@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 {pmid30920344, year = {2019}, author = {Liu, X and Xie, Z and Wang, Y and Sun, Y and Dang, X and Sun, H}, title = {A Dual Role of Amino Acids from Sesbania rostrata Seed Exudates in the Chemotaxis Response of Azorhizobium caulinodans ORS571.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI03190059R}, doi = {10.1094/MPMI-03-19-0059-R}, pmid = {30920344}, issn = {0894-0282}, abstract = {Azorhizobium caulinodans ORS571 can induce nodule formation on the roots and the stems of its host legume, Sesbania rostrata. Plant exudates are essential in the dialogue between microbes and their host plant and, in particular, amino acids can play an important role in the chemotactic response of bacteria. Histidine, arginine, and aspartate, which are the three most abundant amino acids present in S. rostrata seed exudates, behave as chemoattractants toward A. caulinodans. A position-specific-iterated BLAST analysis of the methyl-accepting chemotaxis proteins (MCPs) (chemoreceptors) in the genome of A. caulinodans was performed. Among the 43 MCP homologs, two MCPs harboring a dCache domain were selected as possible cognate amino acid MCPs. After analysis of relative gene expression levels and construction of a gene-deleted mutant strain, one of them, AZC_0821 designed as TlpH, was confirmed to be responsible for the chemotactic response to the three amino acids. In addition, it was found that these three amino acids can also influence chemotaxis of A. caulinodans independently of the chemosensory receptors, by being involved in the increase of the expression level of several che and fla genes involved in the chemotaxis pathway and flagella synthesis. Thus, the contribution of amino acids present in seed exudates is directly related to the role as chemoattractants and indirectly related to the role in the regulation of expression of key genes involved in chemotaxis and motility. This "dual role" is likely to influence the formation of biofilms by A. caulinodans and the host root colonization properties of this bacterium.}, }
@article {pmid30474731, year = {2019}, author = {Hosseinzadeh, S and Shams-Bakhsh, M and Mann, M and Fattah-Hosseini, S and Bagheri, A and Mehrabadi, M and Heck, M}, title = {Distribution and Variation of Bacterial Endosymbiont and "Candidatus Liberibacter asiaticus" Titer in the Huanglongbing Insect Vector, Diaphorina citri Kuwayama.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {206-222}, doi = {10.1007/s00248-018-1290-1}, pmid = {30474731}, issn = {1432-184X}, support = {5300-163//California Citrus Research Board/ ; 2016-70016-24779//National Institute of Food and Agriculture/ ; 8062-22410-006-00-D//Agricultural Research Service/ ; }, mesh = {Animals ; Citrus/*microbiology/parasitology ; Endophytes/genetics/isolation & purification/*physiology ; Female ; Hemiptera/*microbiology/physiology ; Insect Vectors/microbiology/physiology ; Male ; Plant Diseases/*microbiology ; Rhizobiaceae/genetics/isolation & purification/*physiology ; *Symbiosis ; Wolbachia/genetics/isolation & purification/physiology ; }, abstract = {The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is an economic insect pest in most citrus-growing regions and the vector of 'Candidatus Liberibacter asiaticus' (CLas), one of at least three known bacteria associated with Huanglongbing (HLB or citrus greening disease). D. citri harbors bacterial endosymbionts, including Wolbachia pipientis (strain Wolbachia wDi), 'Candidatus Carsonella ruddii,' and 'Candidatus Profftella armatura.' Many important functions of these bacteria can be inferred from their genome sequences, but their interactions with each other, CLas, and their D. citri host are poorly understood. In the present study, the titers of the endosymbionts in different tissues, in each sex, and in insects reared on healthy citrus (referred to as unexposed) and CLas-infected citrus (referred to as CLas-exposed) D. citri were investigated using real-time, quantitative PCR (qPCR) using two different quantitative approaches. Wolbachia and CLas were detected in all insect tissues. The titer of Wolbachia was higher in heads of CLas-exposed males as compared to unexposed males. In males and females, Wolbachia titer was highest in the Malpighian tubules. The highest titer of CLas was observed in the gut. Profftella and Carsonella titers were significantly reduced in the bacteriome of CLas-exposed males compared with that of unexposed males, but this effect was not observed in females. In ovaries of CLas-exposed females, the Profftella and Carsonella titers were increased as compared to non-exposed females. CLas appeared to influence the overall levels of the symbionts but did not drastically perturb the overall microbial community structure. In all the assessed tissues, CLas titer in males was significantly higher than that of females using absolute quantification. These data provide a better understanding of multi-trophic interactions regulating symbiont dynamics in the HLB pathosystem.}, }
@article {pmid30413836, year = {2019}, author = {Villegas-Plazas, M and Wos-Oxley, ML and Sanchez, JA and Pieper, DH and Thomas, OP and Junca, H}, title = {Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {243-256}, doi = {10.1007/s00248-018-1285-y}, pmid = {30413836}, issn = {1432-184X}, support = {KBBE-2009-245226//MAGICPAH/ ; 652-2014//EcosNord-Colciencias/ ; JI-2012//Jóven Investigador - Colciencias/ ; MSc scholarship//Universidad de los Andes/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; Caribbean Region ; Coral Reefs ; *Microbiota ; Panama ; Phylogeny ; Seasons ; Seawater/*chemistry/microbiology ; Symbiosis ; Xestospongia/*microbiology/physiology ; }, abstract = {Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.}, }
@article {pmid30411189, year = {2019}, author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N}, title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {170-184}, doi = {10.1007/s00248-018-1276-z}, pmid = {30411189}, issn = {1432-184X}, support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Urochordata/microbiology/*physiology ; }, abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.}, }
@article {pmid30276419, year = {2019}, author = {Renoz, F and Pons, I and Vanderpoorten, A and Bataille, G and Noël, C and Foray, V and Pierson, V and Hance, T}, title = {Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {159-169}, doi = {10.1007/s00248-018-1265-2}, pmid = {30276419}, issn = {1432-184X}, support = {1.E074.14//Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture/ ; }, mesh = {Animals ; Animals, Wild/microbiology/physiology ; Ants/*microbiology/physiology ; Aphids/classification/genetics/*microbiology/physiology ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Intestines/microbiology/physiology ; Phylogeny ; Serratia/genetics/*physiology ; *Symbiosis ; }, abstract = {Many insects engage in symbiotic associations with diverse assemblages of bacterial symbionts that can deeply impact on their ecology and evolution. The intraspecific variation of symbionts remains poorly assessed while phenotypic effects and transmission behaviors, which are key processes for the persistence and evolution of symbioses, may differ widely depending on the symbiont strains. Serratia symbiotica is one of the most frequent symbiont species in aphids and a valuable model to assess this intraspecific variation since it includes both facultative and obligate symbiotic strains. Despite evidence that some facultative S. symbiotica strains exhibit a free-living capacity, the presence of these strains in wild aphid populations, as well as in insects with which they maintain regular contact, has never been demonstrated. Here, we examined the prevalence, diversity, and tissue tropism of S. symbiotica in wild aphids and associated ants. We found a high occurrence of S. symbiotica infection in ant populations, especially when having tended infected aphid colonies. We also found that the S. symbiotica diversity includes strains found located within the gut of aphids and ants. In the latter, this tissue tropism was found restricted to the proventriculus. Altogether, these findings highlight the extraordinary diversity and versatility of an insect symbiont and suggest the existence of novel routes for symbiont acquisition in insects.}, }
@article {pmid29756135, year = {2018}, author = {Stringlis, IA and Zhang, H and Pieterse, CMJ and Bolton, MD and de Jonge, R}, title = {Microbial small molecules - weapons of plant subversion.}, journal = {Natural product reports}, volume = {35}, number = {5}, pages = {410-433}, doi = {10.1039/c7np00062f}, pmid = {29756135}, issn = {1460-4752}, mesh = {Bacterial Toxins ; Cytokinins/metabolism ; *Genome, Microbial ; Gibberellins/metabolism ; Host-Pathogen Interactions ; Mycotoxins ; Plant Growth Regulators/chemistry/*metabolism ; Plants/metabolism/*microbiology ; Pseudomonas/genetics/metabolism ; Secondary Metabolism ; Siderophores/chemistry/*metabolism ; Symbiosis ; }, abstract = {Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.}, }
@article {pmid29668956, year = {2018}, author = {Telang, A and Skinner, J and Nemitz, RZ and McClure, AM}, title = {Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae).}, journal = {Journal of medical entomology}, volume = {55}, number = {5}, pages = {1170-1181}, doi = {10.1093/jme/tjy056}, pmid = {29668956}, issn = {1938-2928}, mesh = {Animals ; Culex/*microbiology ; Female ; *Metagenome ; Mosquito Vectors/*microbiology ; Symbiosis ; }, abstract = {Mosquitoes are intensely studied as vectors of disease-causing pathogens, but we know relatively less about microbes that naturally reside in mosquitoes. Profiling resident bacteria in mosquitoes can help identify bacterial groups that can be exploited as a strategy of controlling mosquito populations. High-throughput 16S rRNA gene sequencing and traditional culture-based methods were used to identify bacterial assemblages in Culex quinquefasciatus Say (Diptera: Culicidae) in a tissue- and stage-specific design. In parallel, wild host Cx. quinquefasciatus was compared with our domestic strain. 16S rRNA genes survey finds that Cx. quinquefasciatus has taxonomically restricted bacterial communities, with 90% of its bacterial microbiota composed of eight distinctive bacterial groups: Nocardioidaceae (Actinomycetales), Microbacteriaceae (Actinomycetales), Flavobacteriaceae, Rhizobiales, Acetobacteraceae, Rickettsiaceae, Comamondaceae (Burkholderiales), and Enterobacteriaceae. Taking into account both metagenome- and culture-based methods, we suggest three bacterial groups, Acetobacteraceae, Flavobacteriaceae, and Enterobacteriaceae, as candidates for mutualists in Cx. quinquefasciatus. Members of these three bacterial families have been studied as mutualists, or even as symbionts, in other insect groups, so it is quite possible they play similar roles in mosquitoes.}, }
@article {pmid29441375, year = {2018}, author = {Morita, M and Schmidt, EW}, title = {Parallel lives of symbionts and hosts: chemical mutualism in marine animals.}, journal = {Natural product reports}, volume = {35}, number = {4}, pages = {357-378}, pmid = {29441375}, issn = {1460-4752}, support = {R35 GM122521/GM/NIGMS NIH HHS/United States ; U01 TW008163/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/*microbiology ; Biological Products/*chemistry/metabolism ; Bryozoa/chemistry/metabolism ; Crustacea ; Cyanobacteria/chemistry/metabolism ; Halogenated Diphenyl Ethers/chemistry/metabolism ; Porifera/microbiology ; Predatory Behavior ; Ships ; Symbiosis/*physiology ; Tetrodotoxin/metabolism ; Ultraviolet Rays ; Urochordata/metabolism ; }, abstract = {Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.}, }
@article {pmid29338795, year = {2019}, author = {Bhat, AH and Chaubey, AK and Půža, V}, title = {The first report of Xenorhabdus indica from Steinernema pakistanense: co-phylogenetic study suggests co-speciation between X. indica and its steinernematid nematodes.}, journal = {Journal of helminthology}, volume = {93}, number = {1}, pages = {81-90}, doi = {10.1017/S0022149X17001171}, pmid = {29338795}, issn = {1475-2697}, mesh = {Animals ; *Biological Coevolution ; Female ; India ; Insect Control ; Larva/growth & development/parasitology ; Moths/growth & development/parasitology ; *Phylogeny ; *Symbiosis ; Tylenchida/anatomy & histology/*classification/*microbiology/pathogenicity ; Virulence ; Xenorhabdus/*classification/*physiology ; }, abstract = {During a survey in agricultural fields of the sub-humid region of Meerut district, India, two strains of entomopathogenic nematodes, labelled CS31 and CS32, were isolated using the Galleria baiting technique. Based on morphological and morphometric studies, and molecular data, the nematodes were identified as Steinernema pakistanense, making this finding the first report of this species from India. For the first time, we performed a molecular and biochemical characterization of the bacterial symbiont of S. pakistanense. Furthermore, a co-phylogenetic analysis of the bacteria from the monophyletic clade containing a symbiont of S. pakistanense, together with their nematode hosts, was conducted, to test the degree of nematode-bacteria co-speciation. Both isolates were also tested in a laboratory assay for pathogenicity against two major pests, Helicoverpa armigera and Spodoptera litura. The morphology of the Indian isolates corresponds mainly to the original description, with the only difference being the absence of a mucron in first-generation females and missing epiptygmata in the second generation. The sequences of bacterial recA and gyrB genes have shown that the symbiont of S. pakistanense is closely related to Xenorhabdus indica, which is associated with some other nematodes from the 'bicornutum' group. Co-phylogenetic analysis has shown a remarkable congruence between the nematode and bacterial phylogenies, suggesting that, in some lineages within the Steinernema / Xenorhabdus complex, the nematodes and bacteria have undergone co-speciation. In the virulence assay, both strains caused a 100% mortality of both tested insects after 48 h, even at the lowest doses of 25 infective juveniles per insect, suggesting that S. pakistanense could be considered for use in the biocontrol of these organisms in India.}, }
@article {pmid28884173, year = {2018}, author = {Scherlach, K and Hertweck, C}, title = {Mediators of mutualistic microbe-microbe interactions.}, journal = {Natural product reports}, volume = {35}, number = {4}, pages = {303-308}, doi = {10.1039/c7np00035a}, pmid = {28884173}, issn = {1460-4752}, mesh = {Bacteria/metabolism/pathogenicity ; Biological Products/chemistry/*metabolism ; Ecosystem ; Fungi/metabolism/pathogenicity ; Microbial Interactions/*physiology ; Quorum Sensing/physiology ; Secondary Metabolism ; *Symbiosis ; }, abstract = {The co-existence of different microbial species in one habitat is prerequisite for many ecosystem processes. To facilitate co-habitation of ecological niches, intricate mechanisms have evolved that regulate the growth and the behaviour of microbes. A crucial aspect for the establishment and maintenance of a microbial population is the communication among species. Whereas intraspecies communication processes have been widely studied, little is known about the molecular mechanisms underlying interspecies interactions. Through the advance of modern analytical and sequencing technologies, we are now beginning to gain deeper insights into these complex processes. A key feature of microbe-microbe interaction is the secretion of chemical mediators to influence either the microbial partner or co-occurring higher organisms to shape the specific microenvironment. Here we summarize recent advances in understanding the role of natural products as regulators of microbial interaction in various ecological niches. Special attention is paid to mutualistic relationships with relevance for ecology and agriculture as well as medicine.}, }
@article {pmid31319203, year = {2019}, author = {Ingavle, G and Shabrani, N and Vaidya, A and Kale, V}, title = {Mimicking megakaryopoiesisin vitrousing biomaterials: Recent advances and future opportunities.}, journal = {Acta biomaterialia}, volume = {}, number = {}, pages = {}, 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 an adequate availability, expense, risk of bacterial contamination and complications due to immunological reaction. To prevail over our dependence on transfusion of platelets derived from donors, efforts are being made to generate platelets 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 MKsfromvariousstemcellsourcesusing 2D as well as 3D culture approaches in vitro andthedevelopmentofbiomaterials-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 {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 & 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 {pmid30685814, year = {2019}, author = {Morrin, ST and Lane, JA and Marotta, M and Bode, L and Carrington, SD and Irwin, JA and Hickey, RM}, title = {Bovine colostrum-driven modulation of intestinal epithelial cells for increased commensal colonisation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {6}, pages = {2745-2758}, doi = {10.1007/s00253-019-09642-0}, pmid = {30685814}, issn = {1432-0614}, support = {2014058//Teagasc/ ; }, mesh = {Animals ; *Bacterial Adhesion ; Bifidobacterium/metabolism ; Cattle ; Cell Count ; Colostrum/*chemistry ; Epithelial Cells/*microbiology ; Female ; HT29 Cells ; Humans ; Intestinal Mucosa/*cytology/microbiology ; Microarray Analysis ; Oligosaccharides/*chemistry/isolation & purification ; Pregnancy ; *Symbiosis ; Transcriptome ; }, abstract = {Nutritional intake may influence the intestinal epithelial glycome and in turn the available attachment sites for bacteria. In this study, we tested the hypothesis that bovine colostrum may influence the intestinal cell surface and in turn the attachment of commensal organisms. Human HT-29 intestinal cells were exposed to a bovine colostrum fraction (BCF) rich in free oligosaccharides. The adherence of several commensal bacteria, comprising mainly bifidobacteria, to the intestinal cells was significantly enhanced (up to 52-fold) for all strains tested which spanned species that are found across the human lifespan. Importantly, the changes to the HT-29 cell surface did not support enhanced adhesion of the enteric pathogens tested. The gene expression profile of the HT-29 cells following treatment with the BCF was evaluated by microarray analysis. Many so called "glyco-genes" (glycosyltransferases and genes involved in the complex biosynthetic pathways of glycans) were found to be differentially regulated suggesting modulation of the enzymatic addition of sugars to glycoconjugate proteins. The microarray data was further validated by means of real-time PCR. The current findings provide an insight into how commensal microorganisms colonise the human gut and highlight the potential of colostrum and milk components as functional ingredients that can potentially increase commensal numbers in individuals with lower counts of health-promoting bacteria.}, }
@article {pmid29779502, year = {2018}, author = {Buysse, M and Duron, O}, title = {Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks.}, journal = {Parasitology}, volume = {145}, number = {14}, pages = {1969-1978}, doi = {10.1017/S0031182018000793}, pmid = {29779502}, issn = {1469-8161}, mesh = {Alphaproteobacteria/*classification ; Animals ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Female ; Genetic Variation ; Host Specificity ; Ixodes/*microbiology ; Male ; Multilocus Sequence Typing ; *Phylogeny ; *Symbiosis ; }, abstract = {Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.}, }
@article {pmid29234108, year = {2017}, author = {Dimova, T and Terzieva, A and Djerov, L and Dimitrova, V and Nikolov, A and Grozdanov, P and Markova, N}, title = {Mother-to-newborn transmission of mycobacterial L-forms and Vδ2 T-cell response in placentobiome of BCG-vaccinated pregnant women.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17366}, pmid = {29234108}, issn = {2045-2322}, mesh = {BCG Vaccine/administration & dosage/*immunology ; Female ; Humans ; Infant, Newborn ; *Infectious Disease Transmission, Vertical ; Intraepithelial Lymphocytes/*immunology ; L Forms/immunology/*isolation & purification ; Microbiota/*immunology ; Mothers ; Mycobacterium bovis/immunology/*isolation & purification ; Placenta/cytology/*microbiology ; Pregnancy ; Symbiosis/immunology ; T-Lymphocytes ; Tuberculosis/prevention & control ; Vaccination/adverse effects ; }, abstract = {The ability of bacteria to exist as a population of self-replicating forms with defective or entirely missing cell wall (L-forms) is an adaptive mechanism for their survival and reproduction under unfavorable conditions. Bacterial mother-to-fetus transfer is a universal phenomenon in the animal kingdom. However, data about vertical transfer of L bacterial forms are extremely scarce. Bacille Calmette-Guérin is an attenuated strain of M. bovis and the only licensed vaccine used for tuberculosis prevention. We already have shown that filterable L-forms of BCG exist freely in the vaccine and are able to reproduce and to form colonies. The present study was focused on the placental microbiome in the context of mother's BCG vaccination. Here we report an isolation of filterable mycobacterial L-form cultures from gestational tissues and blood of healthy newborns delivered by healthy BCG-vaccinated mothers after normal pregnancy. Of note, vertically transmitted mycobacterial L-forms as a part of placentobiome of the pregnant women didn't influence the number of resident pathogen-reactive Vδ2 cells. Placenta colonization with mycobacterial L-forms occurs by maternal blood-to-decidua transfer very early in gestation. Together, these data showed that BCG L-forms have the capacity to pass trans-placental barrier and that maternal BCG vaccination affects the placentobiome.}, }
@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 = {}, number = {}, pages = {1-4}, 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 = {}, number = {}, pages = {}, 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 {pmid29885477, year = {2018}, author = {Krafsur, ES and Maudlin, I}, title = {Tsetse fly evolution, genetics and the trypanosomiases - A review.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {64}, number = {}, pages = {185-206}, doi = {10.1016/j.meegid.2018.05.033}, pmid = {29885477}, issn = {1567-7257}, mesh = {Animals ; Disease Susceptibility ; *Evolution, Molecular ; *Genetics, Population ; Humans ; Insect Vectors/*genetics/parasitology ; Karyotype ; Phylogeny ; Symbiosis ; Trypanosoma/genetics ; Trypanosomiasis/*epidemiology/parasitology/*transmission ; Tsetse Flies/classification/*genetics/parasitology ; }, abstract = {This reviews work published since 2007. Relative efforts devoted to the agents of African trypanosomiasis and their tsetse fly vectors are given by the numbers of PubMed accessions. In the last 10 years PubMed citations number 3457 for Trypanosoma brucei and 769 for Glossina. The development of simple sequence repeats and single nucleotide polymorphisms afford much higher resolution of Glossina and Trypanosoma population structures than heretofore. Even greater resolution is offered by partial and whole genome sequencing. Reproduction in T. brucei sensu lato is principally clonal although genetic recombination in tsetse salivary glands has been demonstrated in T. b. brucei and T. b. rhodesiense but not in T. b. gambiense. In the past decade most genetic attention was given to the chief human African trypanosomiasis vectors in subgenus Nemorhina e.g., Glossina f. fuscipes, G. p. palpalis, and G. p. gambiense. The chief interest in Nemorhina population genetics seemed to be finding vector populations sufficiently isolated to enable efficient and long-lasting suppression. To this end estimates were made of gene flow, derived from FST and its analogues, and Ne, the size of a hypothetical population equivalent to that under study. Genetic drift was greater, gene flow and Ne typically lesser in savannah inhabiting tsetse (subgenus Glossina) than in riverine forms (Nemorhina). Population stabilities were examined by sequential sampling and genotypic analysis of nuclear and mitochondrial genomes in both groups and found to be stable. Gene frequencies estimated in sequential samplings differed by drift and allowed estimates of effective population numbers that were greater for Nemorhina spp than Glossina spp. Prospects are examined of genetic methods of vector control. The tsetse long generation time (c. 50 d) is a major contraindication to any suggested genetic method of tsetse population manipulation. Ecological and modelling research convincingly show that conventional methods of targeted insecticide applications and traps/targets can achieve cost-effective reduction in tsetse densities.}, }
