanieh, L and Hunt, D and Lensch, S and Cruz, B and Cartwright, HN and Tran, C and Fordyce, PM}, title = {Live imaging of Aiptasia larvae, a model system for coral and anemone bleaching, using a simple microfluidic device.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9275}, doi = {10.1038/s41598-019-45167-2}, pmid = {31239506}, issn = {2045-2322}, abstract = {Coral reefs, and their associated diverse ecosystems, are of enormous ecological importance. In recent years, coral health has been severely impacted by environmental stressors brought on by human activity and climate change, threatening the extinction of several major reef ecosystems. Reef damage is mediated by a process called 'coral bleaching' where corals, sea anemones, and other cnidarians lose their photosynthetic algal symbionts (family Symbiodiniaceae) upon stress induction, resulting in drastically decreased host energy harvest and, ultimately, coral death. The mechanism by which this critical cnidarian-algal symbiosis is lost remains poorly understood. The larvae of the sea anemone, Exaiptasia pallida (commonly referred to as 'Aiptasia') are an attractive model organism to study this process, but they are large (∼100 mm in length, ∼75 mm in diameter), deformable, and highly motile, complicating long-term imaging and limiting study of this critical endosymbiotic relationship in live organisms. Here, we report 'Traptasia', a simple microfluidic device with multiple traps designed to isolate and image individual, live larvae of Aiptasia and their algal symbionts over extended time courses. Using a trap design parameterized via fluid flow simulations and polymer bead loading tests, we trapped Aiptasia larvae containing algal symbionts and demonstrated stable imaging for >10 hours. We visualized algae within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable time-lapsed, high-throughput live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of cnidarian bleaching under different environmental stressors. The 'Traptasia' device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted using the trap optimization data presented here to study a variety of large, motile organisms.}, }
@article {pmid31239394, year = {2019}, author = {Turon, M and Uriz, MJ and Martin, D}, title = {Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00148-19}, pmid = {31239394}, issn = {2379-5077}, abstract = {Sponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllis spp.) and their host sponges (Clathria reinwardti, Amphimedon paraviridis, Neofibularia hartmani, and Aaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of six Haplosyllis species (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabited A. paraviridis and was different from the single species that inhabited A. suberitoides Conversely, two different polychaete species were found in C. reinwardti and N. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCE The symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.}, }
@article {pmid31239345, year = {2019}, author = {Wong, JEMM and Nadzieja, M and Madsen, LH and Bücherl, CA and Dam, S and Sandal, NN and Couto, D and Derbyshire, P and Uldum-Berentsen, M and Schroeder, S and Schwämmle, V and Nogueira, FCS and Asmussen, MH and Thirup, S and Radutoiu, S and Blaise, M and Andersen, KR and Menke, FLH and Zipfel, C and Stougaard, J}, title = {A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {28}, pages = {14339-14348}, doi = {10.1073/pnas.1815425116}, pmid = {31239345}, issn = {1091-6490}, abstract = {The establishment of nitrogen-fixing root nodules in legume-rhizobia symbiosis requires an intricate communication between the host plant and its symbiont. We are, however, limited in our understanding of the symbiosis signaling process. In particular, how membrane-localized receptors of legumes activate signal transduction following perception of rhizobial signaling molecules has mostly remained elusive. To address this, we performed a coimmunoprecipitation-based proteomics screen to identify proteins associated with Nod factor receptor 5 (NFR5) in Lotus japonicus. Out of 51 NFR5-associated proteins, we focused on a receptor-like cytoplasmic kinase (RLCK), which we named NFR5-interacting cytoplasmic kinase 4 (NiCK4). NiCK4 associates with heterologously expressed NFR5 in Nicotiana benthamiana, and directly binds and phosphorylates the cytoplasmic domains of NFR5 and NFR1 in vitro. At the cellular level, Nick4 is coexpressed with Nfr5 in root hairs and nodule cells, and the NiCK4 protein relocates to the nucleus in an NFR5/NFR1-dependent manner upon Nod factor treatment. Phenotyping of retrotransposon insertion mutants revealed that NiCK4 promotes nodule organogenesis. Together, these results suggest that the identified RLCK, NiCK4, acts as a component of the Nod factor signaling pathway downstream of NFR5.}, }
@article {pmid31237779, year = {2019}, author = {Oh, HYP and Visvalingam, V and Wahli, W}, title = {The PPAR-microbiota-metabolic organ trilogy to fine-tune physiology.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {9}, pages = {9706-9730}, doi = {10.1096/fj.201802681RR}, pmid = {31237779}, issn = {1530-6860}, abstract = {The human gut is colonized by commensal microorganisms, predominately bacteria that have coevolved in symbiosis with their host. The gut microbiota has been extensively studied in recent years, and many important findings on how it can regulate host metabolism have been unraveled. In healthy individuals, feeding timing and type of food can influence not only the composition but also the circadian oscillation of the gut microbiota. Host feeding habits thus influence the type of microbe-derived metabolites produced and their concentrations throughout the day. These microbe-derived metabolites influence many aspects of host physiology, including energy metabolism and circadian rhythm. Peroxisome proliferator-activated receptors (PPARs) are a group of ligand-activated transcription factors that regulate various metabolic processes such as fatty acid metabolism. Similar to the gut microbiota, PPAR expression in various organs oscillates diurnally, and studies have shown that the gut microbiota can influence PPAR activities in various metabolic organs. For example, short-chain fatty acids, the most abundant type of metabolites produced by anaerobic fermentation of dietary fibers by the gut microbiota, are PPAR agonists. In this review, we highlight how the gut microbiota can regulate PPARs in key metabolic organs, namely, in the intestines, liver, and muscle. Knowing that the gut microbiota impacts metabolism and is altered in individuals with metabolic diseases might allow treatment of these patients using noninvasive procedures such as gut microbiota manipulation.-Oh, H. Y. P., Visvalingam, V., Wahli, W. The PPAR-microbiota-metabolic organ trilogy to fine-tune physiology.}, }
@article {pmid31237728, year = {2019}, author = {Nadal-Jimenez, P and Griffin, JS and Davies, L and Frost, CL and Marcello, M and Hurst, GDD}, title = {Genetic manipulation allows in vivo tracking of the life cycle of the son-killer symbiont, Arsenophonus nasoniae, and reveals patterns of host invasion, tropism and pathology.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {3172-3182}, doi = {10.1111/1462-2920.14724}, pmid = {31237728}, issn = {1462-2920}, support = {708232//H2020 Marie Skłodowska-Curie Actions/ ; 704382//H2020 Marie Skłodowska-Curie Actions/ ; NE/I01067X/1//Natural Environment Research Council/ ; BB/L014947/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Maternally heritable symbionts are common in arthropods and represent important partners and antagonists. A major impediment to understanding the mechanistic basis of these symbioses has been lack of genetic manipulation tools, for instance, those enabling transgenic GFP expression systems for in vivo visualization. Here, we transform the 'son-killer' reproductive parasite Arsenophonus nasoniae that infects the parasitic wasp Nasonia vitripennis with the plasmid pOM1-gfp, re-introduce this strain to N. vitripennis and then used this system to track symbiont life history in vivo. These data revealed transfer of the symbiont into the fly pupa by N. vitripennis during oviposition and N. vitripennis larvae developing infection over time through feeding. A strong tropism of A. nasoniae to the N. vitripennis ovipositor developed during wasp pupation, which aids onward transmission. The symbiont was also visualized in diapause larvae. Occasional necrotic diapause larvae were observed which displayed intense systemic infection alongside widespread melanotic nodules indicative of an active but failed immune response. Our results provide the foundation for the study of this symbiosis through in vivo tracking of the fate of symbionts through host development, which is rarely achieved in heritable microbe/insect interactions.}, }
@article {pmid31236967, year = {2019}, author = {Chomicki, G and Renner, SS}, title = {Farming by ants remodels nutrient uptake in epiphytes.}, journal = {The New phytologist}, volume = {223}, number = {4}, pages = {2011-2023}, doi = {10.1111/nph.15855}, pmid = {31236967}, issn = {1469-8137}, support = {//Queen's College, University of Oxford/ ; RE 603/20-1//Deutsche Forschungsgemeinschaft/ ; RE 603/20-2//Deutsche Forschungsgemeinschaft/ ; //University of Oxford/ ; }, abstract = {True agriculture - defined by habitual planting, cultivation, harvesting and dependence of a farmer on a crop - is known from fungi farmed by ants, termites or beetles, and plants farmed by humans or ants. Because farmers supply their crops with nutrients, they have the potential to modify crop nutrition over evolutionary time. Here we test this hypothesis in ant/plant farming symbioses. We used field experiments, phylogenetic-comparative analyses and computed-tomography scanning to investigate how the evolution of farming by ants has impacted the nutrition of locally coexisting species in the epiphytic genus Squamellaria (Rubiaceae). Using isotope-labelled mineral and organic nitrogen, we show that specialised ants actively and exclusively fertilise hyperabsorptive warts on the inner walls of plant-formed structures (domatia) where they nest, sharply contrasting with nitrogen provisioning by ants in nonfarming generalist symbioses. Similar hyperabsorptive warts have evolved repeatedly in lineages colonised by farming ants. Our study supports the idea that millions of years of ant agriculture have remodelled plant physiology, shifting from ant-derived nutrients as by-products to active and targeted fertilisation on hyperabsorptive sites. The increased efficiency of ant-derived nutrient provisioning appears to stem from a combination of farming ant behaviour and plant 'crop' traits.}, }
@article {pmid31236871, year = {2019}, author = {Rolim, L and Santiago, TR and Dos Reis Junior, FB and de Carvalho Mendes, I and do Vale, HMM and Hungria, M and Silva, LP}, title = {Identification of soybean Bradyrhizobium strains used in commercial inoculants in Brazil by MALDI-TOF mass spectrometry.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00104-3}, pmid = {31236871}, issn = {1678-4405}, support = {465133/2014-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 02.13.08.001.00.00//Empresa Brasileira de Pesquisa Agropecuária/ ; }, abstract = {Biological nitrogen fixation (BNF) with the soybean crop probably represents the major sustainable technology worldwide, saving billions of dollars in N fertilizers and decreasing water pollution and the emission of greenhouse gases. Accordingly, the identification of strains occupying nodules under field conditions represents a critical step in studies that are aimed at guaranteeing increased BNF contribution. Current methods of identification are mostly based on serology, or on DNA profiles. However, the production of antibodies is restricted to few laboratories, and to obtain DNA profiles of hundreds of isolates is costly and time-consuming. Conversely, the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS technique might represent a golden opportunity for replacing serological and DNA-based methods. However, MALDI-TOF databases of environmental microorganisms are still limited, and, most importantly, there are concerns about the discrimination of protein profiles at the strain level. In this study, we investigated four soybean rhizobial strains carried in commercial inoculants used in over 35 million hectares in Brazil and also in other countries of South America and Africa. A supplementary MALDI-TOF database with the protein profiles of these rhizobial strains was built and allowed the identification of unique profiles statistically supported by multivariate analysis and neural networks. To test this new database, the nodule occupancy by Bradyrhizobium strains in symbiosis with soybean was characterized in a field experiment and the results were compared with serotyping of bacteria by immuno-agglutination. The results obtained by both techniques were highly correlated and confirmed the viability of using the MALDI-TOF MS technique to effectively distinguish bacteria at the strain level.}, }
@article {pmid31236592, year = {2019}, author = {Kenny, NJ and Plese, B and Riesgo, A and Itskovich, VB}, title = {Symbiosis, Selection and Novelty: Freshwater Adaptation in the Unique Sponges of Lake Baikal.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz151}, pmid = {31236592}, issn = {1537-1719}, abstract = {Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. While spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal, and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan 'Benchmarking Universal Single-Copy Orthologs' (BUSCO) set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication and novelty in freshwater sponges compared to marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g. zinc transporter-2), transcription factors (aristaless-related homeobox) and structural proteins (for example actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (for example, colonization and migration patterns) of these key species.}, }
@article {pmid31235587, year = {2019}, author = {Nakayama, T and Nomura, M and Takano, Y and Tanifuji, G and Shiba, K and Inaba, K and Inagaki, Y and Kawata, M}, title = {Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {32}, pages = {15973-15978}, doi = {10.1073/pnas.1902538116}, pmid = {31235587}, issn = {1091-6490}, abstract = {Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.}, }
@article {pmid31234272, year = {2019}, author = {Lan, Q and Liu, C and Ling, S}, title = {Research on Measurement of Symbiosis Degree Between National Fitness and the Sports Industry from the Perspective of Collaborative Development.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ijerph16122191}, pmid = {31234272}, issn = {1660-4601}, abstract = {Clarifying the symbiotic relationship between national fitness and the sports industry has important theoretical and practical significance for the collaborative development of the two. In order to measure and verify the symbiotic relationship between national fitness and the sports industry, we introduce a &quot;symbiosis degree&quot; model test method for the measurement of the symbiotic relationship during 2000-2017 between the two. Our results show that national fitness and the sports industry have symbiotic sufficient and necessary conditions, for both of which there is a symbiotic relationship, and a non-symmetric reciprocal symbiotic mode long-term. Overall, the impact of national fitness on the sports industry is greater than the impact of the sports industry on national fitness. From a structural perspective, there is a certain difference in the mutual influence of national fitness and the sports industry in the field of sports goods and sports services. In a dynamic forecast, we found that national fitness and the sports industry have the development trend of a symmetric reciprocal symbiotic state. Through theoretical studies, data measured and simulated projections, we believe that the symbiosis degree of the measurement model for the detection and prediction of the symbiotic unit of the symbiotic relationship between them to be of practical value.}, }
@article {pmid31233506, year = {2019}, author = {Cui, G and Liew, YJ and Li, Y and Kharbatia, N and Zahran, NI and Emwas, AH and Eguiluz, VM and Aranda, M}, title = {Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia.}, journal = {PLoS genetics}, volume = {15}, number = {6}, pages = {e1008189}, doi = {10.1371/journal.pgen.1008189}, pmid = {31233506}, issn = {1553-7404}, abstract = {The metabolic symbiosis with photosynthetic algae allows corals to thrive in the oligotrophic environments of tropical seas. Different aspects of this relationship have been investigated using the emerging model organism Aiptasia. However, many fundamental questions, such as the nature of the symbiotic relationship and the interactions of nutrients between the partners remain highly debated. Using a meta-analysis approach, we identified a core set of 731 high-confidence symbiosis-associated genes that revealed host-dependent recycling of waste ammonium and amino acid synthesis as central processes in this relationship. Subsequent validation via metabolomic analyses confirmed that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids. We propose that this provides a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. The dependence of this mechanism on symbiont-derived carbon highlights the susceptibility of this symbiosis to changes in carbon translocation, as imposed by environmental stress.}, }
@article {pmid31231402, year = {2019}, author = {Bapaume, L and Laukamm, S and Darbon, G and Monney, C and Meyenhofer, F and Feddermann, N and Chen, M and Reinhardt, D}, title = {VAPYRIN Marks an Endosomal Trafficking Compartment Involved in Arbuscular Mycorrhizal Symbiosis.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {666}, doi = {10.3389/fpls.2019.00666}, pmid = {31231402}, issn = {1664-462X}, abstract = {Arbuscular mycorrhiza (AM) is a symbiosis between plants and AM fungi that requires the intracellular accommodation of the fungal partner in the host. For reciprocal nutrient exchange, AM fungi form intracellular arbuscules that are surrounded by the peri-arbuscular membrane. This membrane, together with the fungal plasma membrane, and the space in between, constitute the symbiotic interface, over which nutrients are exchanged. Intracellular establishment of AM fungi requires the VAPYRIN protein which is induced in colonized cells, and which localizes to numerous small mobile structures of unknown identity (Vapyrin-bodies). In order to characterize the identity and function of the Vapyrin-bodies we pursued a dual strategy. First, we co-expressed fluorescently tagged VAPYRIN with a range of subcellular marker proteins, and secondly, we employed biochemical tools to identify interacting partner proteins of VAPYRIN. As an important tool for the quantitative analysis of confocal microscopic data sets from co-expression of fluorescent proteins, we developed a semi-automated image analysis pipeline that allows for precise spatio-temporal quantification of protein co-localization and of the dynamics of organelle association from movies. Taken together, these experiments revealed that Vapyrin-bodies have an endosomal identity with trans-Golgi features, and that VAPYRIN interacts with a symbiotic R-SNARE of the VAMP721 family, that localizes to the same compartment.}, }
@article {pmid31231333, year = {2019}, author = {Miozzi, L and Vaira, AM and Catoni, M and Fiorilli, V and Accotto, GP and Lanfranco, L}, title = {Arbuscular Mycorrhizal Symbiosis: Plant Friend or Foe in the Fight Against Viruses?.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1238}, doi = {10.3389/fmicb.2019.01238}, pmid = {31231333}, issn = {1664-302X}, abstract = {Plant roots establish interactions with several beneficial soil microorganisms including arbuscular mycorrhizal fungi (AMF). In addition to promoting plant nutrition and growth, AMF colonization can prime systemic plant defense and enhance tolerance to a wide range of environmental stresses and below-ground pathogens. A protective effect of the AMF against above-ground pathogens has also been described in different plant species, but it seems to largely rely on the type of attacker. Viruses are obligate biotrophic pathogens able to infect a large number of plant species, causing massive losses in crop yield worldwide. Despite their economic importance, information on the effect of the AM symbiosis on viral infection is limited and not conclusive. However, several experimental evidences, obtained under controlled conditions, show that AMF colonization may enhance viral infection, affecting susceptibility, symptomatology and viral replication, possibly related to the improved nutritional status and to the delayed induction of pathogenesis-related proteins in the mycorrhizal plants. In this review, we give an overview of the impact of the AMF colonization on plant infection by pathogenic viruses and summarize the current knowledge of the underlying mechanisms. For the cases where AMF colonization increases the susceptibility of plants to viruses, the term &quot;mycorrhiza-induced susceptibility&quot; (MIS) is proposed.}, }
@article {pmid31230564, year = {2019}, author = {Liu, H and Senthilkumar, R and Ma, G and Zou, Q and Zhu, K and Shen, X and Tian, D and Hua, MS and Oelmüller, R and Yeh, KW}, title = {Piriformospora indica-induced phytohormone changes and root colonization strategies are highly host-specific.}, journal = {Plant signaling &amp; behavior}, volume = {14}, number = {9}, pages = {1632688}, doi = {10.1080/15592324.2019.1632688}, pmid = {31230564}, issn = {1559-2324}, abstract = {Piriformospora indica, an endophytic fungus of Sebacinales, has a wide host range and promotes the performance of mono- and eudicot plants. Here, we compare the interaction of P. indica with the roots of seven host plants (Anthurium andraeanum, Arabidopsis thaliana, Brassica campestris, Lycopersicon esculentum, Oncidium orchid, Oryza sativa, and Zea mays). Microscopical analyses showed that the colonization time and the mode of hyphal invasion into the roots differ in the symbiotic interactions. Substantial differences between the species were also observed for the levels and accumulation of jasmonate (JA) and gibberellin (GA) and the transcript levels for genes involved in their syntheses. No obvious correlation could be detected between the endogenous JA and/or GA levels and the time point of root colonization in a given plant species. Our results suggest that root colonization strategies and changes in the two phytohormone levels are highly host-specific.}, }
@article {pmid31230256, year = {2019}, author = {Petrzik, K}, title = {Evolutionary forces at work in partitiviruses.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01680-0}, pmid = {31230256}, issn = {1572-994X}, support = {MEMOBIc//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; RVO60077344//Akademie Věd České Republiky/ ; }, abstract = {The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.}, }
@article {pmid31229798, year = {2019}, author = {Roper, C and Castro, C and Ingel, B}, title = {Xylella fastidiosa: bacterial parasitism with hallmarks of commensalism.}, journal = {Current opinion in plant biology}, volume = {50}, number = {}, pages = {140-147}, doi = {10.1016/j.pbi.2019.05.005}, pmid = {31229798}, issn = {1879-0356}, abstract = {All organisms evolve in the presence of other organisms and these intimate associations are major drivers of evolution. Broadly speaking, these interactions are considered symbioses and can take on a full range of positive, negative or seemingly neutral interactions. Just two examples of these symbiotic interactions are parasitism and commensalism. Parasitism results in one partner benefitting while one partner suffers adverse consequences. Commensalism is a form of symbiosis where one partner benefits and the other partner is neutrally affected. Research efforts are more often focused on understanding parasitic symbioses related to disease, hence, much research is performed on identifying virulence factors to understand the fundamentals of pathogenesis. In turn, much less is understood about the fundamentals of commensal relationships. Here, we will take an introspective look at the plant-associated bacterium, Xylella fastidiosa. In some of its many plant hosts, this bacterium participates in seemingly commensal relationships while in other hosts, it causes devastating diseases that result in epidemics, making it a good model for exploring the determinants of where bacteria fall on the spectrum of parasitic and commensal relationships from both the microbial and the plant host perspective. Recent discoveries in how pathogenic X. fastidiosa imposes self-limiting behaviors upon itself indicate that even in its parasitic form, X. fastidiosa displays hallmarks of a commensal lifestyle. Understanding how commensalism can 'go wrong' and manifest into pathologies in specific hosts is a useful vantage point from which to study the determinants of virulence and pathogenicity.}, }
@article {pmid31229565, year = {2019}, author = {Zhang, R and Yang, Y and Wang, J and Lin, Y and Yan, Y}, title = {Synthetic symbiosis combining plasmid displacement enables rapid construction of phenotype-stable strains.}, journal = {Metabolic engineering}, volume = {55}, number = {}, pages = {85-91}, doi = {10.1016/j.ymben.2019.06.011}, pmid = {31229565}, issn = {1096-7184}, abstract = {Plasmid-based microbial systems have been a major workhorse for chemical and pharmaceutical production. The biosafety issues and elevated industrial cost of antibiotic usage have led to the development of alternative strategies for plasmid selection and maintenance. Such strategies, including auxotrophy complementation, post-segregational killing, operator-repressor and RNA-based interactions often require extensive engineering of various elements and may result in extra metabolic burden in the cells. Herein, we report a design of synthetic symbiosis combining plasmid displacement to construct a phenotype-stable microbial system. By sequestrating an endogenous essential gene folP, cells obtained long-term plasmid maintenance with minimum cost. The phenotype performance was also inherited for up to 80 generations demonstrated by the production of salicylic acid in Escherichia coli. Meanwhile, the temperature-induced curing method of the intermediate plasmids enables rapid engineering. This design can lead to broad applications as a reliable and convenient plasmid-based expression system.}, }
@article {pmid31228837, year = {2019}, author = {Dhaouefi, Z and Toledo-Cervantes, A and Ghedira, K and Chekir-Ghedira, L and Muñoz, R}, title = {Decolorization and phytotoxicity reduction in an innovative anaerobic/aerobic photobioreactor treating textile wastewater.}, journal = {Chemosphere}, volume = {234}, number = {}, pages = {356-364}, doi = {10.1016/j.chemosphere.2019.06.106}, pmid = {31228837}, issn = {1879-1298}, abstract = {The potential of a novel anaerobic/aerobic algal-bacterial photobioreactor for the treatment of synthetic textile wastewater (STWW) was here assessed. Algal-bacterial symbiosis supported total organic carbon, nitrogen and phosphorous removal efficiencies of 78 ± 2%, 47 ± 2% and 26 ± 2%, respectively, at a hydraulic retention time (HRT) of 8 days. A decrease in the HRT from 8 to 4 and 2 days resulted in a slight decrease in organic carbon and phosphate removal, but a sharp decrease in nitrogen removal. Moreover, an efficient decolorization of 99 ± 1% and 96 ± 3% for disperse orange-3 and of disperse blue-1, respectively, was recorded. The effective STWW treatment supported by the anaerobic/aerobic algal-bacterial photobioreactor was confirmed by the reduction in wastewater toxicity towards Raphanus sativus seed germination and growth. These results highlighted the potential of this innovative algal-bacterial photobioreactor configuration for the treatment of textile wastewater and water reuse.}, }
@article {pmid31227910, year = {2019}, author = {Babadi, M and Zalaghi, R and Taghavi, M}, title = {A non-toxic polymer enhances sorghum-mycorrhiza symbiosis for bioremediation of Cd.}, journal = {Mycorrhiza}, volume = {29}, number = {4}, pages = {375-387}, doi = {10.1007/s00572-019-00902-5}, pmid = {31227910}, issn = {1432-1890}, support = {96/3/02/16670//Shahid Chamran University of Ahvaz/ ; }, abstract = {In this study, the effect of a mycorrhizal symbiosis on the translocation of Cd from Cd-polluted soil to sorghum roots was investigated using rhizoboxes. A factorial experiment (two factors including fungus inoculation and Cd contamination) in a completely randomized design with three replicates was performed. In the rhizobox rhizosphere compartment, plants were cultivated in uncontaminated soil and mycorrhizal inoculation (inoculated with Claroideoglomus etunicatum or non-inoculated) was performed, and in the other compartment, the soil was contaminated with Cadmium (Cd) at one of three levels (0, 100 mg kg-1 using a non-toxic organic polymer (poly (N-vinyl succinate))-Cd, or 100 mg kg-1 using Cd-nitrate). Cd pollution resulted in a significant decrease in shoot dry weight (from 7.52 to 6.18 and 6.68 g pot-1, from control to polymer-Cd and nitrate-Cd respectively), root mycorrhizal colonization (from 32.33% to 8.16% and 8.33%), shoot phosphorus concentration (from 3.14 to 2.80 and 2.76 g kg-1), and soil carbohydrate (from 12.05 to 10.74 and 10.24 mg g-1), and also resulted in significant increases in soil glomalin (from 595.55 to 660.52 and 690.39 μg g-1). The use of mycorrhizal fungi increased the glomalin content of the soil and improved the studied parameters. The results revealed the key role of Claroideoglomus etunicatum in translocation of Cd in the rhizobox and also in precise control of Cd concentration of plant tissues (increase or decrease of them depending on Cd composition and Cd availability). Poly(N-vinyl succinate) increased Cd availability and Cd concentration of shoot tissue (5.19 mg kg-1) compared to nitrate-Cd (3.68 mg kg-1) and could be recommended for improving phytoremediation.}, }
@article {pmid31227866, year = {2019}, author = {Mei, YZ and Zhu, YL and Huang, PW and Yang, Q and Dai, CC}, title = {Strategies for gene disruption and expression in filamentous fungi.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {15}, pages = {6041-6059}, doi = {10.1007/s00253-019-09953-2}, pmid = {31227866}, issn = {1432-0614}, support = {2017YFD0800705//Key Technologies Research and Development Program/ ; Project No31570491//National Natural Science Foundation of China (CN)/ ; }, abstract = {Filamentous fungi can produce many valuable secondary metabolites; among these fungi, endophytic fungi play an ecological role in mutualistic symbiosis with plants, including promoting plant growth, disease resistance, and stress resistance. However, the biosynthesis of most secondary metabolites remains unclear, and knowledge of the interaction mechanisms between endophytes and plants is still limited, especially for some novel fungi, due to the lack of genetic manipulation tools for novel species. Herein, we review the newly discovered strategies of gene disruption, such as the CRISPR-Cas9 system, the site-specific recombination Cre/loxP system, and the I-SceI endonuclease-mediated system in filamentous fungi. Gene expression systems contain using integration of target genes into the genome, host-dependent expression cassette construction depending on the host, a host-independent, universal expression system independent of the host, and reporter-guided gene expression for filamentous fungi. Furthermore, the Newly CRISPRi, CRISPRa, and the selection markers were also discussed for gene disruption and gene expression were also discussed. These studies lay the foundation for the biosynthesis of secondary metabolites in these organisms and aid in understanding the ecological function of filamentous fungi.}, }
@article {pmid31222171, year = {2019}, author = {Edgcomb, V}, title = {Symbiotic magnetic motility.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1066-1067}, doi = {10.1038/s41564-019-0489-3}, pmid = {31222171}, issn = {2058-5276}, mesh = {Bacteria ; *Eukaryota ; *Symbiosis ; }, }
@article {pmid31219214, year = {2019}, author = {Muletz-Wolz, CR and Kurata, NP and Himschoot, EA and Wenker, ES and Quinn, EA and Hinde, K and Power, ML and Fleischer, RC}, title = {Diversity and temporal dynamics of primate milk microbiomes.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e22994}, doi = {10.1002/ajp.22994}, pmid = {31219214}, issn = {1098-2345}, support = {RR019970/GF/NIH HHS/United States ; //Directorate for Biological Sciences/ ; //National Institutes of Health/ ; DDIG 0525025//NSF/ ; R24 OD010962/OD/NIH HHS/United States ; R01 DK077639/DK/NIDDK NIH HHS/United States ; R24OD020347//Smithsonian Competitive Grant for Science/ ; //American Society of Primatologists/ ; DDIG: 0746320//NSF/ ; RR000169/GF/NIH HHS/United States ; DK77639//John Capitanio and the California National Primate Research Center/ ; }, abstract = {Milk is inhabited by a community of bacteria and is one of the first postnatal sources of microbial exposure for mammalian young. Bacteria in breast milk may enhance immune development, improve intestinal health, and stimulate the gut-brain axis for infants. Variation in milk microbiome structure (e.g., operational taxonomic unit [OTU] diversity, community composition) may lead to different infant developmental outcomes. Milk microbiome structure may depend on evolutionary processes acting at the host species level and ecological processes occurring over lactation time, among others. We quantified milk microbiomes using 16S rRNA high-throughput sequencing for nine primate species and for six primate mothers sampled over lactation. Our data set included humans (Homo sapiens, Philippines and USA) and eight nonhuman primate species living in captivity (bonobo [Pan paniscus], chimpanzee [Pan troglodytes], western lowland gorilla [Gorilla gorilla gorilla], Bornean orangutan [Pongo pygmaeus], Sumatran orangutan [Pongo abelii], rhesus macaque [Macaca mulatta], owl monkey [Aotus nancymaae]) and in the wild (mantled howler monkey [Alouatta palliata]). For a subset of the data, we paired microbiome data with nutrient and hormone assay results to quantify the effect of milk chemistry on milk microbiomes. We detected a core primate milk microbiome of seven bacterial OTUs indicating a robust relationship between these bacteria and primate species. Milk microbiomes differed among primate species with rhesus macaques, humans and mantled howler monkeys having notably distinct milk microbiomes. Gross energy in milk from protein and fat explained some of the variations in microbiome composition among species. Microbiome composition changed in a predictable manner for three primate mothers over lactation time, suggesting that different bacterial communities may be selected for as the infant ages. Our results contribute to understanding ecological and evolutionary relationships between bacteria and primate hosts, which can have applied benefits for humans and endangered primates in our care.}, }
@article {pmid31218790, year = {2019}, author = {Khatabi, B and Gharechahi, J and Ghaffari, MR and Liu, D and Haynes, PA and McKay, MJ and Mirzaei, M and Salekdeh, GH}, title = {Plant-Microbe Symbiosis: What Has Proteomics Taught Us?.}, journal = {Proteomics}, volume = {19}, number = {16}, pages = {e1800105}, doi = {10.1002/pmic.201800105}, pmid = {31218790}, issn = {1615-9861}, abstract = {Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other &quot;omics&quot; data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based &quot;omic&quot; approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.}, }
@article {pmid31218402, year = {2019}, author = {Motaharpoor, Z and Taheri, H and Nadian, H}, title = {Rhizophagus irregularis modulates cadmium uptake, metal transporter, and chelator gene expression in Medicago sativa.}, journal = {Mycorrhiza}, volume = {29}, number = {4}, pages = {389-395}, doi = {10.1007/s00572-019-00900-7}, pmid = {31218402}, issn = {1432-1890}, abstract = {Arbuscular mycorrhizal fungi (AMF) are considered a potential biotechnological tool for mitigating heavy metal (HM) toxicity. A greenhouse experiment was conducted to evaluate the impacts of the AM fungus Rhizophagus irregularis on cadmium (Cd) uptake, mycorrhizal colonization, and some plant growth parameters of Medicago sativa (alfalfa) in Cd-polluted soils. In addition, expression of two metal chelators (MsPCS1 (phytochelatin synthase) and MsMT2 (metallothionein)) and two metal transporter genes (MsIRT1 and MsNramp1) was analyzed using quantitative real-time PCR (qRT-PCR). Cd addition had a significant negative effect on mycorrhizal colonization. However, AMF symbiosis promoted the accumulation of biomass under both stressed and unstressed conditions compared with non-mycorrhizal (NM) plants. Results also showed that inoculation with R. irregularis significantly reduced shoot Cd concentration in polluted soils. Transcripts abundance of MsPCS1, MsMT2, MsIRT1, and MsNRAMP1 genes were downregulated compared with NM plants indicating that metal sequestration within hyphal fungi probably made Cd concentration insufficient in root cells for induction of these genes. These results suggest that reduction of shoot Cd concentration in M. sativa colonized by R. irregularis could be a promising strategy for safe production of this plant in Cd-polluted soils.}, }
@article {pmid31218384, year = {2019}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {In Vivo Modulation of Arbuscular Mycorrhizal Symbiosis and Soil Quality by Fungal P Solubilizers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01396-6}, pmid = {31218384}, issn = {1432-184X}, support = {PICT 2012 0285//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, abstract = {Phosphorus (P) is an essential nutrient with low bioavailability in soils for plant growth. The use of P solubilization fungi (PSF) has arisen as an eco-friendly strategy to increase this nutrient's bioavailability. The effect of PSF inoculation and its combination with P-transporting organisms (arbuscular mycorrhizal fungi, AMF) on plant growth has been previously studied. However, these studies did not evaluate the combined effect of PSF and AMF inoculation on plant growth, symbiosis, and soil quality. Therefore, the aim of this study is to assess the impact of PSF on the AMF-wheat symbiosis establishment and efficiency, considering the effect on plant growth and soil quality. We performed a greenhouse experiment with wheat under different treatments (+/-AMF: Rhizophagus irregularis; +/-PSF strains: Talaromyces flavus, T. helicus L7B, T. helicus N24, and T. diversus) and measured plant growth, AMF root colonization, symbiotic efficiency, and soil quality indicators. No interaction between PSF and R. irregularis was found in wheat growth, showcasing that their combination is not better than single inoculation. T. helicus strains did not interfere with the AMF-wheat symbiosis establishment, while T. diversus and T. flavus decreased it. The symbiotic efficiency was increased by T. flavus and T. helicus N24, and unchanged with T. helicus L7B and T. diversus inoculation. The soil quality indicators were higher with microbial co-inoculation, particularly the alkaline phosphatases parameter, showing the beneficial role of fungi in soil. This work highlights the importance of microbial interactions in the rhizosphere for crop sustainability and soil quality improvement, assessing the effects of PSF on AMF-wheat symbiosis.}, }
@article {pmid31217550, year = {2019}, author = {Otani, S and Challinor, VL and Kreuzenbeck, NB and Kildgaard, S and Krath Christensen, S and Larsen, LLM and Aanen, DK and Rasmussen, SA and Beemelmanns, C and Poulsen, M}, title = {Disease-free monoculture farming by fungus-growing termites.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8819}, doi = {10.1038/s41598-019-45364-z}, pmid = {31217550}, issn = {2045-2322}, support = {DNRF57//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; CRC 1127 ChemBioSys//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; VKR10101//Villum Fonden (Villum Foundation)/ ; }, abstract = {Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses have been lacking. Here we use culture-dependent and -independent methods to characterise fungus comb mycobiotas from three fungus-growing termite species (two genera). Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing and Illumina MiSeq showed that non-Termitomyces fungi were essentially absent in fungus combs, and that Termitomyces fungal crops are maintained in monocultures as heterokaryons with two or three abundant ITS variants in a single fungal strain. To explore whether the essential absence of other fungi within fungus combs is potentially due to the production of antifungal metabolites by Termitomyces or comb bacteria, we performed in vitro assays and found that both Termitomyces and chemical extracts of fungus comb material can inhibit potential fungal antagonists. Chemical analyses of fungus comb material point to a highly complex metabolome, including compounds with the potential to play roles in mediating these contaminant-free farming conditions in the termite symbiosis.}, }
@article {pmid31217361, year = {2019}, author = {Shinohara, A and Nohara, M and Kondo, Y and Jogahara, T and Nagura-Kato, GA and Izawa, M and Koshimoto, C}, title = {Comparison of the gut microbiotas of laboratory and wild Asian house shrews (Suncus murinus) based on cloned 16S rRNA sequences.}, journal = {Experimental animals}, volume = {}, number = {}, pages = {}, doi = {10.1538/expanim.19-0021}, pmid = {31217361}, issn = {1881-7122}, abstract = {The Asian house shrew, Suncus murinus, is an insectivore (Eulipotyphla, Mammalia) and an important laboratory animal for life-science studies. The gastrointestinal tract of Suncus is simple: the length of the entire intestine is very short relative to body size, the large intestine is quite short, and there are no fermentative chambers such as the forestomach or cecum. These features imply that Suncus has a different nutritional physiology from those of humans and mice, but little is known about whether Suncus utilizes microbial fermentation in the large (LI) or small (SI) intestine. In addition, domestication may affect the gastrointestinal microbial diversity of Suncus. Therefore, we compared the gastrointestinal microbial diversity of Suncus between laboratory and wild Suncus and between the SI and LI (i.e., four groups: Lab-LI, Lab-SI, Wild-LI, and Wild-SI) using bacterial 16S rRNA gene library sequencing analyses with a sub-cloning method. We obtained 759 cloned sequences (176, 174, 195, and 214 from the Lab-LI, Lab-SI, Wild-LI, and Wild-SI samples, respectively), which revealed that the gastrointestinal microbiota of Suncus is rich in Firmicutes (mostly lactic acid bacteria), with few Bacteroidetes. We observed different bacterial communities according to intestinal region in laboratory Suncus, but not in wild Suncus. Furthermore, the gastrointestinal microbial diversity estimates were lower in laboratory Suncus than in wild Suncus. These results imply that Suncus uses lactic acid fermentation in the gut, and that the domestication process altered the gastrointestinal bacterial diversity.}, }
@article {pmid31216282, year = {2019}, author = {Sieber, M and Pita, L and Weiland-Bräuer, N and Dirksen, P and Wang, J and Mortzfeld, B and Franzenburg, S and Schmitz, RA and Baines, JF and Fraune, S and Hentschel, U and Schulenburg, H and Bosch, TCG and Traulsen, A}, title = {Neutrality in the Metaorganism.}, journal = {PLoS biology}, volume = {17}, number = {6}, pages = {e3000298}, doi = {10.1371/journal.pbio.3000298}, pmid = {31216282}, issn = {1545-7885}, abstract = {Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.}, }
@article {pmid31216220, year = {2019}, author = {Plett, KL and Raposo, AE and Anderson, IC and Piller, SC and Plett, JM}, title = {Protein Arginine Methyltransferase Expression Affects Ectomycorrhizal Symbiosis and the Regulation of Hormone Signaling Pathways.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI01190007R}, doi = {10.1094/MPMI-01-19-0007-R}, pmid = {31216220}, issn = {0894-0282}, abstract = {The genomes of all eukaryotic organisms, from small unicellular yeasts to humans, include members of the protein arginine methyltransferase (PRMT) family. These enzymes affect gene transcription, cellular signaling, and function through the posttranslational methylation of arginine residues. Mis-regulation of PRMTs results in serious developmental defects, disease, or death, illustrating the importance of these enzymes to cellular processes. Plant genomes encode almost the full complement of PRMTs found in other higher organisms, plus an additional PRMT found uniquely in plants, PRMT10. Here, we investigate the role of these highly conserved PRMTs in a process that is unique to perennial plants-the development of symbiosis with ectomycorrhizal fungi. We show that PRMT expression and arginine methylation is altered in the roots of the model tree Eucalyptus grandis by the presence of its ectomycorrhizal fungal symbiont Pisolithus albus. Further, using transgenic modifications, we demonstrate that E. grandis-encoded PRMT1 and PRMT10 have important but opposing effects in promoting this symbiosis. In particular, the plant-specific EgPRMT10 has a potential role in the expression of plant hormone pathways during the colonization process and its overexpression reduces fungal colonization success.}, }
@article {pmid31215669, year = {2019}, author = {Page, CE and Leggat, W and Heron, SF and Choukroun, SM and Lloyd, J and Ainsworth, TD}, title = {Seeking Resistance in Coral Reef Ecosystems: The Interplay of Biophysical Factors and Bleaching Resistance under a Changing Climate: The Interplay of a Reef's Biophysical Factors Can Mitigate the Coral Bleaching Response.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {7}, pages = {e1800226}, doi = {10.1002/bies.201800226}, pmid = {31215669}, issn = {1521-1878}, support = {NA14NES4320003//National Oceanic and Atmospheric Administration/ ; DP180103199//Australian Research Council/ ; NA14NES4320003//NOAA/ ; DP180103199//Australian Research Council Discovery Project/ ; }, abstract = {If we are to ensure the persistence of species in an increasingly warm world, of interest is the identification of drivers that affect the ability of an organism to resist thermal stress. Underpinning any organism's capacity for resistance is a complex interplay between biological and physical factors occurring over multiple scales. Tropical coral reefs are a unique system, in that their function is dependent upon the maintenance of a coral-algal symbiosis that is directly disrupted by increases in water temperature. A number of physical factors have been identified as affecting the biological responses of the coral organism under broadscale thermal anomalies. One such factor is water flow, which is capable of modulating both organismal metabolic functioning and thermal environments. Understanding the physiological and hydrodynamic drivers of organism response to thermal stress improves predictive capabilities and informs targeted management responses, thereby increasing the resilience of reefs into the future.}, }
@article {pmid31215061, year = {2019}, author = {Law, SR}, title = {The genetic program at the root of the biological stock exchange.}, journal = {Physiologia plantarum}, volume = {166}, number = {3}, pages = {709-711}, doi = {10.1111/ppl.12980}, pmid = {31215061}, issn = {1399-3054}, mesh = {Gene Expression Regulation, Plant ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; Symbiosis/physiology ; }, abstract = {Beneath the gardens, farmlands and forest floors that surround us, a hidden world blooms in careful cooperation and intense competition. The mutualistic symbiosis of the thread-like hyphae of fungi and plant roots (collectively termed mycorrhizae from the Greek mýkēs - meaning 'fungus', and rhiza - for 'root') is present in the vast majority of plant species. As with most intimate relationships, this symbiosis functions on a principle of 'give and take'. As an autotroph, the plant is able to synthesize all the sugars it requires through photosynthesis; however, its immobility hinders its capacity to forage for nutrients vital for its growth and survival. With an expansive network of hyphae, the heterotrophic fungus is able to locate and remobilize water and nutrients, such as phosphorus (P) and nitrogen (N), and barter them for precious sugars with the plant. An article in this issue of Physiologia Plantarum (Zhao et al. 2019) describes alterations in the genetic programming that takes place in the plant root upon the establishment of this fascinating relationship, which has profound implications for plant productivity and soil management methods.}, }
@article {pmid31214691, year = {2019}, author = {Phillips, AJ and Dornburg, A and Zapfe, KL and Anderson, FE and James, SW and Erséus, C and Moriarty Lemmon, E and Lemmon, AR and Williams, BW}, title = {Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1712-1722}, doi = {10.1093/gbe/evz120}, pmid = {31214691}, issn = {1759-6653}, abstract = {Leeches (Hirudinida) comprise a charismatic, yet often maligned group of organisms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an anchored hybrid enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. Our results suggest that a dramatic reinterpretation of early leech evolution is warranted. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans, but found Acanthobdella to be nested within Oceanobdelliformes. These results cast doubt on the utility of Acanthobdella as a &quot;missing link&quot; used to explain the origin of blood-feeding in hirudineans. Further, our results support a deep divergence between predominantly marine and freshwater lineages, while not supporting the reciprocal monophyly of jawed and proboscis-bearing leeches. To sum up, our phylogenomic resolution of early-diverging leeches provides a necessary foundation for illuminating the evolution of host-symbiont associations and key adaptations that have allowed leeches to colonize a wide diversity of habitats worldwide.}, }
@article {pmid31214211, year = {2019}, author = {Billault-Penneteau, B and Sandré, A and Folgmann, J and Parniske, M and Pawlowski, K}, title = {Dryas as a Model for Studying the Root Symbioses of the Rosaceae.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {661}, doi = {10.3389/fpls.2019.00661}, pmid = {31214211}, issn = {1664-462X}, abstract = {The nitrogen-fixing root nodule symbiosis is restricted to four plant orders: Fabales (legumes), Fagales, Cucurbitales and Rosales (Elaeagnaceae, Rhamnaceae, and Rosaceae). Interestingly all of the Rosaceae genera confirmed to contain nodulating species (i.e., Cercocarpus, Chamaebatia, Dryas, and Purshia) belong to a single subfamily, the Dryadoideae. The Dryas genus is particularly interesting from an evolutionary perspective because it contains closely related nodulating (Dryas drummondii) and non-nodulating species (Dryas octopetala). The close phylogenetic relationship between these two species makes Dryas an ideal model genus to study the genetic basis of nodulation by whole genome comparison and classical genetics. Therefore, we established methods for plant cultivation, transformation and DNA extraction for these species. We optimized seed surface sterilization and germination methods and tested growth protocols ranging from pots and Petri dishes to a hydroponic system. Transgenic hairy roots were obtained by adapting Agrobacterium rhizogenes-based transformation protocols for Dryas species. We compared several DNA extraction protocols for their suitability for subsequent molecular biological analysis. Using CTAB extraction, reproducible PCRs could be performed, but CsCl gradient purification was essential to obtain DNA in sufficient purity for high quality de novo genome sequencing of both Dryas species. Altogether, we established a basic toolkit for the culture, transient transformation and genetic analysis of Dryas sp.}, }
@article {pmid31214134, year = {2019}, author = {Medrano, E and Merselis, DG and Bellantuono, AJ and Rodriguez-Lanetty, M}, title = {Proteomic Basis of Symbiosis: A Heterologous Partner Fails to Duplicate Homologous Colonization in a Novel Cnidarian- Symbiodiniaceae Mutualism.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1153}, doi = {10.3389/fmicb.2019.01153}, pmid = {31214134}, issn = {1664-302X}, abstract = {Reef corals and sea anemones form symbioses with unicellular symbiotic dinoflagellates. The molecular circumventions that underlie the successful intracellular colonization of hosts by symbionts are still largely unknown. We conducted proteomic analyses to determine molecular differences of Exaiptasia pallida anemones colonized by physiologically different symbiont species, in comparison with symbiont-free (aposymbiotic) anemones. We compared one homologous species, Symbiodinium linucheae, that is natively associated with the clonal Exaiptasia strain (CC7) to another heterologous species, Durusdinium trenchii, a thermally tolerant species that colonizes numerous coral species. This approach allowed the discovery of a core set of host genes that are differentially regulated as a function of symbiosis regardless of symbiont species. The findings revealed that symbiont colonization at higher densities requires circumvention of the host cellular immunological response, enhancement of ammonium regulation, and suppression of phagocytosis after a host cell in colonized. Furthermore, the heterologous symbionts failed to duplicate the same level of homologous colonization within the host, evidenced by substantially lower symbiont densities. This reduced colonization of D. trenchii correlated with its inability to circumvent key host systems including autophagy-suppressing modulators, cytoskeletal alteration, and isomerase activity. The larger capability of host molecular circumvention by homologous symbionts could be the result of a longer evolutionary history of host/symbiont interactions, which translates into a more finely tuned symbiosis. These findings are of great importance within the context of the response of reef corals to climate change since it has been suggested that coral may acclimatize to ocean warming by changing their dominant symbiont species.}, }
@article {pmid31213566, year = {2019}, author = {Van Leuven, JT and Mao, M and Xing, DD and Bennett, GM and McCutcheon, JP}, title = {Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.01950-18}, pmid = {31213566}, issn = {2150-7511}, support = {P20 GM104420/GM/NIGMS NIH HHS/United States ; }, abstract = {Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, &quot;Candidatus Hodgkinia cicadicola&quot; (Alphaproteobacteria) and &quot;Ca Sulcia muelleri&quot; (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original &quot;Ca Hodgkinia cicadicola&quot; genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of &quot;Ca Sulcia muelleri&quot; and &quot;Ca Hodgkinia cicadicola&quot; is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5' and 3' ends and seem to undergo nucleotide modification. Surprisingly, we found that most &quot;Ca Hodgkinia cicadicola&quot; and &quot;Ca Sulcia muelleri&quot; tRNAs exist as tRNA halves. We hypothesize that &quot;Ca Sulcia muelleri&quot; and &quot;Ca Hodgkinia cicadicola&quot; tRNAs function in bacterial translation but require host-encoded enzymes to do so.IMPORTANCE The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5' and 3' ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities.}, }
@article {pmid31212139, year = {2019}, author = {Müller, LM and Harrison, MJ}, title = {Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis.}, journal = {Current opinion in plant biology}, volume = {50}, number = {}, pages = {132-139}, doi = {10.1016/j.pbi.2019.05.004}, pmid = {31212139}, issn = {1879-0356}, abstract = {Most land plant species engage in a beneficial interaction with arbuscular mycorrhizal fungi in order to increase mineral nutrient acquisition, in particular the major macronutrient phosphorus (P). Initiation, development, and maintenance of the symbiosis are largely under the control of the host plant and strongly influenced by the plants' P status. Recent advances reveal that phytohormones, microRNAs, and secreted peptides all regulate and integrate development of arbuscular mycorrhizal (AM) symbiosis with the P status of the plant. This occurs through a complex, multi-layered signaling network with crosstalk between phosphate (Pi) starvation signaling pathways and AM symbiosis signaling, and also via direct effects on the AM fungal symbiont. Multiple checkpoints allow the plant to fine-tune symbiosis based on its P status.}, }
@article {pmid31211975, year = {2019}, author = {McCutcheon, JP and Lekberg, Y}, title = {Symbiosis: Fungi as Shrewd Trade Negotiators.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {R570-R572}, doi = {10.1016/j.cub.2019.05.002}, pmid = {31211975}, issn = {1879-0445}, abstract = {Symbiotic fungi associated with plant roots can shuttle a key nutrient through their hyphal network in response to resource inequality. This need-based transport optimizes trade conditions for carbon with plants.}, }
@article {pmid31208116, year = {2019}, author = {Cui, C and Wang, H and Hong, L and Xu, Y and Zhao, Y and Zhou, C}, title = {MtBZR1 Plays an Important Role in Nodule Development in Medicago truncatula.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, doi = {10.3390/ijms20122941}, pmid = {31208116}, issn = {1422-0067}, support = {ZR2018ZC0334//Major Program of Shandong Province Natural Science Foundation/ ; 2015CB943500//Ministry of Science and Technology of the People's Republic of China/ ; 31671507//National Natural Science Foundation of China/ ; 31371235//National Natural Science Foundation of China/ ; }, abstract = {Brassinosteroid (BR) is an essential hormone in plant growth and development. The BR signaling pathway was extensively studied, in which BRASSINAZOLE RESISTANT 1 (BZR1) functions as a key regulator. Here, we carried out a functional study of the homolog of BZR1 in Medicago truncatula R108, whose expression was induced in nodules upon Sinorhizobium meliloti 1021 inoculation. We identified a loss-of-function mutant mtbzr1-1 and generated 35S:MtBZR1 transgenic lines for further analysis at the genetic level. Both the mutant and the overexpression lines of MtBZR1 showed no obvious phenotypic changes under normal growth conditions. After S. meliloti 1021 inoculation, however, the shoot and root dry mass was reduced in mtbzr1-1 compared with the wild type, caused by partially impaired nodule development. The transcriptomic analysis identified 1319 differentially expressed genes in mtbzr1-1 compared with wild type, many of which are involved in nodule development and secondary metabolite biosynthesis. Our results demonstrate the role of MtBZR1 in nodule development in M. truncatula, shedding light on the potential role of BR in legume-rhizobium symbiosis.}, }