@article {pmid29885227, year = {2017}, author = {Twyford, AD}, title = {New insights into the population biology of endoparasitic Rafflesiaceae.}, journal = {American journal of botany}, volume = {104}, number = {10}, pages = {1433-1436}, doi = {10.3732/ajb.1700317}, pmid = {29885227}, issn = {1537-2197}, mesh = {Asia ; Biology ; *Flowers ; *Orobanchaceae ; Symbiosis ; }, abstract = {Parasitic plants demonstrate a diversity of growth strategies, life histories, and developmental and physiological characteristics. Most research to date has focused on a narrow range of parasitic taxa, particularly in the Orobanchaceae, while the other independent origins of parasitism have largely gone unstudied. One type of parasite that has received relatively little attention are the endophytic parasites, which have a fascinating growth strategy where the parasite is embedded within the host tissue, with the flower the only externally visibly plant part. Endophytic growth makes it challenging to understand basic aspects of species biology, such as the size of a given parasite, the number of parasites per host, and the genetic diversity of populations. Recent studies by Barkman et al. (2017) and Pelser et al. (2017) have used microsatellite genotyping to investigate the population biology of endoparasitic Rafflesiaceae species in Asia. They show the potential for extensive parasite spread within a host vine and the strong partitioning of genetic diversity by host. These species are also shown to have an outcrossing mating system. However, these studies suggest different reproductive strategies, one supporting monoecy and one suggesting dioecy. Overall, these studies partly &quot;lift the lid&quot; on the cryptic biology of Rafflesia and the Rafflesiaceae and open the door for future comparative studies between endophytic and free-living parasitic plants.}, }
@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/ ; DE-SC0018409//U.S. Department of Energy/ ; DE-FC02-07ER64494//U.S. Department of Energy/ ; FP7/2007-2013 n° [627266]//European Union Seventh Framework Programme/ ; DEB 1737898//National Science Foundation/ ; }, 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 {pmid29062089, year = {2017}, author = {Duarte, A and Cotter, SC and De Gasperin, O and Houslay, TM and Boncoraglio, G and Welch, M and Kilner, RM}, title = {No evidence of a cleaning mutualism between burying beetles and their phoretic mites.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13838}, pmid = {29062089}, issn = {2045-2322}, support = {310785//European Research Council/International ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Infective Agents/*metabolism ; Bacteria/*classification ; Bodily Secretions/*metabolism ; Breeding ; Coleoptera/*metabolism/microbiology ; Female ; Male ; Mites/classification/*physiology ; Reproduction ; Sexual Behavior, Animal ; *Symbiosis ; }, abstract = {Burying beetles (Nicrophorus vespilloides) breed on small vertebrate carcasses, which they shave and smear with antimicrobial exudates. Producing antimicrobials imposes a fitness cost on burying beetles, which rises with the potency of the antimicrobial defence. Burying beetles also carry phoretic mites (Poecilochirus carabi complex), which breed alongside them on the carcass. Here we test the novel hypothesis that P. carabi mites assist burying beetles in clearing the carcass of bacteria as a side-effect of grazing on the carrion. We manipulated the bacterial environment on carcasses and measured the effect on the beetle in the presence and absence of mites. With next-generation sequencing, we investigated how mites influence the bacterial communities on the carcass. We show that mites: 1) cause beetles to reduce the antibacterial activity of their exudates but 2) there are no consistent fitness benefits of breeding alongside mites. We also find that mites increase bacterial diversity and richness on the carcass, but do not reduce bacterial abundance. The current evidence does not support a cleaning mutualism between burying beetles and P. carabi mites, but more work is needed to understand the functional significance and fitness consequences for the beetle of mite-associated changes to the bacterial community on the carcass.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1016/j.fsi.2019.07.032}, pmid = {31306759}, issn = {1095-9947}, abstract = {As domain species in seep and vent ecosystem, Bathymodiolinae 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 {pmid30901468, year = {2019}, author = {Balakrishnan, B and Luckey, D and Taneja, V}, title = {Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice.}, journal = {Military medicine}, volume = {184}, number = {Suppl 1}, pages = {529-536}, doi = {10.1093/milmed/usy309}, pmid = {30901468}, issn = {1930-613X}, mesh = {Animals ; Autoimmunity/*physiology ; Bifidobacterium/pathogenicity ; Disease Models, Animal ; Enzyme-Linked Immunosorbent Assay/methods ; Gastrointestinal Microbiome/*physiology ; Mice ; *Permeability ; Prevalence ; Symbiosis/physiology ; }, abstract = {OBJECTIVE: Although the etiology of rheumatoid arthritis (RA) is unknown, recent studies have led to the concept that gut dysbiosis may be involved in onset. In this study, we aimed to determine if human gut commensals modulate the immune response and gut epithelial integrity in DQ8 mice.<br><br>METHODS: DQ8 mice were orally gavaged with RA-associated (Eggerthella lenta or Collinsella aerofaciens) and non-associated (Prevotella histicola or Bifidobacterium sp.) on alternate days for 1 week in naïve mice. Some mice were immunized with type II collagen and oral gavage continued for 6 weeks and followed for arthritis. Epithelial integrity was done by FITC-Dextran assay. In addition, cytokines were measured in sera by ELISA and various immune cells were quantified using flow cytometry.<br><br>RESULTS: Gut permeability was increased by the RA-associated bacteria and was sex and age-dependent. In vivo and in vitro observations showed that the RA-non-associated bacteria outgrow the RA-associated bacteria when gavaged or cultured together. Mice gavaged with the RA-non-associated bacteria produced lower levels of pro-inflammatory MCP-1 and MCP-3 and had lower numbers of Inflammatory monocytes CD11c+Ly6c+, when compared to controls. E. lenta treated naïve mice produce Th17 cytokines.<br><br>CONCLUSIONS: Our studies suggest that gut commensals influence immune response in and away from the gut by changing the gut permeability and immunity. Dysbiosis helps the growth of RA-associated bacteria and reduces the beneficial bacteria.}, }
@article {pmid30184201, year = {2018}, author = {Rathi, S and Tak, N and Bissa, G and Chouhan, B and Ojha, A and Adhikari, D and Barik, SK and Satyawada, RR and Sprent, JI and James, EK and Gehlot, HS}, title = {Selection of Bradyrhizobium or Ensifer symbionts by the native Indian caesalpinioid legume Chamaecrista pumila depends on soil pH and other edaphic and climatic factors.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy180}, pmid = {30184201}, issn = {1574-6941}, mesh = {Bradyrhizobium/classification/genetics/*isolation &amp; purification ; Chamaecrista/anatomy &amp; histology/*microbiology/ultrastructure ; Climate ; Hydrogen-Ion Concentration ; India ; Phylogeny ; Rhizobiaceae/classification/genetics/*isolation &amp; purification ; Root Nodules, Plant/anatomy &amp; histology/ultrastructure ; Soil/chemistry ; *Soil Microbiology ; Symbiosis/genetics ; }, abstract = {Nodules of Chamaecrista pumila growing in several locations in India were sampled for anatomical studies and for characterization of their rhizobial microsymbionts. Regardless of their region of origin, the nodules were indeterminate with their bacteroids contained within symbiosomes which were surrounded by pectin. More than 150 strains were isolated from alkaline soils from the Thar Desert (Rajasthan), wet-acidic soils of Shillong (Meghalaya), and from trap experiments using soils from four other states with different agro-ecological regions. Molecular phylogenetic analysis based on five housekeeping (rrs, recA, glnII, dnaK andatpD) and two symbiotic (nodA and nifH) genes was performed for selected strains. Chamaecrista pumila was shown to be nodulated by niche-specific diverse strains of either Ensifer or Bradyrhizobium in alkaline (Thar Desert) to neutral (Tamil Nadu) soils and only Bradyrhizobium strains in acidic (Shillong) soils. Concatenated core gene phylogenies showed four novel Ensifer-MLSA types and nine Bradyrhizobium-MLSA types. Genetically diverse Ensifer strains harbored similar sym genes which were novel. In contrast, significant symbiotic diversity was observed in the Bradyrhizobium strains. The C. pumila strains cross-nodulated Vigna radiata and some wild papilionoid and mimosoid legumes. It is suggested that soil pH and moisture level played important roles in structuring the C. pumila microsymbiont community.}, }
@article {pmid30124811, year = {2018}, author = {Watanabe, K and Suzuki, H and Nishida, T and Mishima, M and Tachibana, M and Fujishima, M and Shimizu, T and Watarai, M}, title = {Identification of novel Legionella genes required for endosymbiosis in Paramecium based on comparative genome analysis with Holospora spp.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy162}, pmid = {30124811}, issn = {1574-6941}, mesh = {Gene Deletion ; Genes, Bacterial ; Genomics ; Holosporaceae/genetics ; Legionella pneumophila/*genetics ; Macrophages/microbiology ; Paramecium/*microbiology ; Symbiosis/*genetics ; }, abstract = {The relationship between Legionella and protist hosts has a huge impact when considering the infectious risk in humans because it facilitates the long-term replication and survival of Legionella in the environment. The ciliate Paramecium is considered to be a protist host for Legionella in natural environments, but the details of their endosymbiosis are largely unknown. In this study, we determined candidate Legionella pneumophila genes that are likely to be involved in the establishment of endosymbiosis in Paramecium caudatum by comparing the genomes of Legionella spp. and Holospora spp. that are obligate endosymbiotic bacteria in Paramecium spp. Among the candidate genes, each single deletion mutant for five genes (lpg0492, lpg0522, lpg0523, lpg2141 and lpg2398) failed to establish endosymbiosis in P. caudatum despite showing intracellular growth in human macrophages. The mutants exhibited no characteristic changes in terms of their morphology, multiplication rate or capacity for modulating the phagosomes in which they were contained, but their resistance to lysozyme decreased significantly. This study provides insights into novel factors required by L. pneumophila for endosymbiosis in P. caudatum, and suggests that endosymbiotic organisms within conspecific hosts may have shared genes related to effective endosymbiosis establishment.}, }
@article {pmid29097716, year = {2017}, author = {Shiu, JH and Keshavmurthy, S and Chiang, PW and Chen, HJ and Lou, SP and Tseng, CH and Justin Hsieh, H and Allen Chen, C and Tang, SL}, title = {Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14933}, pmid = {29097716}, issn = {2045-2322}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Cold-Shock Response ; Heat-Shock Response ; RNA, Ribosomal, 16S/genetics ; Seasons ; Stress, Physiological ; *Symbiosis ; Temperature ; Thermotolerance ; }, abstract = {Seasonal variation in temperature fluctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that different temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4-30.2 and 12.1-23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10-33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities differed between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. Therefore, seasonal acclimation may increase tolerance of coral-associated bacteria to temperature fluctuations.}, }
@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}, support = {RO 2491/4-1//Deutsche Forschungsgemeinschaft/ ; RO 2491/5-2//Deutsche Forschungsgemeinschaft/ ; }, 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 {pmid31294199, year = {2017}, author = {Stamou, GP and Konstadinou, S and Monokrousos, N and Mastrogianni, A and Orfanoudakis, M and Hassiotis, C and Menkissoglu-Spiroudi, U and Vokou, D and Papatheodorou, EM}, title = {The effects of arbuscular mycorrhizal fungi and essential oil on soil microbial community and N-related enzymes during the fungal early colonization phase.}, journal = {AIMS microbiology}, volume = {3}, number = {4}, pages = {938-959}, doi = {10.3934/microbiol.2017.4.938}, pmid = {31294199}, issn = {2471-1888}, abstract = {The arbuscular mycorrhizal fungi (AMF) and the essential oils are both agents of sustainable agriculture, and their independent effects on the community of free-living soil microbes have been explored. In a tomato pot experiment, conducted in a sandy loam mixture, we examined the independent and joint effects of inoculation with the fungus Rhizophagous irregularis and the addition of Mentha spicata essential oil on the structure of the soil microbial community and the activity of soil enzymes involved in the N-cycle, during the pre-symbiosis phase. Plants were grown for 60 days and were inoculated with R. irregularis. Then pots were treated with essential oil (OIL) weekly for a period of a month. Two experimental series were run. The first targeted to examine the effect of inoculation on the microbial community structure by the phospholipid fatty acids analysis (PLFAs), and enzyme activity, and the second to examine the effects of inoculation and essential oil addition on the same variables, under the hypothesis that the joint effect of the two agents would be synergistic, resulting in higher microbial biomass compared to values recorded in singly treated pots. In the AMF pots, N-degrading enzyme activity was dominated by the activity of urease while in the non-inoculated ones by the activities of arylamidase and glutaminase. Higher microbial biomass was found in singly-treated pots (137 and 174% higher in AMF and OIL pots, respectively) compared with pots subjected to both treatments. In these latter pots, higher activity of asparaginase (202 and 162% higher compared to AMF and OIL pots, respectively) and glutaminase (288 and 233% higher compared to AMF and OIL pots, respectively) was found compared to singly-treated ones. Soil microbial biomasses and enzyme activity were negatively associated across all treatments. Moreover, different community composition was detected in pots only inoculated and pots treated only with oil. We concluded that the two treatments produced diverging than synergistic effects on the microbial community composition whereas their joint effect on the activity of asparaginase and glutaminase were synergistic.}, }
@article {pmid31294170, year = {2017}, author = {Muñoz-Azcarate, O and González, AM and Santalla, M}, title = {Natural rhizobial diversity helps to reveal genes and QTLs associated with biological nitrogen fixation in common bean.}, journal = {AIMS microbiology}, volume = {3}, number = {3}, pages = {435-466}, doi = {10.3934/microbiol.2017.3.435}, pmid = {31294170}, issn = {2471-1888}, abstract = {Common bean is one of the most important crops for human feed, and the most important legume for direct consumption by millions of people, especially in developing countries. It is a promiscuous host legume in terms of nodulation, able to associate with a broad and diverse range of rhizobia, although the competitiveness for nodulation and the nitrogen fixation capacity of most of these strains is generally low. As a result, common bean is very inefficient for symbiotic nitrogen fixation, and nitrogen has to be supplied with chemical fertilizers. In the last years, symbiotic nitrogen fixation has received increasing attention as a sustainable alternative to nitrogen fertilizers, and also as a more economic and available one in poor countries. Therefore, optimization of nitrogen fixation of bean-rhizobia symbioses and selection of efficient rhizobial strains should be a priority, which begins with the study of the natural diversity of the symbioses and the rhizobial populations associated. Natural rhizobia biodiversity that nodulates common bean may be a source of adaptive alleles acting through phenotypic plasticity. Crosses between accessions differing for nitrogen fixation may combine alleles that never meet in nature. Another way to discover adaptive genes is to use association genetics to identify loci that common bean plants use for enhanced biological nitrogen fixation and, in consequence, for marker assisted selection for genetic improvement of symbiotic nitrogen fixation. In this review, rhizobial biodiversity resources will be discussed, together with what is known about the loci that underlie such genetic variation, and the potential candidate genes that may influence the symbiosis' fitness benefits, thus achieving an optimal nitrogen fixation capacity in order to help reduce reliance on nitrogen fertilizers in common bean.}, }
@article {pmid31294167, year = {2017}, author = {da-Silva, JR and Alexandre, A and Brígido, C and Oliveira, S}, title = {Can stress response genes be used to improve the symbiotic performance of rhizobia?.}, journal = {AIMS microbiology}, volume = {3}, number = {3}, pages = {365-382}, doi = {10.3934/microbiol.2017.3.365}, pmid = {31294167}, issn = {2471-1888}, abstract = {Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.}, }
@article {pmid31294160, year = {2017}, author = {Silva, LR and Bento, C and Gonçalves, AC and Flores-Félix, JD and Ramírez-Bahena, MH and Peix, A and Velázquez, E}, title = {Legume bioactive compounds: influence of rhizobial inoculation.}, journal = {AIMS microbiology}, volume = {3}, number = {2}, pages = {267-278}, doi = {10.3934/microbiol.2017.2.267}, pmid = {31294160}, issn = {2471-1888}, abstract = {Legumes consumption has been recognized as beneficial for human health, due to their content in proteins, fiber, minerals and vitamins, and their cultivation as beneficial for sustainable agriculture due to their ability to fix atmospheric nitrogen in symbiosis with soil bacteria known as rhizobia. The inoculation with these baceria induces metabolic changes in the plant, from which the more studied to date are the increases in the nitrogen and protein contents, and has been exploited in agriculture to improve the crop yield of several legumes. Nevertheless, legumes also contain several bioactive compounds such as polysaccharides, bioactive peptides, isoflavones and other phenolic compounds, carotenoids, tocopherols and fatty acids, which makes them functional foods included into the nutraceutical products. Therefore, the study of the effect of the rhizobial inoculation in the legume bioactive compounds content is gaining interest in the last decade. Several works reported that the inoculation of different genera and species of rhizobia in several grain legumes, such as soybean, cowpea, chickpea, faba bean or peanut, produced increases in the antioxidant potential and in the content of some bioactive compounds, such as phenolics, flavonoids, organic acids, proteins and fatty acids. Therefore, the rhizobial inoculation is a good tool to enhance the yield and quality of legumes and further studies on this field will allow us to have plant probiotic bacteria that promote the plant growth of legumes improving their functionality.}, }
@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 = {}, number = {}, pages = {}, 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 {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 {pmid30859201, year = {2019}, author = {Grisdale, CJ and Smith, DR and Archibald, JM}, title = {Relative Mutation Rates in Nucleomorph-Bearing Algae.}, journal = {Genome biology and evolution}, volume = {11}, number = {4}, pages = {1045-1053}, doi = {10.1093/gbe/evz056}, pmid = {30859201}, issn = {1759-6653}, mesh = {Biological Evolution ; Cryptophyta/*genetics ; *Genome, Mitochondrial ; *Genome, Plastid ; *Mutation Rate ; Symbiosis ; }, abstract = {Chlorarachniophyte and cryptophyte algae are unique among plastid-containing species in that they have a nucleomorph genome: a compact, highly reduced nuclear genome from a photosynthetic eukaryotic endosymbiont. Despite their independent origins, the nucleomorph genomes of these two lineages have similar genomic architectures, but little is known about the evolutionary pressures impacting nucleomorph DNA, particularly how their rates of evolution compare to those of the neighboring genetic compartments (the mitochondrion, plastid, and nucleus). Here, we use synonymous substitution rates to estimate relative mutation rates in the four genomes of nucleomorph-bearing algae. We show that the relative mutation rates of the host versus endosymbiont nuclear genomes are similar in both chlorarachniophytes and cryptophytes, despite the fact that nucleomorph gene sequences are notoriously highly divergent. There is some evidence, however, for slightly elevated mutation rates in the nucleomorph DNA of chlorarachniophytes-a feature not observed in that of cryptophytes. For both lineages, relative mutation rates in the plastid appear to be lower than those in the nucleus and nucleomorph (and, in one case, the mitochondrion), which is consistent with studies of other plastid-bearing protists. Given the divergent nature of nucleomorph genes, our finding of relatively low evolutionary rates in these genomes suggests that for both lineages a burst of evolutionary change and/or decreased selection pressures likely occurred early in the integration of the secondary endosymbiont.}, }
@article {pmid30531154, year = {2018}, author = {Takashima, Y and Seto, K and Degawa, Y and Guo, Y and Nishizawa, T and Ohta, H and Narisawa, K}, title = {Prevalence and Intra-Family Phylogenetic Divergence of Burkholderiaceae-Related Endobacteria Associated with Species of Mortierella.}, journal = {Microbes and environments}, volume = {33}, number = {4}, pages = {417-427}, doi = {10.1264/jsme2.ME18081}, pmid = {30531154}, issn = {1347-4405}, mesh = {Burkholderiaceae/*classification/genetics/*isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Japan ; Mortierella/*classification/genetics/isolation &amp; purification/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Endofungal bacteria are widespread within the phylum Mucoromycota, and these include Burkholderiaceae-related endobacteria (BRE). However, the prevalence of BRE in Mortierellomycotinan fungi and their phylogenetic divergence remain unclear. Therefore, we examined the prevalence of BRE in diverse species of Mortierella. We surveyed 238 isolates of Mortierella spp. mainly obtained in Japan that were phylogenetically classified into 59 species. BRE were found in 53 isolates consisting of 22 species of Mortierella. Among them, 20 species of Mortierella were newly reported as the fungal hosts of BRE. BRE in a Glomeribacter-Mycoavidus clade in the family Burkholderiaceae were separated phylogenetically into three groups. These groups consisted of a group containing Mycoavidus cysteinexigens, which is known to be associated with M. elongata, and two other newly distinguishable groups. Our results demonstrated that BRE were harbored by many species of Mortierella and those that associated with isolates of Mortierella spp. were more phylogenetically divergent than previously reported.}, }
@article {pmid30487350, year = {2018}, author = {Evans, JS and López-Legentil, S and Erwin, PM}, title = {Comparing Two Common DNA Extraction Kits for the Characterization of Symbiotic Microbial Communities from Ascidian Tissue.}, journal = {Microbes and environments}, volume = {33}, number = {4}, pages = {435-439}, doi = {10.1264/jsme2.ME18031}, pmid = {30487350}, issn = {1347-4405}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; Genetic Techniques/*standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; *Symbiosis ; Urochordata/*microbiology ; }, abstract = {Various DNA extraction methods are often used interchangeably for the characterization of microbial communities despite indications that different techniques produce disparate results. The microbiomes of two ascidian species were herein characterized using two common DNA extraction kits, the DNeasy Blood and Tissue Kit (Qiagen) and the PowerSoil DNA Isolation Kit (Mo Bio Laboratories), followed by next-generation (Illumina) sequencing of partial 16S rRNA genes. Significant differences were detected in microbial community diversity and structure between ascidian species, but not between kits, suggesting similar recovery of biological variation and low technical variation between the two extraction methods for ascidian microbiome characterization.}, }