@article {pmid31207947, year = {2019}, author = {Dominguez, H and Loret, EP}, title = {Ulva lactuca, A Source of Troubles and Potential Riches.}, journal = {Marine drugs}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/md17060357}, pmid = {31207947}, issn = {1660-3397}, abstract = {Ulva lactuca is a green macro alga involved in devastating green tides observed worldwide. These green tides or blooms are a consequence of human activities. Ulva blooms occur mainly in shallow waters and the decomposition of this alga can produce dangerous vapors. Ulva lactuca is a species usually resembling lettuce, but genetic analyses demonstrated that other green algae with tubular phenotypes were U. lactuca clades although previously described as different species or even genera. The capacity for U. lactuca to adopt different phenotypes can be due to environment parameters, such as the degree of water salinity or symbiosis with bacteria. No efficient ways have been discovered to control these green tides, but the Mediterranean seas appear to be protected from blooms, which disappear rapidly in springtime. Ulva contains commercially valuable components, such as bioactive compounds, food or biofuel. The biomass due to this alga collected on beaches every year is beginning to be valorized to produce valuable compounds. This review describes different processes and strategies developed to extract these different valuable components.}, }
@article {pmid31204904, year = {2019}, author = {Zou, H and Zhang, NN and Pan, Q and Zhang, JH and Chen, J and Wei, GH}, title = {Hydrogen Sulfide Promotes Nodulation and Nitrogen Fixation in Soybean-Rhizobia Symbiotic System.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {32}, number = {8}, pages = {972-985}, doi = {10.1094/MPMI-01-19-0003-R}, pmid = {31204904}, issn = {0894-0282}, mesh = {Gasotransmitters/pharmacology ; *Hydrogen Sulfide/pharmacology ; *Nitrogen Fixation/drug effects ; *Plant Root Nodulation/drug effects ; *Rhizobium/physiology ; *Soybeans/microbiology ; Symbiosis/drug effects ; }, abstract = {The rhizobium-legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that an exogenous H2S donor (sodium hydrosulfide [NaHS]) treatment promoted soybean growth, nodulation, and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of Nase component nifH was increased by NaHS treatment in nodules. Quantitative real-time polymerase chain reaction data showed that NaHS treatment upregulated the expressions of symbiosis-related genes nodA, nodC, and nodD of S. fredii. In addition, expression of soybean nodulation marker genes, including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway 2b (GmNSP2b), and nodulation inception genes (GmNIN1a, GmNIN2a, and GmNIN2b), were upregulated. Moreover, the expressions of glutamate synthase (GmGOGAT), asparagine synthase (GmAS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), leghemoglobin (GmLb), and nifH involved in nitrogen metabolism were upregulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in the soybean-rhizobia symbiotic system and enhance the system's nitrogen fixation ability.}, }
@article {pmid31203796, year = {2019}, author = {Ravindran, S and Tambe, AJ and Suthar, JK and Chahar, DS and Fernandes, JM and Desai, V}, title = {Nanomedicine: Bioavailability, Biotransformation and Biokinetics.}, journal = {Current drug metabolism}, volume = {20}, number = {7}, pages = {542-555}, doi = {10.2174/1389200220666190614150708}, pmid = {31203796}, issn = {1875-5453}, abstract = {BACKGROUND: Nanomedicine is increasingly used to treat various ailments. Biocompatibility of nanomedicine is primarily governed by its properties such as bioavailability, biotransformation and biokinetics. One of the major advantages of nanomedicine is enhanced bioavailability of drugs. Biotransformation of nanomedicine is important to understand the pharmacological effects of nanomedicine. Biokinetics includes both pharmacokinetics and toxicokinetics of nanomedicine. Physicochemical parameters of nanomaterials have extensive influence on bioavailability, biotransformation and biokinetics of nanomedicine.<br><br>METHODS: We carried out a structured peer-reviewed research literature survey and analysis using bibliographic databases.<br><br>RESULTS: Eighty papers were included in the review. Papers dealing with bioavailability, biotransformation and biokinetics of nanomedicine are found and reviewed. Bioavailability and biotransformation along with biokinetics are three major factors that determine the biological fate of nanomedicine. Extensive research work has been done for drugs of micron size but studies on nanomedicine are scarce. Therefore, more emphasis in this review is given on the bioavailability and biotransformation of nanomedicine along with biokinetics.<br><br>CONCLUSION: Bioavailability results based on various nanomedicine are summarized in the present work. Biotransformation of nanodrugs as well as nanoformulations is also the focus of this article. Both in vitro and in vivo biotransformation studies on nanodrugs and its excipients are necessary to know the effect of metabolites formed. Biokinetics of nanomedicine is captured in details that are complimentary to bioavailability and biotransformation. Nanomedicine has the potential to be developed as a personalized medicine once its physicochemical properties and its effect on biological system are well understood.}, }
@article {pmid31200330, year = {2019}, author = {Jiang, J and Lu, Y}, title = {Metabolite profiling of Breviolum minutum in response to acidification.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {213}, number = {}, pages = {105215}, doi = {10.1016/j.aquatox.2019.05.017}, pmid = {31200330}, issn = {1879-1514}, abstract = {Coral reefs are in significant decline globally due to climate change and environmental pollution. The ocean is becoming more acidic due to rising atmospheric pCO2, and ocean acidification is considered a major threat to coral reefs. However, little is known about the exact mechanism by which acidification impacts coral symbiosis. As an important component of the symbiotic association, to explore the responses of symbionts could greatly enhance our understanding of this issue. The present work aimed to identify metabolomic changes of Breviolum minutum in acidification (low pH) condition, and investigate the underlying mechanisms responsible. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to determine metabolite profiles after exposure to ambient and acidic conditions. We analysed the resulting metabolite data, and acidification appeared to have little effect on photosynthetic parameters, but it inhibited growth. Marked alterations in metabolite pools were observed in response to acidification that may be important in acclimation to climate change. Acidification may affect the biosynthesis of amino acids and proteins, and thereby inhibit the growth of B. minutum. Metabolites identified using this approach provide targets for future analyses aimed at understanding the responses of Symbiodiniaceae to environmental disturbance.}, }
@article {pmid31197972, year = {2019}, author = {Rader, B and McAnulty, SJ and Nyholm, SV}, title = {Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e858}, doi = {10.1002/mbo3.858}, pmid = {31197972}, issn = {2045-8827}, support = {1R15GM119100/GF/NIH HHS/United States ; IOS-0958006//NSF/ ; IOS-155794//NSF/ ; }, abstract = {The binary association between the squid, Euprymna scolopes, and its symbiont, Vibrio fischeri, serves as a model system to study interactions between beneficial bacteria and the innate immune system. Previous research demonstrated that binding of the squid's immune cells, hemocytes, to V. fischeri is altered if the symbiont is removed from the light organ, suggesting that host colonization alters hemocyte recognition of V. fischeri. To investigate the influence of symbiosis on immune maturation during development, we characterized hemocyte binding and phagocytosis of V. fischeri and nonsymbiotic Vibrio harveyi from symbiotic (sym) and aposymbiotic (apo) juveniles, and wild-caught and laboratory-raised sym and apo adults. Our results demonstrate that while light organ colonization by V. fischeri did not alter juvenile hemocyte response, these cells bound a similar number of V. fischeri and V. harveyi yet phagocytosed only V. harveyi. Our results also indicate that long-term colonization altered the adult hemocyte response to V. fischeri but not V. harveyi. All hemocytes from adult squid, regardless of apo or sym state, both bound and phagocytosed a similar number of V. harveyi while hemocytes from both wild-caught and sym-raised adults bound significantly fewer V. fischeri, although more V. fischeri were phagocytosed by hemocytes from wild-caught animals. In contrast, hemocytes from apo-raised squid bound similar numbers of both V. fischeri and V. harveyi, although more V. harveyi cells were engulfed, suggesting that blood cells from apo-raised adults behaved similarly to juvenile hosts. Taken together, these data suggest that persistent colonization by the light organ symbiont is required for hemocytes to differentially bind and phagocytose V. fischeri. The cellular immune system of E. scolopes likely possesses multiple mechanisms at different developmental stages to promote a specific and life-long interaction with the symbiont.}, }
@article {pmid31197351, year = {2019}, author = {Martínez-Medina, A and Pescador-Azofra, L and Terrón-Camero, L and Pozo, MJ and Romero-Puertas, MC}, title = {Nitric oxide shape plant-fungi interactions.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz289}, pmid = {31197351}, issn = {1460-2431}, abstract = {In their complex environments, plants continuously interact with fungi. While many of those interactions are detrimental for plants and challenge plant capability for growth and survival, others are beneficial improving plant growth and stress tolerance. Accordingly, plants have evolved sophisticated mechanisms to restrict pathogenic interactions while promoting mutualistic relationships. Several studies demonstrated the importance of nitric oxide (NO) in the regulation of plant defence mounted against fungal pathogens. NO triggers a reprograming of defence related gene expression, the production of secondary metabolites with antimicrobial properties and the hypersensitive response. More recent evidences have further shown the regulation of NO during the establishment of plant-fungus mutualistic associations from early steps of the interaction. Indeed NO has been recently shown to be produced by the plant after the recognition of root fungal symbionts, and to be required for the optimal control of the mycorrhizal symbiosis. Although studies dealing with NO function in plant-fungus mutualistic associations are still scarce, experimental data support a different regulation patterns and functions for NO in plant interactions with pathogenic and mutualistic fungi. Here we review recent evidences about NO function in plant-fungus interactions, trying to identify common and differential patterns related to the fungus life-style and their impact on plant health.}, }
@article {pmid31197117, year = {2019}, author = {Lipa, P and Vinardell, JM and Janczarek, M}, title = {Transcriptomic Studies Reveal that the Rhizobium leguminosarum Serine/Threonine Protein Phosphatase PssZ has a Role in the Synthesis of Cell-Surface Components, Nutrient Utilization, and Other Cellular Processes.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, doi = {10.3390/ijms20122905}, pmid = {31197117}, issn = {1422-0067}, abstract = {Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing symbiotic associations with clover plants (Trifolium spp.). Surface polysaccharides, transport systems, and extracellular components synthesized by this bacterium are required for both the adaptation to changing environmental conditions and successful infection of host plant roots. The pssZ gene located in the Pss-I region, which is involved in the synthesis of extracellular polysaccharide, encodes a protein belonging to the group of serine/threonine protein phosphatases. In this study, a comparative transcriptomic analysis of R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt297 carrying a pssZ mutation was performed. RNA-Seq data identified a large number of genes differentially expressed in these two backgrounds. Transcriptome profiling of the pssZ mutant revealed a role of the PssZ protein in several cellular processes, including cell signalling, transcription regulation, synthesis of cell-surface polysaccharides and components, and bacterial metabolism. In addition, we show that inactivation of pssZ affects the rhizobial ability to grow in the presence of different sugars and at various temperatures, as well as the production of different surface polysaccharides. In conclusion, our results identified a set of genes whose expression was affected by PssZ and confirmed the important role of this protein in the rhizobial regulatory network.}, }
@article {pmid31197001, year = {2019}, author = {Mascuch, S and Kubanek, J}, title = {A marine chemical defense partnership.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6445}, pages = {1034-1035}, doi = {10.1126/science.aax8964}, pmid = {31197001}, issn = {1095-9203}, mesh = {*Bacteria ; *Ecosystem ; *Symbiosis ; }, }
@article {pmid31196985, year = {2019}, author = {Zan, J and Li, Z and Tianero, MD and Davis, J and Hill, RT and Donia, MS}, title = {A microbial factory for defensive kahalalides in a tripartite marine symbiosis.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6445}, pages = {}, doi = {10.1126/science.aaw6732}, pmid = {31196985}, issn = {1095-9203}, support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; }, abstract = {Chemical defense against predators is widespread in natural ecosystems. Occasionally, taxonomically distant organisms share the same defense chemical. Here, we describe an unusual tripartite marine symbiosis, in which an intracellular bacterial symbiont (&quot;Candidatus Endobryopsis kahalalidefaciens&quot;) uses a diverse array of biosynthetic enzymes to convert simple substrates into a library of complex molecules (the kahalalides) for chemical defense of the host, the alga Bryopsis sp., against predation. The kahalalides are subsequently hijacked by a third partner, the herbivorous mollusk Elysia rufescens, and employed similarly for defense. &quot;Ca E. kahalalidefaciens&quot; has lost many essential traits for free living and acts as a factory for kahalalide production. This interaction between a bacterium, an alga, and an animal highlights the importance of chemical defense in the evolution of complex symbioses.}, }
@article {pmid31195965, year = {2019}, author = {Dreyer, J and Rautenbach, M and Booysen, E and van Staden, AD and Deane, SM and Dicks, LMT}, title = {Xenorhabdus khoisanae SB10 produces Lys-rich PAX lipopeptides and a Xenocoumacin in its antimicrobial complex.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {132}, doi = {10.1186/s12866-019-1503-x}, pmid = {31195965}, issn = {1471-2180}, support = {not applicable//National Research Foundation/ ; not applicable//BIOPEP Peptide fund/ ; }, abstract = {BACKGROUND: Xenorhabdus spp. live in close symbiosis with nematodes of the Steinernema genus. Steinernema nematodes infect an insect larva and release their symbionts into the haemocoel of the insect. Once released into the haemocoel, the bacteria produce bioactive compounds to create a semi-exclusive environment by inhibiting the growth of bacteria, yeasts and molds. The antimicrobial compounds thus far identified are xenocoumacins, xenortides, xenorhabdins, indole derivatives, xenoamicins, bicornutin and a number of antimicrobial peptides. The latter may be linear peptides such as the bacteriocins xenocin and xenorhabdicin, rhabdopeptides and cabanillasin, or cyclic, such as PAX lipopeptides, taxlllaids, xenobactin and szentiamide. Thus far, production of antimicrobial compounds have been reported for Xenorhabdus nematophila, Xenorhabdus budapestensis, Xenorhabdus cabanillasii, Xenorhabdus kozodoii, Xenorhabdus szentirmaii, Xenorhabdus doucetiae, Xenorhabdus mauleonii, Xenorhabdus indica and Xenorhabdus bovienii. Here we describe, for the first time, PAX lipopeptides and xenocoumacin 2 produced by Xenorhabdus khoisanae. These compounds were identified using ultraperformance liquid chromatography, linked to high resolution electrospray ionisation mass spectrometry and tandem mass spectrometry.<br><br>RESULTS: Cell-free supernatants of X. khoisanae SB10 were heat stable and active against Bacillus subtilis subsp. subtilis, Escherichia coli and Candida albicans. Five lysine-rich lipopeptides from the PAX group were identified in HPLC fractions, with PAX1' and PAX7 present in the highest concentrations. Three novel PAX7 peptides with putative enoyl modifications and two linear analogues of PAX1' were also detected. A small antibiotic compound, yellow in colour and λmax of 314 nm, was recovered from the HPLC fractions and identified as xenocoumacin 2. The PAX lipopeptides and xenocoumacin 2 correlated with the genes and gene clusters in the genome of X. khoisanae SB10.<br><br>CONCLUSION: With UPLC-MS and MSe analyses of compounds in the antimicrobial complex of X. khoisanae SB10, a number of PAX peptides and a xenocoumacin were identified. The combination of pure PAX1' peptide with xenocoumacin 2 resulted in high antimicrobial activity. Many of the fractions did, however, contain labile compounds and some fractions were difficult to resolve. It is thus possible that strain SB10 may produce more antimicrobial compounds than reported here, as suggested by the APE Ec biosynthetic complex. Further research is required to develop these broad-spectrum antimicrobial compounds into drugs that may be used in the fight against microbial infections.}, }
@article {pmid31195952, year = {2019}, author = {Ikram, M and Ali, N and Jan, G and Guljan, F and Khan, N}, title = {Endophytic fungal diversity and their interaction with plants for agriculture sustainability under stressful condition.}, journal = {Recent patents on food, nutrition &amp; agriculture}, volume = {}, number = {}, pages = {}, doi = {10.2174/2212798410666190612130139}, pmid = {31195952}, issn = {1876-1429}, abstract = {Endophytic fungi or endophytes as fascinating group of organism that colonize widely the healthy internal tissues of living plants, and do not cause any symptoms of disease in the host cells. Several decades of study and research have rustled the co-existing endophytes with their host plants, which can significantly influence the formation of metabolic products in plants, its ability to produce new interesting bioactive compound, which are of pharmaceutical, industrial and agricultural importance. The analytical results indicate that the endophytic fungi can confer profound impacts on plant communities by enhancing their growth, increasing their fitness, strengthening their tolerances to abiotic and biotic stresses, enhance defense mechanism and promoting their accumulation of secondary metabolites that provide immunity to the victims. This review focused on the biodiversity and biological roles of endophytic fungi in association with their host plants through reviewing of published research data obtained from the last 30 years.}, }
@article {pmid31195052, year = {2019}, author = {Lee, J and Kim, CH and Jang, HA and Kim, JK and Kotaki, T and Shinoda, T and Shinada, T and Yoo, JW and Lee, BL}, title = {Burkholderia gut symbiont modulates titer of specific juvenile hormone in the bean bug Riptortus pedestris.}, journal = {Developmental and comparative immunology}, volume = {99}, number = {}, pages = {103399}, doi = {10.1016/j.dci.2019.103399}, pmid = {31195052}, issn = {1879-0089}, abstract = {Recent studies have provided molecular evidence that gut symbiotic bacteria modulate host insect development, fitness and reproduction. However, the molecular mechanisms through which gut symbionts regulate these aspects of host physiology remain elusive. To address these questions, we prepared two different Riptortus-Burkholderia insect models, Burkholderia gut symbiont-colonized (Sym) Riptortus pedestris insects and gut symbiont-noncolonized (Apo) insects. Upon LC-MS analyses, juvenile hormone III skipped bisepoxide (JHSB3) was newly identified from Riptortus Apo- and Sym-female and male adults' insect hemolymph and JHSB3 titer in the Apo- and Sym-female insects were measured because JH is important for regulating reproduction in adult insects. The JHSB3 titer in the Sym-females were consistently higher compared to those of Apo-females. Since previous studies reported that Riptortus hexamerin-α and vitellogenin proteins were upregulated by the topical abdominal application of a JH-analog, chemically synthesized JHSB3 was administered to Apo-females. As expected, the hexamerin-α and vitellogenin proteins were dramatically increased in the hemolymph of JHSB3-treated Apo-females, resulting in increased egg production compared to that in Sym-females. Taken together, these results demonstrate that colonization of Burkholderia gut symbiont in the host insect stimulates biosynthesis of the heteroptera-specific JHSB3, leading to larger number of eggs produced and enhanced fitness in Riptortus host insects.}, }
@article {pmid31194818, year = {2019}, author = {Jung, M and Lee, DH}, title = {Abundance and diversity of gut-symbiotic bacteria, the genus Burkholderia in overwintering Riptortus pedestris (Hemiptera: Alydidae) populations and soil in South Korea.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218240}, doi = {10.1371/journal.pone.0218240}, pmid = {31194818}, issn = {1932-6203}, abstract = {Riptortus pedestris is a major agricultural pest on leguminous plants in South Korea and Japan. Recent studies have revealed that R. pedestris can form beneficial symbiosis with bacteria belonging to genus Burkholderia acquired from soil newly for every generation. Although their physiological interactions are relatively well-understood, infection rate and abundance of the Burkholderia in overwintering natural populations of R. pedestris remain unknown. Therefore, the objective of this study was to characterize Burkholderia infection ratio and clade composition of overwintering R. pedestris populations as well as prevalence and diversity of the genus Burkholderia in soil by conducting a two-year field survey. From the field survey, we found 29 overwintering R. pedestris adults in forested areas nearby soybean fields. Diagnostic PCR analysis revealed that overall infection rate of the symbiotic Burkholderia was 93.1% from overwintering adults. Among the Burkholderia-infected R. pedestris, 70.4% of individuals harbored unclassified Burkholderia clades whereas 22.2% and 7.4% of R. pedestris harbor stinkbug-associated beneficial and environmental (SBE) group and Burkholderia cepacia and complex (BCC), respectively. All R. pedestris were infected with a single clade of Burkholderia. In soil, 56.2% of soil samples were Burkholderia positive, and unlike R. pedestris, multiple Burkholderia clades were detected from 62.2% of those samples. Clade composition of the genus Burkholderia in the samples with the bacteria was 91.1%, 60.0%, 31.1% and 8.8% for plant-associated beneficial and environment (PBE), BCC, SBE and unclassified clade, respectively.}, }
@article {pmid31192354, year = {2019}, author = {Liu, Z and Chen, W and Jiao, S and Wang, X and Fan, M and Wang, E and Wei, G}, title = {New Insight into the Evolution of Symbiotic Genes in Black Locust-Associated Rhizobia.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1736-1750}, doi = {10.1093/gbe/evz116}, pmid = {31192354}, issn = {1759-6653}, abstract = {Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.}, }
@article {pmid31191571, year = {2019}, author = {Defrenne, CE and Philpott, TJ and Guichon, SHA and Roach, WJ and Pickles, BJ and Simard, SW}, title = {Shifts in Ectomycorrhizal Fungal Communities and Exploration Types Relate to the Environment and Fine-Root Traits Across Interior Douglas-Fir Forests of Western Canada.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {643}, doi = {10.3389/fpls.2019.00643}, pmid = {31191571}, issn = {1664-462X}, abstract = {Large-scale studies that examine the responses of ectomycorrhizal fungi across biogeographic gradients are necessary to assess their role in mediating current and predicted future alterations in forest ecosystem processes. We assessed the extent of environmental filtering on interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) ectomycorrhizal fungal communities across regional gradients in precipitation, temperature, and soil fertility in interior Douglas-fir dominated forests of western Canada. We also examined relationships between fine-root traits and mycorrhizal fungal exploration types by combining root and fungal trait measurements with next-generation sequencing. Temperature, precipitation, and soil C:N ratio affected fungal community dissimilarity and exploration type abundance but had no effect on α-diversity. Fungi with rhizomorphs (e.g., Piloderma sp.) or proteolytic abilities (e.g., Cortinarius sp.) dominated communities in warmer and less fertile environments. Ascomycetes (e.g., Cenococcum geophilum) or shorter distance explorers, which potentially cost the plant less C, were favored in colder/drier climates where soils were richer in total nitrogen. Environmental filtering of ectomycorrhizal fungal communities is potentially related to co-evolutionary history between Douglas-fir populations and fungal symbionts, suggesting success of interior Douglas-fir as climate changes may be dependent on maintaining strong associations with local communities of mycorrhizal fungi. No evidence for a link between root and fungal resource foraging strategies was found at the regional scale. This lack of evidence further supports the need for a mycorrhizal symbiosis framework that is independent of root trait frameworks, to aid in understanding belowground plant uptake strategies across environments.}, }
@article {pmid31191510, year = {2019}, author = {Habineza, P and Muhammad, A and Ji, T and Xiao, R and Yin, X and Hou, Y and Shi, Z}, title = {The Promoting Effect of Gut Microbiota on Growth and Development of Red Palm Weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera: Dryophthoridae) by Modulating Its Nutritional Metabolism.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1212}, doi = {10.3389/fmicb.2019.01212}, pmid = {31191510}, issn = {1664-302X}, abstract = {Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, is a destructive pest for palm trees worldwide. Recent studies have shown that RPW gut is colonized by microbes and alterations in gut microbiota can significantly modify its hemolymph nutrition content. However, the exact effects of gut microbiota on RPW phenotype and the underlying mechanisms remain elusive. Here germ-free (GF) RPW larvae were generated from dechorionated eggs which were reared on sterilized artificial food under axenic conditions. Compared with controls, the larval development of GF RPW individuals was markedly depressed and their body mass was reduced as well. Furthermore, the content of hemolymph protein, glucose and triglyceride were dropped significantly in GF RPW larvae. Interestingly, introducing gut microbiota into GF individuals could significantly increase the levels of the three nutrition indices. Additionally, it has also been demonstrated that RPW larvae monoassociated with Lactococcus lactis exhibited the same level of protein content with the CR (conventionally reared) insects while feeding Enterobacter cloacae to GF larvae increased their hemolymph triglyceride and glucose content markedly. Consequently, our findings suggest that gut microbiota profoundly affect the development of this pest by regulating its nutrition metabolism and different gut bacterial species show distinct impact on host physiology. Taken together, the establishment of GF and gnotobiotic RPW larvae will advance the elucidation of molecular mechanisms behind the interactions between RPW and its gut microbiota.}, }
@article {pmid31190278, year = {2019}, author = {Lee, SJ and Morse, D and Hijri, M}, title = {Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00903-4}, pmid = {31190278}, issn = {1432-1890}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of &quot;chronobiological individuals&quot; should include &quot;a holobiont&quot; rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.}, }
@article {pmid31189014, year = {2019}, author = {Guo, X and Zhao, Z and Mar, SS and Zhang, D and Saunders, RMK}, title = {A symbiotic balancing act: arbuscular mycorrhizal specificity and specialist fungus gnat pollination in the mycoheterotrophic genus Thismia (Thismiaceae).}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz087}, pmid = {31189014}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Mycorrhizal associations in mycoheterotrophic plants are generally more specialized than in autotrophs. Mycoheterotrophs typically bear small, inconspicuous flowers that often self-pollinate to maximize seed set, although some have structurally complex flowers indicative of xenogamy. A trade-off has previously been proposed between specialization in these above- and below-ground symbioses, although empirical data are lacking.<br><br>METHODS: We used next-generation DNA sequencing to compare the mycorrhizal communities from the roots of a mycoheterotrophic species, Thismia tentaculata (Thismiaceae), and its neighbouring autotrophs. We furthermore conducted detailed assessments of floral phenology and pollination ecology, and performed artificial pollination experiments to determine the breeding system.<br><br>KEY RESULTS: Thismia tentaculata maintains a symbiotic association with a single arbuscular mycorrhizal Rhizophagus species. The flowers are pollinated by a single species of fungus gnats (Corynoptera, Sciaridae), which are attracted by the yellow pigments and are temporarily restrained within the perianth chamber before departing via apertures between the anthers. The plants are self-compatible but predominantly xenogamous.<br><br>CONCLUSIONS: Our findings demonstrate that T. tentaculata maintains highly specialized associations with pollinators and mycorrhizal fungi, both of which are widely distributed. We suggest that specialization in multiple symbiotic interactions is possible in mycoheterotrophs if redundant selective pressures are not exerted to further restrict an already constrained suite of life-history traits.}, }
@article {pmid31186513, year = {2019}, author = {Gabay, Y and Parkinson, JE and Wilkinson, SP and Weis, VM and Davy, SK}, title = {Inter-partner specificity limits the acquisition of thermotolerant symbionts in a model cnidarian-dinoflagellate symbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0429-5}, pmid = {31186513}, issn = {1751-7370}, abstract = {The ability of corals and other cnidarians to survive climate change depends partly on the composition of their endosymbiont communities. The dinoflagellate family Symbiodiniaceae is genetically and physiologically diverse, and one proposed mechanism for cnidarians to acclimate to rising temperatures is to acquire more thermally tolerant symbionts. However, cnidarian-dinoflagellate associations vary in their degree of specificity, which may limit their capacity to alter symbiont communities. Here, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida (commonly referred to as 'Aiptasia'), a model system for the cnidarian-dinoflagellate symbiosis, with simultaneous or sequential mixtures of thermally tolerant and thermally sensitive species of Symbiodiniaceae. We then monitored symbiont success (relative proportional abundance) at normal and elevated temperatures across two to four weeks. All anemones showed signs of bleaching at high temperature. During simultaneous inoculations, the native, thermally sensitive Breviolum minutum colonized polyps most successfully regardless of temperature when paired against the non-native but more thermally tolerant Symbiodinium microadriaticum or Durusdinium trenchii. Furthermore, anemones initially colonized with B. minutum and subsequently exposed to S. microadriaticum failed to acquire the new symbiont. These results highlight how partner specificity may place strong limitations on the ability of certain cnidarians to acquire more thermally tolerant symbionts, and hence their adaptive potential under climate change.}, }
@article {pmid31186318, year = {2019}, author = {Chrostek, E and Gerth, M}, title = {Is Anopheles gambiae a Natural Host of Wolbachia?.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00784-19}, pmid = {31186318}, issn = {2150-7511}, abstract = {Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. Although Wolbachia is present in the majority of terrestrial arthropods, including many disease vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, revealing a high Wolbachia 16S rRNA sequence diversity, low abundance, and a lack of congruence between host and symbiont phylogenies. Here, we reanalyze and discuss recent evidence on the presence of Wolbachia sequences in A. gambiae. We find that although detected at increasing frequencies, the unusual properties of these Wolbachia sequences render them insufficient to diagnose natural infections in A. gambiae Future studies should focus on uncovering the origin of Wolbachia sequence variants in Anopheles and seeking sequence-independent evidence for this new symbiosis. Understanding the ecology of Anopheles mosquitos and their interactions with Wolbachia will be key in designing successful, integrative approaches to limit malaria spread. Although the prospect of using Wolbachia to fight malaria is intriguing, the newly discovered strains do not bring it closer to realization.IMPORTANCEAnopheles gambiae mosquitos are the main vectors of malaria, threatening around half of the world's population. The bacterial symbiont Wolbachia can interfere with disease transmission by other important insect vectors, but until recently, it was thought to be absent from natural A. gambiae populations. Here, we critically analyze the genomic, metagenomic, PCR, imaging, and phenotypic data presented in support of the presence of natural Wolbachia infections in A. gambiae We find that they are insufficient to diagnose Wolbachia infections and argue for the need of obtaining robust data confirming basic Wolbachia characteristics in this system. Determining the Wolbachia infection status of Anopheles is critical due to its potential to influence Anopheles population structure and Plasmodium transmission.}, }
@article {pmid31186308, year = {2019}, author = {Septer, AN}, title = {The Vibrio-Squid Symbiosis as a Model for Studying Interbacterial Competition.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00108-19}, pmid = {31186308}, issn = {2379-5077}, abstract = {The symbiosis between Euprymna scolopes squid and its bioluminescent bacterial symbiont, Vibrio fischeri, is a valuable model system to study a natural, coevolved host-microbe association. Over the past 30 years, researchers have developed and optimized many experimental methods to study both partners in isolation and during symbiosis. These powerful tools, along with a strong foundational knowledge about the system, position the Vibrio-squid symbiosis at the forefront of host-microbe interactions because this system is uniquely suited to investigation of symbiosis from both host and bacterial perspectives. Moreover, the ability to isolate and characterize different strains of V. fischeri has revealed exciting new insights about how different genotypes evolve to compete for a host niche, including deploying interbacterial weapons early during host colonization. This Perspective explores how interbacterial warfare influences the diversity and spatial structure of the symbiotic population, as well as the possible effects that intraspecific competition might have on the host.}, }
@article {pmid31184576, year = {2019}, author = {Gomes, DF and Tullio, LD and Del Cerro, P and Nakatani, AS and Rolla-Santos, AAP and Gil-Serrano, A and Megías, M and Ollero, FJ and Hungria, M}, title = {Regulation of hsnT, nodF and nodE genes in Rhizobium tropici CIAT 899 and their roles in the synthesis of Nod factors and in the symbiosis.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {9}, pages = {990-1000}, doi = {10.1099/mic.0.000824}, pmid = {31184576}, issn = {1465-2080}, abstract = {Rhizobium tropici strain CIAT 899 possesses outstanding agronomic properties as it displays tolerance to environmental stresses, a broad host range and high effectiveness in fixing nitrogen with the common bean (Phaseolus vulgaris L.); in addition, it carries intriguing features such as five copies of the regulatory nodD gene, and the capacity to synthesize a variety of nodulation factors (NFs), even in a flavonoid-independent manner, when submitted to abiotic stresses. However, the roles of several nod genes of the repertoire of CIAT 899 remain to be determined. In this study, we obtained mutants for the hsnT, nodF and nodE genes of CIAT 899 and investigated their expression, NF structures and symbiotic properties. Either in the presence of the flavonoid apigenin, or of salt the expression of hsnT, nodF and nodE in wild-type CIAT 899 was highly up-regulated in comparison to the mutants of all five copies of nodD, indicating the roles that regulatory nodD genes play in the activation of hsnT, nodF and nodE; however, NodD1 was recognized as the main inducer. In total, 29 different NF structures were synthesized by wild-type CIAT 899 induced by apigenin, and 36 when induced by salt, being drastically reduced by mutations in hsnT, nodF and nodE, especially under osmotic stress, with specific changes related to each gene, indicating that the three genes participate in the synthesis of NFs. Mutations in hsnT, nodF and nodE affected differently symbiotic performance (nodule number and shoot dry weight), according to the host plant. Our results indicate that the expression of hsnT, nodF and nodE genes of CIAT 899 is mediated by nodD genes, and although these three genes do not belong to the main set of genes controlling nodulation, they contribute to the synthesis of NFs that will impact symbiotic performance and host specificity.}, }
@article {pmid31182796, year = {2019}, author = {Gruber-Vodicka, HR and Leisch, N and Kleiner, M and Hinzke, T and Liebeke, M and McFall-Ngai, M and Hadfield, MG and Dubilier, N}, title = {Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2.}, journal = {Nature microbiology}, volume = {4}, number = {9}, pages = {1465-1474}, doi = {10.1038/s41564-019-0475-9}, pmid = {31182796}, issn = {2058-5276}, abstract = {Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans1,2. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host3-6. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)7,8 and has a genomic repertoire similar to that of rickettsial parasites9,10, but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations11-13. This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter.}, }
@article {pmid31182497, year = {2019}, author = {Lamouche, F and Chaumeret, A and Guefrachi, I and Barrière, Q and Pierre, O and Guérard, F and Gilard, F and Giraud, E and Dessaux, Y and Gakière, B and Timchenko, T and Kereszt, A and Mergaert, P and Alunni, B}, title = {From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant.}, journal = {Journal of bacteriology}, volume = {201}, number = {17}, pages = {}, doi = {10.1128/JB.00191-19}, pmid = {31182497}, issn = {1098-5530}, abstract = {Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.}, }
@article {pmid31182189, year = {2019}, author = {Strohm, E and Herzner, G and Ruther, J and Kaltenpoth, M and Engl, T}, title = {Nitric oxide radicals are emitted by wasp eggs to kill mold fungi.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43718}, pmid = {31182189}, issn = {2050-084X}, abstract = {Detrimental microbes caused the evolution of a great diversity of antimicrobial defenses in plants and animals. Insects developing underground seem particularly threatened. Here we show that the eggs of a solitary digger wasp, the European beewolf Philanthus triangulum, emit large amounts of gaseous nitric oxide (NO⋅) to protect themselves and their provisions, paralyzed honeybees, against mold fungi. We provide evidence that a NO-synthase (NOS) is involved in the generation of the extraordinary concentrations of nitrogen radicals in brood cells (~1500 ppm NO⋅ and its oxidation product NO2⋅). Sequencing of the beewolf NOS gene revealed no conspicuous differences to related species. However, due to alternative splicing, the NOS-mRNA in beewolf eggs lacks an exon near the regulatory domain. This preventive external application of high doses of NO⋅ by wasp eggs represents an evolutionary key innovation that adds a remarkable novel facet to the array of functions of the important biological effector NO⋅.}, }
@article {pmid31181739, year = {2019}, author = {Hao, Z and Xie, W and Chen, B}, title = {Arbuscular Mycorrhizal Symbiosis Affects Plant Immunity to Viral Infection and Accumulation.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/v11060534}, pmid = {31181739}, issn = {1999-4915}, support = {41571250//National Natural Science Foundation of China/ ; 2016YFC0500702//National Key Research and Development Program of China/ ; }, abstract = {Arbuscular mycorrhizal (AM) fungi, as root symbionts of most terrestrial plants, improve plant growth and fitness. In addition to the improved plant nutritional status, the physiological changes that trigger metabolic changes in the root via AM fungi can also increase the host ability to overcome biotic and abiotic stresses. Plant viruses are one of the important limiting factors for the commercial cultivation of various crops. The effect of AM fungi on viral infection is variable, and considerable attention is focused on shoot virus infection. This review provides an overview of the potential of AM fungi as bioprotection agents against viral diseases and emphasizes the complex nature of plant-fungus-virus interactions. Several mechanisms, including modulated plant tolerance, manipulation of induced systemic resistance (ISR), and altered vector pressure are involved in such interactions. We propose that using &quot;omics&quot; tools will provide detailed insights into the complex mechanisms underlying mycorrhizal-mediated plant immunity.}, }
@article {pmid31181676, year = {2019}, author = {Ho, YS}, title = {Comment to: Qi, Yi, et al. &quot;Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment&quot;, Int. J. Environ. Res. Public Health 2019, 16, 1077.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ijerph16112034}, pmid = {31181676}, issn = {1660-4601}, mesh = {Bibliometrics ; *Public Health ; Symbiosis ; *Waste Water ; }, abstract = {Qi et al. recently published an article in the journal, entitled &quot;Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment&quot; [...].}, }
@article {pmid31179246, year = {2019}, author = {Thapa, V and Roossinck, MJ}, title = {Determinants of Coinfection in the Mycoviruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {169}, doi = {10.3389/fcimb.2019.00169}, pmid = {31179246}, issn = {2235-2988}, }
@article {pmid31178314, year = {2019}, author = {Whiteside, MD and Werner, GDA and Caldas, VEA and Van't Padje, A and Dupin, SE and Elbers, B and Bakker, M and Wyatt, GAK and Klein, M and Hink, MA and Postma, M and Vaitla, B and Noë, R and Shimizu, TS and West, SA and Kiers, ET}, title = {Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {2043-2050.e8}, doi = {10.1016/j.cub.2019.04.061}, pmid = {31178314}, issn = {1879-0445}, abstract = {The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.}, }
@article {pmid31178238, year = {2019}, author = {Spagnoletti, FN and Chiocchio, VM}, title = {Tolerance of dark septate endophytic fungi (DSE) to agrochemicals in vitro.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2019.02.003}, pmid = {31178238}, issn = {0325-7541}, abstract = {Dark septate endophytes (DSE) are a heterogeneous group of fungi, mostly belonging to the Phylum Ascomycota, that are involved in a mutualistic symbiosis with plant roots. The aim of this study is to evaluate the behavior of two strains of DSE isolated from wheat roots of two cropping areas in the province of Buenos Aires, Argentina, against some agrochemicals. Of all the isolates obtained, two strains were identified as Alternaria alternata and Cochliobolus sp. These DSE were found to be tolerant to glyphosate, carbendazim and cypermethrin when evaluated at the recommended agronomic dose (AD), 2 AD and, in some cases, 10 AD. This work contributes to the study of the biology of this group of fungi and their tolerance in the presence of xenobiotics widely used in agriculture.}, }
@article {pmid31177643, year = {2019}, author = {Wang, S and Lu, T and Xue, Q and Xu, K and Cheng, G}, title = {Antioxidation and symbiotic nitrogen fixation function of prxA gene in Mesorhizobium huakuii.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e889}, doi = {10.1002/mbo3.889}, pmid = {31177643}, issn = {2045-8827}, support = {31772399//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; CZY18022//South-Central University for Nationalities/ ; }, abstract = {Peroxiredoxins (Prxs) play an essential role in the antioxidant activity and symbiotic capacity of Mesorhizobium huakuii. A mutation in the M. huakuii prxA gene (encoding a Prx5-like peroxiredoxin) was generated by homologous recombination. The mutation of prxA did not affect M. huakuii growth, but the strain displayed decreased antioxidative capacity under organic cumene hydroperoxide (CUOOH) conditions. The higher resistance of the prxA mutant strain compared with the wild-type strain to more than 1 mmol/L H2 O2 was associated with a significantly higher level of glutathione reductase activity and a significantly lower level of intracellular hydrogen peroxide content. Real-time quantitative PCR showed that under 1 mmol/L H2 O2 conditions, expression of the stress-responsive genes katG and katE was significantly upregulated in the prxA mutant. Although the prxA mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 53.25% reduction in nitrogen fixation capacity. This phenotype was linked to an absence of bacteroid differentiation and deregulation of the transcription of the symbiotic genes nifH, nifD, and fdxN. Expression of the prxA gene was induced during symbiosis. Thus, the PrxA protein is essential for antioxidant capacity and symbiotic nitrogen fixation, playing independent roles in bacterial differentiation and cellular antioxidative systems.}, }
@article {pmid31176943, year = {2019}, author = {Rempel, A and de Souza Sossella, F and Margarites, AC and Astolfi, AL and Steinmetz, RLR and Kunz, A and Treichel, H and Colla, LM}, title = {Bioethanol from Spirulina platensis biomass and the use of residuals to produce biomethane: An energy efficient approach.}, journal = {Bioresource technology}, volume = {288}, number = {}, pages = {121588}, doi = {10.1016/j.biortech.2019.121588}, pmid = {31176943}, issn = {1873-2976}, abstract = {This study aimed to produce bioethanol using Spirulina platensis biomass and the use of saccharification and fermentation wastes of bioethanol production to produce biomethane. The potential for energy generation in each technological route was quantified. Both, the enzymatic hydrolysis of the microalgae polysaccharides and the fermentation process, presented efficiencies above 80%. The fermentation of the hydrolyzate into ethanol was possible without the addition of synthetic nutrients to the must. The direct conversion of Spirulina biomass to biomethane had an energy potential of 16,770 kJ.kg-1, while bioethanol production from the hydrolysed biomass presented 4,664 kJ.kg-1. However, the sum of the energy potential obtained by producing bioethanol followed by the production of biomethane with the saccharification and fermentation residues was 13,945 kJ.kg-1. Despite this, the same raw material was able to produce both biofuels, demonstrating that Spirulina microalgae is a promising alternative to contribute in the field of renewable energies.}, }
@article {pmid31176662, year = {2019}, author = {Olivieri, E and Epis, S and Castelli, M and Varotto Boccazzi, I and Romeo, C and Desirò, A and Bazzocchi, C and Bandi, C and Sassera, D}, title = {Tissue tropism and metabolic pathways of Midichloria mitochondrii suggest tissue-specific functions in the symbiosis with Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {5}, pages = {1070-1077}, doi = {10.1016/j.ttbdis.2019.05.019}, pmid = {31176662}, issn = {1877-9603}, abstract = {A wide range of arthropod species harbour bacterial endosymbionts in various tissues, many of them playing important roles in the fitness and biology of their hosts. In several cases, many different symbionts have been reported to coexist simultaneously within the same host and synergistic or antagonistic interactions can occur between them. While the associations with endosymbiotic bacteria have been widely studied in many insect species, in ticks such interactions are less investigated. The females and immatures of Ixodes ricinus (Ixodidae), the most common hard tick in Europe, harbour the intracellular endosymbiont &quot;Candidatus Midichloria mitochondrii&quot; with a prevalence up to 100%, suggesting a mutualistic relationship. Considering that the tissue distribution of a symbiont might be indicative of its functional role in the physiology of the host, we investigated M. mitochondrii specific localization pattern and the corresponding abundance in selected organs of I. ricinus females. We paired these experiments with in silico analysis of the metabolic pathways of M. mitochondrii, inferred from the available genome sequence, and additionally compared the presence of these pathways in seven other symbionts commonly harboured by ticks to try to obtain a comparative understanding of their biological effects on the tick hosts. M. mitochondrii was found to be abundant in ovaries and tracheae of unfed I. ricinus, and in ovaries, Malpighian tubules and salivary glands of semi-engorged females. These results, together with the in silico metabolic reconstruction allow to hypothesize that the bacterium could play multiple tissue-specific roles in the host, both enhancing the host fitness (supplying essential nutrients, enhancing the reproductive fitness, helping in the anti-oxidative defence, in the energy production and in the maintenance of homeostasis and water balance) and/or for ensuring its presence in the host population (nutrients acquisition, vertical and horizontal transmission). The ability of M. mitochondrii to colonize different tissues allows to speculate that distinctive sub-populations may display different specializations in accordance with tissue tropism. Our hypotheses should be corroborated with future nutritional and physiological experiments for a better understanding of the mechanisms underlying this symbiotic interaction.}, }
@article {pmid31174466, year = {2019}, author = {Baião, GC and Schneider, DI and Miller, WJ and Klasson, L}, title = {The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {465}, doi = {10.1186/s12864-019-5816-9}, pmid = {31174466}, issn = {1471-2164}, support = {2014-4353//Vetenskapsrådet/ ; P28255-B22//Austrian Science Fund/ ; }, abstract = {BACKGROUND: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.<br><br>RESULTS: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.<br><br>CONCLUSIONS: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.}, }
@article {pmid31172251, year = {2019}, author = {Taboada, H and Dunn, MF and Meneses, N and Vargas-Lagunas, C and Buchs, N and Andrade-Domínguez, A and Encarnación, S}, title = {Qualitative changes in proteins contained in outer membrane vesicles produced by Rhizobium etli grown in the presence of the nod gene inducer naringenin.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-019-01682-4}, pmid = {31172251}, issn = {1432-072X}, support = {220790//CONACYT/ ; IN213216//DGAPA-PAPIIT-UNAM/ ; IN207519//DGAPA-PAPIIT-UNAM/ ; }, abstract = {In this work, we compared the proteomic profiles of outer membrane vesicles (OMVs) isolated from Rhizobium etli CE3 grown in minimal medium (MM) with and without exogenous naringenin. One-hundred and seven proteins were present only in OMVs from naringenin-containing cultures (N-OMVs), 57 proteins were unique to OMVs from control cultures lacking naringenin (C-OMVs) and 303 proteins were present in OMVs from both culture conditions (S-OMVs). Although we found no absolute predominance of specific types of proteins in the N-, C- or S-OMV classes, there were categories of proteins that were significantly less or more common in the different OMV categories. Proteins for energy production, translation and membrane and cell wall biogenesis were overrepresented in C-OMVs relative to N-OMVs. Proteins for carbohydrate metabolism and transport and those classified as either general function prediction only, function unknown, or without functional prediction were more common in N-OMVs than C-OMVs. This indicates that naringenin increased the proportion of these proteins in the OMVs, although NodD binding sites were only slightly more common in the promoters of genes for proteins found in the N-OMVs. In addition, OMVs from naringenin-containing cultures contained nodulation factor.}, }
@article {pmid31170026, year = {2019}, author = {Belin, BJ and Tookmanian, EM and de Anda, J and Wong, GCL and Newman, DK}, title = {Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI04190111R}, doi = {10.1094/MPMI-04-19-0111-R}, pmid = {31170026}, issn = {0894-0282}, abstract = {Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here, we demonstrate that the nitrogen-fixation defect conferred by extended hopanoid loss can be fully explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen-fixation levels. Using a single-nodule tracking approach to quantify A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and the presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.}, }
@article {pmid31167992, year = {2019}, author = {Ohbayashi, T and Itoh, H and Lachat, J and Kikuchi, Y and Mergaert, P}, title = {Burkholderia Gut Symbionts Associated with European and Japanese Populations of the Dock Bug Coreus marginatus (Coreoidea: Coreidae).}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {219-222}, doi = {10.1264/jsme2.ME19011}, pmid = {31167992}, issn = {1347-4405}, mesh = {Animals ; Burkholderia/classification/genetics/isolation &amp; purification/*physiology ; DNA, Bacterial/genetics ; Europe ; Female ; Gastrointestinal Tract/anatomy &amp; histology/microbiology ; Heteroptera/anatomy &amp; histology/*microbiology ; Japan ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Insects of the heteropteran superfamilies Coreoidea and Lygaeoidea are consistently associated with symbionts of a specific group of the genus Burkholderia, called the &quot;stinkbug-associated beneficial and environmental (SBE)&quot; group. The symbiosis is maintained by the environmental transmission of symbionts. We investigated European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae). High nymphal mortality in reared aposymbiotic insects suggested an obligate host-symbiont association in this species. Molecular phylogenetic analyses based on 16S rRNA gene sequences revealed that all 173 individuals investigated were colonized by Burkholderia, which were further assigned to different subgroups of the SBE in a region-dependent pattern.}, }
@article {pmid31166165, year = {2019}, author = {Jani, K and Feng, GD and Zhu, HH and Prakash, O and Bandal, J and Rale, V and Shouche, Y and Sharma, A}, title = {Chakrabartia godavariana gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Godavari River, India.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {8}, pages = {2452-2458}, doi = {10.1099/ijsem.0.003512}, pmid = {31166165}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; India ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; Spermidine/analogs &amp; derivatives/chemistry ; Sphingomonadaceae/*classification/isolation &amp; purification ; Ubiquinone/chemistry ; }, abstract = {A Gram-stain-negative, aerobic, yellow-pigmented, oxidase-positive and rod-shaped bacterium, designated PRB40T, was isolated from the Godavari River in India during the course of 'Kumbh Mela', the world's largest mass gathering event. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRB40T formed a lineage within the family Sphingomonadaceae and was distinct from the most closely related genera Sphingorhabdus, Novosphingobiumand Sphingomonas with sequence similarity values ≤95.2 %. Growth of strain PRB40T occurred at 10-40 °C (optimum 30 °C), at pH 6.0-9.0 (pH 7.0) and with 0-0.5 % (w/v) NaCl concentration (0 %). The major respiratory quinone was ubiquinone-10 (Q-10). It contained C17 : 1ω6c, C14 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids. The predominant polar lipids were phospholipid, phosphatidylethanolamine and sphingoglycolipid. It took sym-homospermidine as the major polyamine. The DNA G+C content based on its draft genome sequence was 63.7 mol%. The polyphasic taxonomic analyses indicated that strain PRB40T represents a novel species of a novel genus within the family Sphingomonadaceae, for which the name Chakrabartia godavariana gen. nov., sp. nov. is proposed. The type strain of Chakrabartia godavariana is PRB40T (=MCC 3406T=GDMCC 1.1197T=KCTC 52678T=LMG 29985T).}, }
@article {pmid31166074, year = {2019}, author = {Guerrieri, A and Dong, L and Bouwmeester, HJ}, title = {Role and exploitation of underground chemical signaling in plants.}, journal = {Pest management science}, volume = {75}, number = {9}, pages = {2455-2463}, doi = {10.1002/ps.5507}, pmid = {31166074}, issn = {1526-4998}, support = {670211//H2020 European Research Council/ ; 793795//H2020 Marie Skłodowska-Curie Actions/ ; //Europen Research Council (ERC)/ ; }, abstract = {The soil ecosystem is composed of a mixture of living organisms and non-living matter as well as the complex interactions between them. In the past 100 years or so, agricultural soil ecosystems have been strongly affected by agricultural practices such as tillage and the use of pesticides and fertilizers, which strongly affect soil nutrient composition, pH and biodiversity. In modern pest management, however, the focus is gradually shifting from crop production through agricultural practices to soil ecosystem protection. In this review we discuss how the underground chemical signals secreted by plant roots play a role in keeping the soil ecosystem in balance and how they affect plant fitness by shaping the root biome, increasing nutrient availability, promoting symbiosis, and attracting beneficial organisms and repelling harmful ones, including other plants. We review a number of fascinating cases, such as signaling molecules with dual, positive and negative, functions and bacterial quorum sensing mimicking molecules. Finally, examples of how these compounds can be exploited in modern pest management are reviewed, and the prospects for future developments discussed. © 2019 The Authors. Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid31165947, year = {2019}, author = {Sakamoto, K and Ogiwara, N and Kaji, T and Sugimoto, Y and Ueno, M and Sonoda, M and Matsui, A and Ishida, J and Tanaka, M and Totoki, Y and Shinozaki, K and Seki, M}, title = {Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis.}, journal = {Journal of plant research}, volume = {132}, number = {4}, pages = {541-568}, doi = {10.1007/s10265-019-01117-7}, pmid = {31165947}, issn = {1618-0860}, support = {23380042//Japan Society for the Promotion of Science/ ; }, mesh = {Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant ; Mycorrhizae/*metabolism ; Oligonucleotide Array Sequence Analysis ; Plant Roots/*metabolism/microbiology ; Rhizobium/*metabolism ; Root Nodules, Plant/metabolism/microbiology ; Soybeans/genetics/*metabolism ; Symbiosis ; }, abstract = {Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial-AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.}, }