@article {pmid30289987, year = {2018}, author = {St Leger, AJ and Caspi, RR}, title = {Visions of Eye Commensals: The Known and the Unknown About How the Microbiome Affects Eye Disease.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {11}, pages = {e1800046}, doi = {10.1002/bies.201800046}, pmid = {30289987}, issn = {1521-1878}, support = {EY000184//NEI/NIH/International ; R00 EY025761/EY/NEI NIH HHS/United States ; Z01 EY000184/EY/NEI NIH HHS/United States ; EY000457//NEI/NIH/International ; }, mesh = {Animals ; Corynebacterium/*growth &amp; development ; Eye/*microbiology ; Eye Diseases/*microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Mice ; Microbiota/*physiology ; Symbiosis/*physiology ; }, abstract = {Until recently, the ocular surface is thought by many to be sterile and devoid of living microbes. It is now becoming clear that this may not be the case. Recent and sophisticated PCR analyses have shown that microbial DNA-based &quot;signatures&quot; are present within various ethnic, geographic, and contact lens wearing communities. Furthermore, using a mouse model of ocular surface disease, we have shown that the microbe, Corynebacterium mastitidis (C. mast), can stably colonize the ocular mucosa and that a causal relationship exists between ocular C. mast colonization and beneficial local immunity. While this constitutes proof-of-concept that a bona fide ocular microbiome that tunes immunity can exist at the ocular surface, there remain numerous unanswered questions to be addressed before microbiome-modulating therapies may be successfully developed. Here, the authors will briefly outline what is currently known about the local ocular microbiome as well as microbiomes associated with other sites, and how those sites may play a role in ocular surface immunity. Understanding how commensal microbes affect the ocular surface immune homeostasis has the potential revolutionize how we think about treating ocular surface disease.}, }
@article {pmid30254321, year = {2019}, author = {Flechas, SV and Acosta-González, A and Escobar, LA and Kueneman, JG and Sánchez-Quitian, ZA and Parra-Giraldo, CM and Rollins-Smith, LA and Reinert, LK and Vredenburg, VT and Amézquita, A and Woodhams, DC}, title = {Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {361-373}, doi = {10.1038/s41396-018-0284-9}, pmid = {30254321}, issn = {1751-7370}, mesh = {Animals ; Anura/growth &amp; development/*microbiology ; Bacteria/drug effects/isolation &amp; purification ; Chytridiomycota/*isolation &amp; purification ; Colombia ; *Microbiota ; Mycoses/microbiology/veterinary ; Peptides/analysis/*pharmacology ; Skin/chemistry/microbiology ; Symbiosis ; Sympatry ; }, abstract = {Management of hyper-virulent generalist pathogens is an emergent global challenge, yet for most disease systems we lack a basic understanding as to why some host species suffer mass mortalities, while others resist epizootics. We studied two sympatric species of frogs from the Colombian Andes, which coexist with the amphibian pathogen Batrachochytrium dendrobatidis (Bd), to understand why some species did not succumb to the infection. We found high Bd prevalence in juveniles for both species, yet infection intensities remained low. We also found that bacterial community composition and host defense peptides are specific to amphibian life stages. We detected abundant Bd-inhibitory skin bacteria across life stages and Bd-inhibitory defense peptides post-metamorphosis in both species. Bd-inhibitory bacteria were proportionally more abundant in adults of both species than in earlier developmental stages. We tested for activity of peptides against the skin microbiota and found that in general peptides did not negatively affect bacterial growth and in some instances facilitated growth. Our results suggest that symbiotic bacteria and antimicrobial peptides may be co-selected for, and that together they contribute to the ability of Andean amphibian species to coexist with the global pandemic lineage of Bd.}, }
@article {pmid30228381, year = {2019}, author = {Cooper, MB and Kazamia, E and Helliwell, KE and Kudahl, UJ and Sayer, A and Wheeler, GL and Smith, AG}, title = {Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {334-345}, doi = {10.1038/s41396-018-0274-y}, pmid = {30228381}, issn = {1751-7370}, support = {BB/I013164/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biotin/metabolism ; Chlorophyta/genetics/*metabolism/*microbiology ; Heterotrophic Processes ; Niacin/metabolism ; Phytoplankton/metabolism ; Rhodobacteraceae/*metabolism ; *Symbiosis ; Thiamine/metabolism ; Vitamin B 12/metabolism ; Vitamin B Complex/*metabolism ; }, abstract = {Ostreococcus tauri, a picoeukaryotic alga that contributes significantly to primary production in oligotrophic waters, has a highly streamlined genome, lacking the genetic capacity to grow without the vitamins thiamine (B1) and cobalamin (B12). Here we demonstrate that the B12 and B1 auxotrophy of O. tauri can be alleviated by co-culturing with a heterotrophic bacterial partner Dinoroseobacter shibae, a member of the Rhodobacteraceae family of alpha-proteobacteria, genera of which are frequently found associated with marine algae. D. shibae lacks the complete pathway to synthesise three other B-vitamins: niacin (B3), biotin (B7), and p-aminobenzoic acid (a precursor for folate, B9), and the alga is in turn able to satisfy the reciprocal vitamin requirements of its bacterial partner in a stable long-term co-culture. Bioinformatics searches of 197 representative marine bacteria with sequenced genomes identified just nine species that had a similar combination of traits (ability to make vitamin B12, but missing one or more genes for niacin and biotin biosynthesis enzymes), all of which were from the Rhodobacteraceae. Further analysis of 70 species from this family revealed the majority encoded the B12 pathway, but only half were able to make niacin, and fewer than 13% biotin. These characteristics may have either contributed to or resulted from the tendency of members of this lineage to adopt lifestyles in close association with algae. This study provides a nuanced view of bacterial-phytoplankton interactions, emphasising the complexity of the sources, sinks and dynamic cycling between marine microbes of these important organic micronutrients.}, }
@article {pmid29923795, year = {2018}, author = {Yi, M and Hendricks, WQ and Kaste, J and Charlton, ND and Nagabhyru, P and Panaccione, DG and Young, CA}, title = {Molecular identification and characterization of endophytes from uncultivated barley.}, journal = {Mycologia}, volume = {110}, number = {3}, pages = {453-472}, doi = {10.1080/00275514.2018.1464818}, pmid = {29923795}, issn = {1557-2536}, mesh = {Alkaloids/analysis ; Alleles ; Endophytes/classification/*genetics ; Epichloe/*classification/*genetics/isolation &amp; purification ; *Genetic Variation ; Hordeum/chemistry/genetics/*microbiology ; *Phylogeny ; Seed Bank ; Seeds/*microbiology ; Symbiosis ; }, abstract = {Epichloë species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between Epichloë and their host grasses contribute to plant growth promotion, protection from many pathogens and insect pests, and tolerance to drought stress. Resistance to insect herbivores by endophytes associated with Hordeum species has been previously shown to vary depending on the endophyte-grass-insect combination. We explored the genetic and chemotypic diversity of endophytes present in wild Hordeum species. We analyzed seeds of Hordeum bogdanii, H. brevisubulatum, and H. comosum obtained from the US Department of Agriculture's (USDA) National Plant Germplasm System (NPGS), of which some have been reported as endophyte-infected. Using polymerase chain reaction (PCR) with primers specific to Epichloë species, we were able to identify endophytes in seeds from 17 of the 56 Plant Introduction (PI) lines, of which only 9 lines yielded viable seed. Phylogenetic analyses of housekeeping, alkaloid biosynthesis, and mating type genes suggest that the endophytes of the infected PI lines separate into five taxa: Epichloë bromicola, Epichloë tembladerae, and three unnamed interspecific hybrid species. One PI line contained an endophyte that is considered a new taxonomic group, Epichloë sp. HboTG-3 (H. bogdanii Taxonomic Group 3). Phylogenetic analyses of the interspecific hybrid endophytes from H. bogdanii and H. brevisubulatum indicate that these taxa all have an E. bromicola allele but the second allele varies. We verified in planta alkaloid production from the five genotypes yielding viable seed. Morphological characteristics of the isolates from the viable Hordeum species were analyzed for their features in culture and in planta. In the latter, we observed epiphyllous growth and in some cases sporulation on leaves of infected plants.}, }
@article {pmid29868005, year = {2018}, author = {Zhang, W and Zhu, B and Xu, J and Liu, Y and Qiu, E and Li, Z and Li, Z and He, Y and Zhou, H and Bai, Y and Zhi, F}, title = {Bacteroides fragilis Protects Against Antibiotic-Associated Diarrhea in Rats by Modulating Intestinal Defenses.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {1040}, pmid = {29868005}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/*adverse effects ; Bacterial Infections/*therapy ; *Bacteroides fragilis ; Diarrhea/microbiology/*therapy ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/drug effects ; Intestines/immunology/microbiology ; Male ; Probiotics/administration &amp; dosage/*therapeutic use ; Protective Agents/administration &amp; dosage/therapeutic use ; Rats ; Rats, Sprague-Dawley ; Symbiosis ; }, abstract = {Antibiotic-associated diarrhea (AAD) is iatrogenic diarrhea characterized by disruption of the gut microbiota. Probiotics are routinely used to treat AAD in clinical practice; however, the effectiveness and mechanisms by which probiotics alleviate symptoms remain poorly understood. We previously isolated a non-toxic Bacteroides fragilis strain ZY-312, which has been verified to be beneficial in certain infection disorders. However, the precise role of this commensal bacterium in AAD is unknown. In this study, we successfully established an AAD rat model by exposing rats to appropriate antibiotics. These rats developed diarrhea symptoms and showed alterations in their intestinal microbiota, including overgrowth of some pathogenic bacteria. In addition, gastrointestinal barrier defects, indicated by compromised aquaporin expression, aberrant tight junction proteins, and decreased abundance of mucus-filled goblet cells, were also detected in ADD rats compared with control animals. Of note, oral treatment with B. fragilis strain ZY-312 ameliorated AAD-related diarrhea symptoms by increasing the abundance of specific commensal microbiota. Interestingly, we demonstrated that these changes were coincident with the restoration of intestinal barrier function and enterocyte regeneration in AAD rats. In summary, we identified a potential probiotic therapeutic strategy for AAD and identified the vital roles of B. fragilis strain ZY-312 in modulating the colonic bacterial community and participating in microbiota-mediated epithelial cell proliferation and differentiation.}, }
@article {pmid29608282, year = {2018}, author = {Leonard, SP and Perutka, J and Powell, JE and Geng, P and Richhart, DD and Byrom, M and Kar, S and Davies, BW and Ellington, AD and Moran, NA and Barrick, JE}, title = {Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.}, journal = {ACS synthetic biology}, volume = {7}, number = {5}, pages = {1279-1290}, pmid = {29608282}, issn = {2161-5063}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Bees/*microbiology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gastrointestinal Microbiome/*genetics ; Gene Expression Regulation, Bacterial ; Genetic Engineering/*methods ; Ileum/microbiology ; Microorganisms, Genetically-Modified ; Plasmids ; Promoter Regions, Genetic ; Proteobacteria/*genetics ; Replicon ; Serratia marcescens/genetics/pathogenicity ; Symbiosis ; }, abstract = {Engineering the bacteria present in animal microbiomes promises to lead to breakthroughs in medicine and agriculture, but progress is hampered by a dearth of tools for genetically modifying the diverse species that comprise these communities. Here we present a toolkit of genetic parts for the modular construction of broad-host-range plasmids built around the RSF1010 replicon. Golden Gate assembly of parts in this toolkit can be used to rapidly test various antibiotic resistance markers, promoters, fluorescent reporters, and other coding sequences in newly isolated bacteria. We demonstrate the utility of this toolkit in multiple species of Proteobacteria that are native to the gut microbiomes of honey bees (Apis mellifera) and bumble bees (B ombus sp.). Expressing fluorescent proteins in Snodgrassella alvi, Gilliamella apicola, Bartonella apis, and Serratia strains enables us to visualize how these bacteria colonize the bee gut. We also demonstrate CRISPRi repression in B. apis and use Cas9-facilitated knockout of an S. alvi adhesion gene to show that it is important for colonization of the gut. Beyond characterizing how the gut microbiome influences the health of these prominent pollinators, this bee microbiome toolkit (BTK) will be useful for engineering bacteria found in other natural microbial communities.}, }
@article {pmid29242567, year = {2017}, author = {Guizzo, MG and Parizi, LF and Nunes, RD and Schama, R and Albano, RM and Tirloni, L and Oldiges, DP and Vieira, RP and Oliveira, WHC and Leite, MS and Gonzales, SA and Farber, M and Martins, O and Vaz, IDS and Oliveira, PL}, title = {A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17554}, pmid = {29242567}, issn = {2045-2322}, mesh = {Animals ; Coxiella/drug effects/genetics/*physiology ; Female ; Genome, Bacterial/genetics ; Larva/drug effects/growth &amp; development/microbiology ; Nymph/drug effects/growth &amp; development/microbiology ; Ovum/drug effects/growth &amp; development/microbiology ; Rhipicephalus/growth &amp; development/*microbiology ; *Symbiosis/drug effects ; Tetracycline/pharmacology ; }, abstract = {The cattle tick Rhipicephalus microplus is a hematophagous ectoparasite that causes important economic losses in livestock. Different species of ticks harbor a symbiont bacterium of the genus Coxiella. It was showed that a Coxiella endosymbiont from R. microplus (CERM) is a vertically transmitted mutualist symbiont, comprising 98% of the 16S rRNA sequences in both eggs and larvae. Sequencing of the bacterial genome revealed genes for biosynthetic pathways for several vitamins and key metabolic cofactors that may provide a nutritional complement to the tick host. The CERM was abundant in ovary and Malpighian tubule of fully engorged female. Tetracycline treatment of either the tick or the vertebrate host reduced levels of bacteria in progeny in 74% for eggs and 90% for larvae without major impact neither on the reproductive fitness of the adult female or on embryo development. However, CERM proved to be essential for the tick to reach the adult life stage, as under antibiotic treatment no tick was able to progress beyond the metanymph stage. Data presented here suggest that interference in the symbiotic CERM-R. microplus relationship may be useful to the development of alternative control methods, highlighting the interdependence between ticks and their endosymbionts.}, }
@article {pmid29180695, year = {2017}, author = {Pérez-de-Luque, A and Tille, S and Johnson, I and Pascual-Pardo, D and Ton, J and Cameron, DD}, title = {The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16409}, pmid = {29180695}, issn = {2045-2322}, mesh = {Analysis of Variance ; *Disease Resistance ; Host-Pathogen Interactions ; Mycorrhizae/*physiology ; *Plant Development ; Plant Roots/growth &amp; development/microbiology ; Rhizobiaceae/*physiology ; *Symbiosis ; }, abstract = {Belowground interactions between plant roots, mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR) can improve plant health via enhanced nutrient acquisition and priming of the plant immune system. Two wheat cultivars differing in their ability to form mycorrhiza were (co)inoculated with the mycorrhizal fungus Rhizophagus irregularis and the rhizobacterial strain Pseudomonas putida KT2440. The cultivar with high mycorrhizal compatibility supported higher levels of rhizobacterial colonization than the low compatibility cultivar. Those levels were augmented by mycorrhizal infection. Conversely, rhizobacterial colonization of the low compatibility cultivar was reduced by mycorrhizal arbuscule formation. Single inoculations with R. irregularis or P. putida had differential growth effects on both cultivars. Furthermore, while both cultivars developed systemic priming of chitosan-induced callose after single inoculations with R. irregularis or P. putida, only the cultivar with high mycorrhizal compatibility showed a synergistic increase in callose responsiveness following co-inoculation with both microbes. Our results show that multilateral interactions between roots, mycorrhizal fungi and PGPR can have synergistic effects on growth and systemic priming of wheat.}, }
@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}, 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 hypothesize 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. This article is protected by copyright. All rights reserved.}, }
@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 {pmid30414119, year = {2019}, author = {Schuler, H and Lopez, JA and Doellman, MM and Hood, GR and Egan, SP and Feder, JL}, title = {Target-Enriched Endosymbiont Sequencing (TEEseq): A New High-Throughput Sequencing Approach Applied to the Comprehensive Characterization of Endosymbionts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1858}, number = {}, pages = {195-212}, doi = {10.1007/978-1-4939-8775-7_14}, pmid = {30414119}, issn = {1940-6029}, mesh = {Animals ; Bacterial Proteins/genetics ; Computational Biology/*methods ; DNA, Bacterial/analysis/genetics ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Insecta/*microbiology ; Sequence Analysis, DNA/methods ; *Symbiosis ; Wolbachia/*genetics/isolation &amp; purification/physiology ; }, abstract = {Intracellular bacteria are ubiquitous in the insect world, with perhaps the best-studied example being the alphaproteobacterium, Wolbachia. Like most endosymbionts, Wolbachia cannot be cultivated outside of its host cells, hindering traditional microbial characterization techniques. Furthermore, multiple Wolbachia strains can be present within a single host, and certain strains can be present in densities below the detection limit of current methods. To date, Wolbachia has most commonly been studied using polymerase chain reaction (PCR) amplification and Sanger DNA sequencing by targeting specific genes in the bacterium's genome. PCR amplification and Sanger sequencing of multiple Wolbachia strains requires analysis of individually cloned sequences, which is resource and labor intensive. To help mitigate these difficulties, we present a modified double digest restriction site associated DNA sequencing (ddRADseq) approach to target and sequence in parallel multiple genes by adding restriction enzyme recognition sites to gene-specific PCR primers. Adopting this strategy allows us to uniquely tag and sequence amplicons from multiple hosts simultaneously on an Illumina MiSeq platform. Our approach represents an efficient and cost-effective method to characterize multiple target genes in population surveys.}, }
@article {pmid31287538, year = {2019}, author = {Suzuki, N}, title = {Glycan diversity in the course of vertebrate evolution.}, journal = {Glycobiology}, volume = {}, number = {}, pages = {}, 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}, 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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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 performedsing 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 {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 = {}, number = {}, pages = {}, 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 non-ribosomal 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. 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 all produce the peptides exclusively in symbiosis.}, }
@article {pmid31281920, year = {2019}, author = {de Oliveira, ISR and Jesus, EDC and Ribeiro, TG and da Silva, MSRA 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 = {}, number = {}, 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. caesapiniifolia 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 P. sabiae and a few strains of Rhizobium in the Southeast. On the other hand, the symbionts found in the Northeast were, predominantly, P. 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 to the taxonomical classification of the strains.}, }
@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 {pmid30209224, year = {2018}, author = {Schär, S and Eastwood, R and Arnaldi, KG and Talavera, G and Kaliszewska, ZA and Boyle, JH and Espeland, M and Nash, DR and Vila, R and Pierce, NE}, title = {Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1886}, pages = {}, pmid = {30209224}, issn = {1471-2954}, mesh = {Animals ; Ants/*physiology ; Butterflies/genetics/*physiology ; Electron Transport Complex IV/analysis ; Genes, Mitochondrial ; Insect Proteins/analysis ; Phylogeny ; *Symbiosis ; }, abstract = {The role of specialization in diversification can be explored along two geological axes in the butterfly family Lycaenidae. In addition to variation in host-plant specialization normally exhibited by butterflies, the caterpillars of most Lycaenidae have symbioses with ants ranging from no interactions through to obligate and specific associations, increasing niche dimensionality in ant-associated taxa. Based on mitochondrial sequences from 8282 specimens from 967 species and 249 genera, we show that the degree of ecological specialization of lycaenid species is positively correlated with genetic divergence, haplotype diversity and an increase in isolation by distance. Nucleotide substitution rate is higher in carnivorous than phytophagous lycaenids. The effects documented here for both micro- and macroevolutionary processes could result from increased spatial segregation as a consequence of reduced connectivity in specialists, niche-based divergence or a combination of both. They could also provide an explanation for the extraordinary diversity of the Lycaenidae and, more generally, for diversity in groups of organisms with similar multi-dimensional ecological specialization.}, }
@article {pmid29929732, year = {2018}, author = {Ma, LS and Pellegrin, C and Kahmann, R}, title = {Repeat-containing effectors of filamentous pathogens and symbionts.}, journal = {Current opinion in microbiology}, volume = {46}, number = {}, pages = {123-130}, doi = {10.1016/j.mib.2018.01.007}, pmid = {29929732}, issn = {1879-0364}, mesh = {Amino Acid Motifs ; Fungal Proteins/chemistry/genetics/*metabolism ; Fungi/genetics/*physiology ; Host-Pathogen Interactions ; Plant Diseases/*microbiology ; Plants/*microbiology ; *Symbiosis ; }, abstract = {Pathogenic and symbiotic filamentous microbes secrete effectors which suppress host immune responses and promote a successful colonization. Pathogen effectors are engaged in the arms race with their hosts and because of this they are subject to intense evolutionary pressure. Effectors particularly prone to rapid evolution display repeat-containing domains which can easily expand or contract and accumulate point mutations without altering their original function. In this review we address the diversity of function in such repeat-containing effectors, focus on new findings and point out avenues for future work.}, }
@article {pmid29162937, year = {2017}, author = {Murillo-Rincon, AP and Klimovich, A and Pemöller, E and Taubenheim, J and Mortzfeld, B and Augustin, R and Bosch, TCG}, title = {Spontaneous body contractions are modulated by the microbiome of Hydra.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15937}, pmid = {29162937}, issn = {2045-2322}, mesh = {Animals ; Behavior, Animal ; *Gastrointestinal Microbiome ; Germ-Free Life ; Hydra/*microbiology/*physiology ; Symbiosis ; }, abstract = {Spontaneous contractile activity, such as gut peristalsis, is ubiquitous in animals and is driven by pacemaker cells. In humans, disruption of the contraction pattern leads to gastrointestinal conditions, which are also associated with gut microbiota dysbiosis. Spontaneous contractile activity is also present in animals lacking gastrointestinal tract. Here we show that spontaneous body contractions in Hydra are modulated by symbiotic bacteria. Germ-free animals display strongly reduced and less regular contraction frequencies. These effects are partially restored by reconstituting the natural microbiota. Moreover, soluble molecule(s) produced by symbiotic bacteria may be involved in contraction frequency modulation. As the absence of bacteria does not impair the contractile ability itself, a microbial effect on the pacemakers seems plausible. Our findings indicate that the influence of bacteria on spontaneous contractile activity is present in the early-branching cnidarian hydra as well as in Bilateria, and thus suggest an evolutionary ancient origin of interaction between bacteria and metazoans, opening a window into investigating the roots of human motility disorders.}, }
@article {pmid28873739, year = {2017}, author = {Freire, AL and Ramos, CL and Schwan, RF}, title = {Effect of symbiotic interaction between a fructooligosaccharide and probiotic on the kinetic fermentation and chemical profile of maize blended rice beverages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {100}, number = {Pt 1}, pages = {698-707}, doi = {10.1016/j.foodres.2017.07.070}, pmid = {28873739}, issn = {1873-7145}, mesh = {Adolescent ; Adult ; *Beverages/analysis/microbiology ; Chromatography, High Pressure Liquid ; Fermentation/*physiology ; Fermented Foods/analysis/microbiology ; Humans ; Kinetics ; Lactobacillus/metabolism ; Middle Aged ; Odorants/analysis ; Oligosaccharides/*metabolism ; Oryza/*chemistry ; Probiotics/*metabolism ; Symbiosis/physiology ; Taste ; Yeasts/metabolism ; Young Adult ; Zea mays/*chemistry ; }, abstract = {There is an important demand for the development of new non-dairy probiotic beverages in the functional food market. This work aimed to develop new fermented beverages from maize and rice. Lactobacillus plantarum CCMA 0743, Torulaspora delbrueckii CCMA 0235, and the commercial probiotic Lactobacillus acidophilus LACA 4, were used as a mixed starter culture. Two prebiotic concentrations, 20 and 50g/L fructooligosaccharide (FOS) were tested. The growth of L. acidophilus LACA 4 was favored by 50g/L FOS and after refrigerated storage at 4°C for 28days, its population remained above 107CFU/mL. Lactic and acetic acids were the main organic acids detected, at around 3.7 and 0.5g/L, respectively. Ethanol was present at <5g/L in non-alcoholic beverages. Fifty-five volatile compounds including acids, alcohols, aldehydes, esters, ketones, pyrazines and others, were detected. The sensorial analysis demonstrated that >50% of consumers liked slightly or liked extremely the beverages (scores from 6-9). Therefore, potential symbiotic cereal beverages were successfully obtained using a mix of lactic acid bacteria and yeast as a starter culture. This is an important step in the commercial production of alternative beverages from common food substrates for consumers.}, }
@article {pmid31279967, year = {2019}, author = {Wang, Y and White, MM and Moncalvo, JM}, title = {Diversification of the gut fungi (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera).}, journal = {Molecular phylogenetics and evolution}, volume = {}, 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}, 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 (GxG), other environmental factors (GxE), 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, 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 {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 {pmid30743202, year = {2019}, author = {Dou, J and Zeng, J and Wu, K and Tan, W and Gao, L and Lu, J}, title = {Microbiosis in pathogenesis and intervention of atopic dermatitis.}, journal = {International immunopharmacology}, volume = {69}, number = {}, pages = {263-269}, doi = {10.1016/j.intimp.2019.01.030}, pmid = {30743202}, issn = {1878-1705}, mesh = {Animals ; Biological Therapy/trends ; Dermatitis, Atopic/*microbiology/therapy ; Gastrointestinal Microbiome/*immunology ; Humans ; Immune System ; Skin/microbiology/*pathology ; Symbiosis ; }, abstract = {Atopic dermatitis (AD) is a chronic, non-contagious, inflammatory skin disorder characterized by relapsing eczematous lesions. Its pathogenesis remains incompletely understood. The current evidence has emerged to show that skin and gut microbiome play critical roles in the pathogenesis and progression of AD. Skin mircrobiome mainly refers to skin commensal organisms that promote normal immune system functions and prevent the colonization of pathogens; while gut microbiome can modulate immunologic, metabolic and neuroendocrine functions. With the current knowledge of microbiome effects on the onset of the disease, there are evolving multifarious interventions targeting microbiome for the treatment of AD. In this report, we have reviewed the critical roles of microbiosis in the pathogenesis of AD, summarized potential mechanisms mediated by microbiosis and aimed to enlighten a theoretical basis for its therapeutic applications in the treatment of AD.}, }
@article {pmid30659865, year = {2019}, author = {Vázquez-Medina, R and Ledesma-Durán, A and Aragón, JL}, title = {Patchy spread patterns in three-species bistable systems with facultative mutualism.}, journal = {Bio Systems}, volume = {177}, number = {}, pages = {24-33}, doi = {10.1016/j.biosystems.2019.01.008}, pmid = {30659865}, issn = {1872-8324}, mesh = {Animals ; Ecosystem ; Equidae/*physiology ; *Food Chain ; *Models, Biological ; Models, Statistical ; Perissodactyla/*physiology ; Population Dynamics ; *Predatory Behavior ; Starlings/*physiology ; *Symbiosis ; }, abstract = {A three-species population system under a facultative mutualistic relationship of one of the species is studied. The considered interactions are as follows: facultative between the first species and the second species, obligatory mutualism between the second species and the first one, and the third species is a predator of the first species. For this purpose, we extend the model proposed by Morozov et al., originally used to describe obligatory mutualism, to consider obligatory and facultative mutualism and prove that under adequately selected parameters this system produces a spatial patchy spread of populations or continuous wave fronts. Since the analytical treatment of a three-species model is often prohibitive, we first analyze the interaction between two mutualist species without diffusion and without the presence of the predator. Some parameters are fixed in the bistable regime of the mutualistic species to further consider the influence of the third species. The remaining parameters are then selected to produce patchy patterns under different mortality rates. Finally, the equations of the final three-species system are numerically solved to test the influence of different initial conditions in the formation of patchy populations. It is confirmed that the velocity and the profile of a traveling front are independent on the initial conditions. Our approach opens the way to study more general biological situations.}, }
@article {pmid30470198, year = {2018}, author = {Scolari, F and Attardo, GM and Aksoy, E and Weiss, B and Savini, G and Takac, P and Abd-Alla, A and Parker, AG and Aksoy, S and Malacrida, AR}, title = {Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {169}, pmid = {30470198}, issn = {1471-2180}, support = {R21 AI109263/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Female ; Insect Control ; Male ; *Microbiota ; Reproduction/genetics ; Sex Factors ; *Symbiosis ; Testis ; Transcriptome ; Tsetse Flies/*genetics/*microbiology ; }, abstract = {BACKGROUND: Tsetse flies (Diptera, Glossinidae) display unique reproductive biology traits. Females reproduce through adenotrophic viviparity, nourishing the growing larva into their modified uterus until parturition. Males transfer their sperm and seminal fluid, produced by both testes and male accessory glands, in a spermatophore capsule transiently formed within the female reproductive tract upon mating. Both sexes are obligate blood feeders and have evolved tight relationships with endosymbionts, already shown to provide essential nutrients lacking in their diet. However, the partnership between tsetse and its symbionts has so far been investigated, at the molecular, genomic and metabolomics level, only in females, whereas the roles of microbiota in male reproduction are still unexplored.<br><br>RESULTS: Here we begin unravelling the impact of microbiota on Glossina m. morsitans (G. morsitans) male reproductive biology by generating transcriptomes from the reproductive tissues of males deprived of their endosymbionts (aposymbiotic) via maternal antibiotic treatment and dietary supplementation. We then compared the transcriptional profiles of genes expressed in the male reproductive tract of normal and these aposymbiotic flies. We showed that microbiota removal impacts several male reproductive genes by depressing the activity of genes in the male accessory glands (MAGs), including sequences encoding seminal fluid proteins, and increasing expression of genes in the testes. In the MAGs, in particular, the expression of genes related to mating, immunity and seminal fluid components' synthesis is reduced. In the testes, the absence of symbionts activates genes involved in the metabolic apparatus at the basis of male reproduction, including sperm production, motility and function.<br><br>CONCLUSIONS: Our findings mirrored the complementary roles male accessory glands and testes play in supporting male reproduction and open new avenues for disentangling the interplay between male insects and endosymbionts. From an applied perspective, unravelling the metabolic and functional relationships between tsetse symbionts and male reproductive physiology will provide fundamental information useful to understanding the biology underlying improved male reproductive success in tsetse. This information is of particular importance in the context of tsetse population control via Sterile Insect Technique (SIT) and its impact on trypanosomiasis transmission.}, }
@article {pmid30470187, year = {2018}, author = {Ouedraogo, GMS and Demirbas-Uzel, G and Rayaisse, JB and Gimonneau, G and Traore, AC and Avgoustinos, A and Parker, AG and Sidibe, I and Ouedraogo, AG and Traore, A and Bayala, B and Vreysen, MJB and Bourtzis, K and Abd-Alla, AMM}, title = {Prevalence of trypanosomes, salivary gland hypertrophy virus and Wolbachia in wild populations of tsetse flies from West Africa.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {153}, pmid = {30470187}, issn = {1471-2180}, mesh = {Africa, Western ; Animals ; Cytomegalovirus/*isolation &amp; purification/pathogenicity ; Geography ; Ghana ; Humans ; Insect Vectors/microbiology/parasitology/virology ; Prevalence ; Spiroplasma/isolation &amp; purification ; Symbiosis ; Trypanosoma/*isolation &amp; purification ; Tsetse Flies/*microbiology/*parasitology/*virology ; Wolbachia/*isolation &amp; purification ; }, abstract = {BACKGROUND: Tsetse flies are vectors of African trypanosomes, protozoan parasites that cause sleeping sickness (or human African trypanosomosis) in humans and nagana (or animal African trypanosomosis) in livestock. In addition to trypanosomes, four symbiotic bacteria Wigglesworthia glossinidia, Sodalis glossinidius, Wolbachia, Spiroplasma and one pathogen, the salivary gland hypertrophy virus (SGHV), have been reported in different tsetse species. We evaluated the prevalence and coinfection dynamics between Wolbachia, trypanosomes, and SGHV in four tsetse species (Glossina palpalis gambiensis, G. tachinoides, G. morsitans submorsitans, and G. medicorum) that were collected between 2008 and 2015 from 46 geographical locations in West Africa, i.e. Burkina Faso, Mali, Ghana, Guinea, and Senegal.<br><br>RESULTS: The results indicated an overall low prevalence of SGHV and Wolbachia and a high prevalence of trypanosomes in the sampled wild tsetse populations. The prevalence of all three infections varied among tsetse species and sample origin. The highest trypanosome prevalence was found in Glossina tachinoides (61.1%) from Ghana and in Glossina palpalis gambiensis (43.7%) from Senegal. The trypanosome prevalence in the four species from Burkina Faso was lower, i.e. 39.6% in Glossina medicorum, 18.08%; in Glossina morsitans submorsitans, 16.8%; in Glossina tachinoides and 10.5% in Glossina palpalis gambiensis. The trypanosome prevalence in Glossina palpalis gambiensis was lowest in Mali (6.9%) and Guinea (2.2%). The prevalence of SGHV and Wolbachia was very low irrespective of location or tsetse species with an average of 1.7% for SGHV and 1.0% for Wolbachia. In some cases, mixed infections with different trypanosome species were detected. The highest prevalence of coinfection was Trypanosoma vivax and other Trypanosoma species (9.5%) followed by coinfection of T. congolense with other trypanosomes (7.5%). The prevalence of coinfection of T. vivax and T. congolense was (1.0%) and no mixed infection of trypanosomes, SGHV and Wolbachia was detected.<br><br>CONCLUSION: The results indicated a high rate of trypanosome infection in tsetse wild populations in West African countries but lower infection rate of both Wolbachia and SGHV. Double or triple mixed trypanosome infections were found. In addition, mixed trypanosome and SGHV infections existed however no mixed infections of trypanosome and/or SGHV with Wolbachia were found.}, }
@article {pmid30470185, year = {2018}, author = {Schneider, DI and Parker, AG and Abd-Alla, AM and Miller, WJ}, title = {High-sensitivity detection of cryptic Wolbachia in the African tsetse fly (Glossina spp.).}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {140}, pmid = {30470185}, issn = {1471-2180}, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Female ; In Situ Hybridization, Fluorescence/*methods ; Insect Vectors/microbiology ; Limit of Detection ; Male ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Symbiosis ; Tsetse Flies/*microbiology ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: In African tsetse flies Glossina, spp. detection of bacterial symbionts such as Wolbachia is challenging since their prevalence and distribution are patchy, and natural symbiont titers can range at levels far below detection limit of standard molecular techniques. Reliable estimation of symbiont infection frequency, especially with regard to interrelations between symbionts and their potential impact on host biology, is of pivotal interest in the context of future applications for the control and eradication of Glossina-vectored African trypanosomosis. The presence or absence of symbionts is routinely screened with endpoint polymerase chain reaction (PCR), which has numerous advantages, but reaches its limits, when detecting infections at natural low titer. To not only determine presence of native tsetse symbionts but also to localize them to specific host tissues, fluorescence in situ hybridization (FISH) can be applied. However, classic FISH assays may not detect low-titer infections due to limitations in sensitivity.<br><br>RESULTS: We have compared classic endpoint PCR with high-sensitivity blot-PCR. We demonstrate that the latter technique allows for clear detection of low-titer Wolbachia in the morsitans and palpalis groups while classic endpoint PCR does not. In order to localize Wolbachia in situ in high and low-titer Glossina species, we applied high-end Stellaris® rRNA-FISH. We show that with this high sensitivity method, even low amounts of Wolbachia can be traced in specific tissues. Furthermore, we highlight that more tissues and organs than previously recorded are infested with Wolbachia in subspecies of the morsitans and palpalis groups.<br><br>CONCLUSIONS: Our results demonstrate that overall symbiont infection frequencies as well as the presence in specific host tissues may be underestimated when using low-sensitivity methods. To better understand the complex interrelation of tsetse flies and their native symbionts plus the pathogenic trypanosomes, it is important to consider application of a broader range of high-sensitivity detection tools.}, }
@article {pmid30470184, year = {2018}, author = {Channumsin, M and Ciosi, M and Masiga, D and Turner, CMR and Mable, BK}, title = {Sodalis glossinidius presence in wild tsetse is only associated with presence of trypanosomes in complex interactions with other tsetse-specific factors.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {163}, pmid = {30470184}, issn = {1471-2180}, support = {//Wellcome Trust/United Kingdom ; 093692//Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Animals ; Enterobacteriaceae/*physiology ; Environment ; Female ; Geography ; Kenya ; Male ; Sex Factors ; *Symbiosis ; Tsetse Flies/*microbiology/*parasitology ; }, abstract = {BACKGROUND: Susceptibility of tsetse flies (Glossina spp.) to trypanosomes of both humans and animals has been associated with the presence of the endosymbiont Sodalis glossinidius. However, intrinsic biological characteristics of the flies and environmental factors can influence the presence of both S. glossinidius and the parasites. It thus remains unclear whether it is the S. glossinidius or other attributes of the flies that explains the apparent association. The objective of this study was to test whether the presence of Trypanosoma vivax, T. congolense and T. brucei are related to the presence of S. glossinidius in tsetse flies when other factors are accounted for: geographic location, species of Glossina, sex or age of the host flies.<br><br>RESULTS: Flies (n = 1090) were trapped from four sites in the Shimba Hills and Nguruman regions in Kenya. Sex and species of tsetse (G. austeni, G. brevipalpis, G. longipennis and G. pallidipes) were determined based on external morphological characters and age was estimated by a wing fray score method. The presence of trypanosomes and S. glossinidius was detected using PCR targeting the internal transcribed spacer region 1 and the haemolysin gene, respectively. Sequencing was used to confirm species identification. Generalised Linear Models (GLMs) and Multiple Correspondence Analysis (MCA) were applied to investigate multivariable associations. The overall prevalence of trypanosomes was 42.1%, but GLMs revealed complex patterns of associations: the presence of S. glossinidius was associated with trypanosome presence but only in interactions with other factors and only in some species of trypanosomes. The strongest association was found for T. congolense, and no association was found for T. vivax. The MCA also suggested only a weak association between the presence of trypanosomes and S. glossinidius. Trypanosome-positive status showed strong associations with sex and age while S. glossinidius-positive status showed a strong association with geographic location and species of fly.<br><br>CONCLUSIONS: We suggest that previous conclusions about the presence of endosymbionts increasing probability of trypanosome presence in tsetse flies may have been confounded by other factors, such as community composition of the tsetse flies and the specific trypanosomes found in different regions.}, }
@article {pmid30470183, year = {2018}, author = {Geiger, A and Malele, I and Abd-Alla, AM and Njiokou, F}, title = {Blood feeding tsetse flies as hosts and vectors of mammals-pre-adapted African Trypanosoma: current and expected research directions.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {162}, pmid = {30470183}, issn = {1471-2180}, mesh = {Animals ; *Blood ; Ecosystem ; *Feeding Behavior ; Insect Vectors/microbiology ; Mammals/parasitology ; Symbiosis ; Trypanosoma/physiology ; Trypanosomiasis, African/prevention &amp; control/*transmission ; Tsetse Flies/parasitology/*physiology ; }, abstract = {Research on the zoo-anthropophilic blood feeding tsetse flies' biology conducted, by different teams, in laboratory settings and at the level of the ecosystems- where also co-perpetuate African Trypanosoma- has allowed to unveil and characterize key features of tsetse flies' bacterial symbionts on which rely both (a) the perpetuation of the tsetse fly populations and (b) the completion of the developmental program of the African Trypanosoma. Transcriptomic analyses have already provided much information on tsetse fly genes as well as on genes of the fly symbiotic partners Sodalis glossinidius and Wigglesworthia, which account for the successful onset or not of the African Trypanosoma developmental program. In parallel, identification of the non- symbiotic bacterial communities hosted in the tsetse fly gut has recently been initiated: are briefly introduced those bacteria genera and species common to tsetse flies collected from distinct ecosystems, that could be further studied as potential biologicals preventing the onset of the African Trypanosoma developmental program. Finally, future work will need to concentrate on how to render tsetse flies refractory, and the best means to disseminate them in the field in order to establish an overall refractory fly population.}, }
@article {pmid30470182, year = {2018}, author = {Kariithi, HM and Meki, IK and Schneider, DI and De Vooght, L and Khamis, FM and Geiger, A and Demirbaş-Uzel, G and Vlak, JM and iNCE, IA and Kelm, S and Njiokou, F and Wamwiri, FN and Malele, II and Weiss, BL and Abd-Alla, AMM}, title = {Enhancing vector refractoriness to trypanosome infection: achievements, challenges and perspectives.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {179}, pmid = {30470182}, issn = {1471-2180}, mesh = {Animals ; Female ; Insect Control/methods/organization &amp; administration ; Insect Vectors/parasitology/*physiology ; Microbiota ; Symbiosis/*genetics ; Trypanosoma/genetics ; Trypanosomiasis, African/prevention &amp; control/transmission ; Tsetse Flies/*parasitology/physiology ; }, abstract = {With the absence of effective prophylactic vaccines and drugs against African trypanosomosis, control of this group of zoonotic neglected tropical diseases depends the control of the tsetse fly vector. When applied in an area-wide insect pest management approach, the sterile insect technique (SIT) is effective in eliminating single tsetse species from isolated populations. The need to enhance the effectiveness of SIT led to the concept of investigating tsetse-trypanosome interactions by a consortium of researchers in a five-year (2013-2018) Coordinated Research Project (CRP) organized by the Joint Division of FAO/IAEA. The goal of this CRP was to elucidate tsetse-symbiome-pathogen molecular interactions to improve SIT and SIT-compatible interventions for trypanosomoses control by enhancing vector refractoriness. This would allow extension of SIT into areas with potential disease transmission. This paper highlights the CRP's major achievements and discusses the science-based perspectives for successful mitigation or eradication of African trypanosomosis.}, }
@article {pmid30470181, year = {2018}, author = {De Vooght, L and Van Keer, S and Van Den Abbeele, J}, title = {Towards improving tsetse fly paratransgenesis: stable colonization of Glossina morsitans morsitans with genetically modified Sodalis.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {165}, pmid = {30470181}, issn = {1471-2180}, mesh = {Animals ; Chromosomes, Bacterial ; Enterobacteriaceae/*genetics ; Female ; Green Fluorescent Proteins ; Insect Control/*methods ; Larva/microbiology ; Male ; Microbiota ; Microinjections ; *Organisms, Genetically Modified ; Proof of Concept Study ; Symbiosis ; Tsetse Flies/*microbiology ; }, abstract = {BACKGROUND: Tsetse flies (Glossina sp.) refractory to trypanosome infection are currently being explored as potential tools to contribute in the control of human and animal African trypanosomiasis. One approach to disrupt trypanosome transmission by the tsetse fly vector involves the use of paratransgenesis, a technique that aims to reduce vector competence of disease vectors via genetic modification of their microbiota. An important prerequisite for developing paratransgenic tsetse flies is the stable repopulation of tsetse flies and their progeny with its genetically modified Sodalis symbiont without interfering with host fitness.<br><br>RESULTS: In this study, we assessed by qPCR analysis the ability of a chromosomally GFP-tagged Sodalis (recSodalis) strain to efficiently colonize various tsetse tissues and its transmission to the next generation of offspring using different introduction approaches. When introduced in the adult stage of the fly via thoracic microinjection, recSodalis is maintained at high densities for at least 21 days. However, no vertical transmission to the offspring was observed. Oral administration of recSodalis did not lead to the colonization of either adult flies or their offspring. Finally, introduction of recSodalis via microinjection of third-instar larvae resulted in stably colonized adult tsetse flies. Moreover, the subsequent generations of offspring were also efficiently colonized with recSodalis. We show that proper colonization of the female reproductive tissues by recSodalis is an important determinant for vertical transmission.<br><br>CONCLUSIONS: Intralarval microinjection of recSodalis proves to be essential to achieve optimal colonization of flies with genetically modified Sodalis and its subsequent dissemination into the following generations of progeny. This study provides the proof-of-concept that Sodalis can be used to drive expression of exogenous transgenes in Glossina morsitans morsitans colonies representing a valuable contribution to the development of a paratransgenic tsetse fly based control strategy.}, }