@article {pmid31164991, year = {2019}, author = {Oishi, S and Moriyama, M and Koga, R and Fukatsu, T}, title = {Morphogenesis and development of midgut symbiotic organ of the stinkbug Plautia stali (Hemiptera: Pentatomidae).}, journal = {Zoological letters}, volume = {5}, number = {}, pages = {16}, doi = {10.1186/s40851-019-0134-2}, pmid = {31164991}, issn = {2056-306X}, abstract = {Diverse insects are intimately associated with microbial symbionts, which play a variety of biological roles in their adaptation to and survival in the natural environment. Such insects often possess specialized organs for hosting the microbial symbionts. What developmental processes and mechanisms underlie the formation of the host organs for microbial symbiosis is of fundamental biological interest but poorly understood. Here we investigate the morphogenesis of the midgut symbiotic organ and the process of symbiont colonization therein during the developmental course of the stinkbug Plautia stali. Upon hatching, the midgut is a simple and smooth tube. Subsequently, symbiont colonization to the posterior midgut occurs, and thickening and folding of the midgut epithelium proceed during the first instar period. By the second instar, rudimentary crypts have formed, and their inner cavities are colonized by the symbiotic bacteria. From the second instar to the fourth instar, while the alimentary tract grows and the posterior midgut is established as the symbiotic organ with numerous crypts, the anterior midgut and the posterior midgut are structurally and functionally isolated by a strong constriction in the middle. By the early fifth instar, the midgut symbiotic organ attains the maximal length, but toward the mid fifth instar, the basal region of each crypt starts to constrict and narrow, which deforms the midgut symbiotic organ as a whole into a shorter, thicker and twisted shape. By the late fifth instar to adulthood, the crypts are constricted off, by which the symbiotic bacteria are confined in the crypt cavities and isolated from the midgut main tract, and concurrently, the strong midgut constriction in the middle becomes loose and open, by which the food flow from the anterior midgut to the posterior midgut recovers. This study provides the most detailed and comprehensive descriptions ever reported on the morphogenesis of the symbiotic organ and the process of symbiont colonization in an obligatory insect-bacterium gut symbiotic system. Considering that P. stali is recently emerging as a useful model system for experimentally studying the intimate insect-microbe gut symbiosis, the knowledge obtained in this study establishes the foundation for the further development of this research field.}, }
@article {pmid31163164, year = {2019}, author = {Havird, JC and Forsythe, ES and Williams, AM and Werren, JH and Dowling, DK and Sloan, DB}, title = {Selfish Mitonuclear Conflict.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R496-R511}, doi = {10.1016/j.cub.2019.03.020}, pmid = {31163164}, issn = {1879-0445}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; }, abstract = {Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.}, }
@article {pmid31162896, year = {2019}, author = {Polienko, AK}, title = {[Peculiarities morphology and structure of the uroliths].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {2}, pages = {21-25}, pmid = {31162896}, issn = {1728-2985}, mesh = {Humans ; Microscopy/*methods ; Minerals/*analysis ; Urinary Calculi/*chemistry/*diagnostic imaging/ultrastructure ; }, abstract = {THE AIM: According to statistical data of a number of the countries, have an urolithic disease from 5% to 15% of the population today. A recurrence arises at 50-85% of patients. The purpose of this work was complex studying of morphology, structure, mineral structure of urolit, identification of regularities of their formation, establishment of interrelation between mineral and organic matter in structure of urolit.<br><br>MATERIALS: the urinary stones from the urology departments of hospitals and clinics of the Tomsk region (Russia).<br><br>METHOD: s: crystallomorphological (the study of the surface morphology of uroliths binocular and trinocular microscopes); polarizing optical (study of the mineral composition of uroliths on a polarizing microscope); x-ray crystallography (the study of spectral composition on the apparatus DRON-3); electron microscopic (study of the peculiarities of morphology of crystals in an electron microscope).<br><br>RESULTS: On features of morphology of a surface four types of urolit are allocated: druzovidny, sferolitovy, combined, korallovidny. Structural kinds of urolit: crystal and granular, dendritovidny, combined, rhythmic - zone. In structure of urolit the following types of rhythms are established: zone, granular, combined. In the urolitakh with rhythmic - the zone structure allocated elements of their building: kernel, layer, zone, rhythm. A mineral part of uric stones is presented by the crystals belonging to the classes: oxalates, phosphates, urat .<br><br>SUMMARY: The peculiarities of the morphology of the selected four types of uroliths: druzoid, with, combined, coral. Structural variations uroliths: crystal-grained Shelly, dendritic, combined, rhythmically zoned. In the structure of uroliths, the following types of rhythms: zoned, granular, combined. In urolith with rhythmically zoned structure selected elements of their structure: core, layer, area, rhythm.<br><br>DISCUSSION: Morphological and structural features of the structure of urolites, especially the presence of rhythmic zoning, due to the alternation of layers of mineral and organic matter, indicate a close relationship between the living organism and the organo-mineral aggregate in the human urinary system. With a high degree of confidence we can talk about the symbiosis of living and mineral matter in the human body; as a result of this symbiosis, organic-mineral formations are formed, which are often the further cause of some diseases (for example, urolithiasis and cholelithiasis).<br><br>CONCLUSION: The complex research of uric stones allows to obtain important information on their structure, structure and features of morphology. Morphological and structural features of the structure of urolit, in particular existence of the rhythmic zonality caused by alternation of layers of mineral and organic matter demonstrate close interrelation between a live organism and the organo-mineral unit in an urinary system of the person.}, }
@article {pmid31162893, year = {2019}, author = {Shchuplova, EA and Kuzmin, MD}, title = {[The additional criterion for the diagnosis of purulent-destructive forms of acute pyelonephritis].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {2}, pages = {5-8}, pmid = {31162893}, issn = {1728-2985}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*isolation &amp; purification ; Coinfection/*diagnosis/microbiology ; DNA Probes ; Humans ; In Situ Hybridization, Fluorescence ; Middle Aged ; Pyelonephritis/*diagnosis/*microbiology ; Suppuration/diagnosis ; Young Adult ; }, abstract = {AIM: to develop an additional criterion for objective diagnosis of purulent-destructive forms of acute pyelonephritis.<br><br>MATERIALS AND METHODS: A total of 35 blood samples from patients with acute pyelonephritis aged from 19 to 85 years (mean age was 52 years) were studied. For the analysis, a classical bacteriological method of isolating blood culture and a modern molecular genetic method of fluorescent in situ hybridization (FISH) using DNA probes complementary to species-specific regions of the 16S rRNA gene of microorganisms were used. The obtained results were processed using the Statistica 6.0 program.<br><br>RESULTS: The bacteriological study showed that only in one patient (2.9%) a blood culture was positive, whereas with FISH, polymicrobial infection consisting of two associates was observed in five patients (14.3%), and 207 specific luminescence from different DNA probes were detected in blood samples. The associations of members of the Enterobacteriaceae with S. aureus were 2.4 times more frequent than associations of the Enterobacteriaceae with S. epidermidis, indicating a development of the polymicrobial infection and, accordingly, the development of purulent stage of acute pyelonephritis.<br><br>CONCLUSION: For the diagnosis of acute pyelonephritis, we suggest to use an additional criterion, which consists in applying of FISH method for the detection and simultaneous identification of bacteria that were adhered on the surface of erythrocytes and located intracellularly. This method may allow for the differential diagnosis of serous and purulent stages of acute pyelonephritis.}, }
@article {pmid31161314, year = {2019}, author = {Prasad, S and Pandey, U and Saini, J and Ingalhalikar, M and Pal, PK}, title = {Atrophy of cerebellar peduncles in essential tremor: a machine learning-based volumetric analysis.}, journal = {European radiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00330-019-06269-7}, pmid = {31161314}, issn = {1432-1084}, support = {ECR/2016/000808//Science and Engineering Research Board/ ; }, abstract = {BACKGROUND: Subtle cerebellar signs are frequently observed in essential tremor (ET) and may be associated with cerebellar dysfunction. This study aims to evaluate the macrostructural integrity of the superior, middle, and inferior cerebellar peduncles (SCP, MCP, ICP) and cerebellar gray and white matter (GM, WM) volumes in patients with ET, and compare these volumes between patients with and without cerebellar signs (ETc and ETnc).<br><br>METHODS: Forty patients with ET and 37 age- and gender-matched healthy controls were recruited. Atlas-based region-of-interest analysis of the SCP, MCP, and ICP and automated analysis of cerebellar GM and WM volumes were performed. Peduncular volumes were employed in a multi-variate classification framework to attempt discrimination of ET from controls.<br><br>RESULTS: Significant atrophy of bilateral MCP and ICP and bilateral cerebellar GM was observed in ET. Cerebellar signs were present in 20% of subjects with ET. Comparison of peduncular and cerebellar volumes between ETnc and ETc revealed atrophy of right SCP, bilateral MCP and ICP, and left cerebellar WM in ETc. The multi-variate classifier could discriminate between ET and controls with a test accuracy of 86.66%.<br><br>CONCLUSIONS: Patients with ET have significant atrophy of cerebellar peduncles, particularly the MCP and ICP. Additional atrophy of the SCP is observed in the ETc group. These abnormalities may contribute to the pathogenesis of cerebellar signs in ET.<br><br>KEY POINTS: • Patients with ET have significant atrophy of bilateral middle and inferior cerebellar peduncles and cerebellar gray matter in comparison with healthy controls. • Patients of ET with cerebellar signs have significant atrophy of right superior cerebellar peduncle, bilateral middle and inferior cerebellar peduncle, and left cerebellar white matter in comparison with ET without cerebellar signs. • A multi-variate classifier employing peduncular volumes could discriminate between ET and controls with a test accuracy of 86.66%.}, }
@article {pmid31161283, year = {2019}, author = {Mu, X and Luo, J}, title = {Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-019-03164-8}, pmid = {31161283}, issn = {1420-9071}, support = {2662017QD001//Fundamental Research Funds for the Central Universities/ ; 2017CFB338//Hubei Province Natural Science Foundation of China/ ; 30500487//Research Start-up Fund for Henan Agricultural Universities/ ; }, abstract = {Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.}, }
@article {pmid31160787, year = {2019}, author = {Klimovich, A and Wittlieb, J and Bosch, TCG}, title = {Transgenesis in Hydra to characterize gene function and visualize cell behavior.}, journal = {Nature protocols}, volume = {14}, number = {7}, pages = {2069-2090}, doi = {10.1038/s41596-019-0173-3}, pmid = {31160787}, issn = {1750-2799}, abstract = {The freshwater polyp Hydra is a cnidarian used as a model organism in a number of fields, including the study of the origin and evolution of developmental mechanisms, aging, symbiosis and host-microbe interactions. Here, we describe a procedure for the establishment of stable transgenic Hydra lines by embryo microinjection. The three-stage protocol comprises (i) the design and preparation of a transgenic construct, (ii) the microinjection of the vector into early embryos of Hydra vulgaris, and (iii) the selection and enrichment of mosaic animals in order to develop uniformly transgenic clonal lines. The preparation of a transgenic construct requires ~2 weeks, and transgenic lines can be obtained within 3 months. The method allows constitutive or inducible gain- and loss-of-function approaches, as well as in vivo tracing of individual cells. Hydra polyps carrying transgenic cells reveal functional properties of the ancestral circuitry controlling animal development.}, }
@article {pmid31159921, year = {2019}, author = {Hambleton, EA and Jones, VAS and Maegele, I and Kvaskoff, D and Sachsenheimer, T and Guse, A}, title = {Sterol transfer by atypical cholesterol-binding NPC2 proteins in coral-algal symbiosis.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43923}, pmid = {31159921}, issn = {2050-084X}, support = {GU 1128/3-1//Deutsche Forschungsgemeinschaft/ ; FP7-PEOPLE-2013-CIG//European Commission/ ; 724715//Horizon 2020 Framework Programme/ ; Exploration Grant//Boehringer Ingelheim Stiftung/ ; LTF//European Molecular Biology Organization/ ; Excellence Initiative//Universität Heidelberg/ ; TRR83//Deutsche Forschungsgemeinschaft/ ; SFB1324//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Reef-building corals depend on intracellular dinoflagellate symbionts that provide nutrients. Besides sugars, the transfer of sterols is essential for corals and other sterol-auxotrophic cnidarians. Sterols are important cell components, and variants of the conserved Niemann-Pick Type C2 (NPC2) sterol transporter are vastly up-regulated in symbiotic cnidarians. Types and proportions of transferred sterols and the mechanism of their transfer, however, remain unknown. Using different pairings of symbiont strains with lines of Aiptasia anemones or Acropora corals, we observe both symbiont- and host-driven patterns of sterol transfer, revealing plasticity of sterol use and functional substitution. We propose that sterol transfer is mediated by the symbiosis-specific, non-canonical NPC2 proteins, which gradually accumulate in the symbiosome. Our data suggest that non-canonical NPCs are adapted to the symbiosome environment, including low pH, and play an important role in allowing corals to dominate nutrient-poor shallow tropical seas worldwide.}, }
@article {pmid31159445, year = {2019}, author = {Shen, G and Ju, W and Liu, Y and Guo, X and Zhao, W and Fang, L}, title = {Impact of Urea Addition and Rhizobium Inoculation on Plant Resistance in Metal Contaminated Soil.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ijerph16111955}, pmid = {31159445}, issn = {1660-4601}, abstract = {Legume-rhizobium symbiosis has been heavily investigated for their potential to enhance plant metal resistance in contaminated soil. However, the extent to which plant resistance is associated with the nitrogen (N) supply in symbiont is still uncertain. This study investigates the effect of urea or/and rhizobium (Sinorhizobium meliloti) application on the growth of Medicago sativa and resistance in metals contaminated soil (mainly with Cu). The results show that Cu uptake in plant shoots increased by 41.7%, 69%, and 89.3% with urea treatment, rhizobium inoculation, and their combined treatment, respectively, compared to the control group level. In plant roots, the corresponding values were 1.9-, 1.7-, and 1.5-fold higher than the control group values, respectively. Statistical analysis identified that N content was the dominant variable contributing to Cu uptake in plants. Additionally, a negative correlation was observed between plant oxidative stress and N content, indicating that N plays a key role in plant resistance. Oxidative damage decreased after rhizobium inoculation as the activities of antioxidant enzymes (catalase and superoxide dismutase in roots and peroxidase in plant shoots) were stimulated, enhancing plant resistance and promoting plant growth. Our results suggest that individual rhizobium inoculation, without urea treatment, is the most recommended approach for effective phytoremediation of contaminated land.}, }
@article {pmid31158486, year = {2019}, author = {Titus, BM and Benedict, C and Laroche, R and Gusmão, LC and Van Deusen, V and Chiodo, T and Meyer, CP and Berumen, ML and Bartholomew, A and Yanagi, K and Reimer, JD and Fujii, T and Daly, M and Rodríguez, E}, title = {Phylogenetic relationships among the clownfish-hosting sea anemones.}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106526}, doi = {10.1016/j.ympev.2019.106526}, pmid = {31158486}, issn = {1095-9513}, abstract = {The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test (1) the monophyly of each clownfish-hosting family and genus, (2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and (3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly- and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Stichodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.}, }
@article {pmid31156674, year = {2019}, author = {Gómez-Gallego, T and Benabdellah, K and Merlos, MA and Jiménez-Jiménez, AM and Alcon, C and Berthomieu, P and Ferrol, N}, title = {The Rhizophagus irregularis Genome Encodes Two CTR Copper Transporters That Mediate Cu Import Into the Cytosol and a CTR-Like Protein Likely Involved in Copper Tolerance.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {604}, doi = {10.3389/fpls.2019.00604}, pmid = {31156674}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi increase fitness of their host plants under Cu deficient and toxic conditions. In this study, we have characterized two Cu transporters of the CTR family (RiCTR1 and RiCTR2) and a CTR-like protein (RiCTR3A) of Rhizophagus irregularis. Functional analyses in yeast revealed that RiCTR1 encodes a plasma membrane Cu transporter, RiCTR2 a vacuolar Cu transporter and RiCTR3A a plasma membrane protein involved in Cu tolerance. RiCTR1 was more highly expressed in the extraradical mycelia (ERM) and RiCTR2 in the intraradical mycelia (IRM). In the ERM, RiCTR1 expression was up-regulated by Cu deficiency and down-regulated by Cu toxicity. RiCTR2 expression increased only in the ERM grown under severe Cu-deficient conditions. These data suggest that RiCTR1 is involved in Cu uptake by the ERM and RiCTR2 in mobilization of vacuolar Cu stores. Cu deficiency decreased mycorrhizal colonization and arbuscule frequency, but increased RiCTR1 and RiCTR2 expression in the IRM, which suggest that the IRM has a high Cu demand. The two alternatively spliced products of RiCTR3, RiCTR3A and RiCTR3B, were more highly expressed in the ERM. Up-regulation of RiCTR3A by Cu toxicity and the yeast complementation assays suggest that RiCTR3A might function as a Cu receptor involved in Cu tolerance.}, }
@article {pmid31156662, year = {2019}, author = {Pucciariello, C and Boscari, A and Tagliani, A and Brouquisse, R and Perata, P}, title = {Exploring Legume-Rhizobia Symbiotic Models for Waterlogging Tolerance.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {578}, doi = {10.3389/fpls.2019.00578}, pmid = {31156662}, issn = {1664-462X}, abstract = {Unexpected and increasingly frequent extreme precipitation events result in soil flooding or waterlogging. Legumes have the capacity to establish a symbiotic relationship with endosymbiotic atmospheric dinitrogen-fixing rhizobia, thus contributing to natural nitrogen soil enrichment and reducing the need for chemical fertilization. The impact of waterlogging on nitrogen fixation and legume productivity needs to be considered for crop improvement. This review focuses on the legumes-rhizobia symbiotic models. We aim to summarize the mechanisms underlying symbiosis establishment, nodule development and functioning under waterlogging. The mechanisms of oxygen sensing of the host plant and symbiotic partner are considered in view of recent scientific advances.}, }
@article {pmid31156660, year = {2019}, author = {von Sivers, L and Jaspar, H and Johst, B and Roese, M and Bitterlich, M and Franken, P and Kühn, C}, title = {Brassinosteroids Affect the Symbiosis Between the AM Fungus Rhizoglomus irregularis and Solanaceous Host Plants.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {571}, doi = {10.3389/fpls.2019.00571}, pmid = {31156660}, issn = {1664-462X}, abstract = {Together with several proteins involved in brassinosteroid (BR) signaling and synthesis, the membrane steroid binding protein 1 (MSBP1) was identified within the interactome of the sucrose transporter of tomato (SlSUT2). We asked whether MSBP1 is also involved in BR signaling as assumed for the AtMSBP1 protein from Arabidopsis and whether it impacts root colonization with arbuscular mycorrhizal (AM) fungi in a similar way as shown previously for SlSUT2. In addition, we asked whether brassinosteroids per se affect efficiency of root colonization by AM fungi. We carried out a set of experiments with transgenic tobacco plants with increased and decreased MSBP1 expression levels. We investigated the plant and the mycorrhizal phenotype of these transgenic plants and tested the involvement of MSBP1 in BR metabolism by application of epi-brassinolide and brassinazole, an inhibitor of BR biosynthesis. We show that the phenotype of the transgenic tobacco plants with increased or reduced MSBP1 expression is consistent with an inhibitory role of MSBP1 in BR signaling. MSBP1 overexpression could be mimicked by brassinazole treatment. Interestingly, manipulation of MSBP1 expression in transgenic tobacco plants not only affected plant growth and development, but also the host plant responses toward colonization with AM fungi, as well as arbuscular architecture. Moreover, we observed that brassinosteroids indeed have a direct impact on the nutrient exchange in AM symbiosis and on the biomass production of colonized host plants. Furthermore, arbuscular morphology is affected by changes in MSBP1 expression and brassinolide or brassinazole treatments. We conclude that host plant growth responses and nutrient exchange within the symbiosis with AM fungi is controlled by brassinosteroids and might be impeded by the MSBP1 protein.}, }
@article {pmid31156595, year = {2019}, author = {Bertolazi, AA and de Souza, SB and Ruas, KF and Campostrini, E and de Rezende, CE and Cruz, C and Melo, J and Colodete, CM and Varma, A and Ramos, AC}, title = {Inoculation With Piriformospora indica Is More Efficient in Wild-Type Rice Than in Transgenic Rice Over-Expressing the Vacuolar H+-PPase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1087}, doi = {10.3389/fmicb.2019.01087}, pmid = {31156595}, issn = {1664-302X}, abstract = {Achieving food security in a context of environmental sustainability is one of the main challenges of the XXI century. Two competing strategies to achieve this goal are the use of genetically modified plants and the use of plant growth promoting microorganisms (PGPMs). However, few studies assess the response of genetically modified plants to PGPMs. The aim of this study was to compare the response of over-expressing the vacuolar H+-PPase (AVP) and wild-type rice types to the endophytic fungus; Piriformospora indica. Oryza sativa plants (WT and AVP) were inoculated with P. indica and 30 days later, morphological, ecophysiological and bioenergetic parameters, and nutrient content were assessed. AVP and WT plant heights were strongly influenced by inoculation with P. indica, which also promoted increases in fresh and dry matter of shoot in both genotypes. This may be related with the stimulatory effect of P. indica on ecophysiological parameters, especially photosynthetic rate, stomatal conductance, intrinsic water use efficiency and carboxylation efficiency. However, there were differences between the genotypes concerning the physiological mechanisms leading to biomass increment. In WT plants, inoculation with P. indica stimulated all H+ pumps. However, in inoculated AVP plants, H+-PPase was stimulated, but P- and V-ATPases were inhibited. Fungal inoculation enhanced nutrient uptake in both shoots and roots of WT and AVP plants, compared to uninoculated plants; but among inoculated genotypes, the nutrient uptake was lower in AVP than in WT plants. These results clearly demonstrate that the symbiosis between P. indica and AVP plants did not benefit those plants, which may be related to the inefficient colonization of this fungus on the transgenic plants, demonstrating an incompatibility of this symbiosis, which needs to be further studied.}, }
@article {pmid31153721, year = {2019}, author = {Sobotková, K and Parker, W and Levá, J and Růžková, J and Lukeš, J and Jirků Pomajbíková, K}, title = {Helminth Therapy - From the Parasite Perspective.}, journal = {Trends in parasitology}, volume = {35}, number = {7}, pages = {501-515}, doi = {10.1016/j.pt.2019.04.009}, pmid = {31153721}, issn = {1471-5007}, abstract = {Studies in animal models and humans suggest that intentional exposure to helminths or helminth-derived products may hold promise for treating chronic inflammatory-associated diseases (CIADs). Although the mechanisms underlying 'helminth therapy' are being evaluated, little attention has been paid to the actual organisms in use. Here we examine the notion that, because of the complexity of biological symbiosis, intact helminths rather than helminth-derived products are likely to prove more useful for clinical purposes. Further, weighing potential cost/benefit ratios of various helminths along with other factors, such as feasibility of production, we argue that the four helminths currently in use for CIAD treatments in humans were selected more by happenstance than by design, and that other candidates not yet tested may prove superior.}, }
@article {pmid31152905, year = {2019}, author = {Rostami, M and Rostami, S}, title = {Effect of salicylic acid and mycorrhizal symbiosis on improvement of fluoranthene phytoremediation using tall fescue (Festuca arundinacea Schreb).}, journal = {Chemosphere}, volume = {232}, number = {}, pages = {70-75}, doi = {10.1016/j.chemosphere.2019.05.171}, pmid = {31152905}, issn = {1879-1298}, mesh = {*Biodegradation, Environmental ; Biomass ; Festuca/*metabolism/microbiology ; Fluorenes ; Mycorrhizae/*physiology ; Plant Growth Regulators ; Plant Roots/growth &amp; development ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Salicylic Acid/*metabolism ; Soil ; Soil Microbiology ; Soil Pollutants/*metabolism ; Symbiosis ; }, abstract = {Polycyclic aromatic hydrocarbons are an important group of pollutants that are widely distributed in the environment. The present study aimed to investigate the effect of salicylic acid (a phenolic phytohormone) and mycorrhizal fungi on the growth and phytoremediation ability of tall fescue in the soil contaminated by fluoranthene. The initial concentrations of fluoranthene in this study were 100, 200, and 300 mg kg-1. The experimental treatments were included: T0 uncultivated soil; T1 cultivated soil with tall fescue; T2 cultivated soil with tall fescue + salicylic acid application; T3 cultivated soil with tall fescue + application of mycorrhizal fungi; T4 cultivated soil with tall fescue + salicylic acid and mycorrhizal fungi application; and P planting tall fescue in uncontaminated soil. The removal of fluoranthene was measured after 90 days. Furthermore, at the end of the experiment, the amount of shoot and root biomass, soil bacteria, and dehydrogenase activity were measured. According to the results, in all levels of contamination, removal of fluoranthene in cultivated treatments significantly was higher than uncultivated treatments. Increasing the concentration of fluoranthene had a negative effect on the shoot and root biomass in different treatments. Salicylic acid and mycorrhizal fungi significantly increased the shoot and root biomass and also the number of soil bacteria, dehydrogenase activity, and fluoranthene removal in T2, T3, and T4 treatments compared to T1. At the highest concentration of fluoranthene, as a result of simultaneous application of salicylic acid and mycorrhizal fungi (T4), the fluoranthene removal increased by 63, 21, 13, and 16% in comparison with T0, T1, T2, and T3, respectively. Based on the results, salicylic acid and mycorrhizal fungi, either alone or in combination, have a significant effect on the improvement of phytoremediation potential in tall fescue.}, }
@article {pmid31152194, year = {2019}, author = {Ghorbani, A and Omran, VOG and Razavi, SM and Pirdashti, H and Ranjbar, M}, title = {Piriformospora indica confers salinity tolerance on tomato (Lycopersicon esculentum Mill.) through amelioration of nutrient accumulation, K+/Na+ homeostasis and water status.}, journal = {Plant cell reports}, volume = {38}, number = {9}, pages = {1151-1163}, doi = {10.1007/s00299-019-02434-w}, pmid = {31152194}, issn = {1432-203X}, mesh = {Basidiomycota/*physiology ; Homeostasis ; Lycopersicon esculentum/genetics/*microbiology/physiology ; Nutrients/*metabolism ; Potassium/*metabolism ; Salinity ; Salt Tolerance ; Sodium/*metabolism ; Stress, Physiological ; Symbiosis ; Water/*metabolism ; }, abstract = {KEY MESSAGE: Piriformospora indica confers salt tolerance in tomato seedlings by increasing the uptake of nutrients such as N, P and Ca, improving K+/Na+ homoeostasis by regulating the expression of NHXs, SOS1 and CNGC15 genes, maintaining water status by regulating the expression of aquaporins. Piriformospora indica, an endophytic basidiomycete, has been shown to increase the growth and improve the plants tolerance to stressful conditions, especially salinity, by establishing the arbuscular mycorrhiza-like symbiotic relationship in various plant hosts. In the present research, the effect of NaCl treatment (150 mM) and P. indica inoculation on growth, accumulation of nutrients, the transcription level of genes involved in ionic homeostasis (NHXs, SOS1 and CNGC15) and regulating water status (PIP1;2, PIP2;4, TIP1;1 and TIP2;2) in roots and leaves of tomato seedlings were investigated. The P. indica improved the uptake of N, P, Ca and K, and reduced Na accumulation, and had no significant effect on Cl accumulation in roots and leaves. The endophytic fungus also increased in K+/Na+ ratio in roots and leaves of tomato by regulating the expression of NHX isoforms and upregulating SOS1 and CNGC15 expression. Salinity stress increased the transcription of PIP2;4 gene and reduced the transcription of PIP1;2, TIP1;1 and TIP2;2 genes compared to the control treatment. However, P. indica inoculation upregulated the expression of PIP1;2 and PIP2;4 genes versus non-inoculated plants but did not have a significant effect on TIP1;1 and TIP2;2 expression. These results conclude that the positive effects of P. indica on nutrients accumulation, ionic homeostasis and water status lead to the increased salinity tolerance and the improved plant growth under NaCl treatment.}, }
@article {pmid31152017, year = {2019}, author = {Pesce, C and Oshone, R and Hurst, SG and Kleiner, VA and Tisa, LS}, title = {Stable Transformation of the Actinobacteria Frankia spp.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, doi = {10.1128/AEM.00957-19}, pmid = {31152017}, issn = {1098-5336}, abstract = {A stable and efficient plasmid transfer system was developed for nitrogen-fixing symbiotic actinobacteria of the genus Frankia, a key first step in developing a genetic system. Four derivatives of the broad-host-range cloning vector pBBR1MCS were successfully introduced into different Frankia strains by a filter mating with Escherichia coli strain BW29427. Initially, plasmid pHKT1 that expresses green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 × 10-3, resulting in transformants that were tetracycline resistant and exhibited GFP fluorescence. The presence of the plasmid was confirmed by molecular approaches, including visualization on agarose gel and PCR. Several other pBBR1MCS plasmids were also introduced into F. casuarinae strain CcI3 and other Frankia strains at frequencies ranging from 10-2 to 10-4, and the presence of the plasmids was confirmed by PCR. The plasmids were stably maintained for over 2 years and through passage in a plant host. As a proof of concept, a salt tolerance candidate gene from the highly salt-tolerant Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. Endpoint reverse transcriptase PCR (RT-PCR) showed that the gene was expressed in F. casuarinae strain CcI3. The expression provided an increased level of salt tolerance for the transformant. These results represent stable plasmid transfer and exogenous gene expression in Frankia spp., overcoming a major hurdle in the field. This step in the development of genetic tools in Frankia spp. will open up new avenues for research on actinorhizal symbiosis.IMPORTANCE The absence of genetic tools for Frankia research has been a major hindrance to the associated field of actinorhizal symbiosis and the use of the nitrogen-fixing actinobacteria. This study reports on the introduction of plasmids into Frankia spp. and their functional expression of green fluorescent protein and a cloned gene. As the first step in developing genetic tools, this technique opens up the field to a wide array of approaches in an organism with great importance to and potential in the environment.}, }
@article {pmid31150238, year = {2019}, author = {Zhang, W and Mace, WJ and Matthew, C and Card, SD}, title = {The Impact of Endophyte Infection, Seed Aging, and Imbibition on Selected Sugar Metabolite Concentrations in Seed.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {25}, pages = {6921-6929}, doi = {10.1021/acs.jafc.9b01618}, pmid = {31150238}, issn = {1520-5118}, mesh = {Endophytes/*physiology ; Epichloe/*physiology ; Festuca/growth &amp; development/metabolism/*microbiology/physiology ; Seeds/*growth &amp; development/metabolism/microbiology/physiology ; Sugars/*metabolism ; Symbiosis ; }, abstract = {This study investigated effects of seed aging and imbibition on sugar metabolite concentrations in Epichloë endophyte-infected and endophyte-free seed of tall fescue (Festuca arundinacea Schreb.). Two treatments, namely, accelerated aging and imbibition, were applied to the seeds, with embryo and endosperm tissues analyzed separately. Gas chromatography with flame ionization detection was employed for analysis of sugar metabolites within the seed tissues. Mannitol, ribitol, and trehalose were more abundant in embryo than endosperm tissues and were identified at consistently higher concentrations within endophyte-infected compared to endophyte-free seeds. The ratio of raffinose to sucrose significantly increased with seed aging in both endophyte-free and endophyte-infected embryo tissues, while significantly lower concentrations of trehalose were detected in tissues dissected from aged-seed regardless of endophyte status. This research provides fundamental insight into the metabolic details of endophyte survival in seed and provides a first evaluation of key carbohydrates present in the fungal-plant symbiosis.}, }
@article {pmid31150064, year = {2019}, author = {Weis, VM}, title = {Cell biology of coral symbiosis: Foundational study can inform solutions to the coral reef crisis.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icz067}, pmid = {31150064}, issn = {1557-7023}, abstract = {Coral reefs are faced with almost complete destruction by the end of the century due to global warming unless humanity can cap global temperature rise. There is now a race to develop a diverse set of solutions to save coral reefs. In this perspective, a case is made for understanding of the cell biology of coral-dinoflagellate symbiosis to help inform development of solutions for saving reefs. Laboratory model systems for the study of coral symbiosis, including the sea anemone Exaiptasia pallida, are featured as valuable tools in the fight to save corals. The roles of host innate immunity and inter-partner nutrient dynamics in the onset, ongoing maintenance and dysregulation of symbiosis are reviewed and discussed. Key innate immune genes and pathways, such as glycan-lectin interactions, the sphingosine rheostat and the cytokine TGFβ are shown to modulate a host immune response in the symbiotic state. An upset in the homeostatic inorganic nutrient balance during heat stress and high exogenous nutrient availability is credited with driving the partnership towards dysregulation and coral bleaching. Specific examples are given where knowledge of the cell biology of symbiosis is informing the development of solutions, including studies showing clear limitations in the value of partner switching and acclimatization protocols. Finally, emphasis is placed on rapid advancement of knowledge to try to meet the urgent need for solutions. This includes real-time open communication with colleagues on successes and failures, sharing of resources and information, and working together in the spirit of a collective mission to save coral reefs.}, }
@article {pmid31148385, year = {2019}, author = {Fernandes, S and Vinnakota, R and Kumar, J and Kale, V and Limaye, L}, title = {Improved neural differentiation of normal and abnormal induced pluripotent stem cell lines in the presence of valproic acid.}, journal = {Journal of tissue engineering and regenerative medicine}, volume = {13}, number = {8}, pages = {1482-1496}, doi = {10.1002/term.2904}, pmid = {31148385}, issn = {1932-7005}, support = {BT/PR12696/MED/31/287/2014//Department of Biotechnology, Ministry of Science and Technology/ ; }, abstract = {During the generation of induced pluripotent stem cell (iPSC) lines from cord blood CD34+ cells, a line having complete trisomy of Chromosome 1 and deletion of q23 to qTer of Chromosome 11 was accidentally developed in our lab. The abnormality was consistently detected even at higher passages. These chromosomal anomalies are known to manifest neurological developmental defects. In order to examine if such defects occur during in vitro differentiation of the cell line, we set up a protocol for neural differentiation. Valproic acid (VPA) was earlier reported by us to enhance neural differentiation of placental mesenchymal stem cells. Here, we induced normal and abnormal iPSC lines to neural lineage with/without VPA. Neural differentiation was observed in all four sets, but for both the iPSCs lines, VPA sets performed better. The characteristics tested were morphology, neural filament length, detection of neural markers, and electrophysiology. In summary, the karyotypically abnormal line exhibited efficient neural differentiation. This iPSC line may serve as a useful tool to study abnormalities associated with trisomy 1 and deletion of q23 to qTer of Chromosome 11.}, }
@article {pmid31148173, year = {2019}, author = {An, J and Zeng, T and Ji, C and de Graaf, S and Zheng, Z and Xiao, TT and Deng, X and Xiao, S and Bisseling, T and Limpens, E and Pan, Z}, title = {A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {224}, number = {1}, pages = {396-408}, doi = {10.1111/nph.15975}, pmid = {31148173}, issn = {1469-8137}, support = {2018YFD1000103//National Key Research and Development Program of China/ ; 2017YFD0202001//National Key Research and Development Program of China/ ; 31521092//National Natural Science Foundation of China/ ; Gui Ke AA 18118046//Science and Technology Major Project of Guangxi/ ; GDT20174200001//High-End Foreign Experts Project/ ; 2662018JC039//Fundamental Research Funds for the Central Universities/ ; ERC-2011-AdG294790/ERC_/European Research Council/International ; 530-6CDP21//Koninklijke Nederlandse Akademie van Wetenschappen/ ; }, abstract = {Plants form a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, which facilitates the acquisition of scarce minerals from the soil. In return, the host plants provide sugars and lipids to its fungal partner. However, the mechanism by which the AM fungi obtain sugars from the plant has remained elusive. In this study we investigated the role of potential SWEET family sugar exporters in AM symbiosis in Medicago truncatula. We show that M. truncatula SWEET1b transporter is strongly upregulated in arbuscule-containing cells compared to roots and localizes to the peri-arbuscular membrane, across which nutrient exchange takes place. Heterologous expression of MtSWEET1b in a yeast hexose transport mutant showed that it mainly transports glucose. Overexpression of MtSWEET1b in M. truncatula roots promoted the growth of intraradical mycelium during AM symbiosis. Surprisingly, two independent Mtsweet1b mutants, which are predicted to produce truncated protein variants impaired in glucose transport, exhibited no significant defects in AM symbiosis. However, arbuscule-specific overexpression of MtSWEET1bY57A/G58D , which are considered to act in a dominant-negative manner, resulted in enhanced collapse of arbuscules. Taken together, our results reveal a (redundant) role for MtSWEET1b in the transport of glucose across the peri-arbuscular membrane to maintain arbuscules for a healthy mutually beneficial symbiosis.}, }
@article {pmid31144716, year = {2019}, author = {McDaneld, TG and Kuehn, LA and Keele, JW}, title = {Microbiome of the upper nasal cavity of beef calves prior to weaning12.}, journal = {Journal of animal science}, volume = {97}, number = {6}, pages = {2368-2375}, doi = {10.1093/jas/skz119}, pmid = {31144716}, issn = {1525-3163}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Cattle/*microbiology ; Cattle Diseases/*epidemiology/microbiology ; High-Throughput Nucleotide Sequencing/veterinary ; Incidence ; *Microbiota ; Nasal Cavity/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/epidemiology/microbiology/*veterinary ; Sequence Analysis, DNA ; Symbiosis ; United States/epidemiology ; Weaning ; }, abstract = {Disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. An understanding of the animal's resident respiratory pathogens, in the upper nasal cavity prior to weaning, may help us to understand the impact of these pathogens on incidence of respiratory disease. For this research, the overall goal was to characterize bacterial populations associated with calves at an early age and through time periods prior to weaning in 3 herds at the U.S. Meat Animal Research Center. Nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 40 d of age), preconditioning (approximately 130 d of age), and weaning (approximately 150 d of age) in 2015 and 2016. DNA was extracted from nasal swabs and combined into 2 pools of 10 animals for each sampling time point, in each herd, for a total of 6 pools at each sampling time point and 18 pools for all sampling time points within each year. To evaluate and compare the microbiome of each pooled sample, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Alpha and beta diversity were also measured. Overall, microbial communities were different between combinations of sampling year, herd location, and sampling time prior to weaning as shown by beta diversity. Analysis of these specific respiratory pathogens prior to weaning will present a clearer picture of the distribution of microbial populations in animals prior to weaning and not exhibiting clinical signs of respiratory disease. Therefore, evaluation of the animal's resident bacterial populations in the upper nasal cavity during different phases of the beef production system may help us to understand the impact of the microbiome on incidence of respiratory disease in cattle.}, }
@article {pmid31141960, year = {2019}, author = {Ali, A and Imran Ghani, M and Li, Y and Ding, H and Meng, H and Cheng, Z}, title = {Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China.}, journal = {International journal of molecular sciences}, volume = {20}, number = {11}, pages = {}, doi = {10.3390/ijms20112619}, pmid = {31141960}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci-Tech Innovation Plan/ ; 31772293//National Natural Science Foundation/ ; }, abstract = {Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach-cucumber (SC) and non-heading Chinese cabbage-cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce-cucumber (LLC), coriander-cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host-plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non-heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop-soil sustainable intensification.}, }
@article {pmid31141718, year = {2019}, author = {Liu, XL and Ye, S and Cheng, CY and Li, HW and Lu, B and Yang, WJ and Yang, JS}, title = {Identification and characterization of a symbiotic agglutination-related C-type lectin from the hydrothermal vent shrimp Rimicaris exoculata.}, journal = {Fish &amp; shellfish immunology}, volume = {92}, number = {}, pages = {1-10}, doi = {10.1016/j.fsi.2019.05.057}, pmid = {31141718}, issn = {1095-9947}, abstract = {Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species of hydrothermal vent communities, which inside its gill chamber harbors ectosymbioses with taxonomic invariability while compositional flexibility. Several studies have revealed that the establishment of symbiosis can be initiated and selected by innate immunity-related pattern recognition receptors (PRRs), such as C-type lectins (CTLs). In this research, a CTL was identified in R. exoculata (termed RCTL), which showed high expression at both mRNA and protein levels in the scaphognathite, an organ where the ectosymbionts are attached outside its setae. Linear correlationships were observed between the relative quantities of two major symbionts and the expression of RCTL based on analyzing different shrimp individuals. The recombinant protein of RCTL could recognize and agglutinate the cultivable γ-proteobacterium of Escherichia coli in a Ca2+-dependent manner, obeying a dose-dependent and time-cumulative pattern. Unlike conventional crustacean CTLs, the involvement of RCTL could not affect the bacterial growth, which is a key issue for the successful establishment of symbiosis. These results implied that RCTL might play a critical role in symbiotic recognition and attachment to R. exoculata. It also provides insights to understand how R. exoculata adapted to such a chemosynthesis-based environment.}, }
@article {pmid31140970, year = {2019}, author = {Lynn-Bell, NL and Strand, MR and Oliver, KM}, title = {Bacteriophage acquisition restores protective mutualism.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {9}, pages = {985-989}, doi = {10.1099/mic.0.000816}, pmid = {31140970}, issn = {1465-2080}, abstract = {Insects are frequently infected with inherited facultative symbionts known to provide a range of conditionally beneficial services, including host protection. Pea aphids (Acyrthosiphon pisum) often harbour the bacterium Hamiltonella defensa, which together with its associated bacteriophage A. pisum secondary endosymbiont (APSE) confer protection against an important natural enemy, the parasitic wasp Aphidius ervi. Previous studies showed that spontaneous loss of phage APSE resulted in the complete loss of the protective phenotype. Here, we demonstrate that APSEs can be experimentally transferred into phage-free (i.e. non-protecting) Hamiltonella strains. Unexpectedly, trials using injections of phage particles alone failed, with successful transfer occurring only when APSE and Hamiltonella were simultaneously injected. After transfer, stable establishment of APSE fully restored anti-parasitoid defenses. Thus, phages associated with heritable bacterial symbionts can move horizontally among symbiont strains facilitating the rapid transfer of ecologically important traits although natural barriers may preclude regular exchange.}, }
@article {pmid31139503, year = {2019}, author = {Pochon, X and Wecker, P and Stat, M and Berteaux-Lecellier, V and Lecellier, G}, title = {Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6898}, doi = {10.7717/peerj.6898}, pmid = {31139503}, issn = {2167-8359}, abstract = {High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.}, }
@article {pmid31139158, year = {2019}, author = {Ahmed, HI and Herrera, M and Liew, YJ and Aranda, M}, title = {Long-Term Temperature Stress in the Coral Model Aiptasia Supports the &quot;Anna Karenina Principle&quot; for Bacterial Microbiomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {975}, doi = {10.3389/fmicb.2019.00975}, pmid = {31139158}, issn = {1664-302X}, abstract = {The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.}, }
@article {pmid31138619, year = {2019}, author = {Saint-Leandre, B and Nguyen, SC and Levine, MT}, title = {Diversification and collapse of a telomere elongation mechanism.}, journal = {Genome research}, volume = {29}, number = {6}, pages = {920-931}, doi = {10.1101/gr.245001.118}, pmid = {31138619}, issn = {1549-5469}, support = {R00 GM107351/GM/NIGMS NIH HHS/United States ; R35 GM124684/GM/NIGMS NIH HHS/United States ; }, abstract = {In most eukaryotes, telomerase counteracts chromosome erosion by adding repetitive sequence to terminal ends. Drosophila melanogaster instead relies on specialized retrotransposons that insert exclusively at telomeres. This exchange of goods between host and mobile element-wherein the mobile element provides an essential genome service and the host provides a hospitable niche for mobile element propagation-has been called a &quot;genomic symbiosis.&quot; However, these telomere-specialized, jockey family retrotransposons may actually evolve to &quot;selfishly&quot; overreplicate in the genomes that they ostensibly serve. Under this model, we expect rapid diversification of telomere-specialized retrotransposon lineages and, possibly, the breakdown of this ostensibly symbiotic relationship. Here we report data consistent with both predictions. Searching the raw reads of the 15-Myr-old melanogaster species group, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements account for this retrotransposon lineage diversity. In Drosophila biarmipes, telomere-specialized elements have disappeared completely. De novo assembly of long reads and cytogenetics confirmed this species-specific collapse of retrotransposon-dependent telomere elongation. Instead, telomere-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Telomeric retrotransposon diversification and disappearance suggest that persistently &quot;selfish&quot; machinery shapes telomere elongation across Drosophila rather than completely domesticated, symbiotic mobile elements.}, }
@article {pmid31138324, year = {2019}, author = {Binetruy, F and Dupraz, M and Buysse, M and Duron, O}, title = {Surface sterilization methods impact measures of internal microbial diversity in ticks.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {268}, doi = {10.1186/s13071-019-3517-5}, pmid = {31138324}, issn = {1756-3305}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Biodiversity ; DNA Barcoding, Taxonomic ; Disinfectants/*pharmacology ; Ethanol/pharmacology ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Sodium Hypochlorite/pharmacology ; Specimen Handling/*methods ; Symbiosis ; Ticks/*microbiology ; }, abstract = {BACKGROUND: Ticks are obligate blood feeders transmitting major pathogens worldwide. Over the past few years, considerable research efforts have focused on the diversity, distribution and impact of gut and intracellular bacterial symbionts on tick development and tick-borne pathogen transmission. The study of this internal microbiome requires the use of a sterilization method to remove external (i.e. cuticular) microbes present on the tick's surface and to avoid any further contamination. Several sterilization methods exist, including ethanol- or bleach-based treatments that are both effective in killing microbes but with different potential effects on DNA denaturation.<br><br>METHODS: We examined how these different sterilization methods impact the measure of internal microbial diversity hosted by the Cayenne tick Amblyomma cajennense (sensu stricto). Bacterial barcoding investigations based on 16S rRNA gene sequences were conducted on two batches of 50 individuals each: Ticks of the first batch were sterilized with bleach diluted at 1% and the second batch with 70% ethanol. Tick external microbiome was also determined from cuticle smearing and water samples used for tick washing.<br><br>RESULTS: Bacterial barcoding investigations showed major differences between ethanol- and bleach-treated specimens. Both methods led to the detection of major intracellular bacteria associated with A. cajennense (s.s.) but ethanol-treated ticks always harbored a higher bacterial diversity than bleach-treated ticks. Further examinations of tick gut and tick external microbiome revealed that ethanol-based surface sterilization method is inefficient to eliminate the DNA of external bacteria.<br><br>CONCLUSIONS: We herein provide evidence that studies investigating the internal microbiome of ticks should consider bleach as the gold standard to efficiently remove cuticular bacterial DNA. Indeed, this method does not impact the internal bacterial diversity hosted by ticks and is thus a better method than the ethanol-based one for studying the internal microbiome.}, }
@article {pmid31134003, year = {2019}, author = {Fernández, N and Cabrera, JJ and Varadarajan, AR and Lutz, S and Ledermann, R and Roschitzki, B and Eberl, L and Bedmar, EJ and Fischer, HM and Pessi, G and Ahrens, CH and Mesa, S}, title = {An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {924}, doi = {10.3389/fmicb.2019.00924}, pmid = {31134003}, issn = {1664-302X}, abstract = {The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.}, }
@article {pmid31133991, year = {2019}, author = {Macedo-Raygoza, GM and Valdez-Salas, B and Prado, FM and Prieto, KR and Yamaguchi, LF and Kato, MJ and Canto-Canché, BB and Carrillo-Beltrán, M and Di Mascio, P and White, JF and Beltrán-García, MJ}, title = {Enterobacter cloacae, an Endophyte That Establishes a Nutrient-Transfer Symbiosis With Banana Plants and Protects Against the Black Sigatoka Pathogen.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {804}, doi = {10.3389/fmicb.2019.00804}, pmid = {31133991}, issn = {1664-302X}, abstract = {Banana (Musa spp.) is an important crop worldwide, but black Sigatoka disease caused by the fungus Pseudocercospora fijiensis threatens fruit production. In this work, we examined the potential of the endophytes of banana plants Enterobacter cloacae and Klebsiella pneumoniae, as antagonists of P. fijiensis and support plant growth in nutrient limited soils by N-transfer. The two bacterial isolates were identified by MALDI-TOF mass spectrometry and corroborated by 16S rRNA sequence analysis. Both bacteria were positive for beneficial traits such as N-fixation, indole acetic acid production, phosphate solubilization, negative for 1-aminocyclopropane 1-carboxylic acid deaminase and were antagonistic to P. fijiensis. To measure the effects on plant growth, the two plant bacteria and an E. coli strain (as non-endophyte), were inoculated weekly for 60 days as active cells (AC) and heat-killed cells (HKC) into plant microcosms without nutrients and compared to a water only treatment, and a mineral nutrients solution (MMN) treatment. Bacterial treatments increased growth parameters and prevented accelerated senescence, which was observed for water and mineral nutrients solution (MMN) treatments used as controls. Plants died after the first 20 days of being irrigated with water; irrigation with MMN enabled plants to develop some new leaves, but plants lost weight (-30%) during the same period. Plants treated with bacteria showed good growth, but E. cloacae AC treated plants had significantly greater biomass than the E. cloacae HKC. After 60 days, plants inoculated with E. cloacae AC showed intracellular bacteria within root cells, suggesting that a stable symbiosis was established. To evaluate the transference of organic N from bacteria into the plants, the 3 bacteria were grown with 15NH4Cl or Na15NO3 as the nitrogen source. The 15N transferred from bacteria to plant tissues was measured by pheophytin isotopomer abundance. The relative abundance of the isotopomers m/z 872.57, 873.57, 874.57, 875.57, 876.57 unequivocally demonstrated that plants acquired 15N atoms directly from bacterial cells, using them as a source of N, to support plant growth in restricted nutrient soils. E. cloacae might be a new alternative to promote growth and health of banana crops.}, }
@article {pmid31132110, year = {2019}, author = {Hammer, TJ and Sanders, JG and Fierer, N}, title = {Not all animals need a microbiome.}, journal = {FEMS microbiology letters}, volume = {366}, number = {10}, pages = {}, doi = {10.1093/femsle/fnz117}, pmid = {31132110}, issn = {1574-6968}, abstract = {It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several 'microbiome-free' lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.}, }
@article {pmid31128701, year = {2019}, author = {Yin, Y and Tian, L and Li, X and Huang, M and Liu, L and Wu, P and Li, M and Jiang, H and Wu, G and Chen, Y}, title = {The role of endogenous thiamine produced via THIC in root nodule symbiosis in Lotus japonicus.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {283}, number = {}, pages = {311-320}, doi = {10.1016/j.plantsci.2019.03.011}, pmid = {31128701}, issn = {1873-2259}, mesh = {Lotus/*metabolism/physiology ; Plant Proteins/*metabolism/physiology ; Real-Time Polymerase Chain Reaction ; Rhizobium/metabolism/physiology ; Root Nodules, Plant/*metabolism/physiology ; Symbiosis ; Thiamine/*metabolism/physiology ; Transcriptome ; }, abstract = {Thiamine is a pivotal primary metabolite which is indispensable to all organisms. Although its biosynthetic pathway has been well documented, the mechanism by which thiamine influences the legume-rhizobium symbiosis remains uncertain. Here, we used overexpressing transgenic plants, mutants and grafting experiments to investigate the roles played by thiamine in Lotus japonicus nodulation. ljthic mutants displayed lethal phenotypes and the defect could be overcome by supplementation of thiamine or by overexpression of LjTHIC. Reciprocal grafting between L. japonicus wild-type Gifu B-129 and ljthic showed that the photosynthetic products of the aerial part made a major contribution to overcoming the nodulation defect in ljthic. Overexpression of LjTHIC in Lotus japonicus (OE-LjTHIC) decreased shoot growth and increased the activity of the enzymes 2-oxoglutarate dehydrogenase and pyruvate dehydrogenase. OE-LjTHIC plants exhibited an increase in the number of infection threads and also developed more nodules, which were of smaller size but unchanged nitrogenase activity compared to the wildtype. Taken together, our results suggest that endogenous thiamine produced via LjTHIC acts as an essential nutrient provided by the host plant for rhizobial infection and nodule growth in the Lotus japonicus - rhizobium interaction.}, }