@article {pmid30470179, year = {2018}, author = {Demirbas-Uzel, G and De Vooght, L and Parker, AG and Vreysen, MJB and Mach, RL and Van Den Abbeele, J and Abd-Alla, AMM}, title = {Combining paratransgenesis with SIT: impact of ionizing radiation on the DNA copy number of Sodalis glossinidius in tsetse flies.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {160}, pmid = {30470179}, issn = {1471-2180}, mesh = {Animals ; DNA/*radiation effects ; Enterobacteriaceae/*genetics/*radiation effects ; Enterobacteriaceae Infections ; Female ; Insect Control/*methods ; Insect Vectors/microbiology ; Male ; *Radiation, Ionizing ; Symbiosis ; Tsetse Flies/*microbiology ; }, abstract = {BACKGROUND: Tsetse flies (Diptera: Glossinidae) are the cyclical vectors of the causative agents of African Trypanosomosis, which has been identified as a neglected tropical disease in both humans and animals in many regions of sub-Saharan Africa. The sterile insect technique (SIT) has shown to be a powerful method to manage tsetse fly populations when used in the frame of an area-wide integrated pest management (AW-IPM) program. To date, the release of sterile males to manage tsetse fly populations has only been implemented in areas to reduce transmission of animal African Trypanosomosis (AAT). The implementation of the SIT in areas with Human African Trypanosomosis (HAT) would require additional measures to eliminate the potential risk associated with the release of sterile males that require blood meals to survive and hence, might contribute to disease transmission. Paratransgenesis offers the potential to develop tsetse flies that are refractory to trypanosome infection by modifying their associated bacteria (Sodalis glossinidius) here after referred to as Sodalis. Here we assessed the feasibility of combining the paratransgenesis approach with SIT by analyzing the impact of ionizing radiation on the copy number of Sodalis and the vectorial capacity of sterilized tsetse males.<br><br>RESULTS: Adult Glossina morsitans morsitans that emerged from puparia irradiated on day 22 post larviposition did not show a significant decline in Sodalis copy number as compared with non-irradiated flies. Conversely, the Sodalis copy number was significantly reduced in adults that emerged from puparia irradiated on day 29 post larviposition and in adults irradiated on day 7 post emergence. Moreover, irradiating 22-day old puparia reduced the copy number of Wolbachia and Wigglesworthia in emerged adults as compared with non-irradiated controls, but the radiation treatment had no significant impact on the vectorial competence of the flies.<br><br>CONCLUSION: Although the radiation treatment significantly reduced the copy number of some tsetse fly symbionts, the copy number of Sodalis recovered with time in flies irradiated as 22-day old puparia. This recovery offers the opportunity to combine a paratransgenesis approach - using modified Sodalis to produce males refractory to trypanosome infection - with the release of sterile males to minimize the risk of disease transmission, especially in HAT endemic areas. Moreover, irradiation did not increase the vector competence of the flies for trypanosomes.}, }
@article {pmid30470178, year = {2018}, author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S}, title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {146}, pmid = {30470178}, issn = {1471-2180}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Geography ; High-Throughput Nucleotide Sequencing ; Insect Vectors/*microbiology/parasitology ; Kenya ; Symbiosis ; Trypanosoma/*physiology ; Tsetse Flies/*microbiology/parasitology ; Uganda ; }, abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.<br><br>RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.<br><br>CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.}, }
@article {pmid30470177, year = {2018}, author = {Kame-Ngasse, GI and Njiokou, F and Melachio-Tanekou, TT and Farikou, O and Simo, G and Geiger, A}, title = {Prevalence of symbionts and trypanosome infections in tsetse flies of two villages of the &quot;Faro and Déo&quot; division of the Adamawa region of Cameroon.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {159}, pmid = {30470177}, issn = {1471-2180}, mesh = {Animals ; Cameroon ; Enterobacteriaceae/*isolation &amp; purification ; Insect Vectors/microbiology/parasitology ; Polymerase Chain Reaction ; Prevalence ; *Symbiosis ; Trypanosoma/genetics/isolation &amp; purification ; Tsetse Flies/*microbiology/*parasitology ; Wolbachia/*isolation &amp; purification ; }, abstract = {BACKGROUND: Tsetse flies are vectors of human and animal African trypanosomiasis. In spite of many decades of chemotherapy and vector control, the disease has not been eradicated. Other methods like the transformation of tsetse fly symbionts to render the fly refractory to trypanosome infection are being evaluated. The aim of the present study was to evaluate the association between trypanosome infections and the presence of symbionts in these tsetse species. Tsetse flies were trapped in two villages of the &quot;Faro and Déo&quot; Division of the Adamawa region of Cameroon. In the field, tsetse fly species were identified and their infection by trypanosomes was checked by microscopy. In the laboratory, DNA was extracted from their midguts and the presence of symbionts (Sodalis glossinidius and Wolbachia sp.) and trypanosomes was checked by PCR. Symbionts/trypanosomes association tests were performed.<br><br>RESULTS: Three tsetse fly species including Glossina tachinoides (90.1%), Glossina morsitans submorsitans (9.4%) and Glossina fuscipes fuscipes (0.5%) were caught. In all the population we obtained an occurrence rate of 37.2% for Sodalis glossinidius and 67.6% for Wolbachia irrespective to tsetse flies species. S. glossinidius and Wolbachia sp. occurrence rates were respectively 37 and 68% for G. tachinoides and 28.6 and 59.5% for G. m. submorsitans. Between Golde Bourle and Mayo Dagoum significant differences were observed in the prevalence of symbionts. Prevalence of trypanosomes were 34.8% for Glossina tachinoides and 40.5% for Glossina morsitans submorsitans. In G. tachinoides, the trypanosome infection rates were 11, 2.6 and 13.7%, respectively, for T. brucei s.l., T. congolense forest type and T. congolense savannah type. In G. m. submorsitans, these infection rates were 16.7, 9.5 and, 2.4% respectively, for T. brucei s.l., T. congolense forest type and T. congolense savannah type.<br><br>CONCLUSIONS: The rate of tsetse fly infection by trypanosomes was low compared to those obtained in HAT foci of south Cameroon, and this rate was not statistically linked to the rate of symbiont occurrence. This study allowed to show for the first time the presence of Wolbachia sp. in the tsetse fly sub-species Glossina morsitans submorsitans and Glossina tachinoides.}, }
@article {pmid30308154, year = {2018}, author = {Levy, A and Conway, JM and Dangl, JL and Woyke, T}, title = {Elucidating Bacterial Gene Functions in the Plant Microbiome.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {4}, pages = {475-485}, doi = {10.1016/j.chom.2018.09.005}, pmid = {30308154}, issn = {1934-6069}, mesh = {Genes, Bacterial/*genetics ; Genomics ; Host Microbial Interactions/*genetics ; Metabolomics ; Microbiota/*genetics ; Plants/*microbiology ; Proteomics ; Symbiosis ; Transcriptome ; Whole Genome Sequencing ; }, abstract = {There is a growing appreciation for the important roles microorganisms play in association with plants. Microorganisms are drawn to distinct plant surfaces by the nutrient-rich microenvironment, and in turn some of these colonizing microbes provide mutualistic benefits to their host. The development of plant probiotics to increase crop yield and provide plant resistance against biotic and abiotic stresses, while minimizing chemical inputs, would benefit from a deeper mechanistic understanding of plant-microbe interaction. Technological advances in molecular biology and high-throughput -omics provide stepping stones to the elucidation of critical microbiome gene functions that aid in improving plant performance. Here, we review -omics-based approaches that are propelling forward the current understanding of plant-associated bacterial gene functions, and describe how these technologies have helped unravel key bacterial genes and pathways that mediate pathogenic, beneficial, and commensal host interactions.}, }
@article {pmid28964698, year = {2017}, author = {Ponomarova, O and Gabrielli, N and Sévin, DC and Mülleder, M and Zirngibl, K and Bulyha, K and Andrejev, S and Kafkia, E and Typas, A and Sauer, U and Ralser, M and Patil, KR}, title = {Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.}, journal = {Cell systems}, volume = {5}, number = {4}, pages = {345-357.e6}, pmid = {28964698}, issn = {2405-4712}, support = {//Wellcome Trust/United Kingdom ; FC001134//Cancer Research UK/United Kingdom ; FC001134//Medical Research Council/United Kingdom ; FC001134//Wellcome Trust/United Kingdom ; 200829/Z/16/Z//Wellcome Trust/United Kingdom ; }, mesh = {Fermentation/physiology ; Lactic Acid/*metabolism ; Lactobacillales/*metabolism ; Lactobacillus plantarum/metabolism ; Lactococcus lactis/metabolism ; Nitrogen/*metabolism ; Saccharomyces cerevisiae/metabolism ; Symbiosis/*physiology ; Yeast, Dried/metabolism ; }, abstract = {Many microorganisms live in communities and depend on metabolites secreted by fellow community members for survival. Yet our knowledge of interspecies metabolic dependencies is limited to few communities with small number of exchanged metabolites, and even less is known about cellular regulation facilitating metabolic exchange. Here we show how yeast enables growth of lactic acid bacteria through endogenous, multi-component, cross-feeding in a readily established community. In nitrogen-rich environments, Saccharomyces cerevisiae adjusts its metabolism by secreting a pool of metabolites, especially amino acids, and thereby enables survival of Lactobacillus plantarum and Lactococcus lactis. Quantity of the available nitrogen sources and the status of nitrogen catabolite repression pathways jointly modulate this niche creation. We demonstrate how nitrogen overflow by yeast benefits L. plantarum in grape juice, and contributes to emergence of mutualism with L. lactis in a medium with lactose. Our results illustrate how metabolic decisions of an individual species can benefit others.}, }
@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 fiber 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. Further, 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 programs that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production. This article is protected by copyright. All rights reserved.}, }
@article {pmid31271473, year = {2019}, author = {Leeks, A and Santos, MD 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}, 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 suggests 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, 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}, }
@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}, 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. This article is protected by copyright. All rights reserved.}, }
@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}, abstract = {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, catalyzing 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 and 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. This article is protected by copyright. All rights reserved.}, }
@article {pmid29614286, year = {2018}, author = {Thanbichler, M}, title = {Cell Division: Symbiotic Bacteria Turn It Upside Down.}, journal = {Current biology : CB}, volume = {28}, number = {7}, pages = {R306-R308}, doi = {10.1016/j.cub.2018.02.041}, pmid = {29614286}, issn = {1879-0445}, mesh = {Animals ; Bacteria/cytology ; Cell Division ; Morphogenesis ; Nematoda/*microbiology ; *Symbiosis ; }, abstract = {Symbiotic bacteria of the genus Thiosymbion attach to the surface of their nematode hosts using their poles and divide by longitudinal binary fission. A new study now sheds light on the molecular mechanisms that underlie this peculiar mode of proliferation.}, }
@article {pmid29429621, year = {2018}, author = {Bourguignon, T and Lo, N and Dietrich, C and Šobotník, J and Sidek, S and Roisin, Y and Brune, A and Evans, TA}, title = {Rampant Host Switching Shaped the Termite Gut Microbiome.}, journal = {Current biology : CB}, volume = {28}, number = {4}, pages = {649-654.e2}, doi = {10.1016/j.cub.2018.01.035}, pmid = {29429621}, issn = {1879-0445}, mesh = {Animals ; Bacteria/classification/genetics ; Gastrointestinal Microbiome/*physiology ; Isoptera/*microbiology ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; }, abstract = {The gut microbiota of animals exert major effects on host biology [1]. Although horizontal transfer is generally considered the prevalent route for the acquisition of gut bacteria in mammals [2], some bacterial lineages have co-speciated with their hosts on timescales of several million years [3]. Termites harbor a complex gut microbiota, and their advanced social behavior provides the potential for long-term vertical symbiont transmission, and co-evolution of gut symbionts and host [4-6]. Despite clear evolutionary patterns in the gut microbiota of termites [7], a consensus on how microbial communities were assembled during termite diversification has yet to be reached. Although some studies have concluded that vertical transmission has played a major role [8, 9], others indicate that diet and gut microenvironment have been the primary determinants shaping microbial communities in termite guts [7, 10]. To address this issue, we examined the gut microbiota of 94 termite species, through 16S rRNA metabarcoding. We analyzed the phylogeny of 211 bacterial lineages obtained from termite guts, including their closest relatives from other environments, which were identified using BLAST. The results provided strong evidence for rampant horizontal transfer of gut bacteria between termite host lineages. Although the majority of termite-derived phylotypes formed large monophyletic groups, indicating high levels of niche specialization, numerous other clades were interspersed with bacterial lineages from the guts of other animals. Our results indicate that &quot;mixed-mode&quot; transmission, which combines colony-to-offspring vertical transmission with horizontal colony-to-colony transfer, has been the primary driving force shaping the gut microbiota of termites.}, }
@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 {pmid31258230, year = {2018}, author = {Jaiswal, SK and Naamala, J and Dakora, FD}, title = {Nature and mechanisms of aluminium toxicity, tolerance and amelioration in symbiotic legumes and rhizobia.}, journal = {Biology and fertility of soils}, volume = {54}, number = {3}, pages = {309-318}, doi = {10.1007/s00374-018-1262-0}, pmid = {31258230}, issn = {0178-2762}, abstract = {Recent findings on the effect of aluminium (Al) on the functioning of legumes and their associated microsymbionts are reviewed here. Al represents 7% of solid matter in the Earth's crust and is an important abiotic factor that alters microbial and plant functioning at very early stages. The trivalent Al (Al3+) dominates at pH < 5 in soils and becomes a constraint to legume productivity through its lethal effect on rhizobia, the host plant and their interaction. Al3+ has lethal effects on many aspects of the rhizobia/legume symbiosis, which include a decrease in root elongation and root hair formation, lowered soil rhizobial population, and suppression of nitrogen metabolism involving nitrate reduction, nitrite reduction, nitrogenase activity and the functioning of uptake of hydrogenases (Hup), ultimately impairing the N2 fixation process. At the molecular level, Al is known to suppress the expression of nodulation genes in symbiotic rhizobia, as well as the induction of genes for the formation of hexokinase, phosphodiesterase, phosphooxidase and acid/alkaline phosphatase. Al toxicity can also induce the accumulation of reactive oxygen species and callose, in addition to lipoperoxidation in the legume root elongation zone. Al tolerance in plants can be achieved through over-expression of citrate synthase gene in roots and/or the synthesis and release of organic acids that reverse Al-induced changes in proteins, as well as metabolic regulation by plant-secreted microRNAs. In contrast, Al tolerance in symbiotic rhizobia is attained via the production of exopolysaccharides, the synthesis of siderophores that reduce Al uptake, induction of efflux pumps resistant to heavy metals and the expression of metal-inducible (dmeRF) gene clusters in symbiotic Rhizobiaceae. In soils, Al toxicity is usually ameliorated through liming, organic matter supply and use of Al-tolerant species. Our current understanding of crop productivity in high Al soils suggests that a much greater future accumulation of Al is likely to occur in agricultural soils globally if crop irrigation is increased under a changing climate.}, }
@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 {pmid31260142, year = {2019}, author = {Pellegrin, C and Daguerre, Y and Ruytinx, J and Guinet, F and Kemppainen, M and Dit Frey, NF 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}, 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 a 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, 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 {pmid30737514, year = {2019}, author = {Roth, R and Hillmer, S and Funaya, C and Chiapello, M and Schumacher, K and Lo Presti, L and Kahmann, R and Paszkowski, U}, title = {Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules.}, journal = {Nature plants}, volume = {5}, number = {2}, pages = {204-211}, doi = {10.1038/s41477-019-0365-4}, pmid = {30737514}, issn = {2055-0278}, mesh = {Cell Membrane/microbiology/*ultrastructure ; Electron Microscope Tomography ; Extracellular Vesicles/*metabolism ; Glomeromycota/physiology ; Hyphae/physiology ; Mycorrhizae/cytology/*physiology ; Oryza/cytology/genetics/*microbiology ; Plant Cells/*microbiology ; Plant Leaves/cytology/microbiology/ultrastructure ; Plant Roots/cytology/microbiology/ultrastructure ; Plants, Genetically Modified ; Symbiosis ; Ustilago/pathogenicity ; Zea mays/microbiology ; }, abstract = {During establishment of arbuscular mycorrhizal symbioses, fungal hyphae invade root cells producing transient tree-like structures, the arbuscules, where exchange of photosynthates for soil minerals occurs. Arbuscule formation and collapse lead to rapid production and degradation of plant and fungal membranes, their spatiotemporal dynamics directly influencing nutrient exchange. We determined the ultra-structural details of both membrane surfaces and the interstitial apoplastic matrix by transmission electron microscopy tomography during growth and senescence of Rhizophagus irregularis arbuscules in rice. Invasive growth of arbuscular hyphae was associated with abundant fungal membrane tubules (memtubs) and plant peri-arbuscular membrane evaginations. Similarly, the phylogenetically distant arbuscular mycorrhizal fungus, Gigaspora rosea, and the fungal maize pathogen, Ustilago maydis, developed memtubs while invading host cells, revealing structural commonalities independent of the mutualistic or parasitic outcome of the interaction. Additionally, extracellular vesicles formed continuously in the peri-arbuscular interface from arbuscule biogenesis to senescence, suggesting an involvement in inter-organismic signal and nutrient exchange throughout the arbuscule lifespan.}, }
@article {pmid30518838, year = {2018}, author = {}, title = {Occupying common ground.}, journal = {Nature plants}, volume = {4}, number = {12}, pages = {977}, doi = {10.1038/s41477-018-0336-1}, pmid = {30518838}, issn = {2055-0278}, mesh = {Animals ; Fungi/*classification/genetics/isolation &amp; purification ; Phylogeny ; Plants/classification/genetics/*microbiology ; Symbiosis ; }, }
@article {pmid30397259, year = {2018}, author = {Pecrix, Y and Staton, SE and Sallet, E and Lelandais-Brière, C and Moreau, S and Carrère, S and Blein, T and Jardinaud, MF and Latrasse, D and Zouine, M and Zahm, M and Kreplak, J and Mayjonade, B and Satgé, C and Perez, M and Cauet, S and Marande, W and Chantry-Darmon, C and Lopez-Roques, C and Bouchez, O and Bérard, A and Debellé, F and Muños, S and Bendahmane, A and Bergès, H and Niebel, A and Buitink, J and Frugier, F and Benhamed, M and Crespi, M and Gouzy, J and Gamas, P}, title = {Whole-genome landscape of Medicago truncatula symbiotic genes.}, journal = {Nature plants}, volume = {4}, number = {12}, pages = {1017-1025}, doi = {10.1038/s41477-018-0286-7}, pmid = {30397259}, issn = {2055-0278}, mesh = {DNA Methylation ; *Epigenesis, Genetic ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Genomics ; Medicago truncatula/*genetics ; Multigene Family ; Plant Proteins/genetics ; RNA, Plant/genetics ; RNA, Untranslated/*genetics ; Root Nodules, Plant/genetics ; Symbiosis/*genetics ; }, abstract = {Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.}, }
@article {pmid29044186, year = {2017}, author = {Shehata, HR and Dumigan, C and Watts, S and Raizada, MN}, title = {An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13479}, pmid = {29044186}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; DNA Barcoding, Taxonomic/methods ; *Endophytes ; Lolium/growth &amp; development/microbiology ; *Microbiota ; Phosphates/analysis/*chemistry ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; Zea mays/genetics/*microbiology ; }, abstract = {In the animal microbiome, localization of microbes to specific cell types is well established, but there are few such examples within the plant microbiome which includes endophytes. Endophytes are non-pathogenic microbes that inhabit plants. Root hairs are single cells, equivalent to the nutrient-absorbing intestinal microvilli of animals, used by plants to increase the root surface area for nutrient extraction from soil including phosphorus (P). There has been significant interest in the microbiome of intestinal microvilli but less is known about the root hair microbiome. Here we describe a bacterial endophyte (3F11) from Zea nicaraguensis, a wild corn discovered in a Nicaraguan swamp above rock-P lava flowing from the San Cristobal volcano. Rock-P is insoluble and a major challenge for plants. Following seed coating and germination on insoluble-P, the endophyte colonized epidermal surfaces, ultimately colonizing root hairs intracellularly. The endophyte promoted root hair growth and secreted acids to solubilize rock-P for uptake by a larger root hair surface. The most interesting observation was that a seed-coated endophyte targeted and colonized a critical cell type, root hair cells, consistent with earlier studies. The endophyte maintained its targeting ability in two evolutionary divergent hosts, suggesting that the host recognition machinery is conserved.}, }
@article {pmid29030597, year = {2017}, author = {Schöner, MG and Schöner, CR and Ermisch, R and Puechmaille, SJ and Grafe, TU and Tan, MC and Kerth, G}, title = {Stabilization of a bat-pitcher plant mutualism.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13170}, pmid = {29030597}, issn = {2045-2322}, mesh = {Animals ; Chiroptera/*physiology ; Magnoliopsida/*physiology ; Nitrogen/metabolism ; Symbiosis/*physiology ; }, abstract = {Despite the long persistence of many mutualisms, it is largely unknown which mechanisms stabilize these interactions. This is especially true if only one mutualism partner can choose alternative partners while the other cannot, resulting in a power asymmetry. According to biological market theory the choosing partner should prefer the more dependent partner if the latter offers commodities of higher quality than its competitors. We tested this prediction using Bornean carnivorous pitcher plants (Nepenthes hemsleyana) that strongly rely on faecal nitrogen of bats (Kerivoula hardwickii) which roost inside the pitchers. The bats also roost in furled leaves of various plants. Surprisingly, during field observations the bats did not always choose N. hemsleyana pitchers despite their superior quality but were generally faithful either to pitchers or to furled leaves. In behavioural experiments 21% of the leaf-roosting bats switched to pitchers, while the majority of these bats and all pitcher-roosting individuals were faithful to the roost type in which we had found them. Genetic differentiation cannot explain this faithfulness, which likely results from different roosting traditions. Such traditions could have stabilizing or destabilizing effects on various mutualisms and should be investigated in more detail.}, }
@article {pmid29026213, year = {2017}, author = {Nakayama, T and Inagaki, Y}, title = {Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13075}, pmid = {29026213}, issn = {2045-2322}, mesh = {Cyanobacteria/classification/*genetics/*physiology ; Diatoms/*microbiology ; Evolution, Molecular ; Genomics ; Phylogeny ; Symbiosis/genetics/*physiology ; }, abstract = {Organelle acquisitions via endosymbioses with prokaryotes were milestones in the evolution of eukaryotes. Still, quite a few uncertainties have remained for the evolution in the early stage of organellogenesis. In this respect, rhopalodiacean diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies, are emerging as new models for the study of organellogenesis. The genome for the spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its unique metabolic nature lacking the photosynthetic ability. Nevertheless, the genome sequence of a spheroid body from a single lineage may not be sufficient to depict the evolution of these cyanobacterium-derived intracellular structures as a whole. Here, we report on the complete genome for the spheroid body of Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has been fully determined. Overall, features in genome structure and metabolic capacity, including a lack of photosynthetic ability, were highly conserved between the two spheroid bodies. However, our comparative genomic analyses revealed that the genome of the R. gibberula spheroid body exhibits a lower non-synonymous substitution rate and a slower progression of pseudogenisation than those of E. turgida, suggesting that a certain degree of diversity exists amongst the genomes of obligate endosymbionts in unicellular eukaryotes.}, }
@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 dentofacial 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)/ ; BB/L010305/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/L010305/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, 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 = {}, number = {}, pages = {}, 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 {pmid31245437, year = {2015}, author = {Ono, C and Yoshida, M and Kawano, N and Miyado, K and Umezawa, A}, title = {Staphylococcus epidermidis is involved in a mechanism for female reproduction in mice.}, journal = {Regenerative therapy}, volume = {1}, number = {}, pages = {11-17}, doi = {10.1016/j.reth.2014.12.003}, pmid = {31245437}, issn = {2352-3204}, abstract = {Both external and internal surfaces of organs (e.g., skin, mouth, gut, and intestine) are covered with bacteria, which often contribute to physiological events in host animals. Despite externally opened organs, the presence of bacteria in the mammalian female reproductive tract is uncertain. Here we assessed this problem using wild-type strains of mice, C57BL/6N and ICR. We first demonstrated that bacterial colonies were formed from the oviductal fluid in the C57BL/6N mice with birth experience (&quot;parous&quot;), but not in the mice without birth experience (&quot;non-parous&quot;). Sequence analysis of 16S ribosomal RNA (rRNA) revealed that Staphylococcus epidermidis existed in the oviductal fluid of the parous mice, confirmed by immunohistochemical analysis. Furthermore, extinction of bacterial population with intraperitoneal injection of antibiotics, penicillin G and streptomycin, disturbed the regularly implanted pattern of embryos in ICR mice. Our results indicate that symbiotic S. epidermidis plays a role in interaction between embryo and uterus upon implantation in mice.}, }
@article {pmid30149795, year = {2018}, author = {Brown, AMV}, title = {Endosymbionts of Plant-Parasitic Nematodes.}, journal = {Annual review of phytopathology}, volume = {56}, number = {}, pages = {225-242}, doi = {10.1146/annurev-phyto-080417-045824}, pmid = {30149795}, issn = {1545-2107}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Host-Parasite Interactions ; Nematoda/*microbiology ; Plant Diseases/parasitology/*prevention &amp; control ; Plants/*parasitology ; *Symbiosis ; }, abstract = {Some of the most agriculturally important plant-parasitic nematodes (PPNs) harbor endosymbionts. Extensive work in other systems has shown that endosymbionts can have major effects on host virulence and biology. This review highlights the discovery, development, and diversity of PPN endosymbionts, incorporating inferences from genomic data. Cardinium, reported from five PPN hosts to date, is characterized by its presence in the esophageal glands and other tissues, with a discontinuous distribution across populations, and genomic data suggestive of horizontal gene exchange. Xiphinematobacter occurs in at least 27 species of dagger nematode in the ovaries and gut epithelial cells, where genomic data suggest it may serve in nutritional supplementation. Wolbachia, reported in just three PPNs, appears to have an ancient history in the Pratylenchidae and displays broad tissue distribution and genomic features intermediate between parasitic and reproductive groups. Finally, a model is described that integrates these insights to explain patterns of endosymbiont replacement.}, }
@article {pmid30149793, year = {2018}, author = {Pawlowska, TE and Gaspar, ML and Lastovetsky, OA and Mondo, SJ and Real-Ramirez, I and Shakya, E and Bonfante, P}, title = {Biology of Fungi and Their Bacterial Endosymbionts.}, journal = {Annual review of phytopathology}, volume = {56}, number = {}, pages = {289-309}, doi = {10.1146/annurev-phyto-080417-045914}, pmid = {30149793}, issn = {1545-2107}, mesh = {*Bacterial Physiological Phenomena/genetics ; Evolution, Molecular ; Fungi/genetics/*physiology ; *Symbiosis/genetics ; }, abstract = {Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associations formed by early divergent fungi in the phylum Mucoromycota with heritable EB from two classes, Betaproteobacteria and Mollicutes. These symbioses exemplify novel types of host-symbiont interactions. Studies of these partnerships fuel theoretical models describing mechanisms that stabilize heritable symbioses, control the rate of molecular evolution, and enable the establishment of mutualisms. Lastly, by altering host phenotypes and metabolism, these associations represent an important instrument for probing the basic biology of the Mucoromycota hosts, which remain one of the least explored filamentous fungi.}, }
@article {pmid29915958, year = {2018}, author = {Mi, S and Gu, C and Wu, P and Liu, H and Yan, X and Li, D and Tang, X and Duan, X and Wang, G and Zhang, J}, title = {Improvement of butanol production by the development and co-culture of C. acetobutylicum TSH1 and B. cereus TSH2.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {15}, pages = {6753-6763}, doi = {10.1007/s00253-018-9151-x}, pmid = {29915958}, issn = {1432-0614}, support = {2016YFE0131300//National Key R&amp;D Program of China/ ; 21176141//National Natural Science Foundation of China/ ; }, mesh = {Alcohol Oxidoreductases/metabolism ; Bacillus cereus/*metabolism ; Bacterial Proteins/metabolism ; Butanols/analysis/*metabolism ; Clostridium acetobutylicum/drug effects/*metabolism ; Coculture Techniques ; Fermentation ; Hydrogen-Ion Concentration ; *Metabolic Engineering ; Proteomics ; Symbiosis ; }, abstract = {Butanol fermentation comprises two successive and distinct stages, namely acidogenesis and solventogenesis. The current lack of clarity regarding the underlying metabolic regulation of fermentation impedes improvements in biobutanol production. Here, a proteomics study was performed in the acidogenesis phase, the lowest pH point (transition point), and the solventogenesis phase in the butanol-producing symbiotic system TSH06. Forty-two Clostridium acetobutylicum proteins demonstrated differential expression levels at different stages. The protein level of butanol dehydrogenase increased in the solventogenesis phase, which was in accordance with the trend of butanol concentration. Stress proteins were upregulated either at the transition point or in the solventogenesis phase. The cell division-related protein Maf was upregulated at the transition point. We disrupted the maf gene in C. acetobutylicum TSH1, and Bacillus cereus TSH2 was added to form a new symbiotic system. TSH06△maf produced 13.9 ± 1.0 g/L butanol, which was higher than that of TSH06 (12.3 ± 0.9 g/L). Butanol was furtherly improved in fermentation at variable temperature with neutral red addition for both TSH06 and TSH06△maf. The butanol titer of the maf deletion strain was higher than that of the wild type, although the exact mechanism remains to be determined.}, }
@article {pmid28835914, year = {2017}, author = {Ochsenkühn, MA and Röthig, T and D'Angelo, C and Wiedenmann, J and Voolstra, CR}, title = {The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1602047}, pmid = {28835914}, issn = {2375-2548}, support = {//European Research Council/International ; }, mesh = {Adaptation, Physiological/*drug effects ; Animals ; Anthozoa/*physiology ; Carbohydrates/analysis ; Chromatography, Gas ; Coral Reefs ; Dinoflagellida/*physiology ; Glycerol/*analogs &amp; derivatives/pharmacology ; Metabolomics/methods ; *Osmolar Concentration ; *Salinity ; *Symbiosis ; }, abstract = {The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.}, }
@article {pmid28808685, year = {2017}, author = {Guo, S and Stevens, CA and Vance, TDR and Olijve, LLC and Graham, LA and Campbell, RL and Yazdi, SR and Escobedo, C and Bar-Dolev, M and Yashunsky, V and Braslavsky, I and Langelaan, DN and Smith, SP and Allingham, JS and Voets, IK and Davies, PL}, title = {Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1701440}, pmid = {28808685}, issn = {2375-2548}, mesh = {Adhesins, Bacterial/*chemistry/*metabolism ; Amino Acid Sequence ; Antarctic Regions ; Bacteria/*metabolism ; Binding Sites ; Biofilms ; Diatoms/*microbiology ; Ice Cover/*microbiology ; Ligands ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship ; Symbiosis ; Type I Secretion Systems/genetics ; }, abstract = {Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-μm-long adhesin using a &quot;dissect and build&quot; structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like β-sandwich domains that rigidify on binding Ca2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several &quot;repeats-in-toxin&quot; motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.}, }
@article {pmid28779313, year = {2017}, author = {Szklarzewicz, T and Michalik, A}, title = {Transovarial Transmission of Symbionts in Insects.}, journal = {Results and problems in cell differentiation}, volume = {63}, number = {}, pages = {43-67}, doi = {10.1007/978-3-319-60855-6_3}, pmid = {28779313}, issn = {0080-1844}, mesh = {Animals ; Bacteria/*metabolism ; Fat Body/cytology/microbiology ; Female ; Hemolymph/cytology/microbiology ; Insecta/*anatomy &amp; histology/cytology/*microbiology ; Ovary/cytology/microbiology ; *Symbiosis ; }, abstract = {Many insects, on account of their unbalanced diet, live in obligate symbiotic associations with microorganisms (bacteria or yeast-like symbionts), which provide them with substances missing in the food they consume. In the body of host insect, symbiotic microorganisms may occur intracellularly (e.g., in specialized cells of mesodermal origin termed bacteriocytes, in fat body cells, in midgut epithelium) or extracellularly (e.g., in hemolymph, in midgut lumen). As a rule, symbionts are vertically transmitted to the next generation. In most insects, symbiotic microorganisms are transferred from mother to offspring transovarially within female germ cells. The results of numerous ultrastructural and molecular studies on symbiotic systems in different groups of insects have shown that they have a large diversity of symbiotic microorganisms and different strategies of their transmission from one generation to the next. This chapter reviews the modes of transovarial transmission of symbionts between generations in insects.}, }
@article {pmid28199635, year = {2017}, author = {Martin, WF and Roettger, M and Ku, C and Garg, SG and Nelson-Sathi, S and Landan, G}, title = {Late Mitochondrial Origin Is an Artifact.}, journal = {Genome biology and evolution}, volume = {9}, number = {2}, pages = {373-379}, pmid = {28199635}, issn = {1759-6653}, support = {281357//European Research Council/International ; }, mesh = {*Artifacts ; Genes, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; *Symbiosis ; }, abstract = {The origin of mitochondria was a crucial event in eukaryote evolution. A recent report claimed to provide evidence, based on branch length variation in phylogenetic trees, that the mitochondrion came late in eukaryotic evolution. Here, we reinvestigate their claim with a reanalysis of the published data. We show that the analyses underpinning a late mitochondrial origin suffer from multiple fatal flaws founded in inappropriate statistical methods and analyses, in addition to erroneous interpretations.}, }
@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 = {}, number = {}, pages = {}, 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, L. timberlakei, and L. 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 while 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 towards 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 shows 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 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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {fj201802681RR}, 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 microbial-derived metabolites produced and their concentrations throughout the day. These microbial-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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14724}, pmid = {31237728}, issn = {1462-2920}, 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 A. nasoniae that infects the parasitic wasp N. 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. This article is protected by copyright. All rights reserved.}, }
@article {pmid31236967, year = {2019}, author = {Chomicki, G and Renner, SS}, title = {Farming by ants remodels nutrient uptake in epiphytes.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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 {pmid30919070, year = {2019}, author = {Wang, XX and Hoffland, E and Mommer, L and Feng, G and Kuyper, TW}, title = {Maize varieties can strengthen positive plant-soil feedback through beneficial arbuscular mycorrhizal fungal mutualists.}, journal = {Mycorrhiza}, volume = {29}, number = {3}, pages = {251-261}, doi = {10.1007/s00572-019-00885-3}, pmid = {30919070}, issn = {1432-1890}, support = {U1703232//National Natural Science Foundation of China/ ; }, mesh = {Biomass ; Hyphae/*growth &amp; development/physiology ; Mycorrhizae/*physiology ; Phosphorus/analysis ; Plant Roots/microbiology ; Soil/chemistry ; Soil Microbiology ; *Symbiosis ; Zea mays/*microbiology/physiology ; }, abstract = {Plant-soil feedback (PSF) describes the process whereby plant species modify the soil environment, which subsequently impacts the growth of the same or another plant species. Our aim was to explore PSF by two maize varieties (a landrace and a hybrid variety) and three arbuscular mycorrhizal fungi (AMF) species (Funneliformis mosseae, Claroideoglomus etunicatum, Gigaspora margarita, and the mixture). We carried out a pot experiment with a conditioning and a feedback phase to determine PSF with different species of AMF and with a non-mycorrhizal control. Sterilized soil was conditioned separately by each variety, with or without AMF; in the feedback phase, each soil community was used to grow each in its &quot;home&quot; soil and in the &quot;away&quot; soil. Plant performance was assessed as shoot biomass, phosphorus (P) concentration and P content, and fungal performance was assessed as mycorrhizal colonization and hyphal length density. Both maize varieties were differentially influenced by AMF in the conditioning phase. In the feedback phase, PSF was generally negative for non-mycorrhizal plants or when plants were colonized by G. margarita, whereas PSF was positive in the other three AMF treatments. When plants were grown on home soil, hyphal length density was larger than on away soil. We conclude that different maize varieties can strengthen positive plant-soil feedback for themselves through beneficial mutualists for themselves, but not across the maize varieties.}, }
@article {pmid30470950, year = {2019}, author = {Zhong, C and Zhang, Y and Wei, Y and Meng, J and Chen, Y and Bush, D and Bogusz, D and Franche, C}, title = {The role of Frankia inoculation in casuarina plantations in China.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {1}, pages = {47-56}, doi = {10.1007/s10482-018-1205-7}, pmid = {30470950}, issn = {1572-9699}, support = {CAFYBB2018ZB003//A Specific Program for National Non-profit Scientific Institutions/ ; 2014KJCX017//Forestry Science and Technology Innovation Project of Guangdong/ ; 31470634//National Natural Science Foundation of China/ ; }, mesh = {Agricultural Inoculants/genetics/isolation &amp; purification/*physiology ; China ; Fagales/*growth &amp; development/*microbiology ; Frankia/genetics/isolation &amp; purification/*physiology ; Symbiosis ; Trees/growth &amp; development/microbiology ; }, abstract = {Casuarina trees are planted along the coast from Hainan province in South China to the Zhoushan Islands of Zhejiang province in Southeastern China. Three key species, Casuarina equisetifolia, Casuarina cunninghamiana and Casuarina glauca, are used as windbreaks, in agroforestry systems, and for the production of timber and fuel wood. Frankia have been studied in China since 1984. Today, Frankia research fields are very wide, and cover morphology, physiology and genetic diversity, and the application of inocula for specific purposes on poor quality sites. In this paper, we review the role of Frankia inoculations in nurseries and casuarina plantations in China and discuss the benefits of inoculation.}, }
@article {pmid30460470, year = {2019}, author = {Gtari, M and Benson, DR and Nouioui, I and Dawson, JO and Ghodhbane-Gtari, F}, title = {19th International Meeting on Frankia and Actinorhizal Plants.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {1}, pages = {1-4}, doi = {10.1007/s10482-018-1202-x}, pmid = {30460470}, issn = {1572-9699}, mesh = {Frankia/classification/genetics/*isolation &amp; purification/physiology ; Plant Physiological Phenomena ; Plant Roots/microbiology ; Plants/*microbiology ; Symbiosis ; }, abstract = {It has been 40 years since the first meeting dedicated to Frankia and actinorhizal plants, which was held at Petersham, Massachusetts (reported in Torrey and Tjepkema, 1979). Since then biennial meetings have been organised and held in different venues around the globe (Table 1). The most recent meeting, the &quot;19th International Meeting on Frankia and Actinorhizal Plants&quot;, organised in Hammamet, Tunisia from 17th to 19th of March, 2018, gathered scientists from Algeria, Argentina, Belgium, China, Egypt, France, India, Portugal, Senegal, Sweden, UK, USA and Tunisia. The event was a stimulating opportunity for active researchers to share many advances since the previous meeting held in Montpellier, France (Franche et al. 2016) and to discuss new perspectives in this research field.}, }
@article {pmid30218130, year = {2019}, author = {Bernasconi, R and Stat, M and Koenders, A and Huggett, MJ}, title = {Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {794-807}, doi = {10.1007/s00248-018-1255-4}, pmid = {30218130}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/classification/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.}, }
@article {pmid30187088, year = {2019}, author = {Vallesi, A and Sjödin, A and Petrelli, D and Luporini, P and Taddei, AR and Thelaus, J and Öhrman, C and Nilsson, E and Di Giuseppe, G and Gutiérrez, G and Villalobo, E}, title = {A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {587-596}, doi = {10.1007/s00248-018-1256-3}, pmid = {30187088}, issn = {1432-184X}, mesh = {Antarctic Regions ; DNA Transposable Elements ; Euplotes/*microbiology/physiology ; Francisella/classification/genetics/*isolation &amp; purification/physiology ; Genome, Bacterial ; Phylogeny ; Seawater/microbiology ; Symbiosis ; }, abstract = {The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.}, }
@article {pmid30151860, year = {2018}, author = {Arboleda, E and Hartenstein, V and Martinez, P and Reichert, H and Sen, S and Sprecher, S and Bailly, X}, title = {An Emerging System to Study Photosymbiosis, Brain Regeneration, Chronobiology, and Behavior: The Marine Acoel Symsagittifera roscoffensis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {10}, pages = {e1800107}, doi = {10.1002/bies.201800107}, pmid = {30151860}, issn = {1521-1878}, mesh = {Animals ; Aquatic Organisms ; Behavior, Animal ; Brain/cytology/*physiology ; Chronobiology Phenomena ; Circadian Rhythm/genetics ; Microalgae/physiology ; Microbiota/physiology ; Platyhelminths/*physiology ; Regeneration/*physiology ; Sulfonium Compounds/metabolism ; Symbiosis ; Totipotent Stem Cells/physiology ; }, abstract = {The acoel worm Symsagittifera roscoffensis, an early offshoot of the Bilateria and the only well-studied marine acoel that lives in a photosymbiotic relationship, exhibits a centralized nervous system, brain regeneration, and a wide repertoire of complex behaviors such as circatidal rhythmicity, photo/geotaxis, and social interactions. While this animal can be collected by the thousands and is studied historically, significant progress is made over the last decade to develop it as an emerging marine model. The authors here present the feasibility of culturing it in the laboratory and describe the progress made on different areas, including genomic and tissue architectures, highlighting the associated challenges. In light of these developments, and on the ability to access abundant synchronized embryos, the authors put forward S. roscoffensis as a marine system to revisit questions in the areas of photosymbiosis, regeneration, chronobiology, and the study of complex behaviors from a molecular and evolutionary perspective.}, }
@article {pmid30105505, year = {2019}, author = {Castelli, M and Serra, V and Senra, MVX and Basuri, CK and Soares, CAG and Fokin, SI and Modeo, L and Petroni, G}, title = {The Hidden World of Rickettsiales Symbionts: &quot;Candidatus Spectririckettsia obscura,&quot; a Novel Bacterium Found in Brazilian and Indian Paramecium caudatum.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {748-758}, doi = {10.1007/s00248-018-1243-8}, pmid = {30105505}, issn = {1432-184X}, support = {247658//FP7 People: Marie-Curie Actions/ ; PRA_2016_58//Università di Pisa/ ; }, mesh = {Brazil ; DNA, Bacterial/genetics ; India ; Paramecium caudatum/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsiales/genetics/isolation &amp; purification/*physiology ; *Symbiosis ; }, abstract = {Symbioses between bacteria and eukaryotes are widespread and may have significant impact on the evolutionary history of symbiotic partners. The order Rickettsiales is a lineage of intracellular Alphaproteobacteria characterized by an obligate association with a wide range of eukaryotic hosts, including several unicellular organisms, such as ciliates and amoebas. In this work, we characterized the Rickettsiales symbionts associated with two different genotypes of the freshwater ciliate Paramecium caudatum originated from freshwater environments in distant geographical areas. Phylogenetic analyses based on 16S rRNA gene showed that the two symbionts are closely related to each other (99.4% identity), belong to the family Rickettsiaceae, but are far-related with respect to previously characterized Rickettsiales. Consequently, they were assigned to a new species of a novel genus, namely &quot;Candidatus Spectririckettsia obscura.&quot; Screening on a database of short reads from 16S rRNA gene amplicon-based profiling studies confirmed that bacterial sequences related to the new symbiont are preferentially retrieved from freshwater environments, apparently with extremely scarce occurrence (< 0.1% positive samples). The present work provides new information on the still under-explored biodiversity of Rickettsiales, in particular those associated to ciliate host cells.}, }