@article {pmid31127515, year = {2019}, author = {Symeonides, D and Loizia, P and Zorpas, AA}, title = {Tire waste management system in Cyprus in the framework of circular economy strategy.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-019-05131-z}, pmid = {31127515}, issn = {1614-7499}, abstract = {Worldwide, waste raised from tires counts 1.3-1.5 billion tonnes/year and by the end of 2025, is expected to be more than 2.5 billion tonnes. On 2013, the EU countries reached 3.6 million tonnes of used tires. However, the cheapest treatment method since now is landfilling and is considered to be a major threat for the environment and the public health. In Cyprus, the total tires that were imported on 2015 was 835,142 pieces (5.8% more than the 2014), which were equal to 9638 t, while at the same time, the total waste from those tires were 6629 tonnes. Moreover, the cement industry used 6691 tonnes of tires as alternative fuel. Until now, there are three management systems in place in Cyprus, for the end-of-life tires (ELTs). The collection of ELTs on 2011 was 1817 tonnes while at the end of 2016 was 7201 tonnes. The main treatment methods in Cyprus are the use of ELTs as alternative fuel in cement industry or to produce rubber granules (609-2738 tonnes/year) to be used to construct artificial surfaces or substrate for artificial lawn grounds and limited to pyrolysis (324-837 tonnes/year). At the same time, the environmental fees for the collection of tires varies and depends on the tire category. Furthermore, the market share of ELTs is up to 1.5 million € and the total recovery index from the market is closed to 90% the last 6 years (2013-2017). This paper evaluates and assess the existing tire waste management system (TWMS) in Cyprus in order to promote strength and weakness as well as to propose a holistic management system in insular communities in order to adopt the targets set by the concept of circular economy. The SWOT analysis identified as the main weaknesses the absence from the legislation of specific target for the recovery index of tires and the absence of any centralized logistic system to control the existing management systems while the main threats includes bureaucracy and the absence of technical and economic data which will guarantee the financial viability of a centralized treatment unit.}, }
@article {pmid31126059, year = {2019}, author = {Li, J and Zhao, T and M Shirolkar, M and Li, M and Wang, H and Li, H}, title = {CuO/ZnO Heterojunction Nanorod Arrays Prepared by Photochemical Method with Improved UV Detecting Performance.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/nano9050790}, pmid = {31126059}, issn = {2079-4991}, abstract = {CuO/ZnO heterojunction nanorod arrays were synthesized using a facile photochemical deposition strategy. The morphology of CuO was related to the concentration of Cu2+ in the Cu(NO3)2 solution, UV illumination time, and the air annealing temperature. A possible reaction mechanism was proposed. In the photochemical deposition process, the OH- was generated in the vicinity of the ZnO nanorod arrays and reacted with Cu2+ and NO3- in the solution to form Cu2(NO3)(OH)3/ZnO heterojunction nanorod arrays firstly, which were converted into CuO/ZnO heterojunction nanorod arrays completely after air annealing at a low temperature. The fabricated CuO/ZnO heterojunction nanorod arrays exhibits a well-defined rectifying characteristic and an improved photo-response performance compared with pure ZnO nanorod arrays.}, }
@article {pmid31125808, year = {2019}, author = {Zhang, X and Han, C and Gao, H and Cao, Y}, title = {Comparative transcriptome analysis of the garden asparagus (Asparagus officinalis L.) reveals the molecular mechanism for growth with arbuscular mycorrhizal fungi under salinity stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {20-29}, doi = {10.1016/j.plaphy.2019.05.013}, pmid = {31125808}, issn = {1873-2690}, abstract = {Soil salinity is one of the most abiotic stress factors that severely affects the growth and development of many plants, which can ultimately threaten crop yield. Arbuscular mycorrhiza fungi (AMF) has been proven to be effective in mitigating salinity stress by symbiosis in many crops. Asparagus officinalis are perennial plants grown in saline-alkaline soil, however, limited information on their molecular mechanisms has restricted efficient application of AMF to garden asparagus under salinity stress. In this study, we conducted a transcriptome analysis on the leaves of garden asparagus to identify gene expression under salinity stress. Seedlings were grown in 4 treatments, including non-inoculated AMF using distilled water (NI), inoculated AMF using distilled water (AMF), non-inoculated with salinity stress (NI + S), and inoculated with salinity stress (AMF + S). A total of 6019 novel genes were obtained based on the reference-guided assembly of the garden asparagus transcriptome. Results revealed that 455 differentially expressed genes (DEGs) were identified when comparing NI + S to AMF + S. However, among the up-regulated DEGs, 41 DEGs were down-regulated, while 242 DEGs had no differences in their expression levels when comparing NI to NI + S. These DEGs' expression patterns may be key induced by AMF under salinity stress. Additionally, the GO and KEGG enrichment analyses of 455 DEGs revealed that these genes mainly participate in the improvement of the internal environment in plant cells, nitrogen metabolic-related processes, and possible photoprotection mechanisms. These findings provide insight into enhanced salinity stress adaptation by AMF inoculation, as well as salt-tolerant candidate genes for further functional analyses.}, }
@article {pmid31125438, year = {2019}, author = {Lahari, Z and Ullah, C and Kyndt, T and Gershenzon, J and Gheysen, G}, title = {Strigolactones enhance root-knot nematode (Meloidogyne graminicola) infection in rice by antagonizing the jasmonate pathway.}, journal = {The New phytologist}, volume = {224}, number = {1}, pages = {454-465}, doi = {10.1111/nph.15953}, pmid = {31125438}, issn = {1469-8137}, support = {3G008718W//Fonds Wetenschappelijk Onderzoek/ ; BOF13/GOA/030//Universiteit Gent/ ; }, abstract = {Strigolactones (SLs) are carotenoid-derived plant hormones that also act in the rhizosphere to stimulate germination of root-parasitic plants and enhance plant symbiosis with beneficial microbes. Here, the role of SLs was investigated in the interaction of rice (Oryza sativa) roots with the root-knot nematode Meloidogyne graminicola. Genetic approaches and chemical sprays were used to manipulate SL signaling in rice before infection with M. graminicola. Then, nematode performance was evaluated and plant defense hormones were quantified. Meloidogyne graminicola infection induced SL biosynthesis and signaling and suppressed jasmonic acid (JA)-based defense in rice roots, suggesting a potential role of SLs during nematode infection. Whereas the application of a low dose of the SL analogue GR24 increased nematode infection and decreased jasmonate accumulation, the SL biosynthesis and signaling d mutants were less susceptible to M. graminicola, and constitutively accumulated JA and JA-isoleucine compared with wild-type plants. Spraying with 0.1 μM GR24 restored nematode susceptibility in SL-biosynthesis mutants but not in the signaling mutant. Furthermore, foliar application of the SL biosynthesis inhibitor TIS108 impeded nematode infection and increased jasmonate levels in rice roots. In conclusion, SL signaling in rice suppresses jasmonate accumulation and promotes root-knot nematode infection.}, }
@article {pmid31125425, year = {2019}, author = {Xue, L and Almario, J and Fabiańska, I and Saridis, G and Bucher, M}, title = {Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus.}, journal = {The New phytologist}, volume = {224}, number = {1}, pages = {409-420}, doi = {10.1111/nph.15958}, pmid = {31125425}, issn = {1469-8137}, support = {EXC 1028//The Cluster of Excellence on Plant Sciences (CEPLAS)/ ; BU-2250/12-1//Deutsche Forschungsgemeinschaft/ ; GA-2010-267243//Plant Fellows Program/ ; }, abstract = {Most land plants establish mutualistic interactions with arbuscular mycorrhizal (AM) fungi. Intracellular accommodation of AM fungal symbionts remodels important host traits like root morphology and nutrient acquisition. How mycorrhizal colonization impacts plant microbiota is unclear. To understand the impact of AM symbiosis on fungal microbiota, ten Lotus japonicus mutants impaired at different stages of AM formation were grown in non-sterile natural soil and their root-associated fungal communities were studied. Plant mutants lacking the capacity to form mature arbuscules (arb-) exhibited limited growth performance associated with altered phosphorus (P) acquisition and reduction-oxidation (redox) processes. Furthermore, arb- plants assembled moderately but consistently different root-associated fungal microbiota, characterized by the depletion of Glomeromycota and the concomitant enrichment of Ascomycota, including Dactylonectria torresensis. Single and co-inoculation experiments showed a strong reduction of root colonization by D. torresensis in the presence of AM fungus Rhizophagus irregularis, particularly in arbuscule-forming plants. Our results suggest that impairment of central symbiotic functions in AM host plants leads to specific changes in root microbiomes and in tripartite interactions between the host plant, AM and non-AM fungi. This lays the foundation for mechanistic studies on microbe-microbe and microbe-host interactions in AM symbiosis of the model L. japonicus.}, }
@article {pmid31125282, year = {2019}, author = {Kang, X and Wang, L and Guo, Y and Ul Arifeen, MZ and Cai, X and Xue, Y and Bu, Y and Wang, G and Liu, C}, title = {A Comparative Transcriptomic and Proteomic Analysis of Hexaploid Wheat's Responses to Colonization by Bacillus velezensis and Gaeumannomyces graminis, Both Separately and Combined.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI03190066R}, doi = {10.1094/MPMI-03-19-0066-R}, pmid = {31125282}, issn = {0894-0282}, abstract = {Tritrophic interactions involving a biocontrol agent, a pathogen, and a plant have been analyzed predominantly from the perspective of the biocontrol agent. To explore the adaptive strategies of wheat in response to beneficial, pathogenic, and combined microorganisms, we performed the first comprehensive transcriptomic, proteomic, and biochemical analysis in wheat roots after exposure to Bacillus velezensis CC09, Gaeumannomyces graminis var. tritici, and their combined colonization, respectively. The transcriptional or translational programming of wheat roots inoculated with beneficial B. velezensis showed mild alterations compared with that of pathogenic G. graminis var. tritici. However, the combination of B. velezensis and G. graminis var. tritici activated a larger transcriptional or translational program than for each single microorganism, although the gene expression pattern was similar to that of individual infection by G. graminis var. tritici, suggesting a prioritization of defense against G. graminis var. tritici infection. Surprisingly, pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity made wheat pretreated with B. velezensis more sensitive to subsequent G. graminis var. tritici infection. Additionally, B. velezensis triggered a salicylic acid (SA)-dependent mode of induced systemic resistance that resembles pathogen-induced systemic acquired resistance. Wheat plants mainly depend on SA-mediated resistance, and not that mediated by jasmonic acid (JA), against the necrotrophic pathogen G. graminis var. tritici. Moreover, SA-JA interactions resulted in antagonistic effects regardless of the type of microorganisms in wheat. Further enhancement of SA-dependent defense responses such as lignification to the combined infection was shown to reduce the level of induced JA-dependent defense against subsequent infection with G. graminis var. tritici. Altogether, our results demonstrate how the hexaploid monocot wheat responds to beneficial or pathogenic microorganisms and prolongs the onset of take-all disease through modulation of cell reprogramming and signaling events.}, }
@article {pmid31124196, year = {2019}, author = {McIntosh, M and Serrania, J and Lacanna, E}, title = {A novel LuxR-type solo of Sinorhizobium meliloti, NurR, is regulated by the chromosome replication coordinator, DnaA and activates quorum sensing.}, journal = {Molecular microbiology}, volume = {112}, number = {2}, pages = {678-698}, doi = {10.1111/mmi.14312}, pmid = {31124196}, issn = {1365-2958}, support = {Be 2121/6-2, INST 160/536-1 FUGG//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains eight genes coding for LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long-chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is SinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL-dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti.}, }
@article {pmid31121904, year = {2019}, author = {Zhang, Y and Hu, L and Yu, D and Xu, K and Zhang, J and Li, X and Wang, P and Chen, G and Liu, Z and Peng, C and Li, C and Guo, T}, title = {Integrative Analysis of the Wheat PHT1 Gene Family Reveals A Novel Member Involved in Arbuscular Mycorrhizal Phosphate Transport and Immunity.}, journal = {Cells}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/cells8050490}, pmid = {31121904}, issn = {2073-4409}, abstract = {Phosphorus (P) deficiency is one of the main growth-limiting factors for plants. However, arbuscular mycorrhizal (AM) symbiosis can significantly promote P uptake. Generally, PHT1 transporters play key roles in plants' P uptake, and thus, PHT1 genes have been investigated in some plants, but the regulation and functions of these genes in wheat (TaPHT1) during AM symbiosis have not been studied in depth. Therefore, a comprehensive analysis of TaPHT1 genes was performed, including sequence, phylogeny, cis-elements, expression, subcellular localization and functions, to elucidate their roles in AM-associated phosphate transport and immunity. In total, 35 TaPHT1s were identified in the latest high-quality bread wheat genome, 34 of which were unevenly distributed on 13 chromosomes, and divided into five groups. Sequence analysis indicated that there are 11 types of motif architectures and five types of exon-intron structures in the TaPHT1 family. Duplication mode analysis indicated that the TaPHT1 family has expanded mainly through segmental and tandem duplication events, and that all duplicated gene pairs have been under purifying selection. Transcription analysis of the 35 TaPHT1s revealed that not only known the mycorrhizal-specific genes TaPht-myc, TaPT15-4B (TaPT11) and TaPT19-4D (TaPT10), but also four novel mycorrhizal-specific/inducible genes (TaPT3-2D, TaPT11-4A, TaPT29-6A, and TaPT31-7A) are highly up-regulated in AM wheat roots. Furthermore, the mycorrhizal-specific/inducible genes are significantly induced in wheat roots at different stages of infection by colonizing fungi. Transient Agrobacterium tumefaciens-mediated transformation expression in onion epidermal cells showed that TaPT29-6A is a membrane-localized protein. In contrast to other AM-specific/inducible PHT1 genes, TaPT29-6A is apparently required for the symbiotic and direct Pi pathway. TaPT29-6A-silenced lines exhibited reduced levels of AM fungal colonization and arbuscules, but increased susceptibility to biotrophic, hemi-biotrophic and necrotrophic pathogens. In conclusion, TaPT29-6A was not only essential for the AM symbiosis, but also played vital roles in immunity.}, }
@article {pmid31119081, year = {2019}, author = {Jian, L and Bai, X and Zhang, H and Song, X and Li, Z}, title = {Promotion of growth and metal accumulation of alfalfa by coinoculation with Sinorhizobium and Agrobacterium under copper and zinc stress.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6875}, doi = {10.7717/peerj.6875}, pmid = {31119081}, issn = {2167-8359}, abstract = {The Legume-Rhizobium symbiosis has been proposed as a promising technique for the phytoremediation of contaminated soils due to its beneficial activity in symbiotic nitrogen fixation. However, numerous studies have shown that excessive heavy metals reduce the efficiency of symbiotic nodulation with Rhizobium and inhibit plant growth. In this study, we aimed to evaluate the synergistic effects of IAA-producing bacteria and Rhizobium on Medicago lupulina growth under Cu and Zn stress. Pot experiments showed that 400 mg kg-1 Cu2 + and Zn2 + greatly inhibited plant growth, but dual inoculation of Medicago lupulina with Sinorhizobium meliloti CCNWSX0020 and Agrobacterium tumefaciens CCNWGS0286 significantly increased the number of nodules and plant biomass by enhancing antioxidant activities. Under double stress of 400 mg kg-1 Cu2 + and Zn2 +, the nodule number and nitrogenase activities of dual-inoculated plants were 48.5% and 154.4% higher, respectively, than those of plants inoculated with Sinorhizobium meliloti. The root and above-ground portion lengths of the dual-inoculated plants were 32.6% and 14.1% greater, respectively, than those of the control, while the root and above-ground portion dry weights were 34.3% and 32.2% greater, respectively, than those of the control. Compared with S. meliloti and A. tumefaciens single inoculation, coinoculation increased total Cu uptake by 39.1% and 47.5% and increased total Zn uptake by 35.4% and 44.2%, respectively, under double metal stress conditions. Therefore, coinoculation with Sinorhizobium meliloti and Agrobacterium tumefaciens enhances metal phytoextraction by increasing plant growth and antioxidant activities under Cu/Zn stress, which provides a new approach for bioremediation in heavy metal-contaminated soil.}, }
@article {pmid31118473, year = {2019}, author = {Sproles, AE and Oakley, CA and Matthews, JL and Peng, L and Owen, JG and Grossman, AR and Weis, VM and Davy, SK}, title = {Proteomics quantifies protein expression changes in a model cnidarian colonised by a thermally tolerant but suboptimal symbiont.}, journal = {The ISME journal}, volume = {13}, number = {9}, pages = {2334-2345}, doi = {10.1038/s41396-019-0437-5}, pmid = {31118473}, issn = {1751-7370}, abstract = {The acquisition of thermally tolerant algal symbionts by corals has been proposed as a natural or assisted mechanism of increasing coral reef resilience to anthropogenic climate change, but the cell-level processes determining the performance of new symbiotic associations are poorly understood. We used liquid chromatography-mass spectrometry to investigate the effects of an experimentally induced symbiosis on the host proteome of the model sea anemone Exaiptasia pallida. Aposymbiotic specimens were colonised by either the homologous dinoflagellate symbiont (Breviolum minutum) or a thermally tolerant, ecologically invasive heterologous symbiont (Durusdinium trenchii). Anemones containing D. trenchii exhibited minimal expression of Niemann-Pick C2 proteins, which have predicted biochemical roles in sterol transport and cell recognition, and glutamine synthetases, which are thought to be involved in nitrogen assimilation and recycling between partners. D. trenchii-colonised anemones had higher expression of methionine-synthesising betaine-homocysteine S-methyltransferases and proteins with predicted oxidative stress response functions. Multiple lysosome-associated proteins were less abundant in both symbiotic treatments compared with the aposymbiotic treatment. The differentially abundant proteins are predicted to represent pathways that may be involved in nutrient transport or resource allocation between partners. These results provide targets for specific experiments to elucidate the mechanisms underpinning compensatory physiology in the coral-dinoflagellate symbiosis.}, }
@article {pmid31117021, year = {2019}, author = {Beinart, RA}, title = {The Significance of Microbial Symbionts in Ecosystem Processes.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00127-19}, pmid = {31117021}, issn = {2379-5077}, abstract = {It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.}, }
@article {pmid31117019, year = {2019}, author = {Kleiner, M}, title = {Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00115-19}, pmid = {31117019}, issn = {2379-5077}, abstract = {Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the &quot;expressed&quot; metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.}, }
@article {pmid31115477, year = {2019}, author = {Gómez-Díaz, JS and Montoya-Lerma, J and Muñoz Valencia, V}, title = {Prevalence and Diversity of Endosymbionts in Cassava Whiteflies (Hemiptera: Aleyrodidae) From Colombia.}, journal = {Journal of insect science (Online)}, volume = {19}, number = {3}, pages = {}, doi = {10.1093/jisesa/iez047}, pmid = {31115477}, issn = {1536-2442}, mesh = {Animals ; Hemiptera/genetics/*microbiology ; Manihot ; Nymph/microbiology ; Phylogeny ; Symbiosis ; }, abstract = {Whiteflies cause huge economic losses for cassava (Manihot esculenta Crantz) cultivation. Damage can be caused directly when the insects feed on the phloem and/or indirectly by the transmission of viruses. It has been found that whiteflies maintain a close relationship with some endosymbiotic bacteria and that this interaction produces different effects on host biology and can also facilitate viral transmission. This study aimed to characterize the diversity of secondary endosymbionts (SE) present in whiteflies associated with cassava. Whitefly adults and nymphs were collected from cassava crops at nine locations in Southwestern Colombia. Molecular identification of insects and endosymbionts was carried out using specific mtCOI, wsp, 23s rRNA, and 16s rRNA primers. Phylogenetic trees were constructed from these sequences, both for whitefly species and the endosymbionts found. In addition, morphological identification of whitefly species was made using last instar nymphs. Molecular and morphological evaluation revealed that the most abundant whitefly species was Trialeurodes variabilis (Quaintance) followed by Aleurotrachelus socialis Bondar and Bemisia tuberculata Bondar. One hundred percent of the individuals contained the primary endosymbiont Portiera. The SE Rickettsia, Hamiltonella, Wolbachia, and Fritschea were not detected in the samples tested. Prevalence of Cardinium and Arsenophonus were variable at each locality, Cardinium being most prevalent in A. socialis adults. This study is the first report on the presence of Cardinium and Arsenophonus in A. socialis and T. variabilis. It is also the first report of endosymbiotic diversity in whiteflies associated with cassava in Colombia.}, }
@article {pmid31115264, year = {2019}, author = {Vaidya, A and Singh, S and Limaye, L and Kale, V}, title = {Chimeric feeders of mesenchymal stromal cells and stromal cells modified with constitutively active AKT expand hematopoietic stem cells.}, journal = {Regenerative medicine}, volume = {14}, number = {6}, pages = {535-553}, doi = {10.2217/rme-2018-0157}, pmid = {31115264}, issn = {1746-076X}, abstract = {Aim: To examine whether AKT-modified stromal cells expand human CD34+ hematopoietic stem cells (HSCs). Methods: Coculture, in vitro functional assays, immuno-fluorescence microscopy, flow cytometry. Results: M2-10B4 stromal cells (M2) modified with AKT1 (M2-AKT) expanded primitive CD34+38- HSCs, but affected their functionality. A chimeric feeder layer comprising naive human bone marrow-derived mesenchymal stromal cells and M2-AKT not only overcame the negative effects of M2-AKT, but, unexpectedly, also gave a synergistic effect on the growth and functionality of the HSCs. Conditioned medium of bone marrow stromal cells worked as effectively, but cell-cell contact between HSCs and M2-AKT cells was necessary for the synergistic effect of M2-AKT and bone marrow-derived mesenchymal stromal cells or their CM. Conclusion: Chimeric feeders expand HSCs.}, }
@article {pmid31114600, year = {2019}, author = {Liu, YS and Geng, JC and Sha, XY and Zhao, YX and Hu, TM and Yang, PZ}, title = {Effect of Rhizobium Symbiosis on Low-Temperature Tolerance and Antioxidant Response in Alfalfa (Medicago sativa L.).}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {538}, doi = {10.3389/fpls.2019.00538}, pmid = {31114600}, issn = {1664-462X}, abstract = {Low temperature-induced stress is a major environmental factor limiting the growth and development of plants. Alfalfa (Medicago sativa L.) is a legume well known for its tolerance of extreme environments. In this study, we sought to experimentally investigate the role of rhizobium symbiosis in alfalfa's performance under a low-temperature stress condition. To do this, alfalfa &quot;Ladak+&quot; plants carrying active nodules (AN), inactive nodules (IN), or no nodules (NN) were exposed to an imposed low temperature stress and their survivorship calculated. The antioxidant defense responses, the accumulation of osmotic regulation substances, the cell membrane damage, and the expression of low temperature stress-related genes were determined in both the roots and the shoots of alfalfa plants. We found that more plants with AN survived than those with IN or NN under the same low temperature-stress condition. Greater activity of oxidation protective enzymes was observed in the AN and IN groups, conferring higher tolerance to low temperature in these plants. In addition, rhizobia nodulation also enhanced alfalfa's ability to tolerate low temperature by altering the expression of regulatory and metabolism-associated genes, which resulted in the accumulation of soluble proteins and sugars in the nodulated plants. Taken together, the findings of this study indicate that rhizobium inoculation offers a practical way to promote the persistence and growth potential of alfalfa &quot;Ladak+&quot; in cold areas.}, }
@article {pmid31114559, year = {2019}, author = {González, V and Santamaría, RI and Bustos, P and Pérez-Carrascal, OM and Vinuesa, P and Juárez, S and Martínez-Flores, I and Cevallos, MÁ and Brom, S and Martínez-Romero, E and Romero, D}, title = {Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {910}, doi = {10.3389/fmicb.2019.00910}, pmid = {31114559}, issn = {1664-302X}, abstract = {The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.}, }
@article {pmid31113823, year = {2019}, author = {Serra, L and Macchietto, M and Macias-Muñoz, A and McGill, CJ and Rodriguez, IM and Rodriguez, B and Murad, R and Mortazavi, A}, title = {Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {8}, pages = {2687-2697}, doi = {10.1534/g3.119.400180}, pmid = {31113823}, issn = {2160-1836}, abstract = {Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.}, }
@article {pmid31113629, year = {2019}, author = {Ballinger, MJ and Perlman, SJ}, title = {The defensive Spiroplasma.}, journal = {Current opinion in insect science}, volume = {32}, number = {}, pages = {36-41}, doi = {10.1016/j.cois.2018.10.004}, pmid = {31113629}, issn = {2214-5753}, abstract = {Defensive microbes are of great interest for their roles in arthropod health, disease transmission, and biocontrol efforts. Obligate bacterial passengers of arthropods, such as Spiroplasma, confer protection against the natural enemies of their hosts to improve their own fitness. Although known for less than a decade, Spiroplasma's defensive reach extends to diverse parasites, both microbial and multicellular. We provide an overview of known defensive phenotypes against nematodes, parasitoid wasps, and fungi, and highlight recent studies supporting the role of Spiroplasma-encoded ribosome-inactivating proteins in protection. With cellular features well-suited for life in the hemolymph, broad distribution among invertebrate hosts, and the capacity to repeatedly evolve vertical transmission, Spiroplasma may be uniquely equipped to form intimate, defensive associations to combat extracellular parasites. Along with insights into defensive mechanisms, recent significant advances have been made in male-killing - a phenotype with interesting evolutionary ties to defense. Finally, we look forward to an exciting decade using the genetic tools of Drosophila, and the rapidly-advancing tractability of Spiroplasma itself, to better understand mechanisms and evolution in defensive symbiosis.}, }
@article {pmid31112772, year = {2019}, author = {Bhat, MI and Sowmya, K and Kapila, S and Kapila, R}, title = {Escherichia coli K12: An evolving opportunistic commensal gut microbe distorts barrier integrity in human intestinal cells.}, journal = {Microbial pathogenesis}, volume = {133}, number = {}, pages = {103545}, doi = {10.1016/j.micpath.2019.103545}, pmid = {31112772}, issn = {1096-1208}, mesh = {Caco-2 Cells/cytology/microbiology ; Claudin-1/metabolism ; Cytoskeletal Proteins ; Electric Impedance ; Epithelial Cells/metabolism ; Escherichia coli K12/*pathogenicity/*physiology ; *Gastrointestinal Microbiome ; Gene Expression ; Host Microbial Interactions ; Humans ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Membrane Proteins/metabolism ; Microfilament Proteins/metabolism ; Occludin/genetics/metabolism ; Opportunistic Infections/*microbiology ; Permeability ; RNA, Messenger ; *Symbiosis ; Tight Junction Proteins/metabolism ; Tight Junctions/metabolism ; Zonula Occludens-1 Protein/metabolism ; beta-Defensins/metabolism ; }, abstract = {Commensal enteric microbes under specific conditions viz. immunocompromised system, altered microbiota or uncompetitive niche induce their otherwise dormant pathogenic phenotype to distort host cellular functioning. Here we investigate how under in vitro environment established by using Caco-2 cells, commensal gut microbe E. coli K12 (ATCC 14849) disrupt intestinal epithelial barrier function. Caco-2 cells exposed to E. coli showed the time dependent significant (P < 0.01) decrease in transepithelial electrical resistance (TEER) and concomitantly increased phenol red flux across cell monolayer in contrast to non infected control cells. E. coli infected intestinal cells were observed with suppressed (p < 0.05) mRNA levels of ZO-1, Claudin-1, Occludin and Cingulin-1 in contrast to significantly (p < 0.05) higher PIgR and hbd-2 mRNA fold changes. Immunofluorescent and electron micrographs revealed the disrupted distribution and localisation of specific tight junction proteins (Zo-1 and Claudin-1) and actin filament in E. coli infected Caco-2 cells that ultimately resulted in deformed cellular morphology. Taken together, E. coli K12 under compromised in vitro milieu disrupted the intestinal barrier functions by decreasing the expression of important tight junction genes along with the altered distribution of associated proteins that increased the intestinal permeability as reflected by phenol red flux and TEER values.}, }
@article {pmid31109137, year = {2019}, author = {Ji, J and Zhang, C and Sun, Z and Wang, L and Duanmu, D and Fan, Q}, title = {Genome Editing in Cowpea Vigna unguiculata Using CRISPR-Cas9.}, journal = {International journal of molecular sciences}, volume = {20}, number = {10}, pages = {}, doi = {10.3390/ijms20102471}, pmid = {31109137}, issn = {1422-0067}, abstract = {Cowpea (Vigna unguiculata) is widely cultivated across the world. Due to its symbiotic nitrogen fixation capability and many agronomically important traits, such as tolerance to low rainfall and low fertilization requirements, as well as its high nutrition and health benefits, cowpea is an important legume crop, especially in many semi-arid countries. However, research in Vigna unguiculata is dramatically hampered by the lack of mutant resources and efficient tools for gene inactivation in vivo. In this study, we used clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). We applied the CRISPR/Cas9-mediated genome editing technology to efficiently disrupt the representative symbiotic nitrogen fixation (SNF) gene in Vigna unguiculata. Our customized guide RNAs (gRNAs) targeting symbiosis receptor-like kinase (SYMRK) achieved ~67% mutagenic efficiency in hairy-root-transformed plants, and nodule formation was completely blocked in the mutants with both alleles disrupted. Various types of mutations were observed near the PAM region of the respective gRNA. These results demonstrate the applicability of the CRISPR/Cas9 system in Vigna unguiculata, and therefore should significantly stimulate functional genomics analyses of many important agronomical traits in this unique crop legume.}, }
@article {pmid31109096, year = {2019}, author = {Saridis, G and Chorianopoulou, SN and Ventouris, YE and Sigalas, PP and Bouranis, DL}, title = {An Exploration of the Roles of Ferric Iron Chelation-Strategy Components in the Leaves and Roots of Maize Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/plants8050133}, pmid = {31109096}, issn = {2223-7747}, abstract = {Plants have developed sophisticated mechanisms for acquiring iron from the soil. In the graminaceous species, a chelation strategy is in charge, in order to take up ferric iron from the rhizosphere. The ferric iron chelation-strategy components may also be present in the aerial plant parts. The aim of this work was to search for possible roles of those components in maize leaves. To this end, the expression patterns of ferric iron chelation-strategy components were monitored in the leaves and roots of mycorrhizal and non-mycorrhizal sulfur-deprived maize plants, both before and after sulfate supply. The two levels of sulfur supply were chosen due to the strong impact of this nutrient on iron homeostasis, whilst mycorrhizal symbiosis was chosen as a treatment that forces the plant to optimize its photosynthetic efficiency, in order to feed the fungus. The results, in combination with the findings of our previous works, suggest a role for the aforementioned components in ferric chelation and/or unloading from the xylem vessels to the aerial plant parts. It is proposed that the gene expression of the DMA exporter ZmTOM1 can be used as an early indicator for the establishment of a mycorrhizal symbiotic relationship in maize.}, }
@article {pmid31107632, year = {2019}, author = {Forester, NT and Lane, GA and McKenzie, CM and Lamont, IL and Johnson, LJ}, title = {The Role of SreA-Mediated Iron Regulation in Maintaining Epichloë festucae-Lolium perenne Symbioses.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI03190060R}, doi = {10.1094/MPMI-03-19-0060-R}, pmid = {31107632}, issn = {0894-0282}, abstract = {In ascomycetes and basidiomycetes, iron-responsive GATA-type transcriptional repressors are involved in regulating iron homeostasis, notably to prevent iron toxicity through control of iron uptake. To date, it has been unknown whether this iron regulator contributes toward mutualistic endosymbiosis of microbes with plants, a system where the endophyte must function within the constraints of an in-host existence, including a dependency on the host for nutrient acquisition. Functional characterization of one such protein, SreA from Epichloë festucae, a fungal endosymbiont of cool-season grasses, indicates that regulation of iron homeostasis processes is important for symbiotic maintenance. The deletion of the sreA gene (ΔsreA) led to iron-dependent aberrant hyphal growth and the gradual loss of endophyte hyphae from perennial ryegrass. SreA negatively regulates the siderophore biosynthesis and high-affinity iron uptake systems of E. festucae, similar to other fungi, resulting in iron accumulation in mutants. Our evidence suggests that SreA is involved in the processes that moderate Epichloë iron acquisition from the plant apoplast, because overharvesting of iron in ΔsreA mutants was detected as premature chlorosis of the host using a hydroponic plant growth assay. E. festucae appears to have a tightly regulated iron management system, involving SreA that balances endophyte growth with its survival and prevents overcompetition with the host for iron in the intercellular niche, thus promoting mutualistic associations. Mutations that interfere with Epichloë iron management negatively affect iron-dependent fungal growth and destabilize mutualistic Epichloë -ryegrass associations.}, }
@article {pmid31106828, year = {2019}, author = {Rigo, R and Bazin, J and Crespi, M and Charon, C}, title = {Alternative Splicing in the Regulation of Plant-Microbe Interactions.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcz086}, pmid = {31106828}, issn = {1471-9053}, abstract = {As sessile organisms, plants are continuously exposed to a wide range of biotic interactions. While some biotic interactions are beneficial or even essential for the plant (e.g. rhizobia, mycorrhiza), others such as pathogens are detrimental and require fast adaptation. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of genes they express. In the past few years, high-throughput transcriptome sequencing have revealed that, in addition to transcriptional control of gene expression, post-transcriptional processes, notably alternative splicing (AS), emerged as a key mechanism for gene regulation during plant adaptation to the environment. AS can increase proteome diversity by generating multiple transcripts from a single gene but also can reduce gene expression by yielding isoforms degraded by mechanisms such as nonsense-mediated mRNA decay. In this review, we will summarize recent discoveries detailing the contribution of alternative splicing to the regulation of plant-microbe interactions, with an emphasis on the modulation of immunity receptor function and other components of the signaling pathways that deal with pathogen responses. We will also discuss emerging evidences that AS could contribute to dynamic reprogramming of the plant transcriptome during beneficial interactions, such as the legume-symbiotic interaction.}, }
@article {pmid31106065, year = {2019}, author = {Wright, RM and Strader, ME and Genuise, HM and Matz, M}, title = {Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6849}, doi = {10.7717/peerj.6849}, pmid = {31106065}, issn = {2167-8359}, abstract = {The surface mucus layer of reef-building corals supports feeding, sediment clearing, and protection from pathogenic invaders. As much as half of the fixed carbon supplied by the corals' photosynthetic symbionts is incorporated into expelled mucus. It is therefore reasonable to expect that coral bleaching (disruption of the coral-algal symbiosis) would affect mucus production. Since coral mucus serves as an important nutrient source for the entire reef community, this could have substantial ecosystem-wide consequences. In this study, we examined the effects of heat stress-induced coral bleaching on the composition and antibacterial properties of coral mucus. In a controlled laboratory thermal challenge, stressed corals produced mucus with higher protein (β = 2.1, p < 0.001) and lipid content (β = 15.7, p = 0.02) and increased antibacterial activity (likelihood ratio = 100, p < 0.001) relative to clonal controls. These results are likely explained by the expelled symbionts in the mucus of bleached individuals. Our study suggests that coral bleaching could immediately impact the nutrient flux in the coral reef ecosystem via its effect on coral mucus.}, }
@article {pmid31105111, year = {2019}, author = {Goto, Y}, title = {[REGULATION OF INTESTINAL EPITHELIAL α1, 2-FUCOSE].}, journal = {Arerugi = [Allergy]}, volume = {68}, number = {3}, pages = {151-154}, doi = {10.15036/arerugi.68.151}, pmid = {31105111}, issn = {0021-4884}, mesh = {Fucose/*metabolism ; Humans ; Intestinal Mucosa/*metabolism ; }, }
@article {pmid31103464, year = {2019}, author = {Vander Linden, C and Corbet, C}, title = {Reconciling environment-mediated metabolic heterogeneity with the oncogene-driven cancer paradigm in precision oncology.}, journal = {Seminars in cell &amp; developmental biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcdb.2019.05.016}, pmid = {31103464}, issn = {1096-3634}, abstract = {Precision oncology is the practice of matching one therapy to one specific patient, based on particular genetic tumor alterations, in order to achieve the best clinical response. Despite an expanding arsenal of targeted therapies, many patients still have a poor outcome because tumor cells show a remarkable capacity to develop drug resistance, thereby leading to tumor relapse. Besides genotype-driven resistance mechanisms, tumor microenvironment (TME) peculiarities strongly contribute to generate an intratumoral phenotypic heterogeneity that affects disease progression and treatment outcome. In this Review, we describe how TME-mediated metabolic heterogeneities actively participate to therapeutic failure. We report how a lactate-based metabolic symbiosis acts as a mechanism of adaptive resistance to targeted therapies and we describe the role of mitochondrial metabolism, in particular oxidative phosphorylation (OXPHOS), to support the growth and survival of therapy-resistant tumor cells in a variety of cancers. Finally, we detail potential metabolism-interfering therapeutic strategies aiming to eradicate OXPHOS-dependent relapse-sustaining malignant cells and we discuss relevant (pre)clinical models that may help integrate TME-driven metabolic heterogeneity in precision oncology.}, }
@article {pmid31102241, year = {2019}, author = {Steinfeld, L and Vafaei, A and Rösner, J and Merzendorfer, H}, title = {Chitin Prevalence and Function in Bacteria, Fungi and Protists.}, journal = {Advances in experimental medicine and biology}, volume = {1142}, number = {}, pages = {19-59}, doi = {10.1007/978-981-13-7318-3_3}, pmid = {31102241}, issn = {0065-2598}, mesh = {Adaptive Immunity ; Animals ; Bacteria/*chemistry ; Chitin/*chemistry/immunology ; Fungi/*chemistry ; Humans ; Immunity, Innate ; Mycorrhizae ; Plants ; Signal Transduction ; Symbiosis ; }, abstract = {Chitin is an important structural polysaccharide, which supports and organizes extracellular matrices in a variety of taxonomic groups including bacteria, fungi, protists, and animals. Additionally, chitin has been recognized as a molecule that is required for Rhizobia-legume symbiosis and involved in arbuscular mycorrhizal signaling in the symbiotic interaction between terrestrial plants and fungi. Moreover, it serves as a unique molecular pattern in the plant defense system against pathogenic fungi and parasites, and in the innate and adaptive immune response of mammals and humans. In this review, we will focus on the prevalence and structural function of chitin in bacteria, fungi, and protists, with a particular focus on the evolution of chitin synthases and the function of chitin oligosaccharides as a signaling molecule in symbiosis and immunity.}, }
@article {pmid31101941, year = {2019}, author = {Doni, F and Mispan, MS and Suhaimi, NSM and Ishak, N and Uphoff, N}, title = {Roles of microbes in supporting sustainable rice production using the system of rice intensification.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {13}, pages = {5131-5142}, doi = {10.1007/s00253-019-09879-9}, pmid = {31101941}, issn = {1432-0614}, support = {FRGS/1/2015/SG03/UM/02/3//Ministry of Higher Education Malaysia/ ; BK004-2015//Universiti Malaya/ ; RU006-2017//Universiti Malaya/ ; }, abstract = {The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.}, }
@article {pmid31101921, year = {2019}, author = {Queralt, M and Walker, JKM and de Miguel, AM and Parladé, J and Anderson, IC and Hortal, S}, title = {The ability of a host plant to associate with different symbiotic partners affects ectomycorrhizal functioning.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, doi = {10.1093/femsec/fiz069}, pmid = {31101921}, issn = {1574-6941}, abstract = {Some plants that associate with ectomycorrhizal (ECM) fungi are also able to simultaneously establish symbiosis with other types of partners. The presence of alternative partners that may provide similar benefits may affect ECM functioning. Here we compared potential leucine-aminopeptidase (LA) and acid phosphatase (AP) enzyme activity (involved in N and P cycling, respectively) in ECM fungi of three hosts planted under the same conditions but differing in the type of partners: Pinus (ECM fungi only), Eucalyptus (ECM and arbuscular mycorrhizal -AM- fungi) and Acacia (ECM, AM fungi and rhizobial bacteria). We found that the ECM community on Acacia and Eucalyptus had higher potential AP activity than the Pinus community. The ECM community in Acacia also showed increased potential LA activity compared to Pinus. Morphotypes present in more than one host showed higher potential AP and LA activity when colonizing Acacia than when colonizing another host. Our results suggest that competition with AM fungi and rhizobial bacteria could promote increased ECM activity in Eucalyptus and Acacia. Alternatively, other host-related differences such as ECM community composition could also play a role. We found evidence for ECM physiological plasticity when colonizing different hosts, which might be key for adaptation to future climate scenarios.}, }
@article {pmid31101610, year = {2019}, author = {Feldman, D and Amedi, N and Carmeli, S and Yarden, O and Hadar, Y}, title = {Manipulating the Expression of Small Secreted Protein 1 (Ssp1) Alters Patterns of Development and Metabolism in the White-Rot Fungus Pleurotus ostreatus.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, doi = {10.1128/AEM.00761-19}, pmid = {31101610}, issn = {1098-5336}, abstract = {The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of SSPs at the onset of secondary metabolism, during colony development, and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in the regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analysis was performed during the trophophase and the idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns: OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, the OEssp1 strain exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild type into idiophase. The pigment was produced earlier and in a larger amount in the OEssp1 strain and was absent from the KDssp1 strain. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in the initiation of fruiting body formation as well as earlier aging. We propose that Ssp1 might function as a part of the fungal communication network and regulate the pattern of fungal development and metabolism in P. ostreatusIMPORTANCE Small secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred to as &quot;effectors.&quot; We propose that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging, and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.}, }
@article {pmid31099411, year = {2019}, author = {Bosch, TCG and Guillemin, K and McFall-Ngai, M}, title = {Evolutionary &quot;Experiments&quot; in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host-Microbe Interactions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e1800256}, doi = {10.1002/bies.201800256}, pmid = {31099411}, issn = {1521-1878}, support = {Collaborative Research Centre (CRC) 1182 &quot;Origin//Deutsche Forschungsgemeinschaft/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; P01GM125576//National Institute of General Medical Sciences of the National Institutes of Health/ ; P01 GM125576/GM/NIGMS NIH HHS/United States ; P50GM098911//National Institute of General Medical Sciences of the National Institutes of Health/ ; 5R37AI050661-16//National Institutes of Health/ ; P50GM098911 and P01GM125576.//National Institute of General Medical Sciences of the National Institutes of Health/ ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, abstract = {Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host-microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host-microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.}, }
@article {pmid31097480, year = {2019}, author = {Ishii, Y and Maruyama, S and Takahashi, H and Aihara, Y and Yamaguchi, T and Yamaguchi, K and Shigenobu, S and Kawata, M and Ueno, N and Minagawa, J}, title = {Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {7}, pages = {2337-2347}, doi = {10.1534/g3.118.201012}, pmid = {31097480}, issn = {2160-1836}, abstract = {Stable endosymbiotic relationships between cnidarian animals and dinoflagellate algae are vital for sustaining coral reef ecosystems. Recent studies have shown that elevated seawater temperatures can cause the collapse of their endosymbiosis, known as 'bleaching', and result in mass mortality. However, the molecular interplay between temperature responses and symbiotic states still remains unclear. To identify candidate genes relevant to the symbiotic stability, we performed transcriptomic analyses under multiple conditions using the symbiotic and apo-symbiotic (symbiont free) Exaiptasia diaphana, an emerging model sea anemone. Gene expression patterns showed that large parts of differentially expressed genes in response to heat stress were specific to the symbiotic state, suggesting that the host sea anemone could react to environmental changes in a symbiotic state-dependent manner. Comparative analysis of expression profiles under multiple conditions highlighted candidate genes potentially important in the symbiotic state transition under heat-induced bleaching. Many of these genes were functionally associated with carbohydrate and protein metabolisms in lysosomes. Symbiont algal genes differentially expressed in hospite encode proteins related to heat shock response, calcium signaling, organellar protein transport, and sugar metabolism. Our data suggest that heat stress alters gene expression in both the hosts and symbionts. In particular, heat stress may affect the lysosome-mediated degradation and transportation of substrates such as carbohydrates through the symbiosome (phagosome-derived organelle harboring symbiont) membrane, which potentially might attenuate the stability of symbiosis and lead to bleaching-associated symbiotic state transition.}, }
@article {pmid31095296, year = {2019}, author = {Dabo, M and Jaiswal, SK and Dakora, FD}, title = {Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, doi = {10.1093/femsec/fiz067}, pmid = {31095296}, issn = {1574-6941}, abstract = {The legume host and soil environment play a major role in establishing effective symbiosis with diverse rhizobia for plant growth promotion and nodule formation. The aim of this study was to assess the morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that the isolates were highly diverse in their appearance on yeast mannitol agar plates. The isolates tested also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml-1 and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis showed that soil pH and mineral nutrients significantly influenced bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient which resulted in 45 unique BOX-types. Phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic gene phylogenies suggested that the isolates' sym loci probably relates to the isolates' geographical origin. The results indicated that geographical origin did affect the isolates' phylogenetic placement and could be the basis for allopatric speciation.}, }
@article {pmid31092941, year = {2019}, author = {Steidinger, BS and Crowther, TW and Liang, J and Van Nuland, ME and Werner, GDA and Reich, PB and Nabuurs, GJ and de-Miguel, S and Zhou, M and Picard, N and Herault, B and Zhao, X and Zhang, C and Routh, D and Peay, KG and , }, title = {Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.}, journal = {Nature}, volume = {569}, number = {7756}, pages = {404-408}, doi = {10.1038/s41586-019-1128-0}, pmid = {31092941}, issn = {1476-4687}, abstract = {The identity of the dominant root-associated microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools1,2, sequester carbon3,4 and withstand the effects of climate change5,6. Characterizing the global distribution of these symbioses and identifying the factors that control this distribution are thus integral to understanding the present and future functioning of forest ecosystems. Here we generate a spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species. Our analyses indicate that climate variables-in particular, climatically controlled variation in the rate of decomposition-are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal trees, which represent only 2% of all plant species7, constitute approximately 60% of tree stems on Earth. Ectomycorrhizal symbiosis dominates forests in which seasonally cold and dry climates inhibit decomposition, and is the predominant form of symbiosis at high latitudes and elevation. By contrast, arbuscular mycorrhizal trees dominate in aseasonal, warm tropical forests, and occur with ectomycorrhizal trees in temperate biomes in which seasonally warm-and-wet climates enhance decomposition. Continental transitions between forests dominated by ectomycorrhizal or arbuscular mycorrhizal trees occur relatively abruptly along climate-driven decomposition gradients; these transitions are probably caused by positive feedback effects between plants and microorganisms. Symbiotic nitrogen fixers-which are insensitive to climatic controls on decomposition (compared with mycorrhizal fungi)-are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient that we document provides a spatially explicit quantitative understanding of microbial symbioses at the global scale, and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.}, }
@article {pmid31092601, year = {2019}, author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M}, title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00165-19}, pmid = {31092601}, issn = {2379-5042}, mesh = {Animals ; Bacteria/enzymology/genetics ; *Diet ; Fungi/*growth &amp; development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/microbiology ; Isoptera/*enzymology/*microbiology ; Metagenome ; Phylogeny ; Plant Cells/metabolism ; Sequence Analysis, DNA ; Symbiosis ; Wood/metabolism ; }, abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.}, }
@article {pmid31091180, year = {2019}, author = {Huo, Y and Tong, W and Wang, J and Wang, F and Bai, W and Wang, E and Shi, P and Chen, W and Wei, G}, title = {Rhizobium chutanense sp. nov., isolated from root nodules of Phaseolus vulgaris in China.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {7}, pages = {2049-2056}, doi = {10.1099/ijsem.0.003430}, pmid = {31091180}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; China ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Medicago sativa ; Nucleic Acid Hybridization ; Peas ; Phaseolus/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*classification/isolation &amp; purification ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soybeans ; Symbiosis ; }, abstract = {Two Gram-stain-negative, rod-shaped bacterial strains (C5T and C16), isolated from root nodules of Phaseolus vulgaris L. in Jiangxi Province, PR China, were characterized by using a polyphasic taxonomical approach. The phylogenetic analysis of the 16S rRNA gene and three concatenated housekeeping genes (recA-glnII-atpD) revealed that C5T and C16 were members of the genus Rhizobium, yet were distinct from known species. The case for strain C5T representing a novel species was supported by genomic results. Pairwise digital DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. The genome-based phylogenetic tree reconstructed by using the up-to-date bacterial core gene set consisting of 92 genes showed that the strains formed a monophyletic branch, further supporting this result. The symbiotic genes of nodC and nifH were identified in both strains; each could nodulate Phaseolus vulgaris and Glycine max but not Leucaena leucocephala, Pisum sativum or Medicago sativa plants. Major cellular fatty acids of C5T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 58.8 %), C18 : 1 ω7c 11-methyl (14.2 %) and C18 : 0 (8.1 %). The DNA G+C content of C5T was 61.4 mol%. Based on these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Rhizobium chutanense sp. nov. The type strain is C5T (=CCTCC AB 2018143T=LMG 30777T).}, }
@article {pmid31089128, year = {2019}, author = {Ramakrishna, C and Kujawski, M and Chu, H and Li, L and Mazmanian, SK and Cantin, EM}, title = {Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2153}, doi = {10.1038/s41467-019-09884-6}, pmid = {31089128}, issn = {2041-1723}, mesh = {Acyclovir/therapeutic use ; Animals ; Antiviral Agents/therapeutic use ; B-Lymphocytes/immunology/metabolism ; Bacteroides fragilis/*immunology/metabolism ; Cercopithecus aethiops ; Disease Models, Animal ; Encephalitis, Herpes Simplex/drug therapy/*immunology/virology ; Female ; Gastrointestinal Microbiome/*immunology ; Herpesvirus 1, Human/*immunology/pathogenicity ; Host Microbial Interactions/immunology ; Humans ; Interleukin-10/genetics/immunology/metabolism ; Male ; Mice ; Mice, Knockout ; Polysaccharides, Bacterial/*immunology/metabolism ; Symbiosis/immunology ; T-Lymphocytes/immunology/metabolism ; Vero Cells ; }, abstract = {The gut commensal Bacteroides fragilis or its capsular polysaccharide A (PSA) can prevent various peripheral and CNS sterile inflammatory disorders. Fatal herpes simplex encephalitis (HSE) results from immune pathology caused by uncontrolled invasion of the brainstem by inflammatory monocytes and neutrophils. Here we assess the immunomodulatory potential of PSA in HSE by infecting PSA or PBS treated 129S6 mice with HSV1, followed by delayed Acyclovir (ACV) treatment as often occurs in the clinical setting. Only PSA-treated mice survived, with dramatically reduced brainstem inflammation and altered cytokine and chemokine profiles. Importantly, PSA binding by B cells is essential for induction of regulatory CD4+ and CD8+ T cells secreting IL-10 to control innate inflammatory responses, consistent with the lack of PSA mediated protection in Rag-/-, B cell- and IL-10-deficient mice. Our data reveal the translational potential of PSA as an immunomodulatory symbiosis factor to orchestrate robust protective anti-inflammatory responses during viral infections.}, }
@article {pmid31088928, year = {2019}, author = {Schorn, MA and Jordan, PA and Podell, S and Blanton, JM and Agarwal, V and Biggs, JS and Allen, EE and Moore, BS}, title = {Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00821-19}, pmid = {31088928}, issn = {2150-7511}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biological Products/metabolism ; Cyanobacteria/*genetics/metabolism ; Genomics ; Halogenated Diphenyl Ethers/metabolism ; Indoles/metabolism ; *Metagenomics ; Multigene Family ; Phylogeny ; Porifera/*microbiology ; Pyrroles/metabolism ; Symbiosis/*genetics ; Tropical Climate ; }, abstract = {Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.}, }
@article {pmid31088922, year = {2019}, author = {König, L and Wentrup, C and Schulz, F and Wascher, F and Escola, S and Swanson, MS and Buchrieser, C and Horn, M}, title = {Symbiont-Mediated Defense against Legionella pneumophila in Amoebae.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00333-19}, pmid = {31088922}, issn = {2150-7511}, mesh = {Acanthamoeba castellanii/*microbiology/physiology ; Chlamydiales/*physiology ; Gene Expression ; Humans ; Legionella pneumophila/*pathogenicity ; *Symbiosis ; Virulence ; }, abstract = {Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.IMPORTANCE Bacterial pathogens are generally investigated in the context of disease. To prevent outbreaks, it is essential to understand their lifestyle and interactions with other microbes in their natural environment. Legionella pneumophila is an important human respiratory pathogen that survives and multiplies in biofilms or intracellularly within protists, such as amoebae. Importantly, transmission to humans occurs from these environmental sources. Legionella infection generally leads to rapid host cell lysis. It was therefore surprising to observe that amoebae, including fresh environmental isolates, were well protected during Legionella infection when the bacterial symbiont Protochlamydia amoebophila was also present. Legionella was not prevented from invading amoebae but was impeded in its ability to develop fully virulent progeny and were ultimately cleared in the presence of the symbiont. This study highlights how ecology and virulence of an important human pathogen is affected by a defensive amoeba symbiont, with possibly major consequences for public health.}, }
@article {pmid31088273, year = {2019}, author = {Bell-Roberts, L and Douglas, AE and Werner, GDA}, title = {Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1902}, pages = {20190065}, doi = {10.1098/rspb.2019.0065}, pmid = {31088273}, issn = {1471-2954}, abstract = {Some animal groups associate with the same vertically transmitted microbial symbionts over extended periods of evolutionary time, punctuated by occasional symbiont switches to different microbial taxa. Here we test the oft-repeated suggestion that symbiont switches are linked with host diet changes, focusing on hemipteran insects of the suborder Auchenorrhyncha. These insects include the only animals that feed on plant xylem sap through the life cycle, as well as taxa that feed on phloem sap and plant parenchyma cells. Ancestral state reconstruction provides strong statistical support for a xylem feeding auchenorrhynchan ancestor bearing the dual symbiosis with the primary symbiont Sulcia (Bacteroidetes) and companion symbiont 'β-Sym' (β-proteobacteria). We identified seven dietary transitions from xylem feeding (six to phloem feeding, one to parenchyma feeding), but no reversions to xylem feeding; five evolutionary losses of Sulcia, including replacements by yeast symbionts, exclusively in phloem/parenchyma-feeding lineages; and 14-15 losses of β-Sym, including nine transitions to a different bacterial companion symbiont. Our analysis indicates that, although companion symbiont switching is not associated with shifts in host diet, Sulcia is probably required for xylem-feeding. Furthermore, the ancestral auchenorrhynchan bearing Sulcia and β-Sym probably represents the sole evolutionary origin of xylem feeding in the animal kingdom.}, }
@article {pmid31087385, year = {2019}, author = {Zhou, Y and Ge, S and Jin, L and Yao, K and Wang, Y and Wu, X and Zhou, J and Xia, X and Shi, K and Foyer, CH and Yu, J}, title = {A novel CO2 -responsive systemic signaling pathway controlling plant mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {224}, number = {1}, pages = {106-116}, doi = {10.1111/nph.15917}, pmid = {31087385}, issn = {1469-8137}, support = {2018YFD1000800//the National Key Research and Development of China/ ; 31825023//the National Natural Science Foundation of China/ ; 31430076//the National Natural Science Foundation of China/ ; CARS-25-02A//the Modern Agro-industry Technology Research System of China/ ; (BB/M009130/1//the Biotechnology and Biological Sciences Research Council (BBSRC) UK/ ; }, abstract = {Elevated atmospheric carbon dioxide (eCO2) concentrations promote symbiosis between roots and arbuscular mycorrhizal fungi (AMF), modifying plant nutrient acquisition and cycling of carbon, nitrogen and phosphate. However, the biological mechanisms by which plants transmit aerial eCO2 cues to roots, to alter the symbiotic associations remain unknown. We used a range of interdisciplinary approaches, including gene silencing, grafting, transmission electron microscopy, liquid chromatography tandem mass spectrometry (LC-MS/MS), biochemical methodologies and gene transcript analysis to explore the complexities of environmental signal transmission from the point of perception in the leaves at the apex to the roots. Here we show that eCO2 triggers apoplastic hydrogen peroxide (H2 O2)-dependent auxin production in tomato shoots followed by systemic signaling that results in strigolactone biosynthesis in the roots. This redox-auxin-strigolactone systemic signaling cascade facilitates eCO2 -induced AMF symbiosis and phosphate utilization. Our results challenge the current paradigm of eCO2 effects on AMF and provide new insights into potential targets for manipulation of AMF symbiosis for high nutrient utilization under future climate change scenarios.}, }
@article {pmid31086829, year = {2019}, author = {Burgsdorf, I and Handley, KM and Bar-Shalom, R and Erwin, PM and Steindler, L}, title = {Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00057-19}, pmid = {31086829}, issn = {2379-5077}, abstract = {&quot;Candidatus Synechococcus feldmannii&quot; is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont &quot;Candidatus Synechococcus spongiarum.&quot; Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of &quot;Ca. Synechococcus feldmannii.&quot; By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by &quot;Ca. Synechococcus feldmannii&quot; and free-living cyanobacteria, while they are absent in the obligate symbiont &quot;Ca. Synechococcus spongiarum.&quot; These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on &quot;Ca. Synechococcus feldmannii&quot; its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.}, }
@article {pmid31084944, year = {2019}, author = {González-Pech, RA and Bhattacharya, D and Ragan, MA and Chan, CX}, title = {Genome Evolution of Coral Reef Symbionts as Intracellular Residents.}, journal = {Trends in ecology &amp; evolution}, volume = {34}, number = {9}, pages = {799-806}, doi = {10.1016/j.tree.2019.04.010}, pmid = {31084944}, issn = {1872-8383}, abstract = {Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral-dinoflagellate and other eukaryote-eukaryote symbioses.}, }
@article {pmid31084866, year = {2019}, author = {Ortiz-Castro, R and López-Bucio, J}, title = {Review: Phytostimulation and root architectural responses to quorum-sensing signals and related molecules from rhizobacteria.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {284}, number = {}, pages = {135-142}, doi = {10.1016/j.plantsci.2019.04.010}, pmid = {31084866}, issn = {1873-2259}, mesh = {Host-Pathogen Interactions ; Plant Roots/anatomy &amp; histology/*microbiology/physiology ; Quorum Sensing/*physiology ; Rhizobiaceae/*metabolism ; }, abstract = {Bacteria rely on chemical communication to sense the environment and to retrieve information on their population densities. Accordingly, a vast repertoire of molecules is released, which synchronizes expression of genes, coordinates behavior through a process termed quorum-sensing (QS), and determines the relationships with eukaryotic species. Already identified QS molecules from Gram negative bacteria can be grouped into two main classes, N-acyl-L-homoserine lactones (AHLs) and cyclodipeptides (CDPs), with roles in biofilm formation, bacterial virulence or symbiotic interactions. Noteworthy, plants detect each of these molecules, change their own gene expression programs, re-configurate root architecture, and activate defense responses, improving in this manner their adaptation to natural and agricultural ecosystems. AHLs may act as alarm signals, pathogen and/or microbe-associated molecular patterns, whereas CDPs function as hormonal mimics for plants via their putative interactions with the auxin receptor Transport Inhibitor Response1 (TIR1). A major challenge is to identify the molecular pathways of QS-mediated crosstalk and the plant receptors and interacting proteins for AHLs, CDPs and related signals.}, }
@article {pmid31081746, year = {2019}, author = {Elizalde-Díaz, JP and Hernández-Lucas, I and Medina-Aparicio, L and Dávalos, A and Leija, A and Alvarado-Affantranger, X and García-García, JD and Hernández, G and Garcia-de Los Santos, A}, title = {Rhizobium tropici CIAT 899 copA gene plays a fundamental role in copper tolerance in both free life and symbiosis with Phaseolus vulgaris.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {6}, pages = {651-661}, doi = {10.1099/mic.0.000803}, pmid = {31081746}, issn = {1465-2080}, abstract = {Rhizobium tropici CIAT 899 is a facultative symbiotic diazotroph able to deal with stressful concentrations of metals. Nevertheless the molecular mechanisms involved in metal tolerance have not been elucidated. Copper (Cu2+) is a metal component essential for the heme-copper respiratory oxidases and enzymes that catalyse redox reactions, however, it is highly toxic when intracellular trace concentrations are surpassed. In this study, we report that R. tropici CIAT 899 is more tolerant to Cu2+ than other Rhizobium and Sinorhizobium species. Through Tn5 random mutagenesis we identify a R. tropici mutant strain with a severe reduction in Cu2+ tolerance. The Tn5 insertion disrupted the gene RTCIAT899_CH17575, encoding a putative heavy metal efflux P1B-1-type ATPase designated as copA. Phaseolus vulgaris plants inoculated with the copA::Tn5 mutant in the presence of toxic Cu2+ concentrations showed a drastic reduction in plant and nodule dry weight, as well as nitrogenase activity. Nodules induced by the copA::Tn5 mutant present an increase in H2O2 concentration, lipoperoxidation and accumulate 40-fold more Cu2+ than nodules formed by the wild-type strain. The copA::Tn5 mutant complemented with the copA gene recovered the wild-type symbiotic phenotypes. Therefore, the copA gene is essential for R. tropici CIAT 899 to survive in copper-rich environments in both free life and symbiosis with P. vulgaris plants.}, }
@article {pmid31080889, year = {2019}, author = {Parekh, VS and Jacobs, MA}, title = {Deep learning and radiomics in precision medicine.}, journal = {Expert review of precision medicine and drug development}, volume = {4}, number = {2}, pages = {59-72}, doi = {10.1080/23808993.2019.1585805}, pmid = {31080889}, issn = {2380-8993}, support = {P30 CA006973/CA/NCI NIH HHS/United States ; R01 CA190299/CA/NCI NIH HHS/United States ; U01 CA140204/CA/NCI NIH HHS/United States ; }, abstract = {Introduction: The radiological reading room is undergoing a paradigm shift to a symbiosis of computer science and radiology using artificial intelligence integrated with machine and deep learning with radiomics to better define tissue characteristics. The goal is to use integrated deep learning and radiomics with radiological parameters to produce a personalized diagnosis for a patient.<br><br>Areas covered: This review provides an overview of historical and current deep learning and radiomics methods in the context of precision medicine in radiology. A literature search for 'Deep Learning', 'Radiomics', 'Machine learning', 'Artificial Intelligence', 'Convolutional Neural Network', 'Generative Adversarial Network', 'Autoencoders', Deep Belief Networks&quot;, Reinforcement Learning&quot;, and 'Multiparametric MRI' was performed in PubMed, ArXiv, Scopus, CVPR, SPIE, IEEE Xplore, and NIPS to identify articles of interest.<br><br>Expert opinion: In conclusion, both deep learning and radiomics are two rapidly advancing technologies that will unite in the future to produce a single unified framework for clinical decision support with a potential to completely revolutionize the field of precision medicine.}, }
@article {pmid31079999, year = {2019}, author = {Schlöffel, MA and Käsbauer, C and Gust, AA}, title = {Interplay of plant glycan hydrolases and LysM proteins in plant-Bacteria interactions.}, journal = {International journal of medical microbiology : IJMM}, volume = {309}, number = {3-4}, pages = {252-257}, doi = {10.1016/j.ijmm.2019.04.004}, pmid = {31079999}, issn = {1618-0607}, mesh = {Bacteria/chemistry/metabolism ; Chitin/analogs &amp; derivatives/metabolism ; Chitinases/*metabolism ; *Host Microbial Interactions ; Lysine ; Peptidoglycan/metabolism ; Plant Proteins/chemistry/*metabolism ; Plants/*microbiology ; Receptors, Cell Surface/chemistry/*metabolism ; Signal Transduction ; }, abstract = {Plants are always found together with bacteria and other microbes. Although plants can be attacked by phytopathogenic bacteria, they are more often engaged in neutral or mutualistic bacterial interactions. In the soil, plants associate with rhizobia or other plant growth promoting rhizosphere bacteria; above ground, bacteria colonise plants as epi- and endophytes. For mounting appropriate responses, such as permitting colonisation by beneficial symbionts while at the same time fending off pathogenic invaders, plants need to distinguish between the &quot;good&quot; and the &quot;bad&quot;. Plants make use of proteins containing the lysin motif (LysM) for perception of N-acetylglucosamine containing carbohydrate structures, such as chitooligosaccharides functioning as symbiotic nodulation factors or bacterial peptidoglycan. Moreover, plant hydrolytic enzymes of the chitinase family, which are able to cleave bacterial peptidoglycan or chitooligosaccharides, are essential for cellular signalling induced by rhizobial nodulation factors during symbiosis as well as bacterial peptidoglycan during pathogenesis. Hence, LysM receptors seem to work in concert with hydrolytic enzymes that fine-tune ligand availability to either allow symbiotic interactions or trigger plant immunity.}, }
@article {pmid31078551, year = {2019}, author = {Verdonk, CJ and Sullivan, JT and Williman, KM and Nicholson, L and Bastholm, TR and Hynes, MF and Ronson, CW and Bond, CS and Ramsay, JP}, title = {Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A.}, journal = {Plasmid}, volume = {104}, number = {}, pages = {102416}, doi = {10.1016/j.plasmid.2019.102416}, pmid = {31078551}, issn = {1095-9890}, abstract = {Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSymR7A is the prototypical member of a large family of &quot;symbiosis ICEs&quot; which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a variety of legume species. Mesorhizobial symbiosis ICEs carry a common core of mobilisation genes required for integration, excision and conjugative transfer. IntS of ICEMlSymR7A enables recombination between the ICEMlSymR7A attachment site attP and the 3' end of the phe-tRNA gene. Here we identified putative IntS attP arm (P) sites within the attP region and demonstrated that the outermost P1 and P5 sites demarcated the minimal region for efficient IntS-mediated integration. We also identified the ICEMlSymR7A origin-of-transfer (oriT) site directly upstream of the relaxase-gene rlxS. The ICEMlSymR7A conjugation system mobilised a plasmid carrying the cloned oriT to Escherichia coli in an rlxS-dependent manner. Surprisingly, an in-frame, markerless deletion mutation in the ICEMlSymR7A recombination directionality factor (excisionase) gene rdfS, but not a mutation in intS, abolished mobilisation, suggesting the rdfS deletion tentatively has downstream effects on conjugation or its regulation. In summary, this work defines two critical cis-acting regions required for excision and transfer of ICEMlSymR7A and related ICEs.}, }
@article {pmid31077522, year = {2019}, author = {Songwattana, P and Tittabutr, P and Wongdee, J and Teamtisong, K and Wulandari, D and Teulet, A and Fardoux, J and Boonkerd, N and Giraud, E and Teaumroong, N}, title = {Symbiotic properties of a chimeric Nod-independent photosynthetic Bradyrhizobium strain obtained by conjugative transfer of a symbiotic plasmid.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14650}, pmid = {31077522}, issn = {1462-2920}, support = {//Suranaree University of Technology (SUT)/ ; SUT3-304-55- 36-23//National Research Council of Thailand/ ; JEAI_SymbiTrop//IRD/ ; PHC SIAM 2017 - 38280WF//Franco-Thai Cooperation Program in Higher Education and Research/ ; ANR- 16-CE20-0013//the ANR, grant 'SymEffectors'/ ; }, abstract = {The lateral transfer of symbiotic genes converting a predisposed soil bacteria into a legume symbiont has occurred repeatedly and independently during the evolution of rhizobia. We experimented the transfer of a symbiotic plasmid between Bradyrhizobium strains. The originality of the DOA9 donor is that it harbours a symbiotic mega-plasmid (pDOA9) containing nod, nif and T3SS genes while the ORS278 recipient has the unique property of inducing nodules on some Aeschynomene species in the absence of Nod factors (NFs). We observed that the chimeric strain ORS278-pDOA9* lost its ability to develop a functional symbiosis with Aeschynomene. indica and Aeschynomene evenia. The mutation of rhcN and nodB led to partial restoration of nodule efficiency, indicating that T3SS effectors and NFs block the establishment of the NF-independent symbiosis. Conversely, ORS278-pDOA9* strain acquired the ability to form nodules on Crotalaria juncea and Macroptillium artropurpureum but not on NF-dependent Aeschynomene (A. afraspera and A. americana), suggesting that the ORS278 strain also harbours incompatible factors that block the interaction with these species. These data indicate that the symbiotic properties of a chimeric rhizobia cannot be anticipated due to new combination of symbiotic and non-symbiotic determinants that may interfere during the interaction with the host plant.}, }
@article {pmid31076773, year = {2019}, author = {Shiratake, K and Notaguchi, M and Makino, H and Sawai, Y and Borghi, L}, title = {Petunia PLEIOTROPIC DRUG RESISTANCE 1 Is a Strigolactone Short-Distance Transporter with Long-Distance Outcomes.}, journal = {Plant &amp; cell physiology}, volume = {60}, number = {8}, pages = {1722-1733}, doi = {10.1093/pcp/pcz081}, pmid = {31076773}, issn = {1471-9053}, mesh = {Gene Expression Regulation, Plant ; Lactones/*metabolism ; Membrane Transport Proteins/*metabolism ; Petunia/genetics/*metabolism/physiology ; Plant Proteins/*metabolism ; }, abstract = {Phytohormones of the strigolactone (SL) family have been characterized as negative regulators of lateral bud outgrowth and triggers of symbioses between plants and mycorrhizal fungi. SLs and their precursors are synthesized in root tips as well as along shoot and root vasculature; they either move shoot-wards and regulate plant architecture or are exuded from roots into the soil to establish mycorrhizal symbiosis. Owing to the difficulty in quantification of SL in shoot tissues because of low abundance, it is not yet clear how SL distribution in plants is regulated at short- and long-distances from SL biosynthetic and target tissues. To address this question, we grafted wild-type scions and rootstocks from different petunia mutants for SL biosynthesis/transport and investigated SL activity by quantifying lateral bud outgrowth in the main shoot. Based on these results, we show that (i) the previously reported petunia SL transporter PLEIOTROPIC DRUG RESISTANCE 1 (PDR1) directly accounts for short-distance SL transport and (ii) long-distance transport of SLs seems to be partially and not directly dependent on PDR1. These data suggest that the root-to-shoot transport of SLs occurs either via the vasculature bundle through transporters other than PDR1 or involves SL precursors that are not substrates of PDR1.}, }
@article {pmid31076245, year = {2019}, author = {Brunk, CF and Martin, WF}, title = {Archaeal Histone Contributions to the Origin of Eukaryotes.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {703-714}, doi = {10.1016/j.tim.2019.04.002}, pmid = {31076245}, issn = {1878-4380}, abstract = {The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.}, }
@article {pmid31074496, year = {2019}, author = {Chaudhary, S and Gupta, P and Srivastava, S and Adholeya, A}, title = {Understanding dynamics of Rhizophagus irregularis ontogenesis in axenically developed coculture through basic and advanced microscopic techniques.}, journal = {Journal of basic microbiology}, volume = {59}, number = {8}, pages = {767-774}, doi = {10.1002/jobm.201900138}, pmid = {31074496}, issn = {1521-4028}, support = {//TERI-Deakin Nanobiotechnology Centre/ ; }, mesh = {Axenic Culture ; Biological Ontologies ; Glomeromycota/*growth &amp; development ; Hyphae/growth &amp; development ; *Microscopy/instrumentation ; Mycorrhizae/*growth &amp; development ; Plant Roots/microbiology ; }, abstract = {Detailed information on structural changes that occur during ontogenesis of Rhizophagus irregularis in axenically developed coculture is limited. Our study aims to investigate the series of events that occur during mycorrhizal ontogenesis under axenic condition through basic and advanced microscopic techniques followed by comparison among these to identify the suitable technique for rapid and detailed analysis of mycorrhizal structures. Three stages were identified in mycorrhizal ontogenesis from initiation (preinfection stage of hyphae; its branching, infection and appressoria formation; epidermal opening; and hyphal entry), progression (arbuscular development; hyphal coils and vesicles) to maturity (extraradical spores). Scanning electron microscopy was found to be an efficient tool for studying spatial three-dimensional progression. Adding to the advantages of advanced microscopy, potential of autofluorescence to explore the stages of symbiosis nondestructively was also established. We also report imaging of ultrathin sections by bright field microscopy to provide finer details at subcellular interface. Owing to the merits of nondestructive sampling, ease of sample preparation, autofluorescence (no dye required), no use of toxic chemicals, rapid analysis and in depth characterization confocal laser scanning microscopy was identified as the most preferred technique. The method thus developed can be used for detailed structural inquisition of mycorrhizal symbiosis both in in planta and in an in vitro system.}, }
@article {pmid31073281, year = {2019}, author = {Gao, M and Benge, A and Wu, TJ and Javier, R}, title = {Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Rhizobium Genome for Monitoring the Expression of Rhizobial Genes In Vivo.}, journal = {Biological procedures online}, volume = {21}, number = {}, pages = {8}, doi = {10.1186/s12575-019-0096-y}, pmid = {31073281}, issn = {1480-9222}, abstract = {Background: The soil bacterium Sinorhizobium meliloti and its allies are important nitrogen-fixing bacterial symbionts that cause N2-fixing nodules on the roots of legumes. Chromosomal ß-glucuronidase gene (uidA) transcriptional fusions are frequently used to monitor the expression of bacterial genes during the symbiosis. However, the construction of the fusions is laborious.<br><br>Results: The narrow-host-range, fusion selective plasmid pVMG was constructed and used as a vector for the construction of chromosomal uidA transcriptional fusions in the S. meliloti genome. Translation termination codons were added in all three reading frames upstream of the promoterless uidA in this vector to ensure transcriptional fusions. pVMG replicated to high copy number in Escherichia coli, offering advantages for the isolation of fusion-containing plasmids and the restriction analysis. Genomic locations of uidA fusions were verified in a simple PCR experiment. All these helps reduce the sample processing time and efforts. As a demonstration of its usefulness, the N-acyl homoserine lactone (AHL) signal synthase gene promoter was fused to uidA and shown to be expressed by S. meliloti in the senescence zone of the nodule on the host plant, M. truncatula. This indicates the presence of AHL signals at the late stages of symbiosis.<br><br>Conclusions: A simple, pVMG-based method for construction of chromosomal uidA transcriptional fusions has been successfully used in the model rhizobium S. meliloti. It is also applicable for other rhizobial strains.}, }
@article {pmid31072343, year = {2019}, author = {Chamberlain, NB and Mehari, YT and Hayes, BJ and Roden, CM and Kidane, DT and Swehla, AJ and Lorenzana-DeWitt, MA and Farone, AL and Gunderson, JH and Berk, SG and Farone, MB}, title = {Infection and nuclear interaction in mammalian cells by 'Candidatus Berkiella cookevillensis', a novel bacterium isolated from amoebae.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {91}, doi = {10.1186/s12866-019-1457-z}, pmid = {31072343}, issn = {1471-2180}, support = {R833102//U.S. Environmental Protection Agency/ ; R827111//U.S. Environmental Protection Agency/ ; }, abstract = {BACKGROUND: 'Candidatus Berkiella cookevillensis' and 'Ca. Berkiella aquae' have previously been described as intranuclear bacteria of amoebae. Both bacteria were isolated from amoebae and were described as appearing within the nuclei of Acanthamoeba polyphaga and ultimately lysing their host cells within 4 days. Both bacteria are Gammaproteobacteria in the order Legionellales with the greatest similarity to Coxiella burnetii. Neither bacterium grows axenically in artificial culture media. In this study, we further characterized 'Ca. B. cookevillensis' by demonstrating association with nuclei of human phagocytic and nonphagocytic cell lines.<br><br>RESULTS: Transmission electron microscopy (TEM) and confocal microscopy were used to confirm nuclear co-localization of 'Ca. B. cookevillensis' in the amoeba host A. polyphaga with 100% of cells having bacteria co-localized with host nuclei by 48 h. TEM and confocal microscopy demonstrated that the bacterium was also observed to be closely associated with nuclei of human U937 and THP-1 differentiated macrophage cell lines and nonphagocytic HeLa human epithelial-like cells. Immunofluorescent staining revealed that the bacteria-containing vacuole invaginates the nuclear membranes and appears to cross from the cytoplasm into the nucleus as an intact vacuole.<br><br>CONCLUSION: Results of this study indicate that a novel coccoid bacterium isolated from amoebae can infect human cell lines by associating with the host cell nuclei, either by crossing the nuclear membranes or by deeply invaginating the nuclear membranes. When associated with the nuclei, the bacteria appear to be bound within a vacuole and replicate to high numbers by 48 h. We believe this is the first report of such a process involving bacteria and human cell lines.}, }
@article {pmid31071427, year = {2019}, author = {Rahnama, M and Maclean, P and Fleetwood, DJ and Johnson, RD}, title = {The LaeA orthologue in Epichloë festucae is required for symbiotic interaction with Lolium perenne.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {129}, number = {}, pages = {74-85}, doi = {10.1016/j.fgb.2019.05.001}, pmid = {31071427}, issn = {1096-0937}, abstract = {LaeA is a conserved global regulator of secondary metabolism and development in fungi. It is often required for successful pathogenic interactions. In this study, the laeA homologue in the fungal grass endophyte E. festucae was deleted and functionally characterised in vitro and its role in the mutualistic E. festucae interaction with Lolium perenne (perennial ryegrass) was determined. We showed that laeA in E. festucae is required for normal hyphal morphology, resistance to oxidative stress, and conidiation under nutrient-limited in vitro conditions. In planta studies revealed that laeA is expressed in a tissue-specific manner and is required to form a compatible plant interaction, with the majority of seedlings inoculated with a laeA deletion mutant either dying or being uninfected. In mature infected plants no difference was observed in the number or morphology of endophytic hyphae. However, the number of epiphyllous hyphae were greatly increased. Comparative transcriptomics analyses suggested roles for plant cell wall degradation, fungal cell wall composition, secondary metabolism and small-secreted proteins in Epichloë foliar symbiosis.}, }
@article {pmid31071294, year = {2019}, author = {Brown, EM and Ke, X and Hitchcock, D and Jeanfavre, S and Avila-Pacheco, J and Nakata, T and Arthur, TD and Fornelos, N and Heim, C and Franzosa, EA and Watson, N and Huttenhower, C and Haiser, HJ and Dillow, G and Graham, DB and Finlay, BB and Kostic, AD and Porter, JA and Vlamakis, H and Clish, CB and Xavier, RJ}, title = {Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {668-680.e7}, doi = {10.1016/j.chom.2019.04.002}, pmid = {31071294}, issn = {1934-6069}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, abstract = {Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides-derived sphingolipids including ceramide phosphoinositol and deoxy-sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.}, }
@article {pmid31070991, year = {2019}, author = {Lindsay, PL and Williams, BN and MacLean, A and Harrison, MJ}, title = {A Phosphate-Dependent Requirement for Transcription Factors IPD3 and IPD3L During Arbuscular Mycorrhizal Symbiosis in Medicago truncatula.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI01190006R}, doi = {10.1094/MPMI-01-19-0006-R}, pmid = {31070991}, issn = {0894-0282}, abstract = {During arbuscular mycorrhizal (AM) symbiosis, activation of a symbiosis signaling pathway induces gene expression necessary for accommodation of AM fungi. Here, we focus on pathway components Medicago truncatula INTERACTING PROTEIN OF DOES NOT MAKE INFECTIONS 3 (IPD3) and IPD3 LIKE (IPD3L), which are potential orthologs of Lotus japonicus CYCLOPS, a transcriptional regulator essential for AM symbiosis. In the double mutant ipd3 ipd3l, hyphal entry through the epidermis and overall colonization levels are reduced relative to the wild type but fully developed arbuscules are present in the cortex. In comparison with the wild type, colonization of ipd3 ipd3l is acutely sensitive to higher phosphate levels in the growth medium, with a disproportionate decrease in epidermal penetration, overall colonization, and symbiotic gene expression. When constitutively expressed in ipd3 ipd3l, an autoactive DOES NOT MAKE INFECTIONS 3 induces the expression of transcriptional regulators REDUCED ARBUSCULAR MYCORRHIZA 1 and REQUIRED for ARBUSCULE DEVELOPMENT 1, providing a possible avenue for arbuscule development in the absence of IPD3 and IPD3L. An increased sensitivity of ipd3 ipd3l to GA3 suggests an involvement of DELLA. The data reveal partial redundancy in the symbiosis signaling pathway, which may ensure robust signaling in low-phosphorus environments, while IPD3 and IPD3L maintain signaling in higher-phosphorus environments. The latter may buffer the pathway from short-term variation in phosphorus levels encountered by roots during growth in heterogeneous soil environments.}, }
@article {pmid31069523, year = {2019}, author = {Scott-Brown, AS and Arnold, SEJ and Kite, GC and Farrell, IW and Farman, DI and Collins, DW and Stevenson, PC}, title = {Mechanisms in mutualisms: a chemically mediated thrips pollination strategy in common elder.}, journal = {Planta}, volume = {250}, number = {1}, pages = {367-379}, doi = {10.1007/s00425-019-03176-5}, pmid = {31069523}, issn = {1432-2048}, mesh = {Animals ; *Feeding Behavior ; Female ; Flowers/chemistry/growth &amp; development/physiology ; Inflorescence/chemistry/growth &amp; development/physiology ; Male ; Pollen/chemistry/growth &amp; development/physiology ; Pollination ; Reproduction ; Sambucus nigra/*chemistry/growth &amp; development/physiology ; *Signal Transduction ; Symbiosis ; Thysanoptera/*physiology ; Volatile Organic Compounds/*analysis/metabolism ; }, abstract = {MAIN CONCLUSION: This study provides first evidence of a thrips species pollinating Sambucus nigra and describes how interactions are driven by plant biochemical signalling and moderated by temporal changes in floral chemistry. The concept of flower-feeding thrips as pollinating insects in temperate regions is rarely considered as they are more frequently regarded to be destructive florivores feeding on pollen and surrounding plant tissue. Combining laboratory and field-based studies we examined interactions between Sambucus nigra (elderflower) and Thrips major within their native range to ascertain the role of thrips in the pollination of this species and to determine if floral chemicals mediated flower visits. If thrips provide a pollination service to S. nigra, then this will likely manifest in traits that attract the pollinating taxa at temporally critical points in floral development. T. major were highly abundant in inflorescences of S. nigra, entering flowers when stigmas were pollen-receptive and anthers were immature. When thrips were excluded from the inflorescences, fruit-set failed. Linalool was the major component of the inflorescence headspace with peak abundance coinciding with the highest number of adult thrips visiting flowers. Thrips were absent in buds and their numbers declined again in senescing flowers inversely correlating with the concentration of cyanogenic glycosides recorded in the floral tissue. Our data show that S. nigra floral chemistry mediates the behaviour of pollen-feeding thrips by attracting adults in high numbers to the flowers at pre-anthesis stage, while producing deterrent compounds prior to fruit development. Taking an integrative approach to studying thrips behaviour and floral biology we provide a new insight into the previously ambiguously defined pollination strategies of S. nigra and provide evidence suggesting that the relationship between T. major and S. nigra is mutualistic.}, }
@article {pmid31067698, year = {2019}, author = {Vaz Martins, T and Livina, VN}, title = {What Drives Symbiotic Calcium Signalling in Legumes? Insights and Challenges of Imaging.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092245}, pmid = {31067698}, issn = {1422-0067}, support = {BB/J004553/1; BB/P012574/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Calcium Signaling ; Fabaceae/*metabolism/microbiology ; Microscopy, Fluorescence/methods ; Rhizobium/metabolism/pathogenicity ; *Symbiosis ; }, abstract = {We review the contribution of bioimaging in building a coherent understanding of Ca 2 + signalling during legume-bacteria symbiosis. Currently, two different calcium signals are believed to control key steps of the symbiosis: a Ca 2 + gradient at the tip of the legume root hair is involved in the development of an infection thread, while nuclear Ca 2 + oscillations, the hallmark signal of this symbiosis, control the formation of the root nodule, where bacteria fix nitrogen. Additionally, different Ca 2 + spiking signatures have been associated with specific infection stages. Bioimaging is intrinsically a cross-disciplinary area that requires integration of image recording, processing and analysis. We used experimental examples to critically evaluate previously-established conclusions and draw attention to challenges caused by the varying nature of the signal-to-noise ratio in live imaging. We hypothesise that nuclear Ca 2 + spiking is a wide-range signal involving the entire root hair and that the Ca 2 + signature may be related to cytoplasmic streaming.}, }
@article {pmid31066947, year = {2019}, author = {Muletz-Wolz, CR and Fleischer, RC and Lips, KR}, title = {Fungal disease and temperature alter skin microbiome structure in an experimental salamander system.}, journal = {Molecular ecology}, volume = {28}, number = {11}, pages = {2917-2931}, doi = {10.1111/mec.15122}, pmid = {31066947}, issn = {1365-294X}, support = {//National Park Service/ ; F13B20412//Environmental Protection Agency STAR/ ; }, abstract = {Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species.}, }
@article {pmid31066909, year = {2019}, author = {Martínez-Medina, A and Pescador, L and Fernández, I and Rodríguez-Serrano, M and García, JM and Romero-Puertas, MC and Pozo, MJ}, title = {Nitric oxide and phytoglobin PHYTOGB1 are regulatory elements in the Solanum lycopersicum-Rhizophagus irregularis mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {223}, number = {3}, pages = {1560-1574}, doi = {10.1111/nph.15898}, pmid = {31066909}, issn = {1469-8137}, support = {AGL2015-64990-C2-1-R//Ministerio de Economía y Competitividad/ ; P12BIO296//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; }, abstract = {The regulatory role of nitric oxide (NO) and phytoglobins in plant response to pathogenic and mutualistic microbes has been evidenced. However, little is known about their function in the arbuscular mycorrhizal (AM) symbiosis. We investigated whether NO and phytoglobin PHYTOGB1 are regulatory components in the AM symbiosis. Rhizophagus irregularis in vitro-grown cultures and tomato plants were used to monitor AM-associated NO-related root responses as compared to responses triggered by the pathogen Fusarium oxysporum. A genetic approach was conducted to understand the role of PHYTOGB1 on NO signaling during both interactions. After a common early peak in NO levels in response to both fungi, a specific NO accumulation pattern was triggered in tomato roots during the onset of the AM interaction. PHYTOGB1 was upregulated by the AM interaction. By contrast, the pathogen triggered a continuous NO accumulation and a strong downregulation of PHYTOGB1. Manipulation of PHYTOGB1 levels in overexpressing and silenced roots led to a deregulation of NO levels and altered mycorrhization and pathogen infection. We demonstrate that the onset of the AM symbiosis is associated with a specific NO-related signature in the host root. We propose that NO regulation by PHYTOGB1 is a regulatory component of the AM symbiosis.}, }
@article {pmid31065250, year = {2019}, author = {Irisarri, P and Cardozo, G and Tartaglia, C and Reyno, R and Gutiérrez, P and Lattanzi, FA and Rebuffo, M and Monza, J}, title = {Selection of Competitive and Efficient Rhizobia Strains for White Clover.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {768}, doi = {10.3389/fmicb.2019.00768}, pmid = {31065250}, issn = {1664-302X}, abstract = {The practice of inoculating forage legumes with rhizobia strains is widespread. It is assumed that the inoculated strain determines the performance of the symbiosis and nitrogen fixation rates. However, native-naturalized strains can be competitive, and actual nodule occupancy is often scarcely investigated. In consequence, failures in establishment, and low productivity attributed to poor performance of the inoculant may merely reflect the absence of the inoculated strain in the nodules. This study lays out a strategy followed for selecting a Rhizobium leguminosarum sv. trifolii strain for white clover (Trifolium repens) with competitive nodule occupancy. First, the competitiveness of native-naturalized rhizobia strains selected for their efficiency to fix N2 in clover and tagged with gusA was evaluated in controlled conditions with different soils. Second, three of these experimental strains with superior nodule occupancy plus the currently recommended commercial inoculant, an introduced strain, were tested in the field in 2 years and at two sites. Plant establishment, herbage productivity, fixation of atmospheric N2 (15N natural abundance), and nodule occupancy (ERIC-PCR genomic fingerprinting) were measured. In both years and sites, nodule occupancy of the native-naturalized experimental strains was either higher or similar to that of the commercial inoculant in both primary and secondary roots. The difference was even greater in stolon roots nodules, where nodule occupancy of the native-naturalized experimental strains was at least five times greater. The amount of N fixed per unit plant mass was consistently higher with native-naturalized experimental strains, although the proportion of N derived from atmospheric fixation was similar for all strains. Plant establishment and herbage production, as well as clover contribution in oversown native grasslands, were either similar or higher in white clover inoculated with the native-naturalized experimental strains. These results support the use of our implemented strategy for developing a competitive inoculant from native-naturalized strains.}, }
@article {pmid31064848, year = {2019}, author = {Buchta Rosean, C and Bostic, RR and Ferey, JCM and Feng, TY and Azar, FN and Tung, KS and Dozmorov, MG and Smirnova, E and Bos, PD and Rutkowski, MR}, title = {Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor-Positive Breast Cancer.}, journal = {Cancer research}, volume = {79}, number = {14}, pages = {3662-3675}, doi = {10.1158/0008-5472.CAN-18-3464}, pmid = {31064848}, issn = {1538-7445}, mesh = {*Breast Neoplasms ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Inflammation ; Symbiosis ; Tumor Microenvironment ; }, abstract = {It is unknown why some patients with hormone receptor-positive (HR+) breast cancer present with more aggressive and invasive disease. Metastatic dissemination occurs early in disease and is facilitated by cross-talk between the tumor and tissue environment, suggesting that undefined host-intrinsic factors enhance early dissemination and the probability of developing metastatic disease. Here, we have identified commensal dysbiosis as a host-intrinsic factor associated with metastatic dissemination. Using a mouse model of HR+ mammary cancer, we demonstrate that a preestablished disruption of commensal homeostasis results in enhanced circulating tumor cells and subsequent dissemination to the tumor-draining lymph nodes and lungs. Commensal dysbiosis promoted early inflammation within the mammary gland that was sustained during HR+ mammary tumor progression. Furthermore, dysbiosis enhanced fibrosis and collagen deposition both systemically and locally within the tumor microenvironment and induced significant myeloid infiltration into the mammary gland and breast tumor. These effects were recapitulated both by directly targeting gut microbes using nonabsorbable antibiotics and by fecal microbiota transplantation of dysbiotic cecal contents, demonstrating the direct impact of gut dysbiosis on mammary tumor dissemination. This study identifies dysbiosis as a preexisting, host-intrinsic regulator of tissue inflammation, myeloid recruitment, fibrosis, and dissemination of tumor cells in HR+ breast cancer. SIGNIFICANCE: Identification of commensal dysbiosis as a host-intrinsic factor mediating evolution of metastatic breast cancer allows for development of interventions or diagnostic tools for patients at highest risk for developing metastatic disease.See related commentary by Ingman, p. 3539.}, }
@article {pmid31063471, year = {2019}, author = {Joshi, RK and Mehendale, SM}, title = {Determinants of consistently high HIV prevalence in Indian Districts: A multi-level analysis.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216321}, doi = {10.1371/journal.pone.0216321}, pmid = {31063471}, issn = {1932-6203}, abstract = {INTRODUCTION: Factors associated with persistently high Human Immunodeficiency Virus (HIV) prevalence levels in several districts of India are not well understood. This study was undertaken to determine the association of socio-demographic characteristics, economic factors, awareness about HIV and Sexually Transmitted Infections (STIs), and condom use with consistently high HIV prevalence in the Indian districts and to ascertain whether these associations differed across various regions of India.<br><br>METHODS: This study was carried out including all 640 districts of India. Secondary analysis of data obtained from the Census of India-2011, HIV Sentinel Surveillance in India and District Level Household Survey-III was done. Population profile, socio-economic characteristics, levels of HIV/STI/condom awareness and condom use, were compared between the districts with and without consistently high HIV prevalence. Due to the presence of collinearity among predictor variables, we used principal component analysis and the principal component scores were included as covariates for further analysis. Considering the districts at level 1 and the regions at level 2, multi-level analysis was done by generalised linear mixed models. Variance partition coefficient and median odds ratio were also calculated.<br><br>RESULTS: Sixty-three districts with consistently high HIV prevalence were found clustered in the South and the North-east regions of India. Population size, density and urbanisation were found to be positively associated with consistently high HIV prevalence in these districts. Higher levels of literacy, better socio-economic status, higher proportion of population in reproductive age group and late marriages were positively associated with consistently high HIV prevalence in all regions of India except in the Southern region. Higher levels of knowledge about the role of condoms in HIV prevention and condom use were associated with low HIV prevalence at the district level.<br><br>CONCLUSIONS: Considerable heterogeneity among factors associated with consistently high HIV prevalence at the district level in different regions of India necessitates special region-specific strategies for HIV control. Increasing awareness about HIV alone is not sufficient for controlling the HIV epidemic and there is a need to raise knowledge levels about preventive measures against HIV and promote the use of condoms amongst population.}, }
@article {pmid31062028, year = {2019}, author = {Becerra-Rivera, VA and Dunn, MF}, title = {Polyamine biosynthesis and biological roles in rhizobia.}, journal = {FEMS microbiology letters}, volume = {366}, number = {7}, pages = {}, doi = {10.1093/femsle/fnz084}, pmid = {31062028}, issn = {1574-6968}, abstract = {Polyamines are ubiquitous molecules containing two or more amino groups that fulfill varied and often essential physiological and regulatory roles in all organisms. In the symbiotic nitrogen-fixing bacteria known as rhizobia, putrescine and homospermidine are invariably produced while spermidine and norspermidine synthesis appears to be restricted to the alfalfa microsymbiont Sinorhizobium meliloti. Studies with rhizobial mutants deficient in the synthesis of one or more polyamines have shown that these compounds are important for growth, stress resistance, motility, exopolysaccharide production and biofilm formation. In this review, we describe these studies and examine how polyamines are synthesized and regulated in rhizobia.}, }
@article {pmid31061106, year = {2019}, author = {Pislariu, CI and Sinharoy, S and Torres-Jerez, I and Nakashima, J and Blancaflor, EB and Udvardi, MK}, title = {The Nodule-Specific PLAT Domain Protein NPD1 Is Required for Nitrogen-Fixing Symbiosis.}, journal = {Plant physiology}, volume = {180}, number = {3}, pages = {1480-1497}, doi = {10.1104/pp.18.01613}, pmid = {31061106}, issn = {1532-2548}, abstract = {Symbiotic nitrogen fixation by rhizobia in legume root nodules is a key source of nitrogen for sustainable agriculture. Genetic approaches have revealed important roles for only a few of the thousands of plant genes expressed during nodule development and symbiotic nitrogen fixation. Previously, we isolated >100 nodulation and nitrogen fixation mutants from a population of Tnt1-insertion mutants of Medigaco truncatula Using Tnt1 as a tag to identify genetic lesions in these mutants, we discovered that insertions in a M. truncatula nodule-specific polycystin-1, lipoxygenase, α-toxin (PLAT) domain-encoding gene, MtNPD1, resulted in development of ineffective nodules. Early stages of nodule development and colonization by the nitrogen-fixing bacterium Sinorhizobium meliloti appeared to be normal in the npd1 mutant. However, npd1 nodules ceased to grow after a few days, resulting in abnormally small, ineffective nodules. Rhizobia that colonized developing npd1 nodules did not differentiate completely into nitrogen-fixing bacteroids and quickly degraded. MtNPD1 expression was low in roots but increased significantly in developing nodules 4 d postinoculation, and expression accompanied invading rhizobia in the nodule infection zone and into the distal nitrogen fixation zone. A functional MtNPD1:GFP fusion protein localized in the space surrounding symbiosomes in infected cells. When ectopically expressed in tobacco (Nicotiana tabacum) leaves, MtNPD1 colocalized with vacuoles and the endoplasmic reticulum. MtNPD1 belongs to a cluster of five nodule-specific single PLAT domain-encoding genes, with apparent nonredundant functions.}, }
@article {pmid31059742, year = {2019}, author = {Chaubey, MG and Patel, SN and Rastogi, RP and Srivastava, PL and Singh, AK and Madamwar, D and Singh, NK}, title = {Therapeutic potential of cyanobacterial pigment protein phycoerythrin: in silico and in vitro study of BACE1 interaction and in vivo Aβ reduction.}, journal = {International journal of biological macromolecules}, volume = {134}, number = {}, pages = {368-378}, doi = {10.1016/j.ijbiomac.2019.05.006}, pmid = {31059742}, issn = {1879-0003}, abstract = {Cyanobacteria are an immense source of innovative classes of pharmacologically active compounds exhibiting various biological activities ranging from antioxidants, antibiotics, anticancer, anti-inflammatory to anti-Alzheimer's disease. In the present study, we primarily targeted the inhibition of Beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) by a naturally occurring cyanobacterial protein phycoerythrin (C-PE). BACE1 cleaves amyloid-β precursor protein (APP) and leads to accumulation of neurotoxic amyloid beta (Aβ) plaques in the brain, as an attribute of Alzheimer's disease (AD). Inhibition of BACE1 was measured in terms of their association and dissociation rate constants, thermodynamics of binding using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). The kinetic parameters for enzyme activity were also measured using synthetic decapeptide as a substrate. We further validated the potential of PE by in-vivo histopathological staining of Aβ aggregate mutant Caenorhabditis elegans CL4176 by Thioflavin-T. The present studies pave the way for the application of naturally occurring C-PE as a putative therapeutic drug for the AD.}, }
@article {pmid31059378, year = {2019}, author = {Aasen, DM and Vergara, MN}, title = {New Drug Discovery Paradigms for Retinal Diseases: A Focus on Retinal Organoids.}, journal = {Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1089/jop.2018.0140}, pmid = {31059378}, issn = {1557-7732}, abstract = {Retinal disease represents a growing global problem, both in terms of quality of life and economic impact, yet new therapies are not being developed at a sufficient rate to meet this mounting need. In this context, retinal organoids derived from human induced pluripotent stem cells hold significant promise for improving upon the current drug development process, increasing the speed and efficiency of moving potential therapeutic agents from bench to bedside. These organoid systems display the cell-cell and cell-matrix interactions, cellular heterogeneity, and physiological responses reflective of human biology and, thus, have the ability to replicate retinal disease pathology in a way that 2-dimensional cell cultures and animal models have been heretofore unable to achieve. However, organoid technology is not yet mature enough to meet the high-throughput demands of the first stages of drug screening. Hence, the augmentation of the existing drug development pipeline with retinal organoids, rather than the replacement of existing pathway components, may provide a way to harness the benefits of this improved pathological modeling. In this study, we outline the possible benefits of such a symbiosis, discuss other potential uses, and highlight barriers that remain to be overcome.}, }
@article {pmid31059123, year = {2019}, author = {Sorroche, F and Walch, M and Zou, L and Rengel, D and Maillet, F and Gibelin-Viala, C and Poinsot, V and Chervin, C and Masson-Boivin, C and Gough, C and Batut, J and Garnerone, AM}, title = {Endosymbiotic Sinorhizobium meliloti modulate Medicago root susceptibility to secondary infection via ethylene.}, journal = {The New phytologist}, volume = {223}, number = {3}, pages = {1505-1515}, doi = {10.1111/nph.15883}, pmid = {31059123}, issn = {1469-8137}, support = {ANR-10-LABX-41//Agence Nationale de la Recherche/ ; ANR-15-CE20-0004-01//Agence Nationale de la Recherche/ ; //China Scholarship Council/ ; //Agreenskills mobility programme/ ; }, abstract = {A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cyclic adenosine 3',5'-monophosphate (cAMP) cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction.}, }
@article {pmid31059122, year = {2019}, author = {Zhang, L and Yuan, L and Staehelin, C and Li, Y and Ruan, J and Liang, Z and Xie, Z and Wang, W and Xie, J and Huang, S}, title = {The LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE 1 protein of banana is required for perception of pathogenic and symbiotic signals.}, journal = {The New phytologist}, volume = {223}, number = {3}, pages = {1530-1546}, doi = {10.1111/nph.15888}, pmid = {31059122}, issn = {1469-8137}, support = {31301756//National Natural Science Foundation of China/ ; 31670241//National Natural Science Foundation of China/ ; 31770476//National Natural Science Foundation of China/ ; 201510010270//Science and Technology Program of Guangzhou/ ; 1630052019020//The Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences/ ; }, abstract = {How plants can distinguish pathogenic and symbiotic fungi remains largely unknown. Here, we characterized the role of MaLYK1, a lysin motif receptor kinase of banana. Live cell imaging techniques were used in localization studies. RNA interference (RNAi)-silenced transgenic banana plants were generated to analyze the biological role of MaLYK1. The MaLYK1 ectodomain, chitin beads, chitooligosaccharides (COs) and mycorrhizal lipochitooligosaccharides (Myc-LCOs) were used in pulldown assays. Ligand-induced MaLYK1 complex formation was tested in immunoprecipitation experiments. Chimeric receptors were expressed in Lotus japonicus to characterize the function of the MaLYK1 kinase domain. MaLYK1 was localized to the plasma membrane. MaLYK1 expression was induced by Foc4 (Fusarium oxysporum f. sp. cubense race 4) and diverse microbe-associated molecular patterns. MaLYK1-silenced banana lines showed reduced chitin-triggered defense responses, increased Foc4-induced disease symptoms and reduced mycorrhization. The MaLYK1 ectodomain was pulled down by chitin beads and LCOs or COs impaired this process. Ligand treatments induced MaLYK1 complex formation in planta. The kinase domain of MaLYK1 could functionally replace that of the chitin elicitor receptor kinase 1 (AtCERK1) in Arabidopsis thaliana and of a rhizobial LCO (Nod factor) receptor (LjNFR1) in L. japonicus. MaLYK1 represents a central molecular switch that controls defense- and symbiosis-related signaling.}, }
@article {pmid31058830, year = {2019}, author = {Ngangbam, AK and Mouatt, P and Smith, J and Waters, DLE and Benkendorff, K}, title = {Bromoperoxidase Producing Bacillus spp. Isolated from the Hypobranchial Glands of a Muricid Mollusc Are Capable of Tyrian Purple Precursor Biogenesis.}, journal = {Marine drugs}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/md17050264}, pmid = {31058830}, issn = {1660-3397}, mesh = {Animals ; Bacillus/*genetics/isolation &amp; purification/metabolism ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Branchial Region/metabolism/microbiology ; Gastropoda/*microbiology ; Indoles/analysis ; Mollusca ; Peroxidases/*genetics ; Sequence Analysis, RNA ; Symbiosis ; }, abstract = {The secondary metabolite Tyrian purple, also known as shellfish purple and royal purple, is a dye with historical importance for humans. The biosynthetic origin of Tyrian purple in Muricidae molluscs is not currently known. A possible role for symbiotic bacteria in the production of tyrindoxyl sulphate, the precursor to Tyrian purple stored in the Australian species, Dicathais orbita, has been proposed. This study aimed to culture bacterial symbionts from the purple producing hypobranchial gland, and screen the isolates for bromoperoxidase genes using molecular methods. The ability of bromoperoxidase positive isolates to produce the brominated indole precursor to Tyrian purple was then established by extraction of the culture, and analysis by liquid chromatography-mass spectrometry (LC-MS). In total, 32 bacterial isolates were cultured from D. orbita hypobranchial glands, using marine agar, marine agar with hypobranchial gland aqueous extracts, blood agar, thiosulphate citrate bile salts sucrose agar, and cetrimide agar at pH 7.2. These included 26 Vibrio spp., two Bacillus spp., one Phaeobacter sp., one Shewanella sp., one Halobacillus sp. and one Pseudoalteromonas sp. The two Bacillus species were the only isolates found to have coding sequences for bromoperoxidase enzymes. LC-MS analysis of the supernatant and cell pellets from the bromoperoxidase producing Bacillus spp. cultured in tryptone broth, supplemented with KBr, confirmed their ability to produce the brominated precursor to Tyrian purple, tyrindoxyl sulphate. This study supports a potential role for symbiotic Bacillus spp. in the biosynthesis of Tyrian purple.}, }
@article {pmid31058335, year = {2019}, author = {Gibelin-Viala, C and Amblard, E and Puech-Pages, V and Bonhomme, M and Garcia, M and Bascaules-Bedin, A and Fliegmann, J and Wen, J and Mysore, KS and le Signor, C and Jacquet, C and Gough, C}, title = {The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {223}, number = {3}, pages = {1516-1529}, doi = {10.1111/nph.15891}, pmid = {31058335}, issn = {1469-8137}, support = {DBI-0703285 and IOS-1127155//National Science Foundation/ ; //INRA/ ; //CNRS/ ; //Université Paul Sabatier/ ; ANR-14-CE18-0008-02//French Agence Nationale de la Recherche 'NICE CROPS' project/ ; ANR-10-LABX-41//Laboratoire d'Excellence' LABEX entitled TULIP/ ; }, abstract = {Plant -specific lysin-motif receptor-like kinases (LysM-RLKs) are implicated in the perception of N-acetyl glucosamine-containing compounds, some of which are important signal molecules in plant-microbe interactions. Among these, both lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs) are proposed as arbuscular mycorrhizal (AM) fungal symbiotic signals. COs can also activate plant defence, although there are scarce data about CO production by pathogens, especially nonfungal pathogens. We tested Medicago truncatula mutants in the LysM-RLK MtLYK9 for their abilities to interact with the AM fungus Rhizophagus irregularis and the oomycete pathogen Aphanomyces euteiches. This prompted us to analyse whether A. euteiches can produce COs. Compared with wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. By contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. Aphanomyces euteiches was also shown to produce short COs, mainly CO II, but also CO III and CO IV, and traces of CO V, both ex planta and in planta. MtLYK9 thus has a dual role in plant immunity and the AM symbiosis, which raises questions about the functioning and the ancestral origins of such a receptor protein.}, }