@article {pmid30097664, year = {2018}, author = {Lastovetsky, OA and Ahn, E and Mondo, SJ and Toomer, KH and Zhang, A and Johnson, LM and Pawlowska, TE}, title = {Distribution and population structure of endobacteria in arbuscular mycorrhizal fungi at North Atlantic dunes.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {3001-3013}, pmid = {30097664}, issn = {1751-7370}, mesh = {Burkholderiaceae/genetics/*physiology ; Glomeromycota/genetics/*physiology ; Massachusetts ; Mycorrhizae/genetics/*physiology ; Phylogeny ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; *Symbiosis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF, Glomeromycotina), in addition to forming symbioses with the majority of land plants, harbor vertically transmitted endosymbiotic bacteria 'Candidatus Glomeribacter gigasporarum' (CaGg) and 'Candidatus Moeniiplasma glomeromycotorum' (CaMg). CaGg is a nonessential mutualist of AMF, whereas the lifestyle of CaMg is unknown. To start unraveling the interactions between AMF and their endosymbionts in nature, we examined diversity and distribution of AMF-associated endobacteria in North Atlantic dunes at Cape Cod. Of nearly 500 foredune AMF isolates successfully genotyped during a systematic study, 94% were classified as Gigasporaceae. Two percent of all AMF spores harbored CaGg, and 88% contained CaMg. CaGg was found only in the Gigasporaceae, whereas CaMg was present in Gigasporaceae, Acaulosporaceae, and Diversisporaceae. Incidence of CaGg across AMF was not affected by any of the environmental parameters measured, whereas distribution of CaMg in one of the fungal hosts was impacted by plant density. CaMg populations associated with AMF individuals displayed high levels of genetic diversity but no evidence of gene flow, suggesting that host physical proximity is not sufficient to facilitate horizontal transmission of CaMg. Finally, in addition to a novel lineage of CaGg, we discovered that AMF likely harbor Burkholderia-related bacteria with close phylogenetic affinity to free-living Burkholderia and endobacteria of other Mucoromycota fungi.}, }
@article {pmid30056329, year = {2018}, author = {Mooser, C and Gomez de Agüero, M and Ganal-Vonarburg, SC}, title = {Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective.}, journal = {Current opinion in microbiology}, volume = {44}, number = {}, pages = {50-60}, doi = {10.1016/j.mib.2018.07.007}, pmid = {30056329}, issn = {1879-0364}, mesh = {Animals ; Anti-Bacterial Agents ; Biomedical Research/*methods/*standards/trends ; Disease ; Germ-Free Life ; *Host Microbial Interactions ; Humans ; Models, Animal ; Symbiosis ; }, abstract = {Considering the increasing list of diseases linked to the commensal microbiota, experimental studies of host-microbe interactions are of growing interest. Axenic and differently colonized animal models are inalienable tools to study these interactions. Factors, such as host genetics, diet, antibiotics and litter affect microbiota composition and can be confounding factors in many experimental settings. The use of gnotobiotic mice harboring defined microbiotas of different complexity plus additional housing standardization have thus become a gold standard to study the influence of the microbiome on the host. We highlight here the recent advances, challenges and outstanding goals in gnotobiology with the ambition to contribute to the generation of reliable, reproducible and transferrable results, which form the basis for advances in biomedical research.}, }
@article {pmid30022156, year = {2018}, author = {Goyal, A and Dubinkina, V and Maslov, S}, title = {Multiple stable states in microbial communities explained by the stable marriage problem.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2823-2834}, pmid = {30022156}, issn = {1751-7370}, mesh = {Bacteroides/growth &amp; development/*physiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Polysaccharides/*metabolism ; Symbiosis ; }, abstract = {Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics, and diet shifts, result in transitions to other states. Can we reliably both predict such stable states as well as direct and control transitions between them? Here we present a new conceptual model-inspired by the stable marriage problem in game theory and economics-in which microbial communities naturally exhibit multiple stable states, each state with a different species' abundance profile. Our model's core ingredient is that microbes utilize nutrients one at a time while competing with each other. Using only two ranked tables, one with microbes' nutrient preferences and one with their competitive abilities, we can determine all possible stable states as well as predict inter-state transitions, triggered by the removal or addition of a specific nutrient or microbe. Further, using an example of seven Bacteroides species common to the human gut utilizing nine polysaccharides, we predict that mutual complementarity in nutrient preferences enables these species to coexist at high abundances.}, }
@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 = {}, number = {}, pages = {1-13}, 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 = {}, number = {}, pages = {}, 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 {pmid30911771, year = {2019}, author = {Li, Q and Ren, Y and Fu, X}, title = {Inter-kingdom signaling between gut microbiota and their host.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {76}, number = {12}, pages = {2383-2389}, doi = {10.1007/s00018-019-03076-7}, pmid = {30911771}, issn = {1420-9071}, mesh = {Animals ; Bacteria/*immunology ; Epinephrine/immunology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/microbiology ; Humans ; *Immunity ; Immunity, Cellular ; Inflammation/immunology/microbiology ; Neoplasms/immunology/microbiology ; Norepinephrine/immunology ; *Quorum Sensing ; *Symbiosis ; }, abstract = {The crosstalk between prokaryotic bacteria and eukaryotic gut epithelial cells has opened a new field for research. Quorum sensing system (QS) molecules employed by gut microbiota may play an essential role in host-microbial symbioses of the gut. Recent studies on the gut microbiome will unveil evolved mechanisms of the host to affect bacterial QS and shape bacterial composition. Bacterial autoinducers (AIs) could talk to the host's gut by eliciting proinflammatory effects and modulating the activities of T lymphocyte, macrophage, dendritic cells, and neutrophils. In addition, the gut mucosa could interfere with bacterial AIs by degrading them or secreting AI mimics. Moreover, bacterial AIs and gut hormones epinephrine and noradrenaline may be interchangeable in the crosstalk between the microbiota and human gut. Therefore, inter-kingdom signaling between gut microbiota and host may provide a novel target in the management of gut microbiota-related conditions or diseases in the future.}, }
@article {pmid30841562, year = {2019}, author = {Sottorff, I and Künzel, S and Wiese, J and Lipfert, M and Preußke, N and Sönnichsen, FD and Imhoff, JF}, title = {Antitumor Anthraquinones from an Easter Island Sea Anemone: Animal or Bacterial Origin?.}, journal = {Marine drugs}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/md17030154}, pmid = {30841562}, issn = {1660-3397}, mesh = {Actinobacteria/genetics/isolation &amp; purification/*metabolism ; Animals ; Anthraquinones/*isolation &amp; purification/metabolism ; Antibiotics, Antineoplastic/*isolation &amp; purification/metabolism ; Genome, Bacterial/genetics ; Polynesia ; Sea Anemones/metabolism/*microbiology ; Symbiosis ; }, abstract = {The presence of two known anthraquinones, Lupinacidin A and Galvaquinone B, which have antitumor activity, has been identified in the sea anemone (Gyractis sesere) from Easter Island. So far, these anthraquinones have been characterized from terrestrial and marine Actinobacteria only. In order to identify the anthraquinones producer, we isolated Actinobacteria associated with the sea anemone and obtained representatives of seven actinobacterial genera. Studies of cultures of these bacteria by HPLC, NMR, and HRLCMS analyses showed that the producer of Lupinacidin A and Galvaquinone B indeed was one of the isolated Actinobacteria. The producer strain, SN26_14.1, was identified as a representative of the genus Verrucosispora. Genome analysis supported the biosynthetic potential to the production of these compounds by this strain. This study adds Verrucosispora as a new genus to the anthraquinone producers, in addition to well-known species of Streptomyces and Micromonospora. By a cultivation-based approach, the responsibility of symbionts of a marine invertebrate for the production of complex natural products found within the animal's extracts could be demonstrated. This finding re-opens the debate about the producers of secondary metabolites in sea animals. Finally, it provides valuable information about the chemistry of bacteria harbored in the geographically-isolated and almost unstudied, Easter Island.}, }
@article {pmid30129024, year = {2018}, author = {Suetsugu, K and Ohta, T and Tayasu, I}, title = {Partial mycoheterotrophy in the leafless orchid Cymbidium macrorhizon.}, journal = {American journal of botany}, volume = {105}, number = {9}, pages = {1595-1600}, doi = {10.1002/ajb2.1142}, pmid = {30129024}, issn = {1537-2197}, support = {//Toyota Foundation/International ; 16H02524//JSPS KAKENHI/International ; 17H05016//JSPS KAKENHI/International ; }, mesh = {Chlorophyll/metabolism ; Mycorrhizae ; Orchidaceae/metabolism/*microbiology/physiology ; Symbiosis ; }, abstract = {PREMISE OF THE STUDY: The evolution of full mycoheterotrophy is one of the most interesting topics within plant evolution. The leafless orchid Cymbidium macrorhizon is often assumed to be fully mycoheterotrophic even though it has a green stem and fruit capsule. Here, we assessed the trophic status of this species by analyzing the chlorophyll content and the natural 13 C and 15 N abundance in the sprouting and the fruiting season.<br><br>METHODS: The chlorophyll content was measured in five sprouting and five fruiting individuals of C. macrorhizon that were co-occurring. In addition, their 13 C and 15 N isotopic signatures were compared with those of neighboring autotrophic and partially mycoheterotrophic reference plants.<br><br>KEY RESULTS: Fruiting individuals of C. macrorhizon were found to contain a remarkable amount of chlorophyll compared to their sprouting counterparts. In addition, the natural abundance of 13 C in the tissues of the fruiting plants was slightly depleted relative to the sprouting ones. Linear two-source mixing model analysis revealed that fruiting C. macrorhizon plants obtained approximately 73.7 ± 2.0% of their total carbon from their mycorrhizal fungi when the sprouting individuals were used as the 100% carbon gain standard.<br><br>CONCLUSIONS: Our results indicated that despite its leafless status, fruiting plants of C. macrorhizon were capable of fixing significant quantities of carbon. Considering the autotrophic carbon gain increases during the fruiting season, its photosynthetic ability may contribute to fruit and seed production. These results indicate that C. macrorhizon should, therefore, be considered a partially mycoheterotrophic species rather than fully mycoheterotrophic, at least during the fruiting stage.}, }
@article {pmid30051825, year = {2018}, author = {Chen, C and Linse, K and Uematsu, K and Sigwart, JD}, title = {Cryptic niche switching in a chemosymbiotic gastropod.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1882}, pages = {}, pmid = {30051825}, issn = {1471-2954}, mesh = {Animals ; Body Size ; Gastrointestinal Tract/anatomy &amp; histology ; Gastropoda/anatomy &amp; histology/*physiology ; Hydrothermal Vents ; Metamorphosis, Biological ; Symbiosis ; }, abstract = {Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. 'Metamorphosis' broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropod Gigantopelta chessoia experiences a further, cryptic metamorphosis at body sizes around 5-7 mm. The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term 'cryptometamorphosis' to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.}, }
@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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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 {pmid30642248, year = {2019}, author = {Sibbald, SJ and Hopkins, JF and Filloramo, GV and Archibald, JM}, title = {Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {38}, doi = {10.1186/s12864-018-5412-4}, pmid = {30642248}, issn = {1471-2164}, mesh = {Cercozoa/*genetics ; Cryptophyta/*genetics ; Evolution, Molecular ; *Gene Fusion ; Mutant Chimeric Proteins/*genetics ; Phylogeny ; Symbiosis ; Ubiquitins/*classification/*genetics ; }, abstract = {BACKGROUND: The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms.<br><br>RESULTS: Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life - almost exclusively in phototrophs.<br><br>CONCLUSION: Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis.}, }
@article {pmid28904377, year = {2017}, author = {Rey, F and Costa, ED and Campos, AM and Cartaxana, P and Maciel, E and Domingues, P and Domingues, MRM and Calado, R and Cruz, S}, title = {Kleptoplasty does not promote major shifts in the lipidome of macroalgal chloroplasts sequestered by the sacoglossan sea slug Elysia viridis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11502}, pmid = {28904377}, issn = {2045-2322}, mesh = {Animals ; Chloroplasts/*metabolism ; Chromatography, Liquid ; Gastropoda/*physiology ; Glycolipids/chemistry/metabolism ; *Lipid Metabolism ; Mass Spectrometry ; Molecular Structure ; Photosynthesis ; Seaweed/*metabolism ; *Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Sacoglossan sea slugs, also known as crawling leaves due to their photosynthetic activity, are highly selective feeders that incorporate chloroplasts from specific macroalgae. These &quot;stolen&quot; plastids - kleptoplasts - are kept functional inside animal cells and likely provide an alternative source of energy to their host. The mechanisms supporting the retention and functionality of kleptoplasts remain unknown. A lipidomic mass spectrometry-based analysis was performed to study kleptoplasty of the sacoglossan sea slug Elysia viridis fed with Codium tomentosum. Total lipid extract of both organisms was fractionated. The fraction rich in glycolipids, exclusive lipids from chloroplasts, and the fraction rich in betaine lipids, characteristic of algae, were analysed using hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-LC-MS). This approach allowed the identification of 81 molecular species, namely galactolipids (8 in both organisms), sulfolipids (17 in C. tomentosum and 13 in E. viridis) and betaine lipids (51 in C. tomentosum and 41 in E. viridis). These lipid classes presented similar lipidomic profiles in C. tomentosum and E. viridis, indicating that the necessary mechanisms to perform photosynthesis are preserved during the process of endosymbiosis. The present study shows that there are no major shifts in the lipidome of C. tomentosum chloroplasts sequestered by E. viridis.}, }
@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 = {//American Society of Primatologists/ ; //National Institutes of Health/ ; R24OD020347//Smithsonian Competitive Grant for Science/ ; //Directorate for Biological Sciences/ ; DDIG 0525025//NSF/ ; DDIG: 0746320//NSF/ ; RR000169/GF/NIH HHS/United States ; RR019970/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 = {}, number = {}, pages = {e1800105}, doi = {10.1002/pmic.201800105}, pmid = {31218790}, issn = {1615-9861}, abstract = {Beneficial plant-microbes can 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 which play a critical role in mediating symbiotic plant-microbe interactions and have help to assess the underlying molecular aspects of the symbiotic relationship, including the developmental stages of legume-Rhizobium symbiosis and other non-legume based relationships. Functional proteomics and the study of protein interactions will help provide a better understanding of the protein-protein interaction networks associated with plant-microbe symbiosis and the during the developmental stages of the symbiotic process. 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 to define the factors affecting the outcome of symbiosis. In this review, we provide an update on the current and potential applications of symbiosis based &quot;omic&quot; approaches to dissect different aspects of symbiotic plant interactions. We also discuss the application of proteomics, metaproteomics and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, 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 {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 {pmid30944036, year = {2019}, author = {Couradeau, E and Giraldo-Silva, A and De Martini, F and Garcia-Pichel, F}, title = {Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {55}, doi = {10.1186/s40168-019-0661-2}, pmid = {30944036}, issn = {2049-2618}, mesh = {Cyanobacteria/*classification/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Desert Climate ; *Nitrogen Fixation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocrust microbiome, and the main source of leaked organic carbon. We hypothesized that, by analogy to the rhizosphere of plant roots, M. vaginatus may shape the microbial populations of heterotrophs around it, forming a specialized cyanosphere.<br><br>RESULTS: By physically isolating bundles of M. vaginatus from biocrusts, we were able to study the composition of the microbial populations attached to it, in comparison to the bulk soil crust microbiome by means of high-throughput 16S rRNA sequencing. We did this in two M. vaginatus-dominated biocrust from distinct desert biomes. We found that a small, selected subset of OTUs was significantly enriched in close proximity to M. vaginatus. Furthermore, we also found that a majority of bacteria (corresponding to some two thirds of the reads) were significantly more abundant away from this cyanobacterium. Phylogenetic placements suggest that all typical members of the cyanosphere were copiotrophs and that many were diazotrophs (Additional file 1: Tables S2 and S3). Nitrogen fixation genes were in fact orders of magnitude more abundant in this cyanosphere than in the bulk biocrust soil as assessed by qPCR. By contrary, competition for light, CO2, and low organic carbon concentrations defined at least a part of the OTUs segregating from the cyanobacterium.<br><br>CONCLUSIONS: We showed that M. vaginatus acts as a significant spatial organizer of the biocrust microbiome. On the one hand, it possesses a compositionally differentiated cyanosphere that concentrates the nitrogen-fixing function. We propose that a mutualism based on C for N exchange between M. vaginatus and copiotrophic diazotrophs helps sustains this cyanosphere and that this consortium constitutes the true pioneer community enabling the colonization of nitrogen-poor soils. On the other hand, a large number of biocrust community members segregate away from the vicinity of M. vaginatus, potentially through competition for light or CO2, or because of a preference for oligotrophy.}, }
@article {pmid30935407, year = {2019}, author = {Berglund, F and Österlund, T and Boulund, F and Marathe, NP and Larsson, DGJ and Kristiansson, E}, title = {Identification and reconstruction of novel antibiotic resistance genes from metagenomes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {52}, doi = {10.1186/s40168-019-0670-1}, pmid = {30935407}, issn = {2049-2618}, mesh = {Computational Biology/*methods ; *Drug Resistance, Microbial ; Environmental Microbiology ; Metagenomics ; Software ; Symbiosis ; }, abstract = {BACKGROUND: Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data.<br><br>RESULTS: fARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads.<br><br>CONCLUSIONS: We conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.}, }
@article {pmid29207272, year = {2017}, author = {Dale, C}, title = {Evolution: Weevils Get Tough on Symbiotic Tyrosine.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1282-R1284}, doi = {10.1016/j.cub.2017.10.031}, pmid = {29207272}, issn = {1879-0445}, mesh = {Animals ; Coleoptera/*genetics ; Genome, Bacterial ; Hardness ; Symbiosis/genetics ; Tyrosine/genetics ; Weevils/*genetics ; }, abstract = {Weevils, which represent one of the most diverse groups of terrestrial insects in nature, obtain a tough exoskeleton through the activity of an ancient bacterial symbiont with a tiny genome that serves as a factory for the production of tyrosine.}, }
@article {pmid29207267, year = {2017}, author = {Petitjean, C and Williams, TA}, title = {Evolution: New Gene-Rich Mitochondria Found across the Eukaryotic Tree.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1270-R1271}, doi = {10.1016/j.cub.2017.10.028}, pmid = {29207267}, issn = {1879-0445}, mesh = {Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/genetics ; Symbiosis/genetics ; Trees/genetics ; }, abstract = {Mitochondria are the energy-generating organelles that power eukaryotic cells. Originally descended from endosymbiotic bacteria, their genomes have shrunk during evolution. New analyses suggest that large, gene-rich mitochondrial genomes are more common than previously thought, with interesting implications for eukaryotic genome evolution.}, }
@article {pmid28950079, year = {2017}, author = {Archibald, JM}, title = {Evolution: Protein Import in a Nascent Photosynthetic Organelle.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {R1004-R1006}, doi = {10.1016/j.cub.2017.08.013}, pmid = {28950079}, issn = {1879-0445}, mesh = {*Amoeba ; Biological Evolution ; *Cercozoa ; Photosynthesis ; Plastids ; Symbiosis ; }, abstract = {An amoeba named Paulinella harbours 'chromatophores', cyanobacterium-derived photosynthetic bodies that evolved independent of plastids. Proteomics has shown that hundreds of nucleus-encoded proteins are targeted to the chromatophore, revealing the host cell's contributions to its recently established organelle.}, }
@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, K 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 = {}, 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 post-translational 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 over-expression 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 = {}, number = {}, 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}, 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 = {}, number = {}, pages = {}, 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 'missing link' 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}, 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 {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 = {*Ecosystem ; *Symbiosis ; }, }
@article {pmid30675064, year = {2019}, author = {Tanoue, T and Morita, S and Plichta, DR and Skelly, AN and Suda, W and Sugiura, Y and Narushima, S and Vlamakis, H and Motoo, I and Sugita, K and Shiota, A and Takeshita, K and Yasuma-Mitobe, K and Riethmacher, D and Kaisho, T and Norman, JM and Mucida, D and Suematsu, M and Yaguchi, T and Bucci, V and Inoue, T and Kawakami, Y and Olle, B and Roberts, B and Hattori, M and Xavier, RJ and Atarashi, K and Honda, K}, title = {A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.}, journal = {Nature}, volume = {565}, number = {7741}, pages = {600-605}, doi = {10.1038/s41586-019-0878-z}, pmid = {30675064}, issn = {1476-4687}, support = {DK43351/NH/NIH HHS/United States ; AT009708/NH/NIH HHS/United States ; }, mesh = {Adenocarcinoma/*immunology/pathology/*therapy ; Animals ; Antigens, CD/metabolism ; Bacteria/*classification/immunology/isolation &amp; purification ; CD8-Positive T-Lymphocytes/cytology/*immunology ; Cell Line, Tumor ; Dendritic Cells/immunology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Healthy Volunteers ; Histocompatibility Antigens Class I/immunology ; Humans ; Integrin alpha Chains/metabolism ; Interferon-gamma/biosynthesis/immunology ; Listeria monocytogenes/immunology ; Listeriosis/immunology/microbiology/*prevention &amp; control ; Male ; Mice ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; Symbiosis/*immunology ; Xenograft Model Antitumor Assays ; }, abstract = {There is a growing appreciation for the importance of the gut microbiota as a therapeutic target in various diseases. However, there are only a handful of known commensal strains that can potentially be used to manipulate host physiological functions. Here we isolate a consortium of 11 bacterial strains from healthy human donor faeces that is capable of robustly inducing interferon-γ-producing CD8 T cells in the intestine. These 11 strains act together to mediate the induction without causing inflammation in a manner that is dependent on CD103+ dendritic cells and major histocompatibility (MHC) class Ia molecules. Colonization of mice with the 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models. The 11 strains primarily represent rare, low-abundance components of the human microbiome, and thus have great potential as broadly effective biotherapeutics.}, }