@article {pmid31058096, year = {2019}, author = {Moreno-Altamirano, MMB and Kolstoe, SE and Sánchez-García, FJ}, title = {Virus Control of Cell Metabolism for Replication and Evasion of Host Immune Responses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {95}, doi = {10.3389/fcimb.2019.00095}, pmid = {31058096}, issn = {2235-2988}, abstract = {Over the last decade, there has been significant advances in the understanding of the cross-talk between metabolism and immune responses. It is now evident that immune cell effector function strongly depends on the metabolic pathway in which cells are engaged in at a particular point in time, the activation conditions, and the cell microenvironment. It is also clear that some metabolic intermediates have signaling as well as effector properties and, hence, topics such as immunometabolism, metabolic reprograming, and metabolic symbiosis (among others) have emerged. Viruses completely rely on their host's cell energy and molecular machinery to enter, multiply, and exit for a new round of infection. This review explores how viruses mimic, exploit or interfere with host cell metabolic pathways and how, in doing so, they may evade immune responses. It offers a brief outline of key metabolic pathways, mitochondrial function and metabolism-related signaling pathways, followed by examples of the mechanisms by which several viral proteins regulate host cell metabolic activity.}, }
@article {pmid31057581, year = {2019}, author = {Hossain, MS and Hoang, NT and Yan, Z and Tóth, K and Meyers, BC and Stacey, G}, title = {Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {475}, doi = {10.3389/fpls.2019.00475}, pmid = {31057581}, issn = {1664-462X}, abstract = {MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.}, }
@article {pmid31057515, year = {2019}, author = {Methou, P and Hernández-Ávila, I and Aube, J and Cueff-Gauchard, V and Gayet, N and Amand, L and Shillito, B and Pradillon, F and Cambon-Bonavita, MA}, title = {Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {808}, doi = {10.3389/fmicb.2019.00808}, pmid = {31057515}, issn = {1664-302X}, abstract = {Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female's abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.}, }
@article {pmid31057502, year = {2019}, author = {Rebollar, EA and Harris, RN}, title = {Editorial: Ecology of Amphibian-Microbial Symbioses.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {766}, doi = {10.3389/fmicb.2019.00766}, pmid = {31057502}, issn = {1664-302X}, }
@article {pmid31057424, year = {2019}, author = {Skaljac, M and Vogel, H and Wielsch, N and Mihajlovic, S and Vilcinskas, A}, title = {Transmission of a Protease-Secreting Bacterial Symbiont Among Pea Aphids via Host Plants.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {438}, doi = {10.3389/fphys.2019.00438}, pmid = {31057424}, issn = {1664-042X}, abstract = {Aphids are economically important pest insects that damage plants by phloem feeding and the transmission of plant viruses. Their ability to feed exclusively on nutritionally poor phloem sap is dependent on the obligatory symbiotic bacterium Buchnera aphidicola, but additional facultative symbionts may also be present, a common example of which is Serratia symbiotica. Many Serratia species secrete extracellular enzymes, so we hypothesised that S. symbiotica may produce proteases that help aphids to feed on plants. Molecular analysis, including fluorescence in situ hybridization (FISH), revealed that S. symbiotica colonises the gut, salivary glands and mouthparts (including the stylet) of the pea aphid Acyrthosiphon pisum, providing a mechanism to transfer the symbiont into host plants. S. symbiotica was also detected in plant tissues wounded by the penetrating stylet and was transferred to naïve aphids feeding on plants containing this symbiont. The maintenance of S. symbiotica by repeated transmission via plants may explain the high frequency of this symbiont in aphid populations. Proteomic analysis of the supernatant from a related but cultivable S. symbiotica strain cultured in liquid medium revealed the presence of known and novel proteases including metalloproteases. The corresponding transcripts encoding these S. symbiotica enzymes were detected in A. pisum and in plants carrying the symbiont, although the mRNA was much more abundant in the aphids. Our data suggest that enzymes from S. symbiotica may facilitate the digestion of plant proteins, thereby helping to suppress plant defense, and that the symbionts are important mediators of aphid-plant interactions.}, }
@article {pmid31054574, year = {2019}, author = {Carotenuto, G and Sciascia, I and Oddi, L and Volpe, V and Genre, A}, title = {Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {180}, doi = {10.1186/s12870-019-1791-1}, pmid = {31054574}, issn = {1471-2229}, support = {Dottorati di Ricerca XXXI ciclo//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; Ricerca Locale 2016-2017//Università degli Studi di Torino/ ; }, mesh = {*Cell Nucleus Size ; Image Processing, Computer-Assisted ; Medicago truncatula/*ultrastructure ; Mycorrhizae/*ultrastructure ; Plant Roots/ultrastructure ; }, abstract = {BACKGROUND: The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.<br><br>RESULTS: We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.<br><br>CONCLUSIONS: In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.}, }
@article {pmid31053805, year = {2019}, author = {Kelsey, R}, title = {Magnetotactic symbiosis in marine sediments.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {7}, pages = {398}, doi = {10.1038/s41579-019-0210-9}, pmid = {31053805}, issn = {1740-1534}, }
@article {pmid31053328, year = {2019}, author = {Poinar, G and Vega, FE}, title = {A mid-Cretaceous trichomycete, Priscadvena corymbosa gen. et sp. nov., in Burmese amber.}, journal = {Fungal biology}, volume = {123}, number = {5}, pages = {393-396}, doi = {10.1016/j.funbio.2019.02.007}, pmid = {31053328}, issn = {1878-6146}, mesh = {*Amber ; Animals ; Coleoptera/*microbiology ; *Fossils ; Fungi/*classification/cytology/*isolation &amp; purification ; Microscopy ; Mouth/microbiology ; Myanmar ; }, abstract = {Priscadvena corymbosa gen. et sp. nov., is described from thalli and sporangia emerging from the oral cavity of a click beetle (Coleoptera: Elateridae) in mid-Cretaceous Burmese amber. The fossil contains several features unknown in extant Trichomycetes including a click beetle (Coleoptera: Elateridae) host, spiny, aerial thalli with the entire thallus bearing numerous small uninucleate globular spores and stalks attached to the oral cavity of its host. Based on these features, P. corymbosa gen. et sp. nov. is placed in a new family, Priscadvenaceae fam. nov., and new order, Priscadvenales ord. nov. The new morphological and behavioral features of the fossil add to the diversity of the trichomycetes as currently defined.}, }
@article {pmid31053326, year = {2019}, author = {Arora, P and Wani, ZA and Ahmad, T and Sultan, P and Gupta, S and Riyaz-Ul-Hassan, S}, title = {Community structure, spatial distribution, diversity and functional characterization of culturable endophytic fungi associated with Glycyrrhiza glabra L.}, journal = {Fungal biology}, volume = {123}, number = {5}, pages = {373-383}, doi = {10.1016/j.funbio.2019.02.003}, pmid = {31053326}, issn = {1878-6146}, mesh = {Anti-Infective Agents/metabolism ; Endophytes/*classification/genetics/*isolation &amp; purification/physiology ; Fungi/*classification/genetics/*isolation &amp; purification/physiology ; Glycyrrhiza/*microbiology ; India ; Plant Development ; *Symbiosis ; }, abstract = {A total of 266 endophytic fungal isolates were recovered from 1019 tissue segments of Glycyrrhiza glabra collected from four different locations in the North-Western Himalayas. The endophytes grouped into 21 genera and 38 different taxa. The host had strong affinity for the genus Phoma, followed by Fusarium. The species richness was highest at the sub-tropical location, followed by the sub-temperate location and the temperate locations, respectively. The tissue specificity of endophytes was also evident. Some endophytes showed potential antimicrobial activity against phyto-pathogens indicating that they may be helpful to the host in evading pathogens. All the endophytic taxa produced the plant growth promoting hormone, indole acetic acid (IAA), though in varying concentrations. None of these endophytes caused any symptoms of disease in co-cultivation with the tissue cultured plants. Further, all the endophytes had a positive influence on the phenolic and flavonoid content of the host. Three endophytes, Stagonosporopsis cucurbitacearum, Bionectria sp. and Aspergillus terreus also increased the host root (rhizome) and shoot growth visibly. Such endophytes are potential candidates for developing endophyte-based technologies for sustainable cultivation and enhanced productivity of G. glabra. This is the first report of community structure and biological properties of fungal endophytes associated with G. glabra.}, }
@article {pmid31051397, year = {2019}, author = {Moshiri, F and Ebrahimi, H and Ardakani, MR and Rejali, F and Mousavi, SM}, title = {Biogeochemical distribution of Pb and Zn forms in two calcareous soils affected by mycorrhizal symbiosis and alfalfa rhizosphere.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {241-248}, doi = {10.1016/j.ecoenv.2019.04.055}, pmid = {31051397}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; Glomeromycota/*drug effects/genetics ; Iran ; Lead/*analysis ; Medicago sativa/growth &amp; development/*microbiology ; Mycorrhizae/chemistry/*drug effects ; Random Allocation ; Research Design ; *Rhizosphere ; Soil/chemistry ; Soil Pollutants/*analysis ; Symbiosis ; Zinc/*analysis ; }, abstract = {Using of arbuscular mycorrhizal fungi (AMF) has emerged as a new technique to alleviate the toxic metals stress through changing their chemical behavior. The present work was conducted as a factorial arrangement based on a completely randomized design to study the inoculation effects of Glomus intraradices, Glomus mosseae and Glomus etunicatum, on Pb and Zn fractions in the rhizosphere of alfalfa by using rhizobox technique in two agricultural soils with different Zn and Pb concentrations [with low (LH) and high (HH) concentration levels]. The results showed that AMF colonization promoted plant growth and lowered the shoot and root Pb and shoot Zn concentrations in the studied soils compared to uninoculated treatments. Mycorrhizal colonization significantly increased the Ca(NO3)2- extractable Zn and ORG-Zn (respectively 500 and 59.6% more than the uninoculated treatment) and decreased the OXI-Zn (20.32% less than the none inoculated treatment) in the HH soil. By contrast, mycorrhizae slightly increased the CARB, OXI and ORG-Zn forms in the LH soil compared to the uninoculation condition. In the AMF- treated HH soil, an increase was recorded in the Ca(NO3)2- extractable Pb, EXCH-Pb and CARB-Pb (respectively, 17.65, 3.09 and 14.22% compared to the none inoculated treatment) and a decrease in the OXI and ORG-Pb forms (respectively, 28.79 and 13.51% compared to the uninoculated treatment). A reverse status was observed for Pb changes in the LH soil. Depending on the contamination level, the mycorrhizal inoculation differentially affected the Pb and Zn fractions at different distances from the root surface. In the LH soil, at <5 mm distance (i.e. rhizospheric soil), the mycorrhizal inoculation decreased the CARB (about 17.99%) and OXI -Zn (about 29.63%) forms compared to bulk soil (i.e. > 5 mm distance) while ORG-Zn was increased up to 48.63%. However, Ca(NO3)2- extractable, CARB and ORG-Pb was increased in rhizosphere soil (respectively, 89.33, 3.84 and 6.14%) and OXI-Pb was decreased up to 10.36% compared to the bulk soil. In the HH soil, mycorrhizal inoculation increased the CARB and OXI-Zn (respectively, 1.76 and 5.71%) and OXI-Pb fractions (11.56%) compared to the <5 mm distances. Whereas, it reduced the Ca(NO3)2- extractable, EXCH, and ORG-Zn (Respectively, 52.70, 19.19 and 30.16%) and Ca(NO3)2- extractable, CARB and ORG-Pb (respectively, 47.18, 3.70 and 5.79%). These results revealed that depending on the soil contamination level and nature of the element, AMF colonization affects biogeochemical fractions of the metals and their accumulation in the plant tissues.}, }
@article {pmid31051335, year = {2019}, author = {Molinero-Rosales, N and Martín-Rodríguez, JÁ and Ho-Plágaro, T and García-Garrido, JM}, title = {Identification and expression analysis of the arbuscular mycorrhiza-inducible Rieske non-heme oxygenase Ptc52 gene from tomato.}, journal = {Journal of plant physiology}, volume = {237}, number = {}, pages = {95-103}, doi = {10.1016/j.jplph.2019.04.009}, pmid = {31051335}, issn = {1618-1328}, mesh = {Amino Acid Sequence ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Lycopersicon esculentum/enzymology/*genetics/microbiology ; Mycorrhizae/*physiology ; Oxygenases/chemistry/*genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Promoter Regions, Genetic ; Sequence Alignment ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) formation enhances plant growth and fitness through improved uptake of water and mineral nutrients in exchange for carbon compounds to the AM fungus. The fungal structure for the reciprocal exchange of nutrients in the symbiosis is the arbuscule, and defence genes expressed in cells containing arbuscules could play a role in the control of hyphal spread and arbuscule formation in the root. We characterized and analyzed the Ptc52 gene from tomato (SlPtc52), a member of the gene family of non-heme oxygenases, whose function has been related to the lethal leaf spot 1 (Lls1) lesion mimic phenotype in plants which is sometimes associated with enhanced disease resistance. Sequence analysis of the SlPTC52 protein revealed conserved typical motifs from non-heme oxygenases, including a Rieske [2Fe-2S] motif, a mononuclear non-heme iron-binding motif and a C-terminal CxxC motif. The level of transcript accumulation was low in stem, flower and green fruits, and high in leaves. Although SlPtc52 expression was perceptible at low levels in roots, its expression increased concomitantly with AM fungus root colonization. Tomato non-mycorrhizal hairy roots expressing the GUS protein under the control of promoter SlPtc52 exhibited GUS activity in the endodermis, the apical meristem of the root tip and in the lateral root primordium. AM fungal colonization also resulted in intensive GUS activity that clearly corresponds to cortical cells containing arbuscules. SlPtc52 gene silencing led to a delay in root colonization and a decrease in arbuscular abundance, suggesting that SlPTC52 plays a regulatory role during AM symbiosis.}, }
@article {pmid31049565, year = {2019}, author = {Samba-Louaka, A and Delafont, V and Rodier, MH and Cateau, E and Héchard, Y}, title = {Free-living amoebae and squatters in the wild: ecological and molecular features.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {4}, pages = {415-434}, doi = {10.1093/femsre/fuz011}, pmid = {31049565}, issn = {1574-6976}, mesh = {Amoeba/genetics/*physiology/virology ; Bacteria/*classification/virology ; Bacterial Physiological Phenomena ; Biological Evolution ; *Ecosystem ; Genetic Variation ; }, abstract = {Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.}, }
@article {pmid31049371, year = {2019}, author = {Rahnama, M and Maclean, P and Fleetwood, DJ and Johnson, RD}, title = {Comparative transcriptomics analysis of compatible wild type and incompatible ΔlaeA mutant strains of Epichloë festucae in association with perennial ryegrass.}, journal = {Data in brief}, volume = {24}, number = {}, pages = {103843}, doi = {10.1016/j.dib.2019.103843}, pmid = {31049371}, issn = {2352-3409}, abstract = {Epichloë festucae fungi form bioprotective endophytic symbioses with perennial ryegrass. Although this interaction is economically important, relatively little is known about the molecular processes and regulatory genes that are involved in establishing a compatible symbiosis. The present study utilised next-generation sequencing to investigate the genes required for establishing a compatible symbiotic interaction between E. festucae and perennial ryegrass. A comparative transcriptomics study, comparing the compatible symbiotic interaction of E. festucae/perennial ryegrass with the incompatible interaction of a ΔlaeA mutant strain of E.festucae/perennial ryegrass, was performed two weeks after inoculation. Differentially expressed genes were identified and classified according to gene ontology and functional annotation analyses. The raw data of this study have been deposited at SRA database with the BioProject ID PRJNA513830.}, }
@article {pmid31041384, year = {2019}, author = {Dutta, AK and Choudhary, E and Wang, X and Záhorszka, M and Forbak, M and Lohner, P and Jessen, HJ and Agarwal, N and Korduláková, J and Jessen-Trefzer, C}, title = {Trehalose Conjugation Enhances Toxicity of Photosensitizers against Mycobacteria.}, journal = {ACS central science}, volume = {5}, number = {4}, pages = {644-650}, doi = {10.1021/acscentsci.8b00962}, pmid = {31041384}, issn = {2374-7943}, abstract = {Trehalose is a natural glucose-derived disaccharide found in the cell wall of mycobacteria. It enters the mycobacterial cell through a highly specific trehalose transporter system. Subsequently, trehalose is equipped with mycolic acid species and is incorporated into the cell wall as trehalose monomycolate or dimycolate. Here, we investigate the phototoxicity of several photosensitizer trehalose conjugates and take advantage of the promiscuity of the extracellular Ag85 complex, which catalyzes the attachment of mycolic acids to trehalose and its analogues. We find that processing by Ag85 enriches and tethers photosensitizer trehalose conjugates directly into the mycomembrane. Irradiation of the conjugates triggers singlet oxygen formation, killing mycobacterial cells more efficiently, as compared to photosensitizers without trehalose conjugation. The conjugates are potent antimycobacterial agents that are, per se, affected neither by permeability issues nor by detoxification mechanisms via drug efflux. They could serve as interesting scaffolds for photodynamic therapy of mycobacterial infections.}, }
@article {pmid31038750, year = {2019}, author = {Gomes, SIF and van Bodegom, PM and Merckx, VSFT and Soudzilovskaia, N}, title = {Environmental drivers for cheaters of arbuscular mycorrhizal symbiosis in tropical rainforests.}, journal = {The New phytologist}, volume = {223}, number = {3}, pages = {1575-1583}, doi = {10.1111/nph.15876}, pmid = {31038750}, issn = {1469-8137}, support = {VIDI 016.161.318//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {Hundreds of nonphotosynthetic mycoheterotrophic plant species cheat the arbuscular mycorrhizal symbiosis. Their patchy local occurrence suggests constraints by biotic and abiotic factors, among which the role of soil chemistry and nutrient status has not been investigated. Here, we examine the edaphic drivers predicting the local-scale distribution of mycoheterotrophic plants in two lowland rainforests in South America. We compared soil chemistry and nutrient status in plots where mycoheterotrophic plants were present with those without these plants. Soil pH, soil nitrate, and the interaction between soil potassium and nitrate concentrations were the best predictors for the occurrence of mycoheterotrophic plants in these tropical rainforests. Mycoheterotrophic plant occurrences decreased with a rise in each of these predictors. This indicates that these plants are associated with low-fertility patches. Such low-fertility conditions coincide with conditions that potentially favour a weak mutualism between plants and arbuscular mycorrhizal fungi according to the trade balance model. Our study points out which soil properties favour the cheating of arbuscular mycorrhizal networks in tropical forests. The patchy occurrence of mycoheterotrophic plants suggests that local soil heterogeneity causes the stability of arbuscular mycorrhizal networks to vary at a very small scale.}, }
@article {pmid31037067, year = {2019}, author = {Pons, I and Renoz, F and Noël, C and Hance, T}, title = {Circulation of the Cultivable Symbiont Serratia symbiotica in Aphids Is Mediated by Plants.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {764}, doi = {10.3389/fmicb.2019.00764}, pmid = {31037067}, issn = {1664-302X}, abstract = {Symbiosis is a common phenomenon in nature that substantially affects organismal ecology and evolution. Fundamental questions regarding how mutualistic associations arise and evolve in nature remain, however, poorly studied. The aphid-Serratia symbiotica bacterium interaction represents a valuable model to study mechanisms shaping these symbiotic interspecific interactions. S. symbiotica strains capable of living independently of aphid hosts have recently been isolated. These strains probably resulted from horizontal transfers and could be an evolutionary link to an intra-organismal symbiosis. In this context, we used the tripartite interaction between the aphid Aphis fabae, a cultivable S. symbiotica bacterium, and the host plant Vicia faba to evaluate the bacterium ability to circulate in this system, exploring its environmental acquisition by aphids and horizontal transmission between aphids via the host plant. Using molecular analyses and fluorescence techniques, we showed that the cultivable S. symbiotica can enter the plants and induce new bacterial infections in aphids feeding on these new infected plants. Remarkably, we also found that the bacterium can have positive effects on the host plant, mainly at the root level. Furthermore, our results demonstrated that cultivable S. symbiotica can be horizontally transferred from infected to uninfected aphids sharing the same plant, providing first direct evidence that plants can mediate horizontal transmission of certain strains of this symbiont species. These findings highlight the importance of considering symbiotic associations in complex systems where microorganisms can circulate between different compartments. Our study can thus have major implications for understanding the multifaceted interactions between microbes, insects and plants.}, }
@article {pmid31036911, year = {2019}, author = {Monteil, CL and Vallenet, D and Menguy, N and Benzerara, K and Barbe, V and Fouteau, S and Cruaud, C and Floriani, M and Viollier, E and Adryanczyk, G and Leonhardt, N and Faivre, D and Pignol, D and López-García, P and Weld, RJ and Lefevre, CT}, title = {Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1088-1095}, doi = {10.1038/s41564-019-0432-7}, pmid = {31036911}, issn = {2058-5276}, abstract = {Mutualistic symbioses are often a source of evolutionary innovation and drivers of biological diversification1. Widely distributed in the microbial world, particularly in anoxic settings2,3, they often rely on metabolic exchanges and syntrophy2,4. Here, we report a mutualistic symbiosis observed in marine anoxic sediments between excavate protists (Symbiontida, Euglenozoa)5 and ectosymbiotic Deltaproteobacteria biomineralizing ferrimagnetic nanoparticles. Light and electron microscopy observations as well as genomic data support a multi-layered mutualism based on collective magnetotactic motility with division of labour and interspecies hydrogen-transfer-based syntrophy6. The guided motility of the consortia along the geomagnetic field is allowed by the magnetic moment of the non-motile ectosymbiotic bacteria combined with the protist motor activity, which is a unique example of eukaryotic magnetoreception7 acquired by symbiosis. The nearly complete deltaproteobacterial genome assembled from a single consortium contains a full magnetosome gene set8, but shows signs of reduction, with the probable loss of flagellar genes. Based on the metabolic gene content, the ectosymbiotic bacteria are anaerobic sulfate-reducing chemolithoautotrophs that likely reduce sulfate with hydrogen produced by hydrogenosome-like organelles6 underlying the plasma membrane of the protist. In addition to being necessary hydrogen sinks, ectosymbionts may provide organics to the protist by diffusion and predation, as shown by magnetosome-containing digestive vacuoles. Phylogenetic analyses of 16S and 18S ribosomal RNA genes from magnetotactic consortia in marine sediments across the Northern and Southern hemispheres indicate a host-ectosymbiont specificity and co-evolution. This suggests a historical acquisition of magnetoreception by a euglenozoan ancestor from Deltaproteobacteria followed by subsequent diversification. It also supports the cosmopolitan nature of this type of symbiosis in marine anoxic sediments.}, }
@article {pmid31036280, year = {2019}, author = {Shah, NK}, title = {Decision Support in Transfusion Medicine and Blood Banking.}, journal = {Clinics in laboratory medicine}, volume = {39}, number = {2}, pages = {269-279}, doi = {10.1016/j.cll.2019.01.006}, pmid = {31036280}, issn = {1557-9832}, abstract = {Clinical decision support (CDS) can greatly enhance patient blood management through optimizing ordering and providing patient-specific information. At present, modeling and prediction have small roles in inventory management; they will likely have increasing applications to help guide donor center collections based on real-time demand to meet more dispersed needs. Transfusion side-effects management for both donor and recipients is an area ripe for intervention by CDS to enable proactive actions. Last, CDS and broader prediction will 1 day function alongside and seamlessly along many of our major processes to create a human-computer symbiosis.}, }
@article {pmid31035831, year = {2019}, author = {Pandey, S}, title = {Heterotrimeric G-Protein Signaling in Plants: Conserved and Novel Mechanisms.}, journal = {Annual review of plant biology}, volume = {70}, number = {}, pages = {213-238}, doi = {10.1146/annurev-arplant-050718-100231}, pmid = {31035831}, issn = {1545-2123}, abstract = {Heterotrimeric GTP-binding proteins are key regulators of a multitude of signaling pathways in all eukaryotes. Although the core G-protein components and their basic biochemistries are broadly conserved throughout evolution, the regulatory mechanisms of G proteins seem to have been rewired in plants to meet specific needs. These proteins are currently the focus of intense research in plants due to their involvement in many agronomically important traits, such as seed yield, organ size regulation, biotic and abiotic stress responses, symbiosis, and nitrogen use efficiency. The availability of massive sequence information from a variety of plant species, extensive biochemical data generated over decades, and impressive genetic resources for plant G proteins have made it possible to examine their role, unique properties, and novel regulation. This review focuses on some recent advances in our understanding of the mechanistic details of this critical signaling pathway to enable the precise manipulation and generation of plants to meet future needs.}, }
@article {pmid31034469, year = {2019}, author = {Dietel, AK and Merker, H and Kaltenpoth, M and Kost, C}, title = {Selective advantages favour high genomic AT-contents in intracellular elements.}, journal = {PLoS genetics}, volume = {15}, number = {4}, pages = {e1007778}, doi = {10.1371/journal.pgen.1007778}, pmid = {31034469}, issn = {1553-7404}, abstract = {Extrachromosomal genetic elements such as bacterial endosymbionts and plasmids generally exhibit AT-contents that are increased relative to their hosts' DNA. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes such as a mutational bias towards increased A+T. Here we show experimentally that an increased AT-content of host-dependent elements can be selectively favoured. Manipulating the nucleotide composition of bacterial cells by introducing A+T-rich or G+C-rich plasmids, we demonstrate that cells containing GC-rich plasmids are less fit than cells containing AT-rich plasmids. Moreover, the cost of GC-rich elements could be compensated by providing precursors of G+C, but not of A+T, thus linking the observed fitness effects to the cytoplasmic availability of nucleotides. Accordingly, introducing AT-rich and GC-rich plasmids into other bacterial species with different genomic GC-contents revealed that the costs of G+C-rich plasmids decreased with an increasing GC-content of their host's genomic DNA. Taken together, our work identifies selection as a strong evolutionary force that drives the genomes of intracellular genetic elements toward higher A+T contents.}, }
@article {pmid31033207, year = {2019}, author = {Horta, A and Alves, C and Pinteus, S and Lopes, C and Fino, N and Silva, J and Ribeiro, J and Rodrigues, D and Francisco, J and Rodrigues, A and Pedrosa, R}, title = {Identification of Asparagopsis armata-associated bacteria and characterization of their bioactive potential.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e00824}, doi = {10.1002/mbo3.824}, pmid = {31033207}, issn = {2045-8827}, support = {265896//FP7 Food, Agriculture and Fisheries, Biotechnology/ ; PTDC/MAR-BIO/6149/2014//Fundação para a Ciência e a Tecnologia/ ; SAICTPAC/0019/2015 - LISBOA-01-0145-FEDER-016405//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/103255/2014//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/120250/2016//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/96203/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/97764/2013//Fundação para a Ciência e a Tecnologia/ ; UID/MAR/04292/2019//Fundação para a Ciência e a Tecnologia/ ; Centro-01-0145-FEDER-000018//Centro 2020 program, Portugal 2020, European Union, European Regional Development Fund/ ; }, abstract = {Macroalgae-associated bacteria have already proved to be an interesting source of compounds with therapeutic potential. Accordingly, the main aim of this study was to characterize Asparagopsis armata-associated bacteria community and evaluate their capacity to produce substances with antitumor and antimicrobial potential. Bacteria were selected according to their phenotype and isolated by the streak plate technique. The identification was carried out by the RNA ribosomal 16s gene amplification through PCR techniques. The antimicrobial activities were evaluated against seven microorganisms (Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella enteritidis, Staphylococcus aureus, Saccharomyces cerevisiae, Candida albicans) by following their growth through spectrophotometric readings. Antitumor activities were evaluated in vitro on human cell lines derived from hepatocellular (HepG-2) and breast carcinoma (MCF-7) using the MTT method. The present work identified a total of 21 bacteria belonging to the genus Vibrio, Staphylococcus, Shewanella, Alteromonadaceae, Bacillus, Cobetia, and Photobacterium, with Vibrio being the most abundant (42.86%). The extract of Shewanella sp. ASP 26 bacterial strain induced the highest antimicrobial activity, namely against Bacillus subtilis and Staphylococcus aureus with an IC50 of 151.1 and 346.8 μg/mL, respectively. These bacteria (Shewanella sp.) were also the ones with highest antitumor potential, demonstrating antiproliferative activity on HepG-2 cells. Asparagopsis armata-associated bacteria revealed to be a potential source of compounds with antitumor and antibacterial activity.}, }
@article {pmid31033101, year = {2019}, author = {Taerum, SJ and Jasso-Selles, DE and Wilson, M and Ware, JL and Sillam-Dussès, D and Šobotník, J and Gile, GH}, title = {Molecular Identity of Holomastigotes (Spirotrichonymphea, Parabasalia) with Descriptions of Holomastigotes flavipes n. sp. and Holomastigotes tibialis n. sp.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12739}, pmid = {31033101}, issn = {1550-7408}, support = {//College of Liberal Arts and Sciences and the School of Life Sciences, Arizona State University/ ; CZ.02.1.01/0.0/0.0/16_019/0000803//OP RDE/ ; }, abstract = {Holomastigotes is a protist genus (Parabasalia: Spirotrichonymphea) that resides in the hindguts of &quot;lower&quot; termites. It can be distinguished from other parabasalids by spiral flagellar bands that run along the entire length of the cell, an anterior nucleus, a reduced or absent axostyle, the presence of spherical vesicles inside the cells, and the absence of ingested wood particles. Eight species have been described based on their morphology so far, although no molecular data were available prior to this study. We determined the 18S rRNA gene sequences of Holomastigotes from the hindguts of Hodotermopsis sjostedti, Reticulitermes flavipes, Reticulitermes lucifugus, and Reticulitermes tibialis. Phylogenetic analyses placed all sequences in an exclusive and well-supported clade with the type species, Holomastigotes elongatum from R. lucifugus. However, the phylogenetic position of Holomastigotes within the Spirotrichonymphea was not resolved. We describe two new species, Holomastigotes flavipes n. sp. and Holomastigotes tibialis n. sp., inhabiting the hindguts of R. flavipes and R. tibialis, respectively.}, }
@article {pmid31031793, year = {2019}, author = {Evelin, H and Devi, TS and Gupta, S and Kapoor, R}, title = {Mitigation of Salinity Stress in Plants by Arbuscular Mycorrhizal Symbiosis: Current Understanding and New Challenges.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {470}, doi = {10.3389/fpls.2019.00470}, pmid = {31031793}, issn = {1664-462X}, abstract = {Modern agriculture is facing twin challenge of ensuring global food security and executing it in a sustainable manner. However, the rapidly expanding salinity stress in cultivable areas poses a major peril to crop yield. Among various biotechnological techniques being used to reduce the negative effects of salinity, the use of arbuscular mycorrhizal fungi (AMF) is considered to be an efficient approach for bio-amelioration of salinity stress. AMF deploy an array of biochemical and physiological mechanisms that act in a concerted manner to provide more salinity tolerance to the host plant. Some of the well-known mechanisms include improved nutrient uptake and maintenance of ionic homeostasis, superior water use efficiency and osmoprotection, enhanced photosynthetic efficiency, preservation of cell ultrastructure, and reinforced antioxidant metabolism. Molecular studies in past one decade have further elucidated the processes involved in amelioration of salt stress in mycorrhizal plants. The participating AMF induce expression of genes involved in Na+ extrusion to the soil solution, K+ acquisition (by phloem loading and unloading) and release into the xylem, therefore maintaining favorable Na+:K+ ratio. Colonization by AMF differentially affects expression of plasma membrane and tonoplast aquaporins (PIPs and TIPs), which consequently improves water status of the plant. Formation of AM (arbuscular mycorrhiza) surges the capacity of plant to mend photosystem-II (PSII) and boosts quantum efficiency of PSII under salt stress conditions by mounting the transcript levels of chloroplast genes encoding antenna proteins involved in transfer of excitation energy. Furthermore, AM-induced interplay of phytohormones, including strigolactones, abscisic acid, gibberellic acid, salicylic acid, and jasmonic acid have also been associated with the salt tolerance mechanism. This review comprehensively covers major research advances on physiological, biochemical, and molecular mechanisms implicated in AM-induced salt stress tolerance in plants. The review identifies the challenges involved in the application of AM in alleviation of salt stress in plants in order to improve crop productivity.}, }
@article {pmid31031789, year = {2019}, author = {Hajheidari, M and Koncz, C and Bucher, M}, title = {Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {454}, doi = {10.3389/fpls.2019.00454}, pmid = {31031789}, issn = {1664-462X}, abstract = {The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.}, }
@article {pmid31031015, year = {2019}, author = {Tounsi-Hammami, S and Le Roux, C and Dhane-Fitouri, S and De Lajudie, P and Duponnois, R and Ben Jeddi, F}, title = {Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {4}, pages = {448-456}, doi = {10.1016/j.syapm.2019.04.002}, pmid = {31031015}, issn = {1618-0984}, mesh = {Genetic Variation ; Lupinus/genetics/growth &amp; development/*microbiology ; *Phylogeny ; Plant Root Nodulation/*genetics ; Rhizobium/*classification/*genetics/physiology ; Root Nodules, Plant/genetics/growth &amp; development/microbiology ; Soil/chemistry ; *Soil Microbiology ; Symbiosis/genetics ; Tunisia ; }, abstract = {With a view to introducing white lupin (Lupinus albus L.) for cultivation in Tunisian calcareous soils, compatible indigenous rhizobia for nitrogen-fixing symbiosis were investigated and characterized. Two L. albus varieties, Mekna and Lumen, were used to trap rhizobia in soil samples collected from 56 sites with high active lime contents (0-49%). Nodulation occurred in only 15 soils. The local variety, Mekna, developed significantly more root nodules and had a trapping capacity in more soils than the imported variety Lumen. A phylogenetic analysis based on the partial 16S-23S ribosomal RNA internal transcribed spacer region (ITS) and multi-locus sequence analysis (MLSA) of three chromosomal housekeeping genes, recA, atpD and dnaK, showed that strains were affiliated to Agrobacterium, Rhizobium, and Neorhizobium, with large internal diversity, including separate lineages. Infectivity tests highlighted some nodulation specificity at the plant variety level, since the strains originating from Mekna could only nodulate this variety, while strains trapped in Lumen could nodulate both varieties. When inoculated, almost all strains resulted in a significant increase in plant shoot dry weight on L. albus. Although Agrobacterium sp. strains isolated from L. albus could nodulate and had a plant growth promoting effect, no nodA and nodC genes could be amplified. This is discussed together with the absence of bradyrhizobia and the general infrequency of L. albus-nodulating rhizobia in Tunisian soils. The adapted and efficient rhizobial strains reported here were promising candidates for inoculant development and represent a contribution towards successful cultivation of L. albus in Tunisia, especially the most promising Mekna variety.}, }
@article {pmid31030835, year = {2019}, author = {Bosák, J and Hrala, M and Pirková, V and Micenková, L and Čížek, A and Smola, J and Kučerová, D and Vacková, Z and Budinská, E and Koláčková, I and Šmajs, D}, title = {Porcine pathogenic Escherichia coli strains differ from human fecal strains in occurrence of bacteriocin types.}, journal = {Veterinary microbiology}, volume = {232}, number = {}, pages = {121-127}, doi = {10.1016/j.vetmic.2019.04.003}, pmid = {31030835}, issn = {1873-2542}, mesh = {Animals ; Bacterial Adhesion ; Bacteriocins/*genetics ; Carrier Proteins/genetics ; Colicins/*genetics ; Diarrhea/microbiology ; Enterotoxigenic Escherichia coli/genetics/*pathogenicity ; Escherichia coli Proteins/genetics ; Feces/microbiology ; Fimbriae Proteins/genetics ; Gastrointestinal Tract/microbiology ; Humans ; Iron/metabolism ; Phylogeny ; Plasmids ; Polymerase Chain Reaction ; Shiga-Toxigenic Escherichia coli/genetics/*pathogenicity ; Swine ; Symbiosis ; Virulence Factors/genetics ; }, abstract = {Enterotoxigenic and Shiga-toxigenic Escherichia coli (i.e., ETEC and STEC) are important causative agents of human and animal diseases. In humans, infections range from mild diarrhea to severe life-threating conditions, while infections of piglets result in lower weight gain and higher pig mortality with the accompanying significant economic losses. In this study, frequencies of four phylogenetic groups, fourteen virulence- and thirty bacteriocin determinants were analyzed in a set of 443 fecal E. coli isolates from diseased pigs and compared to a previously characterized set of 1283 human fecal E. coli isolates collected in the same geographical region. In addition, these characteristics were compared among ETEC, STEC, and non-toxigenic porcine E. coli isolates. Phylogenetic group A was prevalent among porcine pathogenic E. coli isolates, whereas the frequency of phylogroup B2, adhesion/invasion (fimA, pap, sfa, afaI, ial, ipaH, and pCVD432) and iron acquisition (aer and iucC) determinants were less frequent compared to human fecal isolates. Additionally, porcine isolates differed from human isolates relative to the spectrum of produced bacteriocins. While human fecal isolates encoded colicins and microcins with a similar prevalence, porcine pathogenic E. coli isolates produced predominantly colicins (94% of isolates); especially colicins B (42.6%), M (40.1%), and Ib (34.0%), which are encoded on large conjugative plasmids. The observed high prevalence of these colicin determinants suggests the importance of large colicinogenic plasmids and/or the importance of colicin production in intestinal inflammatory conditions.}, }
@article {pmid31029964, year = {2019}, author = {Ryszka, P and Lichtscheidl, I and Tylko, G and Turnau, K}, title = {Symbiotic microbes of Saxifraga stellaris ssp. alpigena from the copper creek of Schwarzwand (Austrian Alps) enhance plant tolerance to copper.}, journal = {Chemosphere}, volume = {228}, number = {}, pages = {183-194}, doi = {10.1016/j.chemosphere.2019.04.084}, pmid = {31029964}, issn = {1879-1298}, mesh = {Austria ; Bacteria ; Copper/*toxicity ; *Drug Tolerance ; Ecology ; Endophytes/*physiology ; Fungi ; Plant Roots/microbiology ; Plant Shoots/microbiology ; Saxifragaceae/*microbiology ; Soil Pollutants ; *Symbiosis ; }, abstract = {Saxifraga stellaris var. alpigena grows as one of the very few higher plants in the copper rich area of the &quot;blue creek&quot; in Austria. Two endophytes were isolated from it: Mortierella sp. (fungus), and Stenotrophomonas maltophilia (bacterium). Both microbes were practically inseparable due to resistance of the bacteria to the antibiotics tested. On PDA media, the fungus showed higher tolerance to copper than the bacterium, which disappeared from both the media and the surface of the fungus in the presence of 150 μM of Cu. However, at this Cu concentration, the bacteria were still detectable inside the mycelium and reappeared on the outside when transferred to media of lower Cu concentration. Microscopic studies of in vitro cultivated plants showed that the fungus was present in both, the roots and shoots of the plant. The effects of endophytes on plant performance were assessed in rhizoboxes filled with Cu-rich substratum; plants inoculated with both microbes showed better growth, survival and photosynthesis performance than the non-inoculated controls. The results of this study prove the beneficial influence of the isolated endophytes on the Cu tolerance of S. stellaris, and indicate the ecological potential of applying microbial consortia to plants under extreme environmental conditions.}, }
@article {pmid31029716, year = {2019}, author = {Buyuktimkin, B and Zafar, H and Saier, MH}, title = {Comparative genomics of the transportome of Ten Treponema species.}, journal = {Microbial pathogenesis}, volume = {132}, number = {}, pages = {87-99}, doi = {10.1016/j.micpath.2019.04.034}, pmid = {31029716}, issn = {1096-1208}, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/genetics/immunology/metabolism ; Biofilms/drug effects/growth &amp; development ; Carrier Proteins/classification/*genetics/*metabolism ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; Genome Size ; Genomics/*methods ; Host-Pathogen Interactions ; Humans ; Immune Evasion ; Porins/genetics/immunology ; Proteome ; Species Specificity ; Substrate Specificity ; Symbiosis ; Syphilis/microbiology ; Treponema/*classification/*genetics/pathogenicity/*physiology ; Treponema pallidum/genetics ; }, abstract = {Treponema is a diverse bacterial genus, the species of which can be pathogenic, symbiotic, or free living. These treponemes can cause various diseases in humans and other animals, such as periodontal disease, bovine digital dermatitis and animal skin lesions. However, the most important and well-studied disease of treponemes that affects humans is 'syphilis'. This disease is caused by Treponema pallidum subspecie pallidum with 11-12 million new cases around the globe on an annual basis. In this study we analyze the transportome of ten Treponema species, with emphasis on the types of encoded transport proteins and their substrates. Of the ten species examined, two (T. primitia and T. azonutricium) reside as symbionts in the guts of termites; six (T. pallidum, T. paraluiscuniculi, T. pedis, T. denticola, T. putidum and T. brennaborense) are pathogens of either humans or animals, and T. caldarium and T. succinifaciens are avirulent species, the former being thermophilic. All ten species have a repertoire of transport proteins that assists them in residing in their respective ecological niches. For instance, oral pathogens use transport proteins that take up nutrients uniquely present in their ecosystem; they also encode multiple multidrug/macromolecule exporters that protect against antimicrobials and aid in biofilm formation. Proteins of termite gut symbionts convert cellulose into other sugars that can be metabolized by the host. As often observed for pathogens and symbionts, several of these treponemes have reduced genome sizes, and their small genomes correlate with their dependencies on the host. Overall, the transportomes of T. pallidum and other pathogens have a conglomerate of parasitic lifestyle-assisting proteins. For example, a T. pallidum repeat protein (TprK) mediates immune evasion; outer membrane proteins (OMPs) allow nutrient uptake and end product export, and several ABC transporters catalyze sugar uptake, considered pivotal to parasitic lifestyles. Taken together, the results of this study yield new information that may help open new avenues of treponeme research.}, }
@article {pmid31028027, year = {2019}, author = {Onchuru, TO and Kaltenpoth, M}, title = {Established Cotton Stainer Gut Bacterial Mutualists Evade Regulation by Host Antimicrobial Peptides.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {13}, pages = {}, doi = {10.1128/AEM.00738-19}, pmid = {31028027}, issn = {1098-5336}, abstract = {Symbioses with microorganisms are ubiquitous in nature and confer important ecological traits to animal hosts but also require control mechanisms to ensure homeostasis of the symbiotic interactions. In addition to protecting hosts against pathogens, animal immune systems recognize, respond to, and regulate mutualists. The gut bacterial symbionts of the cotton stainer bug, Dysdercus fasciatus, elicit an immune response characterized by the upregulation of c-type lysozyme and the antimicrobial peptide pyrrhocoricin in bugs with their native gut microbiota compared to that in dysbiotic insects. In this study, we investigated the impact of the elicited antimicrobial immune response on the established cotton stainer gut bacterial symbiont populations. To this end, we used RNA interference (RNAi) to knock down immunity-related genes hypothesized to regulate the symbionts, and we subsequently measured the effect of this silencing on host fitness and on the abundance of the major gut bacterial symbionts. Despite successful downregulation of target genes by both ingestion and injection of double-stranded RNA (dsRNA), the silencing of immunity-related genes had no effect on either host fitness or the qualitative and quantitative composition of established gut bacterial symbionts, indicating that the host immune responses are not actively involved in the regulation of the nutritional and defensive gut bacterial mutualists. These results suggest that close associations of bacterial symbionts with their hosts can result in the evolution of mechanisms ensuring that symbionts remain insensitive to host immunological responses, which may be important for the evolutionary stability of animal-microbe symbiotic associations.IMPORTANCE Animal immune systems are central for the protection of hosts against enemies by preventing or eliminating successful infections. However, in the presence of beneficial bacterial mutualists, the immune system must strike a balance of not killing the beneficial symbionts while at the same time preventing enemy attacks. Here, using the cotton stainer bug, we reveal that its long-term associated bacterial symbionts are insensitive to the host's immune effectors, suggesting adaptation to the host's defenses, thereby strengthening the stability of the symbiotic relationship. The ability of the symbionts to elicit host immune responses but remain insensitive themselves may be a mechanism by which the symbionts prime hosts to fight future pathogenic infections.}, }
@article {pmid31027924, year = {2019}, author = {Alami, S and Lamin, H and Bouhnik, O and El Faik, S and Filali-Maltouf, A and Abdelmoumen, H and Bedmar, EJ and Missbah El Idrissi, M}, title = {Astragalus algarbiensis is nodulated by the genistearum symbiovar of Bradyrhizobium spp. in Morocco.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {4}, pages = {440-447}, doi = {10.1016/j.syapm.2019.03.004}, pmid = {31027924}, issn = {1618-0984}, mesh = {Astragalus Plant/*microbiology ; Biodiversity ; Bradyrhizobium/*classification/genetics ; Cytisus/microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Morocco ; *Phylogeny ; Plant Root Nodulation/*genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis/genetics ; }, abstract = {Astragalus algarbiensis is a wild herbaceous legume growing in Maamora, the most important cork oak forest in northern Africa. It is a plant of great importance as fodder in silvopastoral systems, and in the restoration of poor and degraded soils. The purpose of this study was to describe the biodiversity of rhizobia nodulating this plant and determine their identity. Out of 80 bacterial isolates, 56 strains isolated from root nodules of A. algarbiensis were characterized. ERIC-PCR fingerprinting grouped the strains in two main clusters containing 29 and 27 isolates, respectively, and the amplified ribosomal DNA restriction analysis (ARDRA) generated two different ribotypes. Based on both the ERIC-PCR and ARDRA results, representative strains As21 and As36 were selected for further genetic studies. The nearly complete 16S rRNA gene sequences of As21 and As36 showed that they were closely related to Bradyrhizobium cytisi CTAW11T with similarity values of 99.84% and 99.77%, respectively. Concatenation of atpD, recA, gyrB and dnaK housekeeping gene sequences indicated that strains As21 and As36 had a 95.22% similarity but they showed values of 95.80% and 94.97% with B. cytisi CTAW11T, respectively. The sequencing of the symbiotic nodC gene of the two strains revealed 97.20% and 97.76% identities, respectively, with that of B. cytisi CTAW11T isolated from Cytisus villosus growing in the Moroccan Rif Mountains. Furthermore, the phylogenic analysis showed that the strains isolated from A. algarbiensis clustered with B. cytisi and B. rifense within the bradyrhizobia genistearum symbiovar and may constitute two novel genospecies.}, }
@article {pmid31027729, year = {2019}, author = {Duchatelet, L and Delroisse, J and Flammang, P and Mahillon, J and Mallefet, J}, title = {Etmopterus spinax, the velvet belly lanternshark, does not use bacterial luminescence.}, journal = {Acta histochemica}, volume = {121}, number = {4}, pages = {516-521}, doi = {10.1016/j.acthis.2019.04.010}, pmid = {31027729}, issn = {1618-0372}, abstract = {Marine organisms are able to produce light using either their own luminous system, called intrinsic bioluminescence, or symbiotic luminous bacteria, called extrinsic bioluminescence. Among bioluminescent vertebrates, Osteichthyes are known to harbor both types of bioluminescence, while no study has so far addressed the potential use of intrinsic/extrinsic luminescence in elasmobranchs. In sharks, two families are known to emit light: Etmopteridae and Dalatiidae. The deep-sea bioluminescent Etmopteridae, Etmopterus spinax, has received a particular interest over the past fifteen years and its bioluminescence control was investigated in depth. However, the nature of the shark luminous system still remains enigmatic. The present work was undertaken to assess whether the light of this shark species originates from a bioluminescent bacterial symbiosis. Using fluorescent in situ hybridization (FISH) and transmission electron microscopy (TEM) image analyses, this study supports the conclusion that the bioluminescence in the deep-sea lanternshark, Etmopterus spinax, is not of bacterial origin.}, }
@article {pmid31025899, year = {2019}, author = {Smigielski, L and Laubach, EM and Pesch, L and Glock, JML and Albrecht, F and Slusarenko, A and Panstruga, R and Kuhn, H}, title = {Nodulation Induces Systemic Resistance of Medicago truncatula and Pisum sativum Against Erysiphe pisi and Primes for Powdery Mildew-Triggered Salicylic Acid Accumulation.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {32}, number = {9}, pages = {1243-1255}, doi = {10.1094/MPMI-11-18-0304-R}, pmid = {31025899}, issn = {0894-0282}, abstract = {Plants encounter beneficial and detrimental microorganisms both above- and belowground and the health status of the plant depends on the composition of this pan-microbiome. Beneficial microorganisms contribute to plant nutrition or systemically or locally protect plants against pathogens, thus facilitating adaptation to a variety of environments. Induced systemic resistance, caused by root-associated microbes, manifests as aboveground resistance against necrotrophic pathogens and is mediated by jasmonic acid/ethylene-dependent signaling. By contrast, systemic acquired resistance relies on salicylic acid (SA) signaling and confers resistance against secondary infection by (hemi)biotrophic pathogens. To investigate whether symbiotic rhizobia that are ubiquitously found in natural ecosystems are able to modulate resistance against biotrophs, we tested the impact of preestablished nodulation of Medicago truncatula and pea (Pisum sativum) plants against infection by the powdery mildew fungus Erysiphe pisi. We found that root symbiosis interfered with fungal penetration of M. truncatula and reduced asexual spore formation on pea leaves independently of symbiotic nitrogen fixation. Improved resistance of nodulated plants correlated with elevated levels of free SA and SA-dependent marker gene expression upon powdery mildew infection. Our results suggest that nodulation primes the plants systemically for E. pisi-triggered SA accumulation and defense gene expression, resulting in increased resistance.}, }
@article {pmid31025880, year = {2019}, author = {Togo, A and Dufour, JC and Lagier, JC and Dubourg, G and Raoult, D and Million, M}, title = {Repertoire of human breast and milk microbiota: a systematic review.}, journal = {Future microbiology}, volume = {14}, number = {}, pages = {623-641}, doi = {10.2217/fmb-2018-0317}, pmid = {31025880}, issn = {1746-0921}, mesh = {Abscess/microbiology ; Archaea/classification/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification ; Breast/*microbiology ; Breast Feeding ; Colostrum/microbiology ; Databases, Factual ; Dysbiosis ; Female ; Humans ; Mastitis/microbiology ; *Microbiota ; Milk, Human/*microbiology ; Symbiosis ; }, abstract = {Breastfeeding is a major determinant of human health. Breast milk is not sterile and ecological large-scale sequencing methods have revealed an unsuspected microbial diversity that plays an important role. However, microbiological analysis at the species level has been neglected while it is a prerequisite before understanding which microbe is associated with symbiosis or dysbiosis, and health or disease. We review the currently known bacterial repertoire from the human breast and milk microbiota using a semiautomated strategy. Total 242 articles from 38 countries, 11,124 women and 15,489 samples were included. Total 820 species were identified mainly composed of Proteobacteria and Firmicutes. We report variations according to the analytical method (culture or molecular method), the anatomical site (breast, colostrum or milk) and the infectious status (healthy control, mastitis, breast abscess, neonatal infection). In addition, we compared it with the other human repertoires. Finally, we discuss its putative origin and role in health and disease.}, }
@article {pmid31024611, year = {2019}, author = {Janwa, H and Massey, SE and Velev, J and Mishra, B}, title = {On the Origin of Biomolecular Networks.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {240}, doi = {10.3389/fgene.2019.00240}, pmid = {31024611}, issn = {1664-8021}, support = {U54 CA193313/CA/NCI NIH HHS/United States ; }, abstract = {Biomolecular networks have already found great utility in characterizing complex biological systems arising from pairwise interactions amongst biomolecules. Here, we explore the important and hitherto neglected role of information asymmetry in the genesis and evolution of such pairwise biomolecular interactions. Information asymmetry between sender and receiver genes is identified as a key feature distinguishing early biochemical reactions from abiotic chemistry, and a driver of network topology as biomolecular systems become more complex. In this context, we review how graph theoretical approaches can be applied not only for a better understanding of various proximate (mechanistic) relations, but also, ultimate (evolutionary) structures encoded in such networks from among all types of variations they induce. Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory, whereby sender and receiver gene players accrue benefit from gene duplication, leading to a preferential attachment mode of network growth. The study of the resulting dynamics suggests many mathematical/computational problems, the majority of which are intractable yet yield to efficient approximation algorithms, when studied through an algebraic graph theoretic lens. We relegate for future work the role of other possible generalizations, additionally involving horizontal gene transfer, sexual recombination, endo-symbiosis, etc., which enrich the underlying graph theory even further.}, }
@article {pmid31024597, year = {2019}, author = {Dolgikh, AV and Kirienko, AN and Tikhonovich, IA and Foo, E and Dolgikh, EA}, title = {The DELLA Proteins Influence the Expression of Cytokinin Biosynthesis and Response Genes During Nodulation.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {432}, doi = {10.3389/fpls.2019.00432}, pmid = {31024597}, issn = {1664-462X}, abstract = {The key event that initiates nodule organogenesis is the perception of bacterial signal molecules, the Nod factors, triggering a complex of responses in epidermal and cortical cells of the root. The Nod factor signaling pathway interacts with plant hormones, including cytokinins and gibberellins. Activation of cytokinin signaling through the homeodomain-containing transcription factors KNOX is essential for nodule formation. The main regulators of gibberellin signaling, the DELLA proteins are also involved in regulation of nodule formation. However, the interaction between the cytokinin and gibberellin signaling pathways is not fully understood. Here, we show in Pisum sativum L. that the DELLA proteins can activate the expression of KNOX and BELL transcription factors involved in regulation of cytokinin metabolic and response genes. Consistently, pea la cry-s (della1 della2) mutant showed reduced ability to upregulate expression of some cytokinin metabolic genes during nodulation. Our results suggest that DELLA proteins may regulate cytokinin metabolism upon nodulation.}, }
@article {pmid31024537, year = {2019}, author = {Pantazi, E and Powell, N}, title = {Group 3 ILCs: Peacekeepers or Troublemakers? What's Your Gut Telling You?!.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {676}, doi = {10.3389/fimmu.2019.00676}, pmid = {31024537}, issn = {1664-3224}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {A complex network of interactions exists between the microbiome, the epithelium, and immune cells that reside along the walls of the gastrointestinal tract. The intestinal immune system has been assigned with the difficult task of discriminating between commensal, harmless bacteria, and invading pathogens that translocate across the epithelial monolayer. Importantly, it is trained to maintain tolerance against commensals, and initiate protective immune responses against pathogens to secure intestinal homeostasis. Breakdown of this fine balance between the host and its intestinal microbiota can lead to intestinal inflammation and subsequently to development of inflammatory bowel disease (IBD). A decade since their discovery, innate lymphoid cells (ILCs) are now recognized as important regulators of intestinal homeostasis. ILC3s have emerged as a critical subset in the gut. They are the most phenotypically diverse ILC population and interact directly with numerous different cell types (haematopoietic and non-haematopoeitic), as well as interface with the bacterial flora. In addition to their contribution to intestinal pathogen immunity, they also mitigate against tissue damage occurring following acute injury, by facilitating tissue repair and regeneration, a key function in the maintenance of intestinal homeostasis. However, in chronic inflammation the tables are turned and ILC3s may acquire a pro-inflammatory phenotype in the gut. Chronic ILC activation can lead to persistent inflammation contributing to IBD and/or colorectal cancer. In this review, we discuss current knowledge of group 3 ILCs and their contributions to intestinal homeostasis and disease leading to novel therapeutic targets and clinical approaches that may inform novel treatment strategies for immune-mediated disorders, including IBD.}, }
@article {pmid31022406, year = {2019}, author = {Eckstein, S and Heermann, R}, title = {Regulation of Phenotypic Switching and Heterogeneity in Photorhabdus luminescens Cell Populations.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmb.2019.04.015}, pmid = {31022406}, issn = {1089-8638}, abstract = {Phenotypic heterogeneity in bacterial cell populations allows genetically identical organisms to different behavior under similar environmental conditions. The Gram-negative bacterium Photorhabdus luminescens is an excellent organism to study phenotypic heterogeneity since their life cycle involves a symbiotic interaction with soil nematodes as well as a pathogenic association with insect larvae. Phenotypic heterogeneity is highly distinct in P. luminescens. The bacteria exist in two phenotypic forms that differ in various morphologic and phenotypic traits and are therefore distinguished as primary (1°) and secondary (2°) cells. The 1 cells are bioluminescent, pigmented, produce several secondary metabolites and exo-enzymes, and support nematode growth and development. The 2° cells lack all these 1°-specific phenotypes. The entomopathogenic nematodes carry 1° cells in their upper gut and release them into an insect's body after slipping inside. During insect infection, up to the half number of 1° cells undergo phenotypic switching and convert to 2° cells. Since the 2° cells are not able to live in nematode symbiosis any more, they cannot re-associate with their symbiosis partners after the infection and remain in the soil. Phenotypic switching in P. luminescens has to be tightly regulated since a high switching frequency would lead to a complete break-down of the nematode-bacteria life cycle. Here, we present the main regulatory mechanisms known to-date that are important for phenotypic switching in P. luminescens cell populations and discuss the biological reason as well as the fate of the 2° cells in the soil.}, }
@article {pmid31021099, year = {2019}, author = {Bhattacharya, A and Paul, A and Chakrabarti, D and DasGupta, M}, title = {Gatekeeper-Activation Loop Cross-Talk Determines Distinct Autoactivation States of Symbiosis Receptor Kinase.}, journal = {Biochemistry}, volume = {58}, number = {19}, pages = {2419-2431}, doi = {10.1021/acs.biochem.9b00071}, pmid = {31021099}, issn = {1520-4995}, abstract = {Plant receptor-like kinases (RLKs) have a Tyr in the &quot;gatekeeper&quot; position adjacent to the hinge region. The gatekeeper is phosphorylated in several RLKs, including symbiosis receptor kinase (SYMRK), but the significance of this remains unknown. Gatekeeper substitution did not inactivate Arachis hypogaea SYMRK but affected autophosphorylation at selected sites. Herein, we show that nonphosphorylatable gatekeepers (Y670F and Y670A) restrict SYMRK to be a Ser/Thr kinase with a basal level of phosphorylation (∼5 P/polypeptide, termed state I) whereas phosphorylatable gatekeepers (Y670 and Y670T) allowed SYMRK to be dual specific (Ser/Thr/Tyr) with a maximal level of phosphorylation (∼10 P/polypeptide, termed state II). State II SYMRKs were phosphorylated on gatekeeper residues, and the phosphocode in their activation segment was distinct from state I. The kcat/ Km for substrate phosphorylation was ∼10-fold higher for state II, though for autophosphorylation, it was comparable with those of state I SYMRKs. To identify other determinants of state I features, we mutagenized all nine sites where phosphorylation was affected by nonphosphorylatable gatekeepers (Y670F and Y670A). Only two such mutants, S754A and S757A, located on the activation loop failed to phosphorylate gatekeeper Tyr and restricted SYMRK in state I. Double mutants like Y670F/S754A retained the features of state I, but Y670F/S757A was significantly inactivated, indicating a nonphosphorylatable gatekeeper can bypass phosphorylation of S754 but not S757 in the activation segment. We propose a working model for the hierarchical phosphorylation of SYMRK on gatekeeper and activation segments for its pS757-mediated activation as a Ser/Thr kinase in selfie mode (autophosphorylation) to a pS754/pY670-mediated activation as a Ser/Thr/Tyr kinase that functions in dual mode (both autophosphorylation and substrate phosphorylation).}, }
@article {pmid31020397, year = {2019}, author = {Tsyganova, AV and Seliverstova, EV and Brewin, NJ and Tsyganov, VE}, title = {Bacterial release is accompanied by ectopic accumulation of cell wall material around the vacuole in nodules of Pisum sativum sym33-3 allele encoding transcription factor PsCYCLOPS/PsIPD3.}, journal = {Protoplasma}, volume = {256}, number = {5}, pages = {1449-1453}, doi = {10.1007/s00709-019-01383-1}, pmid = {31020397}, issn = {1615-6102}, support = {16-16-10035//Russian Science Foundation/ ; }, abstract = {Pisum sativum symbiotic mutant SGEFix--2 carries the sym33-3 allele of the gene Sym33, encoding transcription factor PsCYCLOPS/PsIPD3. Previously, strong host cell defence reactions were identified in nodules of this mutant. In the present study, new manifestations of defence reactions were revealed in 28-day-old white nodules in which bacterial release had occurred. These nodules were investigated using histochemical staining of pectin and suberin and by immunogold localisation of three components of pectin: highly methyl-esterified homogalacturonan (HG) recognised by monoclonal antibody JIM7, low methyl-esterified HG recognised by JIM5 and linear (1-4)-β-D-galactan side-chain of rhamnogalacturonan I (RG I) recognised by LM5. In the mutant, but not in the wild-type, cell wall material was deposited around the vacuole in the uninfected cells, in cells containing infection threads and in the infected cells. The deposits around the vacuole were marked with JIM7 and LM5 antibodies but not with JIM5, suggesting that they contain newly formed cell wall material. Deposition was accompanied by suberin accumulation. This is the first report that deposition of cell wall material around the vacuole may be associated with the defence reaction in ineffective nodules. In addition, hypertrophic infection droplets labelled with JIM7 were identified. In the matrix of some infection threads, RG I recognised a pectic gel component. Callose deposits in the cell walls and in the walls of infection threads were occasionally observed. The observations suggest that an important function of transcriptional factor CYCLOPS/IPD3 is the suppression of defence reactions during establishment of the legume-rhizobial symbiosis.}, }
@article {pmid31018578, year = {2019}, author = {Mamontova, T and Afonin, AM and Ihling, C and Soboleva, A and Lukasheva, E and Sulima, AS and Shtark, OY and Akhtemova, GA and Povydysh, MN and Sinz, A and Frolov, A and Zhukov, VA and Tikhonovich, IA}, title = {Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {8}, pages = {}, doi = {10.3390/molecules24081603}, pmid = {31018578}, issn = {1420-3049}, support = {16-16-00118//Russian Science Foundation/ ; }, mesh = {Bacteria/growth &amp; development ; Biomass ; Chromatography, High Pressure Liquid ; Fungi/physiology ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genotype ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Mycorrhizae/physiology ; Peas/chemistry/*genetics/metabolism/microbiology ; Plant Proteins/classification/genetics/*isolation &amp; purification ; Plant Root Nodulation/genetics ; Proteome/classification/genetics/*isolation &amp; purification ; Proteomics/methods ; Seeds/chemistry/*genetics/metabolism ; Soil Microbiology ; Symbiosis/*genetics ; Tandem Mass Spectrometry ; }, abstract = {Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.}, }
@article {pmid31018159, year = {2019}, author = {Béthencourt, L and Boubakri, H and Taib, N and Normand, P and Armengaud, J and Fournier, P and Brochier-Armanet, C and Herrera-Belaroussi, A}, title = {Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation.}, journal = {Research in microbiology}, volume = {170}, number = {4-5}, pages = {202-213}, doi = {10.1016/j.resmic.2019.04.002}, pmid = {31018159}, issn = {1769-7123}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics ; Frankia/*genetics/*physiology ; Gene Expression Profiling ; Genome, Bacterial/genetics ; Monophenol Monooxygenase/genetics ; Proteogenomics ; Proteome/genetics/metabolism ; Spores, Bacterial/*genetics/*metabolism ; Stress, Physiological/genetics ; }, abstract = {Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with sporulation occurring within host cells. The molecular determinants controlling Frankia sporulation have not been yet described. In order to highlight, for the first time, the molecular players potentially involved in Frankia sporulation, we conducted (i) a comparison of protein contents between Frankia spores and hyphae and (ii) a comparative genomic analysis of Frankia proteomes with sporulating and non-sporulating Actinobacteria. Among the main results, glycogen-metabolism related proteins, as well as oxidative stress response and protease-like proteins were overdetected in hyphae, recalling lytic processes that allow Streptomyces cells to erect sporogenic hyphae. Several genes encoding transcriptional regulators, including GntR-like, appeared up-regulated in spores, as well as tyrosinase, suggesting their potential role in mature spore metabolism. Finally, our results highlighted new proteins potentially involved in Frankia sporulation, including a pyrophosphate-energized proton pump and YaaT, described as involved in the phosphorelay allowing sporulation in Bacillus subtilis, leading us to discuss the role of a phosphorelay in Frankia sporulation.}, }
@article {pmid31016002, year = {2019}, author = {Pogoda, CS and Keepers, KG and Nadiadi, AY and Bailey, DW and Lendemer, JC and Tripp, EA and Kane, NC}, title = {Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria.}, journal = {Ecology and evolution}, volume = {9}, number = {7}, pages = {4245-4263}, doi = {10.1002/ece3.5056}, pmid = {31016002}, issn = {2045-7758}, abstract = {Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.}, }
@article {pmid31015472, year = {2019}, author = {Molina-Santiago, C and Pearson, JR and Navarro, Y and Berlanga-Clavero, MV and Caraballo-Rodriguez, AM and Petras, D and García-Martín, ML and Lamon, G and Haberstein, B and Cazorla, FM and de Vicente, A and Loquet, A and Dorrestein, PC and Romero, D}, title = {The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1919}, doi = {10.1038/s41467-019-09944-x}, pmid = {31015472}, issn = {2041-1723}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; BacBio 637971//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/International ; AGL2016-78662-R//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/International ; }, mesh = {Bacillus subtilis/*genetics/growth &amp; development/metabolism ; Bacterial Proteins/genetics/metabolism ; Colony Count, Microbial ; Cucurbitaceae/*microbiology ; Extracellular Matrix/*metabolism ; *Gene Expression Regulation, Bacterial ; Microbial Interactions/*genetics ; Phosphotransferases/genetics/metabolism ; Plant Leaves/microbiology ; Protein Kinases/genetics/metabolism ; Pseudomonas chlororaphis/*genetics/growth &amp; development/metabolism ; Seeds/microbiology ; Spores, Bacterial/genetics/growth &amp; development/metabolism ; Symbiosis/physiology ; Type VI Secretion Systems/genetics/metabolism ; }, abstract = {Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.}, }
@article {pmid31011888, year = {2019}, author = {Bengyella, L and Iftikhar, S and Nawaz, K and Fonmboh, DJ and Yekwa, EL and Jones, RC and Njanu, YMT and Roy, P}, title = {Biotechnological application of endophytic filamentous bipolaris and curvularia: a review on bioeconomy impact.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {5}, pages = {69}, doi = {10.1007/s11274-019-2644-7}, pmid = {31011888}, issn = {1573-0972}, support = {3240223450//The World Academy of Sciences (TWAS)/ ; }, mesh = {*Ascomycota/classification/enzymology/metabolism ; Biodegradation, Environmental ; *Bioengineering ; Biofuels ; Biological Control Agents ; *Biotechnology ; Biotransformation ; *Endophytes/classification/enzymology/metabolism ; Fertilizers ; Flocculation ; Fungal Viruses ; Herbicides ; Metallurgy ; Nanoparticles ; Soil/chemistry ; Symbiosis ; Thermotolerance ; Uranium ; }, abstract = {The filamentous Bipolaris and Curvularia genera consist of species known to cause severe diseases in plants and animals amounting to an estimated annual loss of USD $10 billion worldwide. Despite the harmful effect of Bipolaris and Curvularia species, scarce attention is paid on beneficial areas where the fungi are used in industrial processes to generate biotechnological products. Catalytic potential of Bipolaris and Curvularia species in the production of biodiesel, bioflucculant, biosorbent, and mycoherbicide are promising for the bioeconomy. It is herein demonstrated that knowledge-based application of some endophytic Bipolaris and Curvularia species are indispensable vectors of sustainable economic development. In the twenty-first century, India, China, and the USA have taken progress in the biotechnological application of these fungi to generate wealth. As such, some Bipolaris and Curvularia species significantly impact on global crop improvement, act as catalyst in batch-reactors for biosynthesis of industrial enzymes and medicines, bioengineer of green-nanoparticle, agent of biofertilizer, bioremediation and bio-hydrometallurgy. For the first time, this study discusses the current advances in biotechnological application of Bipolaris and Curvularia species and provide new insights into the prospects of optimizing their bioengineering potential for developing bioeconomy.}, }
@article {pmid31011810, year = {2019}, author = {Shitole, AA and Raut, PW and Sharma, N and Giram, P and Khandwekar, AP and Garnaik, B}, title = {Electrospun polycaprolactone/hydroxyapatite/ZnO nanofibers as potential biomaterials for bone tissue regeneration.}, journal = {Journal of materials science. Materials in medicine}, volume = {30}, number = {5}, pages = {51}, doi = {10.1007/s10856-019-6255-5}, pmid = {31011810}, issn = {1573-4838}, abstract = {Fabricating a bioartificial bone graft possessing structural, mechanical and biological properties mimicking the real bone matrix is a major challenge in bone tissue engineering. Moreover, the developed materials are prone to microbial invasion leading to biomaterial centered infections which might limit their clinical translation. In the present study, biomimetic nanofibrous scaffolds of Poly ɛ-caprolactone (PCL)/nano-hydroxyapatite (nHA) were electrospun with 1wt%, 5wt%, 10wt%, 15wt% and 30wt% of zinc oxide (ZnO) nanoparticles in order to understand the optimal concentration range of (ZnO) nanoparticles balancing both biocompatibility and osteoregeneration. The developed nanofibrous scaffolds were successfully characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDAX), contact angle, fourier transform infrared spectroscopy (FTIR), wide-angle X-Ray diffraction (WAXD), brunaueremmett Teller (BET) surface area and tensile testing. Biocompatibility of the developed scaffolds at in vitro level was evaluated by culturing MG-63 cells and investigating the impact on cell viability, proliferation, protein adsorption, alkaline phosphatase (ALP) activity and biomineralization. The PCL/nHA scaffolds exhibited a 1.2-fold increase in cell viability and proliferation, while incorporation of ZnO nanoparticles to PCL/nHA imparted antimicrobial activity to the scaffolds with a progressive increase in the antimicrobial efficacy with increasing ZnO concentration. The results of cell viability were supported by ALP activity and mineralization assay, wherein, PCL/nHA/ZnO scaffolds showed higher ALP activity and better mineralization capacity as compared to pristine PCL. Although, the PCL/nHA/ZnO scaffolds with 10, 15 and 30wt% of ZnO particles exhibited superior antimicrobial efficacy against both gram-negative (E. coli) and gram-positive (S. aureus) bacteria, a significant decrease in the cell viability and mechanical properties was observed at higher concentrations of ZnO namely 15 and 30%. Amongst the various ZnO concentrations studied optimal cell viability, antimicrobial effect and mechanical strength were observed at 10wt.% ZnO concentration. Thus, the present study revealed that the biomimetic tri-component PCL/nHA/ZnO scaffolds with ZnO concentration range of ≤ 10% could be ideal for achieving optimal biocompatibility (cell proliferation, biomineralization, and antimicrobial capacity) and mechanical stability thus making it a promising biomaterial substrate for bone tissue regeneration.}, }
@article {pmid31011805, year = {2019}, author = {Guerrero-Galán, C and Calvo-Polanco, M and Zimmermann, SD}, title = {Ectomycorrhizal symbiosis helps plants to challenge salt stress conditions.}, journal = {Mycorrhiza}, volume = {29}, number = {4}, pages = {291-301}, doi = {10.1007/s00572-019-00894-2}, pmid = {31011805}, issn = {1432-1890}, abstract = {Soil salinity is an environmental condition that is currently increasing worldwide. Plant growth under salinity induces osmotic stress and ion toxicity impairing root water and nutrient absorption, but the association with beneficial soil microorganisms has been linked to an improved adaptation to this constraint. The ectomycorrhizal (ECM) symbiosis has been proposed as a key factor for a better tolerance of woody species to salt stress, thanks to the reduction of sodium (Na+) uptake towards photosynthetic organs. Although no precise mechanisms for this enhanced plant salt tolerance have been described yet, in this review, we summarize the knowledge accumulated so far on the role of ECM symbiosis. Moreover, we propose several strategies by which ECM fungi might help plants, including restriction of Na+ entrance into plant tissues and improvement of mineral nutrition and water balances. This positive effect of ECM fungi has been proven in field assays and the results obtained point to a promising application in forestry cultures and reforestation.}, }
@article {pmid31011585, year = {2019}, author = {Wang, S and Ye, Q and Zeng, X and Qiao, S}, title = {Functions of Macrophages in the Maintenance of Intestinal Homeostasis.}, journal = {Journal of immunology research}, volume = {2019}, number = {}, pages = {1512969}, doi = {10.1155/2019/1512969}, pmid = {31011585}, issn = {2314-7156}, mesh = {Animals ; *Homeostasis ; Humans ; Inflammation/immunology ; Inflammatory Bowel Diseases/immunology ; Intestinal Mucosa/*immunology ; Intestines/immunology/physiology ; Macrophages/*immunology ; Mice ; Symbiosis ; }, abstract = {Intestinal macrophages constitute the largest pool of macrophages in the body and have emerged as crucial sentinels for pathogen recognition and elimination. The source and development of intestinal macrophages, as well as their distinct properties have been well documented. Intestinal macrophages exert their functions in the maintenance of intestinal homeostasis by shaping host-microbiota symbiosis, managing gut inflammation, crosstalking with T cells, and facilitating wound repair. Recently, nutritional regulation of intestinal macrophages has attracted substantial attention and is becoming a promising approach to disease prevention and control. Understanding the mechanisms employed by intestinal macrophages in mediating intestinal immune homeostasis and inflammation, as well as the mode of action of dietary nutrients in the modulating functions of intestinal macrophages, represents an opportunity to prevent and control inflammatory bowel diseases.}, }
@article {pmid31008572, year = {2019}, author = {Green, KA and Eaton, CJ and Savoian, MS and Scott, B}, title = {A homologue of the fungal tetraspanin Pls1 is required for Epichloë festucae expressorium formation and establishment of a mutualistic interaction with Lolium perenne.}, journal = {Molecular plant pathology}, volume = {20}, number = {7}, pages = {961-975}, doi = {10.1111/mpp.12805}, pmid = {31008572}, issn = {1364-3703}, support = {MAU1301//Tertiary Education Commission/ ; }, abstract = {Epichloë festucae is an endophytic fungus that forms a mutualistic symbiotic association with the grass host Lolium perenne. Endophytic hyphae exit the host by an appressorium-like structure known as an expressorium. In plant-pathogenic fungi, the tetraspanin Pls1 and the NADPH oxidase component Nox2 are required for appressorium development. Previously we showed that the homologue of Nox2, NoxB, is required for E. festucae expressorium development and establishment of a mutualistic symbiotic interaction with the grass host. Here we used a reverse genetics approach to functionally characterize the role of the E. festucae homologue of Pls1, PlsA. The morphology and growth of ΔplsA in axenic culture was comparable to wild-type. The tiller length of plants infected with ΔplsA was significantly reduced. Hyphae of ΔplsA had a proliferative pattern of growth within the leaves of L. perenne with increased colonization of the intercellular spaces and the vascular bundles. The ΔplsA mutant was also defective in expressorium development although the phenotype was not as severe as for ΔnoxB, highlighting potentially distinct roles for PlsA and NoxB in signalling through the NoxB complex. Hyphae of ΔplsA proliferate below the cuticle surface but still occasionally form an expressorium-like structure that enables the mutant hyphae to exit the leaf to grow on the surface. These expressoria still form a septin ring-like structure at the point of cuticle exit as found in the wild-type strain. These results establish that E. festucae PlsA has an important, but distinct, role to NoxB in expressorium development and plant symbiosis.}, }
@article {pmid31006611, year = {2019}, author = {Vila, A and Estrada-Peña, A and Altet, L and Cusco, A and Dandreano, S and Francino, O and Halos, L and Roura, X}, title = {Endosymbionts carried by ticks feeding on dogs in Spain.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {848-852}, doi = {10.1016/j.ttbdis.2019.04.003}, pmid = {31006611}, issn = {1877-9603}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification/*pathogenicity ; DNA, Bacterial/genetics ; Dermacentor/microbiology ; Dogs/*parasitology ; Feeding Behavior ; Female ; Ixodidae/microbiology ; Male ; Polymerase Chain Reaction ; Rhipicephalus sanguineus/microbiology ; Spain ; *Symbiosis ; Tick Infestations/microbiology/*veterinary ; Tick-Borne Diseases/microbiology/*veterinary ; Ticks/*microbiology ; }, abstract = {Studies on tick microbial communities historically focused on tick-borne pathogens. However, there is an increasing interest in capturing relationships among non-pathogenic endosymbionts and exploring their relevance for tick biology. The present study included a total of 1600 adult ticks collected from domestic dogs in 4 different biogeographical regions of Spain. Each pool formed by 1 to 10 halves of individuals representing one specific ticks species was examined by PCR for the presence of Coxiellaceae, Rickettsia spp., Rickettsiales, Wolbachia spp., and other bacterial DNA. Of the pools analyzed, 92% tested positive for endosymbiont-derived DNA. Coxiella spp. endosymbionts were the most prevalent microorganisms, being always present in Rhipicephalus sanguineus sensu lato (s.l.) pools. Rickettsia spp. DNA was detected in 60% of Dermacentor reticulatus pools and 40% of R. sanguineus s.l. pools, with a higher diversity of Rickettsia species in R. sanguineus s.l. pools. Our study reveals a negative relationship of Rickettsia massiliae with the presence of tick-borne pathogens in the same pool of ticks. An additional endosymbiont, 'Candidatus Rickettsiella isopodorum', was only detected in D. reticulatus pools. Data from this study indicate that dogs in Spain are exposed to several endosymbionts. Due to the importance of tick-borne pathogens, characterizing the role of endosymbionts for tick physiology and prevalence, may lead to novel control strategies.}, }
@article {pmid31006112, year = {2019}, author = {Kazenel, MR and Kivlin, SN and Taylor, DL and Lynn, JS and Rudgers, JA}, title = {Altitudinal gradients fail to predict fungal symbiont responses to warming.}, journal = {Ecology}, volume = {100}, number = {8}, pages = {e02740}, doi = {10.1002/ecy.2740}, pmid = {31006112}, issn = {1939-9170}, abstract = {Climate change is shifting altitudinal species ranges, with potential to disrupt species interactions. Altitudinal gradient studies and warming experiments can both increase understanding of climate effects on species interactions, but few studies have used both together to improve predictions. We examined whether plant-fungal symbioses responded similarly to altitude and 23 yr of experimental warming. Root- and leaf-associated fungi, which can mediate plants' climate sensitivity, responded divergently to elevation vs. warming. Fungal colonization, diversity, and composition varied with altitude, but climate variables were generally weak predictors; other factors such as host plant identity, plant community composition, or edaphic variables likely drive fungal altitudinal distributions. Manipulated warming altered fungal colonization, but not composition or diversity. Leaf symbionts were more sensitive to climate and experimental warming than root symbionts. Altitudinal patterns and responses to warming differed among host plant species and fungal groups, indicating that predicting climate effects on symbioses will require tracking both host and symbiont identities. Combining experimental and observational methods can yield valuable insight into how climate change may alter plant-symbiont interactions, but our results indicate that altitude does not always serve as an adequate proxy for warming effects on fungal symbionts of plants.}, }
@article {pmid31006045, year = {2019}, author = {Prasad, S and Shah, A and Bhalsing, KS and Ingalhalikar, M and Saini, J and Pal, PK}, title = {Clinical correlates of abnormal subcortical volumes in Essential Tremor.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {126}, number = {5}, pages = {569-576}, doi = {10.1007/s00702-019-02004-0}, pmid = {31006045}, issn = {1435-1463}, support = {ECR/2016/000808//Science and Engineering Research Board/ ; }, abstract = {Essential tremor (ET) is considered to be a neurodegenerative disorder and it is plausible that the observed motor and non-motor symptoms may be attributable to functional alterations secondary to abnormalities of subcortical nuclei. This study aims to compare the volumes of subcortical nuclei in patients with ET to ascertain neuroimaging correlates of motor and non-motor features of ET. Forty patients of ET and 40 age- and gender-matched healthy controls (HC) were enrolled in this study. Tremor severity was quantified with the Fahn-Tolosa-Marin tremor rating scale. Patients of ET with and without a rest tremor were also compared. Structural imaging was performed on a 3T scanner, and volumes of subcortical structures were obtained using Freesurfer. There was no difference in total brain volume between ET and HC. However, compared to HC, significantly lower volumes of bilateral thalamus, hippocampus, and ventral diencephalon were observed in patients with ET. A significantly higher volume was observed in the right caudate nucleus, pallidum, amygdala, and bilateral putamen, and nucleus accumbens. No difference was observed between patients of ET with and without a rest tremor. Patients with ET have significant alterations in volumes of subcortical nuclei, which are not limited to the motor domain and include structures involved in cognitive and behavioral functions. These results add to the growing concept of a neurodegenerative pathophysiology of ET with abnormalities extending beyond the cerebellum.}, }
@article {pmid31005641, year = {2019}, author = {Zhu, S and Feng, S and Xu, Z and Qin, L and Shang, C and Feng, P and Wang, Z and Yuan, Z}, title = {Cultivation of Chlorella vulgaris on unsterilized dairy-derived liquid digestate for simultaneous biofuels feedstock production and pollutant removal.}, journal = {Bioresource technology}, volume = {285}, number = {}, pages = {121353}, doi = {10.1016/j.biortech.2019.121353}, pmid = {31005641}, issn = {1873-2976}, abstract = {In order to assess viability of microalgae cultivation using unsterilized dairy-derived liquid digestate (DLD) for simultaneous biofuels feedstock production and contaminant removal, four DLD concentrations (25%, 50%, 75% and 100%) were used to grow Chlorella vulgaris in batch photobioreactors (PBRs). The 25% DLD was an ideal alternative medium in that high growth rate (0.69 d-1), high lipid productivity (112.9 mg L-1 d-1) as well as high nutrient removal were attained. The high DLD concentration caused inhibition of microalgal growth, where COD was more inhibitive than ammonium. The presence of bacteria did not influence microalgae production because of limited growth. Microalgal growth reduced the richness and diversity of bacterial community. Furthermore, the species of Bacteroidetes, Candidatus Saccharibacteria, and Chlamydiae rather than Proteobacteria benefited microalgal-bacterial symbiosis. These findings contribute to better application of microalgal-bacterial system for large-scale microalgae cultivation as well as environmental sustainability.}, }
@article {pmid31003984, year = {2019}, author = {Ogran, A and Yardeni, EH and Keren-Paz, A and Bucher, T and Jain, R and Gilhar, O and Kolodkin-Gal, I}, title = {The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {13}, pages = {}, doi = {10.1128/AEM.00512-19}, pmid = {31003984}, issn = {1098-5336}, abstract = {Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria.IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.}, }
@article {pmid31001301, year = {2019}, author = {Lamouche, F and Bonadé-Bottino, N and Mergaert, P and Alunni, B}, title = {Symbiotic Efficiency of Spherical and Elongated Bacteroids in the Aeschynomene-Bradyrhizobium Symbiosis.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {377}, doi = {10.3389/fpls.2019.00377}, pmid = {31001301}, issn = {1664-462X}, abstract = {The legume-rhizobium symbiosis is a major supplier of fixed nitrogen in the biosphere and constitutes a key step of the nitrogen biogeochemical cycle. In some legume species belonging to the Inverted Repeat Lacking Clade (IRLC) and the Dalbergioids, the differentiation of rhizobia into intracellular nitrogen-fixing bacteroids is terminal and involves pronounced cell enlargement and genome endoreduplication, in addition to a strong loss of viability. In the Medicago truncatula-Sinorhizobium spp. system, the extent of bacteroid differentiation correlates with the level of symbiotic efficiency. Here, we used different physiological measurements to compare the symbiotic efficiency of photosynthetic bradyrhizobia in different Aeschynomene spp. (Dalbergioids) hosts inducing different bacteroid morphotypes associated with increasing ploidy levels. The strongly differentiated spherical bacteroids were more efficient than the less strongly differentiated elongated ones, providing a higher mass gain to their hosts. However, symbiotic efficiency is not solely correlated with the extent of bacteroid differentiation especially in spherical bacteroid-inducing plants, suggesting the existence of other factors controlling symbiotic efficiency.}, }
@article {pmid31001272, year = {2019}, author = {Khare, SP and Shetty, A and Biradar, R and Patta, I and Chen, ZJ and Sathe, AV and Reddy, PC and Lahesmaa, R and Galande, S}, title = {NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {667}, doi = {10.3389/fimmu.2019.00667}, pmid = {31001272}, issn = {1664-3224}, abstract = {SATB1 is a genome organizer protein that is expressed in a lineage specific manner in CD4+ T-cells. SATB1 plays a crucial role in expression of multiple genes throughout the thymic development and peripheral differentiation of T cells. Although SATB1 function has been subjected to intense investigation, regulation of SATB1 gene expression remains poorly understood. Analysis of RNA-seq data revealed multiple transcription start sites at the upstream regulatory region of SATB1. We further demonstrated that SATB1 gene is expressed via alternative promoters during T-helper (Th) cell differentiation. The proximal promoter &quot;P1&quot; is used more by the naïve and activated CD4+ T-cells whereas the middle &quot;P2&quot; and the distal &quot;P3&quot; promoters are used at a significantly higher level by polarized T-helper cells. Cytokine and TCR signaling play crucial roles toward SATB1 alternative promoter usage. Under Th2 polarization conditions, transcription factor STAT6, which operates downstream of the cytokine signaling binds to the P2 and P3 promoters. Genetic perturbation by knockout and chemical inhibition of STAT6 activation resulted in the loss of P2 and P3 promoter activity. Moreover, chemical inhibition of activation of NF-κB, a transcription factor that operates downstream of the TCR signaling, also resulted in reduced P2 and P3 promoter usage. Furthermore, usage of the P1 promoter correlated with lower SATB1 protein expression whereas P2 and P3 promoter usage correlated with higher SATB1 protein expression. Thus, the promoter switch might play a crucial role in fine-tuning of SATB1 protein expression in a cell type specific manner.}, }
@article {pmid31001223, year = {2019}, author = {Sun, Y and Xie, Z and Sui, F and Liu, X and Cheng, W}, title = {Identification of Cbp1, a c-di-GMP Binding Chemoreceptor in Azorhizobium caulinodans ORS571 Involved in Chemotaxis and Nodulation of the Host Plant.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {638}, doi = {10.3389/fmicb.2019.00638}, pmid = {31001223}, issn = {1664-302X}, abstract = {Cbp1, a chemoreceptor containing a PilZ domain was identified in Azorhizobium caulinodans ORS571, a nitrogen-fixing free-living soil bacterium that induces nodule formation in both the roots and stems of the host legume Sesbania rostrata. Chemoreceptors are responsible for sensing signals in the chemotaxis pathway, which guides motile bacteria to beneficial niches and plays an important role in the establishment of rhizobia-legume symbiosis. PilZ domain proteins are known to bind the second messenger c-di-GMP, an important regulator of motility, biofilm formation and virulence. Cbp1 was shown to bind c-di-GMP through the conserved RxxxR motif of its PilZ domain. A mutant strain carrying a cbp1 deletion was impaired in chemotaxis, a feature that could be restored by genetic complementation. Compared with the wild type strain, the Δcbp1 mutant displayed enhanced aggregation and biofilm formation. The Δcbp1 mutant induced functional nodules when inoculated individually. However, the Δcbp1 mutant was less competitive than the wild type in competitive root colonization and nodulation. These data are in agreement with the hypothesis that the c-di-GMP binding chemoreceptor Cbp1 in A. caulinodans is involved in chemotaxis and nodulation.}, }
@article {pmid31001143, year = {2019}, author = {Zhou, Z and Zhao, S and Tang, J and Liu, Z and Wu, Y and Wang, Y and Lin, S}, title = {Altered Immune Landscape and Disrupted Coral-Symbiodinium Symbiosis in the Scleractinian Coral Pocillopora damicornis by Vibrio coralliilyticus Challenge.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {366}, doi = {10.3389/fphys.2019.00366}, pmid = {31001143}, issn = {1664-042X}, abstract = {Vibrio coralliilyticus is known to cause coral diseases, especially under environmental perturbation, but its impact on coral physiology and underpinning mechanism is poorly understood. In the present study, we investigated cytological, immunological, and metatranscriptomic responses of the scleractinian coral Pocillopora damicornis to V. coralliilyticus infection. The density and chlorophyll content of symbiotic zooxanthellae decreased significantly at 12 and 24 h after Vibrio challenge. The activities of antioxidant enzymes such as superoxide dismutase and catalase, nitric oxide synthase, phenoloxidase (PO), and the activation level of caspase3 all rose significantly in P. damicornis after Vibrio challenge. In the metatranscriptomic analysis, we found 10 significantly upregulated genes in the symbionts at 24 h after the challenge, which were mostly involved in the metabolism of nucleic acid and polysaccharide, and 133 significantly down-regulated symbiont genes, which were mainly related to amino acid catabolism and transport. Meanwhile, 1432 significantly upregulated coral genes were revealed, highly overrepresented in GO terms that are mostly related to the regulation of immune response, the regulation of cytokine production, and innate immune response. Furthermore, at 24 h after Vibrio challenge, 890 coral genes were significantly downregulated, highly overrepresented in four GO terms implicated in defense response. These results in concert suggest that V. coralliilyticus infection triggered the innate immune response including the redox, PO, and apoptosis systems, but repressed the response of the complement system in the scleractinian coral P. damicornis, accompanied by symbiont density decrease and symbiosis collapse through disordering the metabolism of the symbionts. These findings shed light on the molecular regulatory processes underlying bleaching and degradation of P. damicornis resulting from the infection of V. coralliilyticus.}, }
@article {pmid31000761, year = {2019}, author = {Fortier, J and Truax, B and Gagnon, D and Lambert, F}, title = {Abiotic and biotic factors controlling fine root biomass, carbon and nutrients in closed-canopy hybrid poplar stands on post-agricultural land.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6296}, doi = {10.1038/s41598-019-42709-6}, pmid = {31000761}, issn = {2045-2322}, abstract = {Fine roots (diameter <2 mm) have a pivotal role in resource acquisition, symbiosis development, and for elemental cycling in forests. Various abiotic and biotic factors affect their biomass and nutrient content. Understanding the effect of these factors on root traits could improve biogeochemical modelling, nutrient management and ecosystem services provision in planted forests. Data from 14-year old poplars planted along a fertility/climatic gradient in Southeastern Canada, show that live fine root biomass varied with genotype and environment, was negatively correlated to soil fertility, and uncorrelated to tree size. Dead fine root biomass varied with genotype and peaked during fall and in colder environments with slower element cycling. Root chemistry also varied with environment, genotype and season. The genotype producing recalcitrant leaf litter had the highest root biomass, suggesting a compensation strategy. Along the studied gradient, plasticity level observed for some root traits (biomass, element contents) was genotype-specific and high for some genotypes. Regionally, such plasticity patterns should be considered in elemental budgets, for nutrient management and ecosystem services provision in plantations (carbon storage, nutrient retention). The small inter-site aboveground productivity differences observed suggest that plasticity in fine root growth may contribute to overcome nutrient limitations on less fertile marginal lands.}, }
@article {pmid31000545, year = {2019}, author = {Alai, S and Ghattargi, VC and Gautam, M and Dhotre, DP and Patel, K and Pawar, SP and Kumar, R and Shaligram, U and Deobagkar, D and Gairola, S}, title = {Genome Sequence of Bordetella pertussis Vaccine Strain BP 165.}, journal = {Microbiology resource announcements}, volume = {8}, number = {16}, pages = {}, doi = {10.1128/MRA.00150-19}, pmid = {31000545}, issn = {2576-098X}, abstract = {Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis Various vaccine reference strains are used globally for the production of such vaccines. We report here a draft genome sequence for Bordetella pertussis strain BP 165, which is used by the Serum Institute of India in the production of acellular pertussis vaccine.}, }
@article {pmid30999960, year = {2019}, author = {Sabūnas, V and Radzijevskaja, J and Sakalauskas, P and Petkevičius, S and Karvelienė, B and Žiliukienė, J and Lipatova, I and Paulauskas, A}, title = {Dirofilaria repens in dogs and humans in Lithuania.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {177}, doi = {10.1186/s13071-019-3406-y}, pmid = {30999960}, issn = {1756-3305}, support = {VP1-3.1-ŠMM-01-V-02-003//Lietuvos Mokslo Taryba (LT)/ ; }, mesh = {Adult ; Aged ; Animals ; Child ; *Dirofilaria repens/microbiology ; Dirofilariasis/epidemiology/*parasitology ; Dog Diseases/epidemiology/*parasitology ; Dogs ; Eye Diseases/parasitology ; Female ; Humans ; Lithuania/epidemiology ; Male ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Prevalence ; Symbiosis ; Wolbachia/isolation &amp; purification ; }, abstract = {BACKGROUND: In Lithuania, the first case of canine subcutaneous dirofilariosis was recorded in 2010. Since then, an increasing number of cases of canine dirofilariosis have been documented in different veterinary clinics throughout the country. Human dirofilariosis was diagnosed in Lithuania for the first time in September 2011. However, to the authors' knowledge, there are no published data on the presence and prevalence of autochthonous dirofilariosis in dogs and humans in the country. The present study provides information about the predominant species and prevalence of Dirofilaria in dogs and describes the cases of human dirofilariosis in Lithuania. It also outlines PCR detection of the bacterial endosymbiont Wolbachia that contributes to the inflammatory features of filarioid infection.<br><br>RESULTS: A total of 2280 blood samples and six adult worms from pet and shelter dogs were collected in the central and eastern regions of Lithuania in 2013-2015. Based on their morphological appearance, morphometric measurements and molecular analysis, all the adult nematodes were identified as Dirofilaria repens. The diagnosis of microfilariae in blood samples was based on blood smear analysis and Knott's test. The PCR and sequence analysis of the ribosomal DNA ITS2 region and cox1 gene confirmed the presence of D. repens. Overall, 61 (2.7%) of the 2280 blood samples were found to be positive for the presence of D. repens. The infection rate of D. repens was significantly higher in shelter dogs (19.0%; 19/100) than in pet dogs (1.9%; 42/2180) (χ2 = 100.039, df = 1, P < 0.0001). Forty-nine DNA samples of D. repens-infected dogs were tested for the presence of the bacterial endosymbiont Wolbachia and, of these, 40 samples (81.6%) were found to be positive. Three ocular and six subcutaneous cases of human dirofilariosis were diagnosed in Lithuania in the period 2011-2018.<br><br>CONCLUSIONS: To the authors' knowledge, this is the first report of autochthonous D. repens infection in dogs and humans in Lithuania. The present data demonstrate that D. repens is the main etiological agent of dirofilariosis in Lithuania. The DNA of the filarioid endosymbiotic bacterium Wolbachia was detected in the vast majority of dogs infected with D. repens.}, }
@article {pmid30999182, year = {2019}, author = {Bharti, A and Garg, N}, title = {SA and AM symbiosis modulate antioxidant defense mechanisms and asada pathway in chickpea genotypes under salt stress.}, journal = {Ecotoxicology and environmental safety}, volume = {178}, number = {}, pages = {66-78}, doi = {10.1016/j.ecoenv.2019.04.025}, pmid = {30999182}, issn = {1090-2414}, mesh = {Antioxidants/*metabolism ; Ascorbic Acid/metabolism ; Cicer/drug effects/*metabolism/microbiology ; Genotype ; Glomeromycota/*metabolism ; Mycorrhizae/*metabolism ; Oxidation-Reduction ; Oxidative Stress/drug effects ; Salicylic Acid/metabolism/*pharmacology ; *Salt Stress ; Salt Tolerance ; Seeds/drug effects/metabolism/microbiology ; Symbiosis ; }, abstract = {Salt stress disturbs redox homeostasis by perturbing equilibrium between generation and removal of reactive oxygen species (ROS), which alters the normal metabolism of plants through membrane damage, lipid peroxidation and denaturation of proteins. Salicylic acid (SA) seed priming and arbuscular mycorrhizal (AM) fungi impart salt tolerance in legumes by maintaining redox balance. The present investigation focused on the relative and combined applications of SA and Rhizoglomus intraradices in scavenging ROS in Cicer arietinum L. (chickpea) genotypes (salt tolerant-PBG 5, relatively sensitive-BG 256) subjected to salt stress. Despite the enhanced antioxidant mechanisms under salt stress, ROS (superoxide, O2- and hydrogen peroxide, H2O2) accumulation increased significantly and induced lipid peroxidation and lipoxygenase (LOX) activities, which disrupted membrane stability, more in BG 256 than PBG 5. Salt stress also caused redox imbalance by lowering ascorbate/dehydroascorbate (ASA/DHA) and reduced glutathione/oxidized glutathione (GSH/GSSG) ratios, indicating that redox-homeostasis was crucial for salt-tolerance. Exogenous SA was more promising in reducing ROS-generation and lipid-peroxidation, which provided higher membrane stability as compared to AM inoculation. Although, the enzymatic antioxidants were more active in SA treated plants, yet, AM inoculation outperformed in increasing reformative enzyme activities of Foyer-Halliwell-Asada cycle, which resulted in higher plant biomass in a genotype-dependent manner. SA increased AM root colonization and provided functional complementarity to R. intraradices and thereby strengthening antioxidant defense mechanisms through their cumulative contribution. The study suggested the use of +SA+AM as an eco-friendly tool in imparting salt tolerance in chickpea genotypes subjected to long-term salinity.}, }
@article {pmid30995278, year = {2019}, author = {Leinonen, PH and Helander, M and Vázquez-de-Aldana, BR and Zabalgogeazcoa, I and Saikkonen, K}, title = {Local adaptation in natural European host grass populations with asymmetric symbiosis.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215510}, doi = {10.1371/journal.pone.0215510}, pmid = {30995278}, issn = {1932-6203}, abstract = {Recent work on microbiomes is revealing the wealth and importance of plant-microbe interactions. Microbial symbionts are proposed to have profound effects on fitness of their host plants and vice versa, especially when their fitness is tightly linked. Here we studied local adaptation of host plants and possible fitness contribution of such symbiosis in the context of abiotic environmental factors. We conducted a four-way multi-year reciprocal transplant experiment with natural populations of the perennial grass Festuca rubra s.l. from northern and southern Finland, Faroe Islands and Spain. We included F. rubra with and without transmitted symbiotic fungus Epichloë that is vertically transmitted via host seed. We found local adaptation across the European range, as evidenced by higher host fitness of the local geographic origin compared with nonlocals at three of the four studied sites, suggesting that selection pressures are driving evolution in different directions. Abiotic factors did not result in strong fitness effects related to Epichloë symbiosis, indicating that other factors such as herbivory are more likely to contribute to fitness differences between plants naturally occurring with or without Epichloë. Nevertheless, in the case of asymmetric symbiosis that is obligatory for the symbiont, abiotic conditions that affect performance of the host, may also cause selective pressure for the symbiont.}, }
@article {pmid30993446, year = {2019}, author = {Singh, AN and Sharma, N}, title = {Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer.}, journal = {The protein journal}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10930-019-09832-9}, pmid = {30993446}, issn = {1875-8355}, abstract = {The Sonic hedgehog signalling is known to play a crucial role in regulating embryonic development, cancer stem cell maintenance and tissue patterning. Dysregulated hedgehog signalling has been reported to affect tumorigenesis and drug response in various human malignancies. Epigenetic therapy relying on DNA methyltransferase and Histone deacetylase inhibitors are being proposed as potential drug candidates considering their efficiency in preventing development of cancer progenitor cells, killing drug resistant cells and also dictating &quot;on/off&quot; switch of tumor suppressor genes and oncogenes. In this docking approach, epigenetic modulators were virtually screened for their efficiency in inhibiting key regulators of SHH pathway viz., sonic hedgehog, Smoothened and Gli using polypharmacological approach. The control drugs and epigenetic modulators were docked with PDB protein structures using AutoDock vina and further checked for their drug-likeness properties. Further molecular dynamics simulation using VMD and NAMD, and MMP/GBSA energy calculation were employed for verifying the stability and entropy of the ligand-receptor complex. EPZ-6438 and GSK 343 (EZH2 inhibitors), CHR 3996 and Mocetinostat (HDAC inhibitors), GSK 126 (HKMT inhibitor) and UNC 1215 (L3MBTL3 antagonist) exhibited multiple-targeted approach in modulating HH signalling. This is the first study to report these epigenetic drugs as potential multi-targeted hedgehog pathway inhibitors. Thus, epigenetic polypharmacology approach can be explored as a better alternative to challenges of acute long term toxicity and drug resistance occurring due to traditional single targeted chemotherapy in the future.}, }
@article {pmid30991952, year = {2019}, author = {Dhaygude, K and Nair, A and Johansson, H and Wurm, Y and Sundström, L}, title = {The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {301}, doi = {10.1186/s12864-019-5665-6}, pmid = {30991952}, issn = {1471-2164}, support = {252411 and 284666 (Centre of Excellence in Biological Interactions)//Academy of Finland/ ; BB/K004204/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/L00626X/1//Natural Environment Research Council/ ; }, mesh = {Animals ; Ants/*genetics/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Insect/genetics ; *Genomics ; Symbiosis/*genetics ; Wolbachia/*genetics/*physiology ; }, abstract = {BACKGROUND: Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict.<br><br>RESULTS: In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes.<br><br>CONCLUSION: We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.}, }
@article {pmid30991927, year = {2019}, author = {Dixon, GB and Kenkel, CD}, title = {Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1901}, pages = {20190111}, doi = {10.1098/rspb.2019.0111}, pmid = {30991927}, issn = {1471-2954}, abstract = {Heritable symbioses have been critical for the evolution of life. The genetic consequences of evolving a heritable symbiosis from the perspective of the symbiont are well established, but concomitant changes in the host remain unresolved. In stony corals, heritable, vertical transmission has evolved repeatedly, providing a unique opportunity to investigate the genomic basis of this complex trait. We conducted a comparative analysis of 25 coral transcriptomes to identify orthologous genes exhibiting signatures of positive selection and convergent amino acid substitutions in vertically transmitting lineages. The frequency of convergence events tends to be higher among vertically transmitting lineages, consistent with the proposed role of selection in driving the evolution of convergent transmission mode phenotypes. Of 10 774 orthologous genes, 403 exhibited at least one molecular convergence event and evidence of positive selection in at least one vertically transmitting lineage. Functional enrichments among these top candidate genes include processes previously implicated in symbiosis including endocytosis, immune response, cytoskeletal protein binding and cytoplasmic membrane-bounded vesicles. Finally, several novel candidates were identified among 100 genes showing evidence of positive selection at the particular convergence event, highlighting the value of our approach for generating new insight into host mechanisms associated with the evolution of heritable symbioses.}, }
@article {pmid30991290, year = {2019}, author = {Ezra, H}, title = {On the relationship between road safety research and the practice of road design and operation.}, journal = {Accident; analysis and prevention}, volume = {128}, number = {}, pages = {114-131}, doi = {10.1016/j.aap.2019.03.016}, pmid = {30991290}, issn = {1879-2057}, mesh = {Accident Prevention/*methods ; Accidents, Traffic/prevention &amp; control ; Built Environment/*standards ; *Decision Making ; Humans ; Research/standards ; Safety ; }, abstract = {How do the findings of road safety research affect the practice by which the road infrastructure is built and operated? The question is seldom asked. I discuss the complexities of the research-practice symbiosis in the light of two historical anecdotes. These allow me to point out several issues of concern. My general conclusion is that the relationship, as it evolved over time, is unpremeditated and occasionally dysfunctional. Issues of concern are the lightness with which decisions affecting road-user safety can be based on opinion that is unsupported by evidence, that such opinions can trump inconvenient evidence, that research findings can be willfully distorted or disregarded, that questionable results can be given a ring of consensual truth, and that the questions which research asks and what findings get published are at times influenced by external interest. In sum, the concern is that practice is not sufficiently evidence-based. Road users have a right to expect that decisions substantially affecting their safety take into account fact-based expectation of safety consequences. It is therefore time to endow the research-practice relationship with a premeditated and purposeful structure.}, }
@article {pmid30990223, year = {2019}, author = {Mathé-Hubert, H and Kaech, H and Ganesanandamoorthy, P and Vorburger, C}, title = {Evolutionary costs and benefits of infection with diverse strains of Spiroplasma in pea aphids.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {7}, pages = {1466-1481}, doi = {10.1111/evo.13740}, pmid = {30990223}, issn = {1558-5646}, support = {CRSII3_154396//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {The heritable endosymbiont Spiroplasma infects many insects and has repeatedly evolved the ability to protect its hosts against different parasites. Defenses do not come for free to the host, and theory predicts that more costly symbionts need to provide stronger benefits to persist in host populations. We investigated the costs and benefits of Spiroplasma infections in pea aphids (Acyrthosiphon pisum), testing 12 bacterial strains from three different clades. Virtually all strains decreased aphid lifespan and reproduction, but only two had a (weak) protective effect against the parasitoid Aphidius ervi, an important natural enemy of pea aphids. Spiroplasma-induced fitness costs were variable, with strains from the most slowly evolving clade reaching higher titers and curtailing aphid lifespan more strongly than other strains. Some Spiroplasma strains shared their host with a second endosymbiont, Regiella insecticola. Although the result of an unfortunate handling error, these co-infections proved instructive, because they showed that the cost of infection with Spiroplasma may be attenuated in the presence of Regiella. These results suggest that mechanisms other than protection against A. ervi maintain pea aphid infections with diverse strains of Spiroplasma, and that studying them in isolation will not provide a complete picture of their effects on host fitness.}, }
@article {pmid30990167, year = {2019}, author = {Zhou, YL and Ślipiński, A and Ren, D and Parker, J}, title = {A Mesozoic clown beetle myrmecophile (Coleoptera: Histeridae).}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.44985}, pmid = {30990167}, issn = {2050-084X}, support = {31402008//National Natural Science Foundation of China/ ; 20150064//International Postdoctoral Exchange Fellowship/ ; }, abstract = {Complex interspecies relationships are widespread among metazoans, but the evolutionary history of these lifestyles is poorly understood. We describe a fossil beetle in 99-million-year-old Burmese amber that we infer to have been a social impostor of the earliest-known ant colonies. Promyrmister kistneri gen. et sp. nov. belongs to the haeteriine clown beetles (Coleoptera: Histeridae), a major clade of 'myrmecophiles'-specialized nest intruders with dramatic anatomical, chemical and behavioral adaptations for colony infiltration. Promyrmister reveals that myrmecophiles evolved close to the emergence of ant eusociality, in colonies of stem-group ants that predominate Burmese amber, or with cryptic crown-group ants that remain largely unknown at this time. The clown beetle-ant relationship has been maintained ever since by the beetles host-switching to numerous modern ant genera, ultimately diversifying into one of the largest radiations of symbiotic animals. We infer that obligate behavioral symbioses can evolve relatively rapidly, and be sustained over deep time.}, }
@article {pmid30990122, year = {2019}, author = {Shah, S and Thapa, BB and Chand, K and Pradhan, S and Singh, A and Varma, A and Sen Thakuri, L and Joshi, P and Pant, B}, title = {Piriformospora indica promotes the growth of the in-vitro-raised Cymbidium aloifolium plantlet and their acclimatization.}, journal = {Plant signaling &amp; behavior}, volume = {14}, number = {6}, pages = {1596716}, doi = {10.1080/15592324.2019.1596716}, pmid = {30990122}, issn = {1559-2324}, abstract = {Cymbidium aloifolium is known for its ornamental and medicinal values. It has been listed as threatened orchid species. In this study, in vitro propagated C. aloifolium plantlets were interacted with the Piriformospora indica. The growth assay was performed for 45 days; the plant growth pattern such as number and length of roots and shoots were measured. Microscopic study of the root section stained by trypan blue was done to detect the peloton formation. The methanol extracts of the fungal colonized plant as well as uncolonized (control) plant were prepared and various metabolites were identified by gas chromatography mass spectroscopy. Acclimatization was done in a substrate composition of coco peat: gravel: charcoal in ratio 2:2:1. P. indica-colonized plantlet showed the highest growth with the formation of clamdospore in the root section. The growth regulator such as auxin, ascorbic acid, andrographolide, hexadecanoic acid, and DL-proline were identified. After three months of field transfer, plantlet colonized by P. indica survived and remained healthy as compared to uncolonized control plantlet.}, }
@article {pmid30989804, year = {2019}, author = {Mediavilla, O and Geml, J and Olaizola, J and Oria-de-Rueda, JA and Baldrian, P and Martín-Pinto, P}, title = {Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13395}, pmid = {30989804}, issn = {1751-7915}, support = {VA050P17//Junta de Castilla y León/ ; //University of Valladolid programme 'Ayudas para estancias breves en el desarrollo de Tesis Doctorales. Convocatoria 2016'/ ; 2018//Naturalis Biodiversity Center/ ; //European Social Fund/ ; }, abstract = {Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.}, }
@article {pmid30989446, year = {2019}, author = {Zhang, Z and Ke, D and Hu, M and Zhang, C and Deng, L and Li, Y and Li, J and Zhao, H and Cheng, L and Wang, L and Yuan, H}, title = {Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis.}, journal = {Plant molecular biology}, volume = {100}, number = {3}, pages = {265-283}, doi = {10.1007/s11103-019-00857-3}, pmid = {30989446}, issn = {1573-5028}, support = {182300410063//Natural Science Foundation of Henan Provincial Science and Technology/ ; 18A180031//key scientific research projects of Henan higher education institutions/ ; 31400213//National Natural Science Foundation of China/ ; 2015, 2016//Funding scheme for young core teachers of Xinyang Normal University/ ; 2017//Nanhu Scholars Program for Young Scholars of XYNU/ ; }, mesh = {Ammonia/metabolism ; Fabaceae/genetics/*metabolism ; Gene Expression Regulation, Plant ; Lotus/genetics/*metabolism ; Mass Spectrometry ; Mitogen-Activated Protein Kinase 6/genetics/metabolism ; Nitrogen Fixation ; Phosphoproteins/physiology ; Phosphorylation ; Plant Proteins/genetics/*metabolism ; Plant Roots/metabolism ; Proteomics/*methods ; RNA Splicing ; RNA, Plant/metabolism ; Rhizobium/genetics/*physiology ; Root Nodules, Plant/genetics/growth &amp; development/*metabolism ; *Signal Transduction ; Symbiosis/*physiology ; Transcription Factors ; }, abstract = {KEY MESSAGE: Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.}, }
@article {pmid30989396, year = {2019}, author = {Deveau, A and Clowez, P and Petit, F and Maurice, JP and Todesco, F and Murat, C and Harroué, M and Ruelle, J and Le Tacon, F}, title = {New insights into black truffle biology: discovery of the potential connecting structure between a Tuber aestivum ascocarp and its host root.}, journal = {Mycorrhiza}, volume = {29}, number = {3}, pages = {219-226}, doi = {10.1007/s00572-019-00892-4}, pmid = {30989396}, issn = {1432-1890}, support = {ANR-11-LABX 0002 01//ANR/ ; }, mesh = {Ascomycota/*physiology ; Carbon/metabolism ; Fruiting Bodies, Fungal/*physiology ; Genes, Mating Type, Fungal ; Mycorrhizae ; Polymerase Chain Reaction ; *Symbiosis ; Trees/*microbiology ; }, abstract = {According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed. We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles. Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type.}, }
@article {pmid30989224, year = {2019}, author = {Chong, RA and Park, H and Moran, NA}, title = {Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola.}, journal = {Molecular biology and evolution}, volume = {36}, number = {7}, pages = {1481-1489}, doi = {10.1093/molbev/msz082}, pmid = {30989224}, issn = {1537-1719}, abstract = {An evolutionary consequence of uniparentally transmitted symbiosis is degradation of symbiont genomes. We use the system of aphids and their maternally inherited obligate endosymbiont, Buchnera aphidicola, to explore the evolutionary process of genome degradation. We compared complete genome sequences for 39 Buchnera strains, including 23 newly sequenced symbiont genomes from diverse aphid hosts. We reconstructed the genome of the most recent shared Buchnera ancestor, which contained 616 protein-coding genes, and 39 RNA genes. The extent of subsequent gene loss varied across lineages, resulting in modern genomes ranging from 412 to 646 kb and containing 354-587 protein-coding genes. Loss events were highly nonrandom across loci. Genes involved in replication, transcription, translation, and amino acid biosynthesis are largely retained, whereas genes underlying ornithine biosynthesis, stress responses, and transcriptional regulation were lost repeatedly. Aside from losses, gene order is almost completely stable. The main exceptions involve movement between plasmid and chromosome locations of genes underlying tryptophan and leucine biosynthesis and supporting nutrition of aphid hosts. This set of complete genomes enabled tests for signatures of positive diversifying selection. Of 371 Buchnera genes tested, 29 genes show strong support for ongoing positive selection. These include genes encoding outer membrane porins that are expected to be involved in direct interactions with hosts. Collectively, these results indicate that extensive genome reduction occurred in the ancestral Buchnera prior to aphid diversification and that reduction has continued since, with losses greater in some lineages and for some loci.}, }
@article {pmid30987816, year = {2019}, author = {Morris, LA and Voolstra, CR and Quigley, KM and Bourne, DG and Bay, LK}, title = {Nutrient Availability and Metabolism Affect the Stability of Coral-Symbiodiniaceae Symbioses.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {678-689}, doi = {10.1016/j.tim.2019.03.004}, pmid = {30987816}, issn = {1878-4380}, abstract = {Coral reefs rely upon the highly optimized coral-Symbiodiniaceae symbiosis, making them sensitive to environmental change and susceptible to anthropogenic stress. Coral bleaching is predominantly attributed to photo-oxidative stress, yet nutrient availability and metabolism underpin the stability of symbioses. Recent studies link symbiont proliferation under nutrient enrichment to bleaching; however, the interactions between nutrients and symbiotic stability are nuanced. Here, we demonstrate how bleaching is regulated by the forms and ratios of available nutrients and their impacts on autotrophic carbon metabolism, rather than algal symbiont growth. By extension, historical nutrient conditions mediate host-symbiont compatibility and bleaching tolerance over proximate and evolutionary timescales. Renewed investigations into the coral nutrient metabolism will be required to truly elucidate the cellular mechanisms leading to coral bleaching.}, }
@article {pmid30986120, year = {2019}, author = {Si, Z and Yang, Q and Liang, R and Chen, L and Chen, D and Li, Y}, title = {Digalactosyldiacylglycerol Synthase Gene MtDGD1 Plays an Essential Role in Nodule Development and Nitrogen Fixation.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {32}, number = {9}, pages = {1196-1209}, doi = {10.1094/MPMI-11-18-0322-R}, pmid = {30986120}, issn = {0894-0282}, abstract = {Little is known about the genes participating in digalactosyldiacylglycerol (DGDG) synthesis during nodule symbiosis. Here, we identified full-length MtDGD1, a synthase of DGDG, and characterized its effect on symbiotic nitrogen fixation in Medicago truncatula. Immunofluorescence and immunoelectron microscopy showed that MtDGD1 was located on the symbiosome membranes in the infected cells. β-Glucuronidase histochemical staining revealed that MtDGD1 was highly expressed in the infection zone of young nodules as well as in the whole mature nodules. Compared with the control, MtDGD1-RNA interference transgenic plants exhibited significant decreases in nodule number, symbiotic nitrogen fixation activity, and DGDG abundance in the nodules, as well as abnormal nodule and symbiosome development. Overexpression of MtDGD1 resulted in enhancement of nodule number and nitrogen fixation activity. In response to phosphorus starvation, the MtDGD1 expression level was substantially upregulated and the abundance of nonphospholipid DGDG was significantly increased in the roots and nodules, accompanied by corresponding decreases in the abundance of phospholipids such as phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. Overall, our results indicate that DGD1 contributes to effective nodule organogenesis and nitrogen fixation by affecting the synthesis and content of DGDG during symbiosis.}, }
@article {pmid30984121, year = {2019}, author = {Deja-Sikora, E and Mercy, L and Baum, C and Hrynkiewicz, K}, title = {The Contribution of Endomycorrhiza to the Performance of Potato Virus Y-Infected Solanaceous Plants: Disease Alleviation or Exacerbation?.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {516}, doi = {10.3389/fmicb.2019.00516}, pmid = {30984121}, issn = {1664-302X}, abstract = {Solanaceae, comprising meaningful crops (as potato, tomato, pepper, eggplant, and tobacco), can benefit from a symbiosis with arbuscular mycorrhizal fungi (AMF), which improve plant fitness and support plant defense against pathogens. Currently, those crops are likely the most impacted by Potato virus Y (PVY). Unfortunately, the effects of AM symbiosis on the severity of disease induced by PVY in solanaceous crops remain uncertain, partly because the interplay between AMF and PVY is poorly characterized. To shed some light on this issue, available studies on interactions in tripartite association between the host plant, its fungal colonizer, and viral pathogen were analyzed and discussed. Although the best-documented PVY transmission pathway is aphid-dependent, PVY infections are also observed in the absence of insect vector. We hypothesize the existence of an additional pathway for virus transmission involving AMF, in which the common mycorrhizal network (CMN) may act as a potential bridge. Therefore, we reviewed (1) the significance of AM colonization for the course of disease, (2) the potential of AMF networks to act as vectors for PVY, and (3) the consequences for crop breeding and production of AM biofertilizers.}, }
@article {pmid30984118, year = {2019}, author = {Ek-Ramos, MJ and Gomez-Flores, R and Orozco-Flores, AA and Rodríguez-Padilla, C and González-Ochoa, G and Tamez-Guerra, P}, title = {Bioactive Products From Plant-Endophytic Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {463}, doi = {10.3389/fmicb.2019.00463}, pmid = {30984118}, issn = {1664-302X}, abstract = {Endophytes constitute plant-colonizing microorganisms in a mutualistic symbiosis relationship. They are found in most ecosystems reducing plant crops' biotic and abiotic stressors by stimulating immune responses, excluding plant pathogens by niche competition, and participating in antioxidant activities and phenylpropanoid metabolism, whose activation produces plant defense, structural support, and survival molecules. In fact, metabolomic studies have demonstrated that endophyte genes associated to specific metabolites are involved in plant growth promotion (PGP) by stimulating plant hormones production such as auxins and gibberellins or as plant protective agents against microbial pathogens, cancer, and insect pests, but eco-friendly and eco-safe. A number of metabolites of Gram-positive endophytes isolated from agriculture, forest, mangrove, and medicinal plants, mainly related to the Firmicutes phyla, possess distinctive biocontrol and plant growth-promoting activities. In general, Actinobacteria and Bacillus endophytes produce aromatic compounds, lipopeptides, plant hormones, polysaccharides, and several enzymes linked to phenylpropanoid metabolism, thus representing high potential for PGP and crop management strategies. Furthermore, Actinobacteria have been shown to produce metabolites with antimicrobial and antitumor activities, useful in agriculture, medicine, and veterinary areas. The great endophytes diversity, their metabolites production, and their adaptation to stress conditions make them a suitable and unlimited source of novel metabolites, whose application could reduce agrochemicals usage in food and drugs production.}, }
@article {pmid30979392, year = {2019}, author = {Jaspers, C and Fraune, S and Arnold, AE and Miller, DJ and Bosch, TCG and Voolstra, CR and , }, title = {Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.}, journal = {Zoology (Jena, Germany)}, volume = {133}, number = {}, pages = {81-87}, doi = {10.1016/j.zool.2019.02.007}, pmid = {30979392}, issn = {1873-2720}, mesh = {Animals ; *Microbiota ; Symbiosis ; }, abstract = {Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.}, }
@article {pmid30978547, year = {2019}, author = {Munzi, S and Cruz, C and Corrêa, A}, title = {When the exception becomes the rule: An integrative approach to symbiosis.}, journal = {The Science of the total environment}, volume = {672}, number = {}, pages = {855-861}, doi = {10.1016/j.scitotenv.2019.04.038}, pmid = {30978547}, issn = {1879-1026}, mesh = {Animals ; Anthozoa/microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {Symbiosis, mainly due to the advances in -omics technology and to the microbiome revolution, is being increasingly acknowledged as fundamental to explain any aspect of life existence. Previously considered an exception, a peculiar characteristic of few systems like lichens, corals and mycorrhizas, symbiosis is nowadays recognized as the rule, with the microbiome being part of all living entities and systems. However, our knowledge of the ecological meaning and functioning of many symbiotic systems is still limited. Here, we discuss a new, integrative approach based on current findings that looks at commonalities among symbiotic systems to produce theoretical models and conceptual knowledge that would allow a more efficient exploitation of symbiosis-based biotechnologies. The microbiome recruitment and assemblage processes are indicated as one of the potential targets where a holistic approach could bring advantages. Finally, we reflect on the potential socio-economic and environmental consequences of a symbiotic view of the world, where co-dependence is the matrix of life.}, }
@article {pmid30977796, year = {2019}, author = {Salinero-Lanzarote, A and Pacheco-Moreno, A and Domingo-Serrano, L and Durán, D and Ormeño-Orrillo, E and Martínez-Romero, E and Albareda, M and Palacios, JM and Rey, L}, title = {The Type VI secretion system of Rhizobium etli Mim1 has a positive effect in symbiosis.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz054}, pmid = {30977796}, issn = {1574-6941}, abstract = {The Type VI secretion systems (T6SSs) allow bacteria to translocate effector proteins to other bacteria or to eukaryotic cells. However, little is known about the role of T6SS in endosymbiotic bacteria. In this work we describe the T6SS of Rhizobium etli Mim1, a bacteria able to effectively nodulate common beans. Structural genes and those encoding possible effectors have been identified in a 28-gene DNA region of R. etli Mim1 pRetMIM1f plasmid. Immunodetection of Hcp protein, a conserved key structural component of T6SS systems, indicates that this secretion system is active at high cell densities, in the presence of root exudates, and in bean nodules. Rhizobium etli mutants affected in T6SS structural genes produced plants with lower dry weight and smaller nodules than the wild-type strain, indicating for the first time that the T6SS plays a positive role in Rhizobium-legume symbiosis.}, }
@article {pmid30977533, year = {2019}, author = {Wu, Z and Wang, M and Yang, S and Chen, S and Chen, X and Liu, C and Wang, S and Wang, H and Zhang, B and Liu, H and Qin, R and Wang, X}, title = {A global coexpression network of soybean genes gives insights into the evolution of nodulation in nonlegumes and legumes.}, journal = {The New phytologist}, volume = {223}, number = {4}, pages = {2104-2119}, doi = {10.1111/nph.15845}, pmid = {30977533}, issn = {1469-8137}, support = {2016YFD0100700//The National Key Research and Development Program of China/ ; 2662015PY020//Huazhong Agricultural University/ ; 2014RC002//Huazhong Agricultural University/ ; 91535104//The National Natural Science Foundation of China/ ; 31430046//The National Natural Science Foundation of China/ ; 2015M582235//The Chinese Postdoctoral Science Foundation/ ; 2015CB910200//The National Key Basic Research Foundation of China/ ; }, abstract = {A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events before the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation.}, }
@article {pmid30976084, year = {2019}, author = {Kim, GB and Son, SU and Yu, HJ and Mun, JH}, title = {MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5952}, doi = {10.1038/s41598-019-42407-3}, pmid = {30976084}, issn = {2045-2322}, support = {PJ012251//Rural Development Administration (RDA)/ ; PJ012421//Rural Development Administration (RDA)/ ; }, abstract = {Gibberellin (GA) plays a controversial role in the legume-rhizobium symbiosis. Recent studies have shown that the GA level in legumes must be precisely controlled for successful rhizobial infection and nodule organogenesis. However, regulation of the GA level via catabolism in legume roots has not been reported to date. Here, we investigate a novel GA inactivating C20-GA2-oxidase gene MtGA2ox10 in Medicago truncatula. RNA sequencing analysis and quantitative polymerase chain reaction revealed that MtGA2ox10 was induced as early as 6 h post-inoculation (hpi) of rhizobia and reached peak transcript abundance at 12 hpi. Promoter::β-glucuronidase fusion showed that the promoter activity was localized in the root infection/differentiation zone during the early stage of rhizobial infection and in the vascular bundle of the mature nodule. The CRISPR/Cas9-mediated deletion mutation of MtGA2ox10 suppressed infection thread formation, which resulted in reduced development and retarded growth of nodules on the Agrobacterium rhizogenes-transformed roots. Over-expression of MtGA2ox10 in the stable transgenic plants caused dwarfism, which was rescued by GA3 application, and increased infection thread formation but inhibition of nodule development. We conclude that MtGA2ox10 plays an important role in the rhizobial infection and the development of root nodules through fine catabolic tuning of GA in M. truncatula.}, }
@article {pmid30976027, year = {2019}, author = {Lefoulon, E and Vaisman, N and Frydman, HM and Sun, L and Foster, JM and Slatko, BE}, title = {Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5939}, doi = {10.1038/s41598-019-42454-w}, pmid = {30976027}, issn = {2045-2322}, abstract = {Symbiosis is a major force of evolutionary change, influencing virtually all aspects of biology, from population ecology and evolution to genomics and molecular/biochemical mechanisms of development and reproduction. A remarkable example is Wolbachia endobacteria, present in some parasitic nematodes and many arthropod species. Acquisition of genomic data from diverse Wolbachia clades will aid in the elucidation of the different symbiotic mechanisms(s). However, challenges of de novo assembly of Wolbachia genomes include the presence in the sample of host DNA: nematode/vertebrate or insect. We designed biotinylated probes to capture large fragments of Wolbachia DNA for sequencing using PacBio technology (LEFT-SEQ: Large Enriched Fragment Targeted Sequencing). LEFT-SEQ was used to capture and sequence four Wolbachia genomes: the filarial nematode Brugia malayi, wBm, (21-fold enrichment), Drosophila mauritiana flies (2 isolates), wMau (11-fold enrichment), and Aedes albopictus mosquitoes, wAlbB (200-fold enrichment). LEFT-SEQ resulted in complete genomes for wBm and for wMau. For wBm, 18 single-nucleotide polymorphisms (SNPs), relative to the wBm reference, were identified and confirmed by PCR. A limit of LEFT-SEQ is illustrated by the wAlbB genome, characterized by a very high level of insertion sequences elements (ISs) and DNA repeats, for which only a 20-contig draft assembly was achieved.}, }
@article {pmid30975812, year = {2019}, author = {Gogoleva, NE and Nikolaichik, YA and Ismailov, TT and Khlopko, YA and Dmitrieva, SA and Konnova, TA and Ermekkaliev, TS and Safronova, VI and Belimov, AA and Gogolev, YV}, title = {Complete Genome Sequence of Abscisic Acid-Metabolizing Rhizobacterium Rhodococcus sp. Strain P1Y.}, journal = {Microbiology resource announcements}, volume = {8}, number = {15}, pages = {}, doi = {10.1128/MRA.01591-18}, pmid = {30975812}, issn = {2576-098X}, abstract = {Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABA-utilizing Rhodococcus sp. strain P1Y, isolated from the rice (Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequence data.}, }
@article {pmid30972304, year = {2019}, author = {Choudhary, E and Sharma, R and Kumar, Y and Agarwal, N}, title = {Conditional Silencing by CRISPRi Reveals the Role of DNA Gyrase in Formation of Drug-Tolerant Persister Population in Mycobacterium tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {70}, doi = {10.3389/fcimb.2019.00070}, pmid = {30972304}, issn = {2235-2988}, abstract = {Drug tolerance in mycobacterial pathogens is a global concern. Fluoroquinolone (FQ) treatment is widely used for induction of persisters in bacteria. Although FQs that target DNA gyrase are currently used as second-line anti-tuberculosis (TB) drugs, little is known about their impact on Mycobacterium tuberculosis (Mtb) persister formation. Here we explored the CRISPRi-based genetic repression for better understanding the effect of DNA gyrase depletion on Mtb physiology and response to anti-TB drugs. We find that suppression of DNA gyrase drastically affects intra- and extracellular growth of Mtb. Interestingly, gyrase depletion in Mtb leads to activation of RecA/LexA-mediated SOS response and drug tolerance via induction of persister subpopulation. Chemical inhibition of RecA in gyrase-depleted bacteria results in reversion of persister phenotype and better killing by antibiotics. This study provides evidence that inhibition of SOS response can be advantageous in improving the efficacy of anti-TB drugs and shortening the duration of current TB treatment.}, }
@article {pmid30972043, year = {2019}, author = {Mills, JG and Brookes, JD and Gellie, NJC and Liddicoat, C and Lowe, AJ and Sydnor, HR and Thomas, T and Weinstein, P and Weyrich, LS and Breed, MF}, title = {Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {550}, doi = {10.3389/fmicb.2019.00550}, pmid = {30972043}, issn = {1664-302X}, abstract = {A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.}, }
@article {pmid30971198, year = {2019}, author = {Malinich, EA and Wang, K and Mukherjee, PK and Kolomiets, M and Kenerley, CM}, title = {Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {280}, doi = {10.1186/s12864-019-5651-z}, pmid = {30971198}, issn = {1471-2164}, support = {2016-67013-24730//National Institute of Food and Agriculture/ ; }, mesh = {Energy Metabolism ; *Gene Expression Profiling ; Plant Roots/*microbiology ; Trichoderma/*genetics/metabolism/*physiology ; Zea mays/*microbiology ; }, abstract = {BACKGROUND: Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex.<br><br>RESULTS: We present a model of T. virens - maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots.<br><br>CONCLUSIONS: T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens - maize symbiosis.}, }
@article {pmid30968126, year = {2019}, author = {Berger, A and Boscari, A and Frendo, P and Brouquisse, R}, title = {Nitric oxide signaling, metabolism and toxicity in nitrogen-fixing symbiosis.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz159}, pmid = {30968126}, issn = {1460-2431}, abstract = {The interactions between legumes and Rhizobia lead to the establishment of a symbiotic relationship characterized by the formation of a new organ, the nodule, which facilitates the fixation of atmospheric nitrogen (N2) by nitrogenase through the creation of a hypoxic environment. Significant amounts of nitric oxide (NO) accumulate at different stages of nodule development, suggesting that NO performs specific signaling and/or metabolic functions during symbiosis. NO, which regulates nodule gene expression, accumulates to high levels in hypoxic nodules. NO accumulation is considered to assist energy metabolism within the hypoxic environment of the nodule via a phytoglobin/NO-mediated respiration process. NO is a potent inhibitor of the activity of nitrogenase and other plant/bacterial enzymes, acting as a developmental signal in the induction of nodule senescence. Hence, key questions concern the relative importance of the signaling/metabolic functions of NO versus its toxic action and how NO levels are regulated to be compatible with nitrogen fixation functions. This review analyses these paradoxical roles of NO at various stages of symbiosis, and highlights the role of plant phytoglobins and bacterial hemoproteins in the control of NO accumulation.}, }
@article {pmid30967024, year = {2019}, author = {Kang, L}, title = {Overview: biotic signalling for smart pest management.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1767}, pages = {20180306}, doi = {10.1098/rstb.2018.0306}, pmid = {30967024}, issn = {1471-2970}, abstract = {Biotic signalling refers to species or phylogenetic-clade-specific signals that elicit adaptive and acceptable responses within and among organisms. It is not only the molecular basis of the ecological relationships among different species, such as parasitism, symbiosis and predation, but also serves as ideal targets that can be used to manipulate these ecological relationships. This concept was proposed by a group of scientists from the Chinese Academy of Sciences (CAS) and actively pursued in a five-year research project in 2014 funded by the CAS ($40 million), entitled 'Decoding biotic interactions and mechanism for target management of agricultural pests'. The multi-disciplinary project aimed at a systematic investigation of the intra-species and inter-species and interactions via biotic signalling, with the ultimate goal being the development of novel methods to manage the pest insects and diseases. We hereby propose a topic 'Biotic signalling sheds light on smart pest control' as a theme issue for the Philosophical Transactions of the Royal Society B. It contains a total of 18 reviews and research articles under the topic of signalling manipulation for pest management. Unravelling these complex interactions among plants, microbial pathogens and insects holds promise for developing novel strategies to protect crop plants without compromising agricultural productivity and environmental health. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.}, }
@article {pmid30963950, year = {2019}, author = {Uchiumi, Y and Ohtsuki, H and Sasaki, A}, title = {Evolution of self-limited cell division of symbionts.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1895}, pages = {20182238}, doi = {10.1098/rspb.2018.2238}, pmid = {30963950}, issn = {1471-2954}, abstract = {In mutualism between unicellular hosts and their endosymbionts, symbiont's cell division is often synchronized with its host's, ensuring the permanent relationship between endosymbionts and their hosts. The evolution of synchronized cell division thus has been considered to be an essential step in the evolutionary transition from symbionts to organelles. However, if symbionts would accelerate their cell division without regard for the synchronization with the host, they would proliferate more efficiently. Thus, it is paradoxical that symbionts evolve to limit their own division for synchronized cell division. Here, we theoretically explore the condition for the evolution of self-limited cell division of symbionts, by assuming that symbionts control their division rate and that hosts control symbionts' death rate by intracellular digestion and nutrient supply. Our analysis shows that symbionts can evolve to limit their own cell division. Such evolution occurs if not only symbiont's but also host's benefit through symbiosis is large. Moreover, the coevolution of hosts and symbionts leads to either permanent symbiosis where symbionts proliferate to keep pace with their host, or the arms race between symbionts that behave as lytic parasites and hosts that resist them by rapid digestion.}, }
@article {pmid30963860, year = {2019}, author = {Skelton, J and Johnson, AJ and Jusino, MA and Bateman, CC and Li, Y and Hulcr, J}, title = {A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1894}, pages = {20182127}, doi = {10.1098/rspb.2018.2127}, pmid = {30963860}, issn = {1471-2954}, abstract = {Thousands of species of ambrosia beetles excavate tunnels in wood to farm fungi. They maintain associations with particular lineages of fungi, but the phylogenetic extent and mechanisms of fidelity are unknown. We test the hypothesis that selectivity of their mycangium enforces fidelity at coarse phylogenetic scales, while permitting promiscuity among closely related fungal mutualists. We confirm a single evolutionary origin of the Xylosandrus complex-a group of several xyleborine genera that farm fungi in the genus Ambrosiella. Multi-level co-phylogenetic analysis revealed frequent symbiont switching within major Ambrosiella clades, but not between clades. The loss of the mycangium in Diuncus, a genus of evolutionary cheaters, was commensurate with the loss of fidelity to fungal clades, supporting the hypothesis that the mycangium reinforces fidelity. Finally, in vivo experiments tracked symbiotic compatibility throughout the symbiotic life cycle of Xylosandrus compactus and demonstrated that closely related Ambrosiella symbionts are interchangeable, but the probability of fungal uptake in the mycangium was significantly lower in more phylogenetically distant species of symbionts. Symbiont loads in experimental subjects were similar to wild-caught beetles. We conclude that partner choice in ambrosia beetles is achieved in the mycangium, and co-phylogenetic inferences can be used to predict the likelihood of specific symbiont switches.}, }
@article {pmid30962361, year = {2019}, author = {Jäckle, O and Seah, BKB and Tietjen, M and Leisch, N and Liebeke, M and Kleiner, M and Berg, JS and Gruber-Vodicka, HR}, title = {Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {17}, pages = {8505-8514}, doi = {10.1073/pnas.1818995116}, pmid = {30962361}, issn = {1091-6490}, abstract = {Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant'Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29-4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca R. santandreae's versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts-serving as the primary energy storage for its animal host.}, }
@article {pmid30961763, year = {2019}, author = {Jin, Y and Kim, HU and Hong, S and Shin, C and Kulkarni, A and Kim, T}, title = {Effect of Copper Foil Crystal Orientation on Graphene Quality Synthesized by Chemical Vapor Deposition.}, journal = {Journal of nanoscience and nanotechnology}, volume = {19}, number = {9}, pages = {5942-5948}, doi = {10.1166/jnn.2019.16599}, pmid = {30961763}, issn = {1533-4880}, abstract = {Line defects such as wrinkles are believed to change the electrical properties of graphene. However, they are often observed in graphene grown via chemical vapor deposition; hence, it is important to study the impact of the substrate condition on graphene quality. In this work, graphene was synthesized on various copper domains with different crystal orientations and surface morphologies. During the synthesis process, three typical crystal orientations were obtained Cu(001), Cu(101), and Cu(111) showing different surface morphologies with various densities of wrinkles. Graphene wrinkles along with copper wrinkles were studied using atomic force microscopy and Kelvin probe force microscopy. The quality of graphene on different crystal orientations and morphologies was evaluated as well. It was found that different crystallographic orientations lead to different degrees of wrinkle and roughness. In addition, these wrinkle defects exhibited characteristic surface potential variations and the density of substrate wrinkles was closely associated with the uniformity of graphene and led to a disordered structure and low crystallinity.}, }
@article {pmid30958898, year = {2019}, author = {Zlatogursky, VV and Gerasimova, EA and Drachko, D and Klimov, VI and Shɨshkin, Y and Plotnikov, AO}, title = {Pinjata ruminata gen. et sp. n.-A New Member of Centrohelid Family Yogsothothidae (Haptista: Centroplasthelida) from the Brackish River.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12737}, pmid = {30958898}, issn = {1550-7408}, support = {16-34-60102_mol_a_dk//RFBR/ ; 18-44-560009_r_a//RFBR/ ; }, abstract = {A new genus and species of centrohelid heliozoan Pinjata ruminata from the Tuzlukkol' River (Orenburg Region of Russia) and Gor'koe Lake (Chelyabinsk Region of Russia) is studied with light- and electron microscopy. Pinjata ruminata has two types of plate scales, partially running up the sides of the axopodia. Inner plate scales (3.2-4.9 × 1.5-2.6 μm) are flat, ovate-oblong and have a broad axial thickening and a thin electron-dense border. Outer plate scales (4.2-6.7 × 1.5-3.0 μm) are concave, elongated, of irregular shape, often curved, and broadened towards one end. Roundish depressions are forming two rows on both sides of the narrow axial thickening. The cells are attached to the substratum. Molecular phylogenetic analysis based on the SSU rDNA robustly placed P. ruminata in the family Yogsothothidae. This position is confirmed with the presence of five panacanthocystid increase regions. The morphology of the new genus is in a good accordance with diagnosis of the family. The status of a genus &quot;Heteroraphidiophrys&quot; is discussed. Other potential findings of Pinjata from literature are analyzed. Pinjata represents the third lineage of centrohelids, characterized with the presence of only tangentially oriented plate scales. The halophilic nature of Yogsothothidae is suggested.}, }
@article {pmid30957149, year = {2019}, author = {Wu, QS and He, JD and Srivastava, AK and Zou, YN and Kuča, K}, title = {Mycorrhizas enhance drought tolerance of citrus by altering root fatty acid compositions and their saturation levels.}, journal = {Tree physiology}, volume = {39}, number = {7}, pages = {1149-1158}, doi = {10.1093/treephys/tpz039}, pmid = {30957149}, issn = {1758-4469}, abstract = {Arbuscular mycorrhizas (AMs) have the ability to enhance drought tolerance of citrus, but the underlying mechanisms have not been clearly elucidated. Considering the strong association of cell membrane fatty acid (FA) unsaturation with plant drought tolerance, the present study hypothesized that AM fungi (AMF) modulated the composition and unsaturation of FAs to enhance drought tolerance of host plants. Drought-sensitive citrus rootstocks, trifoliate orange (Poncirus trifoliata) seedlings, were inoculated with AMF (Funneliformis mosseae) for 3 months and were subsequently exposed to drought stress (DS) for 8 weeks. Mycorrhizal seedlings exhibited better plant growth performance, higher leaf water potential and lower root abscisic acid concentrations under both well-watered (WW) and DS conditions. Arbuscular mycorrhiza fungus inoculation considerably increased root methyl oleate (C18:1), methyl linoleate (C18:2) and methyl linolenate (C18:3N3) concentrations under both WW and DS conditions, and root methyl palmitoleate (C16:1) concentrations under WW, while it decreased root methyl stearate (C18:0) levels under both WW and DS. These changes in the composition of FAs of mycorrhized roots resulted in higher unsaturation index of root FAs, which later aided in reducing the oxidative damage on account of lower concentration of malondialdehyde and superoxide radicals. The changes of these FAs were a result of AMF-up-regulating root FA desaturase 2 (PtFAD2), FA desaturase 6 (PtFAD6) and Δ9 FA desaturase (PtΔ9) genes under WW and PtFAD2, PtFAD6 and Δ15 FA desaturase (PtΔ15) genes under DS conditions. Our results confirmed that mycorrhization brought significant changes in root FA compositions, in addition to regulation of gene expression responsible for increasing the unsaturation level of FAs, a predisposing physiological event for better drought tolerance of citrus.}, }
@article {pmid30955777, year = {2019}, author = {McCauley, M and Goulet, TL}, title = {Caribbean gorgonian octocorals cope with nutrient enrichment.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {621-628}, doi = {10.1016/j.marpolbul.2019.02.067}, pmid = {30955777}, issn = {1879-3363}, mesh = {Ammonia/metabolism ; Animals ; Anthozoa/*physiology ; Carbon ; Caribbean Region ; Chlorophyll ; Dinoflagellida/*physiology ; Nitrogen/*metabolism ; Nutrients/metabolism ; Phosphates/metabolism ; Phosphorus/*metabolism ; Symbiosis ; }, abstract = {Corals inhabit oligotrophic waters, thriving amidst limited nutrients such as nitrogen and phosphorous. When nutrient levels increase, usually due to human activity, the symbiosis of dinoflagellates (family Symbiodiniaceae) with scleractinian corals can break down. Although gorgonian corals dominate many Caribbean reefs, the impact of enrichment on them and their algae is understudied. We exposed two gorgonian species, Pseudoplexaura porosa and Eunicea tourneforti, to elevated concentrations of either ammonium (10 μM or 50 μM) or phosphate (4 μM). Enrichment with 10 μM ammonium increased chlorophyll content and algal density in both species, whereas the host biochemical composition was unaffected. Exposure to 50 μM ammonium only reduced the quantum yield in P. porosa and mitotic indices in both species. Conversely, algal carbon and nitrogen content within E. tourneforti increased with 4 μM phosphate exposure. These gorgonian species coped with short-term nutrient enrichment, furthering our understanding of the success of Caribbean gorgonians.}, }
@article {pmid30953569, year = {2019}, author = {Arimoto, A and Hikosaka-Katayama, T and Hikosaka, A and Tagawa, K and Inoue, T and Ueki, T and Yoshida, MA and Kanda, M and Shoguchi, E and Hisata, K and Satoh, N}, title = {A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, doi = {10.1093/gigascience/giz023}, pmid = {30953569}, issn = {2047-217X}, abstract = {BACKGROUND: Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.<br><br>FINDINGS: To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.<br><br>CONCLUSIONS: Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.}, }
@article {pmid30953430, year = {2019}, author = {Landmann, F}, title = {The Wolbachia Endosymbionts.}, journal = {Microbiology spectrum}, volume = {7}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.BAI-0018-2019}, pmid = {30953430}, issn = {2165-0497}, mesh = {Animals ; Arthropods/microbiology ; Filarioidea/microbiology ; Host Microbial Interactions/*physiology ; Insecta/microbiology ; Symbiosis ; Wolbachia/classification/genetics/pathogenicity/*physiology ; }, abstract = {The Wolbachia endosymbionts encompass a large group of intracellular bacteria of biomedical and veterinary relevance, closely related to Anaplasma, Ehrlichia, and Rickettsia. This genus of Gram-negative members of the Alphaproteobacteria does not infect vertebrates but is instead restricted to ecdysozoan species, including terrestrial arthropods and a family of parasitic filarial nematodes, the Onchocercidae. The Wolbachia profoundly impact not only the ecology and evolution but also the reproductive biology of their hosts, through a wide range of symbiotic interactions. Because they are essential to the survival and reproduction of their filarial nematode hosts, they represent an attractive target to fight filariasis. Their abilities to spread through insect populations and to affect vector competence through pathogen protection have made Wolbachia a staple for controlling vector-borne diseases. Estimated to be present in up to 66% of insect species, the Wolbachia are probably the most abundant endosymbionts on earth. Their success resides in their unique capacity to infect and manipulate the host germ line to favor their vertical transmission through the maternal lineage. Because the Wolbachia resist genetic manipulation and growth in axenic culture, our understanding of their biology is still in its infancy. Despite these limitations, the &quot;-omics&quot; revolution combined with the use of well-established and emerging experimental host models is accelerating our comprehension of the host phenotypes caused by Wolbachia, and the identification of Wolbachia effectors is ongoing.}, }
@article {pmid30952658, year = {2019}, author = {Mohammed, M and Jaiswal, SK and Dakora, FD}, title = {Insights into the Phylogeny, Nodule Function, and Biogeographic Distribution of Microsymbionts Nodulating the Orphan Kersting's Groundnut [Macrotyloma geocarpum (Harms) Marechal &amp; Baudet] in African Soils.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {11}, pages = {}, doi = {10.1128/AEM.00342-19}, pmid = {30952658}, issn = {1098-5336}, abstract = {Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal &amp; Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date there is little information on the phylogeny and functional traits of its microsymbionts, aspects that are much needed for its conservation and improvement. This study explored the morphogenetic diversity, phylogenetic relationships, and N2-fixing efficiency of Kersting's groundnut rhizobial isolates from contrasting environments in Ghana, South Africa, and Mozambique. BOX-PCR fingerprinting revealed high diversity among the rhizobial populations, which was influenced by geographic origin. Of the 164 isolates evaluated, 130 BOX-PCR types were identified at a 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA genes and multilocus sequence analysis of protein-coding genes (atpD, glnII, gyrB, and rpoB) and symbiotic genes (nifH and nodC) showed that Kersting's groundnut is primarily nodulated by members of the genus Bradyrhizobium, which are closely related to Bradyrhizobium vignae 7-2T, Bradyrhizobium kavangense 14-3T, Bradyrhizobium subterraneum 58-2-1T, Bradyrhizobium pachyrhizi PAC48T, the type strain of Bradyrhizobium elkanii, and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N2 fixation and induced greater nodulation, leaf chlorophyll concentration, and photosynthetic rates in their homologous host than did the 5 mM KNO3-fed plants and/or the commercial Bradyrhizobium sp. strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing.IMPORTANCE Rhizobia play important roles in agroecosystems, where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the microsymbionts nodulating Kersting's groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N2-fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of microsymbionts nodulating a neglected cultivated legume and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting's groundnut found in this study offers an opportunity for future studies to properly describe, characterize, and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.}, }
@article {pmid30952451, year = {2019}, author = {Camacho, M and Medina, C and Rodríguez-Navarro, DN and Temprano Vera, F}, title = {Biodiversity of rhizobia present in plant nodules of Biserrula pelecinus across Southwest Spain.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {3}, pages = {415-421}, doi = {10.1016/j.syapm.2019.03.005}, pmid = {30952451}, issn = {1618-0984}, abstract = {Biodiversity studies of native Mesorhizobium spp. strains able to nodulate the annual herbaceous legume Biserrula pelecinus L. in soils from Southwest Spain have been carried out. One or two isolates per plant, 30 in total, were randomly selected for further characterization. There was no association between the presence of mesorhizobia nodulating-B. pelecinus and the chemical or textural properties of the soils. The isolates were tested for their symbiotic effectiveness on this forage legume under greenhouse conditions and characterized on the basis of physiological parameters: carbon source utilisation (API 50CH), 16S rRNA sequencing and ERIC-PCR, lipopolysaccharide, protein and plasmid profiles. Our results show that in spite of the great diversity found among the native isolates, most of them belong to the genus Mesorhizobium, the exception being strain B24 which sequence matches 97.52% with Neorhizobium huautlense; this is the first description of a Neorhizobium strain effectively nodulating-biserrula plants. Results of a field trial indicated that some of these isolates could be recommended as inoculants for this legume. B24=DSM 28743=CECT 8815; ENA (HF955513) 16S rRNA sequences of isolates B13, B18, B26, B30 and B1 are deposited at ENA under numbers LS999402 to LS999406, respectively.}, }
@article {pmid30951191, year = {2019}, author = {Benavent-González, A and Raggio, J and Villagra, J and Blanquer, JM and Pintado, A and Rozzi, R and Green, TGA and Sancho, LG}, title = {High nitrogen contribution by Gunnera magellanica and nitrogen transfer by mycorrhizas drive an extraordinarily fast primary succession in sub-Antarctic Chile.}, journal = {The New phytologist}, volume = {223}, number = {2}, pages = {661-674}, doi = {10.1111/nph.15838}, pmid = {30951191}, issn = {1469-8137}, support = {CTM2015-64728-C2-1-R//Ministerio de Economía y Competitividad/ ; CTM2012-38222-CO2-01//Ministerio de Economía y Competitividad/ ; BES-2013-062945//Ministerio de Economía y Competitividad/ ; }, abstract = {Chronosequences at the forefront of retreating glaciers provide information about colonization rates of bare surfaces. In the northern hemisphere, forest development can take centuries, with rates often limited by low nutrient availability. By contrast, in front of the retreating Pia Glacier (Tierra del Fuego, Chile), a Nothofagus forest is in place after only 34 yr of development, while total soil nitrogen (N) increased from near zero to 1.5%, suggesting a strong input of this nutrient. We measured N-fixation rates, carbon fluxes, leaf N and phosphorus contents and leaf δ15 N in the dominant plants, including the herb Gunnera magellanica, which is endosymbiotically associated with a cyanobacterium, in order to investigate the role of N-fixing and mycorrhizal symbionts in N-budgets during successional transition. G. magellanica presented some of the highest nitrogenase activities yet reported (potential maximal contribution of 300 kg N ha-1 yr-1). Foliar δ15 N results support the framework of a highly efficient N-uptake and transfer system based on mycorrhizas, with c. 80% of N taken up by the mycorrhizas potentially transferred to the host plant. Our results suggest the symbiosis of G. magellanica with cyanobacteria, and trees and shrubs with mycorrhizas, to be the key processes driving this rapid succession.}, }
@article {pmid30950432, year = {2019}, author = {Tiwari, R and Negandhi, H and Zodpey, S}, title = {Forecasting the future need and gaps in requirements for public health professionals in India up to 2026.}, journal = {WHO South-East Asia journal of public health}, volume = {8}, number = {1}, pages = {56-65}, doi = {10.4103/2224-3151.255351}, pmid = {30950432}, issn = {2304-5272}, mesh = {Forecasting/*methods ; Health Policy/trends ; Humans ; India ; Needs Assessment/*trends ; Public Health/methods/statistics &amp; numerical data ; Students, Public Health/*statistics &amp; numerical data ; Workforce/*standards/trends ; }, abstract = {Current ambitious reforms in India mean that public health professionals (PHPs) will become an increasingly vital component of the health workforce. Despite a rapid growth in schools of public health in India, uptake of places by students without a medical background is low. This paper reports the results of an exercise to estimate the baseline supply of, and need for, PHPs in India in 2017 and to forecast possible supply-need scenarios up to 2026. Supply was estimated using the stock and flow approach and the service-target approach was used to estimate need. The additional need resulting from development of a new public health cadre, as stated in the National Health Policy 2017, was also included. Supply-need gaps were forecast according to three scenarios, which varied according to the future intensity of policy intervention to increase occupancy of training places for PHPs from a non-medical background: &quot;best guess&quot; (no intervention), &quot;optimistic&quot; (feasible intervention), and &quot;aspirational&quot; (significant intervention) scenarios. In the best guess scenario in 2017, i.e. with a low non-medical place occupancy of 60%, there is a supply-need gap of around 28 000 PHPs. In the absence of any intervention to increase place occupancy, this shortfall is forecast to increase to 45 000 PHPs by the year 2026. By contrast, in the aspirational scenario, i.e. with a high place occupancy of 75% for non-medical places, the baseline gap for 2017 of almost 26 000 PHPs reduces by 2026 to around 21 000 PHPs. By 2026, most new PHPs will be produced by public health training programmes offered by institutions other than medical colleges. Without significant interventions, India is likely to have a significant shortfall in PHPs in 2026. Policy-makers will have to carefully examine issues surrounding the current low uptake of non-medical public health seats and review the current framework regulating training of PHPs, in order to respond adequately to future requirements.}, }
@article {pmid30950320, year = {2019}, author = {Ingavle, G and Vaidya, A and Kale, V}, title = {Constructing Three-Dimensional Microenvironments Using Engineered Biomaterials for Hematopoietic Stem Cell Expansion.}, journal = {Tissue engineering. Part B, Reviews}, volume = {25}, number = {4}, pages = {312-329}, doi = {10.1089/ten.TEB.2018.0286}, pmid = {30950320}, issn = {1937-3376}, abstract = {IMPACT STATEMENT: This review discusses designing novel biomaterial-based hematopoietic stem cell (HSC) expansion strategies that would contribute to the field of hematopoiesis and also proposes possible approaches for HSC expansion using interpenetrating network hydrogels, emulsion templated polymers poly(HIPEs) (high internal phase emulsion templated polymers), and three-dimensional cell printing, which could provide optimal environment for HSC attachment, proliferation, and differentiation. These novel approaches could improve the efficacy of bone marrow transplantation and also offer new insights in the field of regenerative biology.}, }
@article {pmid30949766, year = {2019}, author = {Rajan, A and Valla, JM and Alappatt, JA and Sharda, M and Shah, A and Ingalhalikar, M and Singh, NC}, title = {Wired for musical rhythm? A diffusion MRI-based study of individual differences in music perception.}, journal = {Brain structure &amp; function}, volume = {224}, number = {5}, pages = {1711-1722}, doi = {10.1007/s00429-019-01868-y}, pmid = {30949766}, issn = {1863-2661}, abstract = {Music perceptual abilities are subjective and exhibit high inter-individual variability. Twenty-nine participants with varying degrees of musical training were tested for musical perception ability with the Profile of Music Perception Skills (PROMS) and brain structural measures obtained via diffusion tensor imaging. Controlling for the period of training, TBSS results showed that individuals with better musical perception abilities showed increased deviations from linear anisotropy in the corpus callosum. Specifically, mode of anisotropy in the genu and body of the corpus callosum was negatively correlated with music perception score suggesting the presence of crossing fibers. A multi-compartment model of crossing fibers revealed a significant positive relation for partial volumes of secondary fiber populations with timing aspects of music perception. Our results suggest that inter-hemispheric connectivity differences in the anterior parts of the corpus callosum may reflect innate differences in the processing of the rhythmic aspects of music.}, }
@article {pmid30949751, year = {2019}, author = {Hughey, MC and Sokol, ER and Walke, JB and Becker, MH and Belden, LK}, title = {Ecological Correlates of Large-Scale Turnover in the Dominant Members of Pseudacris crucifer Skin Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01372-0}, pmid = {30949751}, issn = {1432-184X}, support = {DEB-1136640//National Science Foundation/ ; D10ZO-028//Morris Animal Foundation/ ; }, abstract = {Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing. We found that skin bacterial communities on frogs were less diverse than, and structurally distinct from, the surrounding habitat. Frog skin was typically dominated by one of two bacterial OTUs: at western sites, a Proteobacteria dominated the community, whereas eastern sites were dominated by an Actinobacteria. Using a metacommunity framework, we then sought to identify factors explaining small- and large-scale variation in community structure-that is, among hosts within a pond, and among ponds spanning the study transect. We focused on the presence of a fungal skin pathogen, Batrachochytrium dendrobatidis (Bd) as one potential driver of variation. We found no direct link between skin bacterial community structure and Bd infection status of individual frog hosts. Differences in pond-level community structure, however, were explained by Bd infection prevalence. Importantly, Bd infection prevalence itself was correlated with numerous other environmental factors; thus, skin bacterial diversity may be influenced by a complex suite of extrinsic factors. Our findings indicate that large-scale factors and processes merit consideration when seeking to understand microbiome diversity.}, }
@article {pmid30949677, year = {2019}, author = {Pillonel, T and Bertelli, C and Aeby, S and de Barsy, M and Jacquier, N and Kebbi-Beghdadi, C and Mueller, L and Vouga, M and Greub, G}, title = {Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship.}, journal = {Genome biology and evolution}, volume = {11}, number = {4}, pages = {1334-1344}, doi = {10.1093/gbe/evz072}, pmid = {30949677}, issn = {1759-6653}, mesh = {Animals ; Chlamydiales/*genetics/metabolism ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Host-Parasite Interactions ; Ixodes/*microbiology ; Symbiosis ; }, abstract = {The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named &quot;Candidatus Rhabdochlamydia helvetica&quot; whereas only few thousand reads mapped to the genome of &quot;Candidatus Midichloria mitochondrii,&quot; a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.}, }
@article {pmid30948550, year = {2019}, author = {Vizentin-Bugoni, J and Tarwater, CE and Foster, JT and Drake, DR and Gleditsch, JM and Hruska, AM and Kelley, JP and Sperry, JH}, title = {Structure, spatial dynamics, and stability of novel seed dispersal mutualistic networks in Hawai'i.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6435}, pages = {78-82}, doi = {10.1126/science.aau8751}, pmid = {30948550}, issn = {1095-9203}, mesh = {Animals ; Hawaii ; Human Activities ; Humans ; *Introduced Species ; *Seed Dispersal ; *Symbiosis ; }, abstract = {Increasing rates of human-caused species invasions and extinctions may reshape communities and modify the structure, dynamics, and stability of species interactions. To investigate how such changes affect communities, we performed multiscale analyses of seed dispersal networks on O'ahu, Hawai'i. Networks consisted exclusively of novel interactions, were largely dominated by introduced species, and exhibited specialized and modular structure at local and regional scales, despite high interaction dissimilarity across communities. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide. Our findings suggest that shared evolutionary history is not a necessary process for the emergence of complex network structure, and interaction patterns may be highly conserved, regardless of species identity and environment. Introduced species can quickly become well integrated into novel networks, making restoration of native ecosystems more challenging than previously thought.}, }
@article {pmid30946516, year = {2019}, author = {Wei, X and Feng, C and Li, XH and Mao, XX and Luo, HB and Zhang, DM and Rong, L and Xie, ZY and Yu, X and Li, J and Ye, WC and Huang, XJ and Zhang, CX}, title = {Enantiomeric Polyketides from the Starfish-Derived Symbiotic Fungus Penicillium sp. GGF16-1-2.}, journal = {Chemistry &amp; biodiversity}, volume = {16}, number = {6}, pages = {e1900052}, doi = {10.1002/cbdv.201900052}, pmid = {30946516}, issn = {1612-1880}, support = {81741160//NSFC/ ; 2015A020216017//Science and Technology Planning Project of Guangdong Province/ ; 2017A020217008//Science and Technology Planning Project of Guangdong Province/ ; 2014A030313411//Natural Science Foundation of Guangdong Province/ ; XH20170110//The Fire Plan Project of the Guangzhou University of Chinese Medicine/ ; 2016003//Open Subject of State Key Laboratory of Marine Resources Utilization in the South China Sea of Hainan University/ ; //Open Subject of Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/ ; }, mesh = {Animals ; Cell Line, Tumor ; Cell Survival/drug effects ; Crystallography, X-Ray ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Humans ; Molecular Conformation ; Penicillium/chemistry/*metabolism ; Polyketides/*chemistry/isolation &amp; purification/pharmacology ; Starfish/*microbiology ; Stereoisomerism ; Symbiosis ; }, abstract = {One new racemic mixture, penicilliode A (1) and four pairs of enantiomeric polyketides, penicilliode B and C (2 and 3) and coniochaetone B and C (4 and 5), were obtained from the starfish-derived symbiotic fungus Penicillium sp. GGF16-1-2. Interestingly, the strain GGF16-1-2 can produce enantiomers. The absolute configuration of 1 was determined by X-ray diffraction (XRD) analysis, and the absolute configurations of 2-4 were determined by the optical rotation (OR) values and electronic circular dichroism (ECD) calculations. Compounds 1-5 were firstly isolated from the marine-derived fungus Penicillium as racemates, and 2-5 were separated by HPLC with a chiral stationary phase. All the compounds were evaluated for their antibacterial, cytotoxic and inhibitory activities against PDE4D2.}, }
@article {pmid30944875, year = {2019}, author = {Vannier, N and Mony, C and Bittebiere, AK and Theis, KR and Rosenberg, E and Vandenkoornhuyse, P}, title = {Clonal Plants as Meta-Holobionts.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00213-18}, pmid = {30944875}, issn = {2379-5077}, abstract = {The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all p