@article {pmid29924441, year = {2018}, author = {Barfield, SJ and Aglyamova, GV and Bay, LK and Matz, MV}, title = {Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes.}, journal = {Molecular ecology}, volume = {27}, number = {15}, pages = {3103-3115}, doi = {10.1111/mec.14774}, pmid = {29924441}, issn = {1365-294X}, mesh = {Acclimatization ; Animals ; Anthozoa/*genetics ; Climate Change ; Coral Reefs ; Symbiosis/genetics/physiology ; }, abstract = {Reef-building corals can increase their resistance to heat-induced bleaching through adaptation and acclimatization and/or by associating with a more thermo-tolerant strain of algal symbiont (Symbiodinium sp.). Here, we show that these two adaptive pathways interact. We collected Acropora millepora corals from two contrasting thermal environments on the Great Barrier Reef: cooler, mid-latitude Orpheus Island, where all corals hosted a heat-sensitive clade C Symbiodinium, and warmer, low-latitude Wilkie Island, where corals hosted either a clade C or a more thermo-tolerant clade D. Corals were kept in a benign common garden to reveal differences in baseline gene expression, reflecting prior adaptation/long-term acclimatization. Model-based analysis identified gene expression differences between Wilkie and Orpheus corals that were negatively correlated with previously described transcriptome-wide signatures of heat stress, signifying generally elevated thermotolerance of Wilkie corals. Yet, model-free analyses of gene expression revealed that Wilkie corals hosting clade C were distinct from Wilkie corals hosting clade D, whereas Orpheus corals were more variable. Wilkie corals hosting clade C symbionts exhibited unique functional signatures, including downregulation of histone proteins and ion channels and upregulation of chaperones and RNA processing genes, putatively representing constitutive &quot;frontloading&quot; of stress response genes. Furthermore, clade C Symbiodinium exhibited constitutive expression differences between Wilkie and Orpheus, indicative of contrasting life history strategies. Our results demonstrate that hosting alternative Symbiodinium types is associated with different pathways of local adaptation for the coral host. These interactions could play a significant role in setting the direction of genetic adaptation to global warming in the two symbiotic partners.}, }
@article {pmid28171752, year = {2017}, author = {de Vries, J and Archibald, JM}, title = {Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?.}, journal = {Current biology : CB}, volume = {27}, number = {3}, pages = {R103-R105}, doi = {10.1016/j.cub.2016.12.006}, pmid = {28171752}, issn = {1879-0445}, mesh = {Biological Evolution ; *Cyanobacteria ; Fresh Water ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {Photosynthetic eukaryotes are the product of an endosymbiotic event between a eukaryotic host and a cyanobacterium that became today's plastid. A new phylogenomic study suggests that the closest relative of plastids among extant cyanobacteria is the recently discovered freshwater-dwelling Gloeomargarita lithophora.}, }
@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 {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 {pmid30830203, year = {2019}, author = {Marcionetti, A and Rossier, V and Roux, N and Salis, P and Laudet, V and Salamin, N}, title = {Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {869-882}, doi = {10.1093/gbe/evz042}, pmid = {30830203}, issn = {1759-6653}, mesh = {Animals ; *Biological Evolution ; Genome Components ; Perciformes/*genetics ; *Sea Anemones ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.}, }
@article {pmid30715356, year = {2019}, author = {Pizarro, D and Dal Grande, F and Leavitt, SD and Dyer, PS and Schmitt, I and Crespo, A and Thorsten Lumbsch, H and Divakar, PK}, title = {Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {721-730}, doi = {10.1093/gbe/evz027}, pmid = {30715356}, issn = {1759-6653}, mesh = {Genes, Mating Type, Fungal/*genetics ; *Genome, Fungal ; Lichens/*genetics ; *Reproduction, Asexual ; Symbiosis ; }, abstract = {Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi-homothallism versus heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group.}, }
@article {pmid30715330, year = {2019}, author = {Irwin, NAT and Keeling, PJ}, title = {Extensive Reduction of the Nuclear Pore Complex in Nucleomorphs.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {678-687}, doi = {10.1093/gbe/evz029}, pmid = {30715330}, issn = {1759-6653}, mesh = {Cercozoa/*genetics ; Cryptophyta/*genetics ; *Nuclear Pore ; Nuclear Pore Complex Proteins/*genetics ; *Symbiosis ; }, abstract = {The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved among eukaryotes. Potential exceptions to this are nucleomorphs: Highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here, we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologs. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.}, }
@article {pmid30311871, year = {2018}, author = {Taylor, MJ and Bordenstein, SR and Slatko, B}, title = {Microbe Profile: Wolbachia: a sex selector, a viral protector and a target to treat filarial nematodes.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {11}, pages = {1345-1347}, doi = {10.1099/mic.0.000724}, pmid = {30311871}, issn = {1465-2080}, support = {R01 AI132581/AI/NIAID NIH HHS/United States ; R21 AI133522/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropods/*microbiology ; Filarioidea/*microbiology ; Genome, Bacterial/genetics ; Host Specificity/*physiology ; Humans ; Symbiosis/physiology ; Wolbachia/*genetics/*physiology ; }, abstract = {Wolbachia is the most widespread genus of endosymbiotic bacteria in the animal world, infecting a diverse range of arthropods and nematodes. A broad spectrum of associations from parasitism to mutualism occur, with a tendency to drive reproductive manipulation or influence host fecundity to spread infection through host populations. These varied effects of Wolbachia are exploited for public health benefits. Notably, the protection of insect hosts from viruses is being tested as a potential control strategy for human arboviruses, and the mutualistic relationship with filarial nematodes makes Wolbachia a target for antibiotic therapy of human and veterinary nematode diseases.}, }
@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 = {}, number = {}, pages = {MPMI01190003R}, doi = {10.1094/MPMI-01-19-0003-R}, pmid = {31204904}, issn = {0894-0282}, 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 = {}, number = {}, pages = {}, 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 the 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>METHOD: We carried out a structured peer-reviewed research literature survey and analysis using bibliographic databases.<br><br>RESULTS: Seventy-nine 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 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 complementary 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 is well understood.}, }
@article {pmid30516980, year = {2018}, author = {Bell, TJ and Draper, SL and Centanni, M and Carnachan, SM and Tannock, GW and Sims, IM}, title = {Characterization of Polysaccharides from Feijoa Fruits (Acca sellowiana Berg.) and Their Utilization as Growth Substrates by Gut Commensal Bacteroides Species.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {50}, pages = {13277-13284}, doi = {10.1021/acs.jafc.8b05080}, pmid = {30516980}, issn = {1520-5118}, mesh = {Bacteroides/*growth &amp; development/metabolism ; Feijoa/*chemistry/metabolism ; Fruit/chemistry/metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Plant Extracts/*chemistry/metabolism ; Symbiosis ; }, abstract = {Polysaccharides from feijoa fruit were extracted and analyzed; the composition of these polysaccharides conforms to those typically found in the primary cell walls of eudicotyledons. The two major polysaccharide extracts consisted of mainly pectic polysaccharides and hemicellulosic polysaccharides [xyloglucan (77%) and arabinoxylan (16%)]. A collection of commensal Bacteroides species was screened for growth in culture using these polysaccharide preparations and placed into five categories based on their preference for each substrate. Most of the species tested could utilize the pectic polysaccharides, but growth on the hemicellulose was more limited. Constituent sugar and glycosyl linkage analysis showed that species that grew on the hemicellulose fraction showed differences in their preference for the two polysaccharides in this preparation. Our data demonstrate that the members of the genus Bacteroides show differential hydrolysis of pectic polysaccharides, xyloglucan, and arabinoxylan, which might influence the structure and metabolic activities of the microbiota in the human gut.}, }
@article {pmid30358445, year = {2018}, author = {Sigwart, JD and Chen, C}, title = {Comparative Oxygen Consumption of Gastropod Holobionts from Deep-Sea Hydrothermal Vents in the Indian Ocean.}, journal = {The Biological bulletin}, volume = {235}, number = {2}, pages = {102-112}, doi = {10.1086/699326}, pmid = {30358445}, issn = {1939-8697}, mesh = {Animals ; Gastropoda/*metabolism ; *Hydrothermal Vents ; Indian Ocean ; Oxygen Consumption/*physiology ; Symbiosis/*physiology ; Temperature ; }, abstract = {Physiological traits are the foundation of an organism's success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23-25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the &quot;trophosome&quot; does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.}, }
@article {pmid30053110, year = {2018}, author = {Burke, GR and Simmonds, TJ and Sharanowski, BJ and Geib, SM}, title = {Rapid Viral Symbiogenesis via Changes in Parasitoid Wasp Genome Architecture.}, journal = {Molecular biology and evolution}, volume = {35}, number = {10}, pages = {2463-2474}, doi = {10.1093/molbev/msy148}, pmid = {30053110}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Animals ; Baculoviridae/*genetics ; *Biological Evolution ; Gene Expression Regulation, Viral ; *Genome, Insect ; Host-Parasite Interactions/*genetics ; Symbiosis ; Wasps/genetics/*virology ; }, abstract = {Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of the genus Fopius, this recent acquisition allows an unprecedented opportunity to examine early endogenization events. Massive amounts of virus-like particles (VLPs) are produced in wasp ovaries. Unlike most endogenous viruses of parasitoid wasps, the VLPs do not contain DNA, translating to major differences in parasitism-promoting strategies. Rapid changes include genomic rearrangement, loss of DNA processing proteins, and wasp control of viral gene expression. These events precede the full development of tissue-specific viral gene expression observed in older associations. These data indicate that viral endogenization can rapidly result in functional and evolutionary changes associated with genomic novelty and adaptation in parasitoids.}, }
@article {pmid29900626, year = {2018}, author = {van Oppen, MJH and Bongaerts, P and Frade, P and Peplow, LM and Boyd, SE and Nim, HT and Bay, LK}, title = {Adaptation to reef habitats through selection on the coral animal and its associated microbiome.}, journal = {Molecular ecology}, volume = {27}, number = {14}, pages = {2956-2971}, doi = {10.1111/mec.14763}, pmid = {29900626}, issn = {1365-294X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; Anthozoa/*genetics/growth &amp; development/microbiology ; *Coral Reefs ; Dinoflagellida/*genetics/growth &amp; development ; Ecosystem ; Gene Flow ; Genetics, Population ; Genome/genetics ; Microbiota/genetics ; Photosynthesis/genetics ; Symbiosis/*genetics ; }, abstract = {Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically, and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.}, }
@article {pmid29746094, year = {2018}, author = {Zúñiga, A and Fuente, F and Federici, F and Lionne, C and Bônnet, J and de Lorenzo, V and González, B}, title = {An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth.}, journal = {ACS synthetic biology}, volume = {7}, number = {6}, pages = {1519-1527}, doi = {10.1021/acssynbio.8b00002}, pmid = {29746094}, issn = {2161-5063}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Arabidopsis/*growth &amp; development/*microbiology ; Cupriavidus/genetics/*metabolism ; Feedback, Physiological ; Gene Expression Regulation, Bacterial ; Indoleacetic Acids/*metabolism ; Metabolic Engineering/*methods ; Microorganisms, Genetically-Modified ; Plant Roots/microbiology ; Plasmids/genetics ; Quorum Sensing ; Symbiosis ; }, abstract = {The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.}, }
@article {pmid29588346, year = {2018}, author = {Chen, Y and Chaudhary, N and Yang, N and Granato, A and Turner, JA and Howard, SL and Devereaux, C and Zuo, T and Shrestha, A and Goel, RR and Neuberg, D and Wesemann, DR}, title = {Microbial symbionts regulate the primary Ig repertoire.}, journal = {The Journal of experimental medicine}, volume = {215}, number = {5}, pages = {1397-1415}, pmid = {29588346}, issn = {1540-9538}, support = {P40 OD010995/OD/NIH HHS/United States ; R01 AI113217/AI/NIAID NIH HHS/United States ; R01 AI121394/AI/NIAID NIH HHS/United States ; T32 AI007306/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; B-Lymphocytes/immunology ; Bacteria/*metabolism ; Clone Cells ; Germ-Free Life ; Immunity, Mucosal ; Immunoglobulin Heavy Chains/metabolism ; Immunoglobulin Variable Region/metabolism ; Immunoglobulins/*metabolism ; Intestine, Small/microbiology ; Mice, Inbred C57BL ; Receptors, Antigen, B-Cell/metabolism ; Spleen/cytology ; *Symbiosis ; T-Lymphocytes/cytology ; }, abstract = {The ability of immunoglobulin (Ig) to recognize pathogens is critical for optimal immune fitness. Early events that shape preimmune Ig repertoires, expressed on IgM+ IgD+ B cells as B cell receptors (BCRs), are poorly defined. Here, we studied germ-free mice and conventionalized littermates to explore the hypothesis that symbiotic microbes help shape the preimmune Ig repertoire. Ig-binding assays showed that exposure to conventional microbial symbionts enriched frequencies of antibacterial IgM+ IgD+ B cells in intestine and spleen. This enrichment affected follicular B cells, involving a diverse set of Ig-variable region gene segments, and was T cell-independent. Functionally, enrichment of microbe reactivity primed basal levels of small intestinal T cell-independent, symbiont-reactive IgA and enhanced systemic IgG responses to bacterial immunization. These results demonstrate that microbial symbionts influence host immunity by enriching frequencies of antibacterial specificities within preimmune B cell repertoires and that this may have consequences for mucosal and systemic immunity.}, }
@article {pmid29431439, year = {2018}, author = {Miller, JH and Field, JJ and Kanakkanthara, A and Owen, JG and Singh, AJ and Northcote, PT}, title = {Marine Invertebrate Natural Products that Target Microtubules.}, journal = {Journal of natural products}, volume = {81}, number = {3}, pages = {691-702}, doi = {10.1021/acs.jnatprod.7b00964}, pmid = {29431439}, issn = {1520-6025}, mesh = {Animals ; Aquatic Organisms/*chemistry ; Bacteria/drug effects ; Biological Products/*chemistry ; Humans ; Invertebrates/*chemistry ; Microtubules/*metabolism ; Symbiosis/drug effects ; }, abstract = {Marine natural products as secondary metabolites are a potential major source of new drugs for treating disease. In some cases, cytotoxic marine metabolites target the microtubules of the eukaryote cytoskeleton for reasons that will be discussed. This review covers the microtubule-targeting agents reported from sponges, corals, tunicates, and molluscs and the evidence that many of these secondary metabolites are produced by bacterial symbionts. The review finishes by discussing the directions for future development and production of clinically relevant amounts of these natural products and their analogues through aquaculture, chemical synthesis, and biosynthesis by bacterial symbionts.}, }
@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 {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 = {}, 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 = {}, number = {}, pages = {}, 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 {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 {pmid30806054, year = {2019}, author = {Du, J and Jiang, S and Wei, J and Shen, Y and Ni, J}, title = {[Co-expression of lignocellulase from termite and their endosymbionts].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {35}, number = {2}, pages = {244-253}, doi = {10.13345/j.cjb.180235}, pmid = {30806054}, issn = {1000-3061}, mesh = {Animals ; Cellulase ; Cellulose ; Hydrolysis ; *Isoptera ; Lignin ; Symbiosis ; beta-Glucosidase ; }, abstract = {Natural lignocellulosic materials contain cellulose, hemicellulose, and lignin. Cellulose hydrolysis to glucose requires a series of lignocellulases. Recently, the research on the synergistic effect of lignocellulases has become a new research focus. Here, four lignocellulase genes encoding β-glucosidase, endo-1,4-β-glucanase, xylanase and laccase from termite and their endosymbionts were cloned into pETDuet-1 and pRSFDuet-1 and expressed in Escherichia coli. After SDS-PAGE analysis, the corresponding protein bands consistent with the theoretical values were observed and all the proteins showed enzyme activities. We used phosphoric acid swollen cellulose (PASC) as substrate to measure the synergistic effect of crude extracts of co-expressing enzymes and the mixture of single enzyme. The co-expressed enzymes increased the degradation efficiency of PASC by 44% compared with the single enzyme mixture; while the degradation rate increased by 34% and 20%, respectively when using filter paper and corn cob pretreated with phosphoric acid as substrates. The degradation efficiency of the co-expressed enzymes was higher than the total efficiency of the single enzyme mixture.}, }
@article {pmid30708172, year = {2019}, author = {Shaikevich, E and Bogacheva, A and Rakova, V and Ganushkina, L and Ilinsky, Y}, title = {Wolbachia symbionts in mosquitoes: Intra- and intersupergroup recombinations, horizontal transmission and evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {24-34}, doi = {10.1016/j.ympev.2019.01.020}, pmid = {30708172}, issn = {1095-9513}, mesh = {Aedes/microbiology ; Alleles ; Animals ; Anopheles/genetics ; *Biological Evolution ; Culicidae/*microbiology ; Databases, Genetic ; *Gene Transfer, Horizontal ; Haplotypes/genetics ; Humans ; Mosquito Vectors/microbiology ; Multilocus Sequence Typing ; Phylogeny ; *Recombination, Genetic ; Species Specificity ; *Symbiosis ; Wolbachia/*genetics ; }, abstract = {Many mosquitoes harbour Wolbachia symbionts that could affect the biology of their host in different ways. Evolutionary relationships of mosquitoes' Wolbachia infection, geographical distribution and symbiont prevalence in many mosquito species are not yet clear. Here, we present the results of Wolbachia screening of 17 mosquito species of four genera-Aedes, Anopheles, Coquillettidia and Culex collected from five regions of Eastern Europe and the Caucasus in 2012-2016. Based on multilocus sequence typing (MLST) data previously published and generated in this study, we try to reveal genetic links between mosquitoes' and other hosts' Wolbachia. The Wolbachia symbionts are found in Culex pipiens, Aedes albopictus and Coquillettidia richiardii and for the first time in Aedes cinereus and Aedes cantans, which are important vectors of human pathogens. Phylogenetic analysis demonstrated multiple origins of infection in mosquitoes although the one-allele-criterion approach revealed links among B-supergroup mosquito Wolbachia with allele content of lepidopteran hosts. The MLST gene content of strain wAlbA from the A-supergroup is linked with different ant species. Several cases of intersupergroup recombinations were found. One of them occurred in the wAlbaB strain of Aedes albopictus, which contains the coxA allele of the A-supergroup, whereas other loci, including wsp, belong to supergroup B. Other cases are revealed for non-mosquito symbionts and they exemplified genetic exchanges of A, B and F supergroups. We conclude that modern Wolbachia diversity in mosquitoes and in many other insect taxa is a recent product of strain recombination and symbiont transfers.}, }
@article {pmid30665024, year = {2019}, author = {Kitamoto, M and Tokuda, G and Watanabe, H and Arioka, M}, title = {Characterization of CBM36-containing GH11 endoxylanase NtSymX11 from the hindgut metagenome of higher termite Nasutitermes takasagoensis displaying prominent catalytic activity.}, journal = {Carbohydrate research}, volume = {474}, number = {}, pages = {1-7}, doi = {10.1016/j.carres.2019.01.003}, pmid = {30665024}, issn = {1873-426X}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*chemistry/enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Calcium/chemistry ; Cloning, Molecular ; Endo-1,4-beta Xylanases/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Glucuronates/chemistry/*metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Isoptera/*microbiology ; Kinetics ; Metagenome ; Oligosaccharides/chemistry/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Symbiosis/physiology ; Temperature ; Xylans/chemistry/*metabolism ; }, abstract = {Symbionts in the gut of termites are expected to be large sources of enzymes involved in lignocellulose degradation, but their biotechnological potential has not been fully explored. In this study, we expressed, purified, and biochemically characterized a glycoside hydrolase family 11 xylanase, NtSymX11, from a symbiotic bacterium of the higher termite, Nasutitermes takasagoensis. NtSymX11 is a multimodular enzyme consisting of a catalytic domain and two tandem carbohydrate-binding modules (CBM36). The pH and temperature optima of NtSymX11 were pH 6.0 and 40 °C, respectively. By comparing the properties of full-length and truncated variants of NtSymX11, it was shown that CBM36 decreases the enzyme stability at acidic pH and high temperature. The main products from xylohexaose and various xylan substrates were X1-X3 xylooligosaccharides. Analysis of kinetic parameters indicated that NtSymX11 displays an outstanding catalytic performance when compared to other reported xylanases, and CBM36 enhances the activity by increasing the affinity to the substrate. Addition of Ca2+ boosted the activity of full-length enzyme, but not the truncated variant lacking the CBM, against the insoluble substrate, suggesting that CBM36 plays a role in the Ca2+-dependent increase of catalytic efficiency.}, }
@article {pmid30344303, year = {2018}, author = {Jankauskaitė, L and Misevičienė, V and Vaidelienė, L and Kėvalas, R}, title = {Lower Airway Virology in Health and Disease-From Invaders to Symbionts.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {54}, number = {5}, pages = {}, pmid = {30344303}, issn = {1648-9144}, mesh = {Adaptive Immunity ; Asthma/immunology/virology ; Bacteria/virology ; Bacteriophages/genetics ; Chronic Disease ; Humans ; Immunity, Innate ; Lung/*virology ; Lung Diseases/*virology ; *Microbiota ; Symbiosis ; Virus Diseases/immunology/*virology ; Viruses/*pathogenicity ; }, abstract = {Studies of human airway virome are relatively recent and still very limited. Culture-independent microbial techniques showed growing evidence of numerous viral communities in the respiratory microbial ecosystem. The significance of different acute respiratory viruses is already known in the pathogenesis of chronic conditions, such as asthma, cystic fibrosis (CF), or chronic obstructive lung disease (COPD), and their exacerbations. Viral pathogens, such as influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, or rhinovirus, have been associated with impaired immune response, acute exacerbations, and decrease in lung function in chronic lung diseases. However, more data have attributed a role to Herpes family viruses or the newly identified Anelloviridae family of viruses in chronic diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), or CF. Impaired antiviral immunity, bacterial colonization, or used medication, such as glucocorticoids or antibiotics, contribute to the imbalance of airway microbiome and may shape the local viral ecosystem. A specific part of virome, bacteriophages, frames lung microbial communities through direct contact with its host, the specific bacteria known as Pseudomonas aeruginosa or their biofilm formation. Moreover, antibiotic resistance is induced through phages via horizontal transfer and leads to more severe exacerbations of chronic airway conditions. Morbidity and mortality of asthma, COPD, CF, and IPF remains high, despite an increased understanding and knowledge about the impact of respiratory virome in the pathogenesis of these conditions. Thus, more studies focus on new prophylactic methods or therapeutic agents directed toward viral⁻host interaction, microbial metabolic function, or lung microbial composition rearrangement.}, }
@article {pmid30343053, year = {2018}, author = {Li, J and Han, M and Yu, J}, title = {Simple paratransgenic mosquitoes models and their dynamics.}, journal = {Mathematical biosciences}, volume = {306}, number = {}, pages = {20-31}, doi = {10.1016/j.mbs.2018.10.005}, pmid = {30343053}, issn = {1879-3134}, mesh = {Animals ; Animals, Genetically Modified ; Bacteria/*genetics/pathogenicity ; Disease Transmission, Infectious ; Female ; Host Microbial Interactions ; Host-Parasite Interactions ; Humans ; Malaria/prevention &amp; control/transmission ; Male ; Mathematical Concepts ; *Models, Biological ; Mosquito Vectors/growth &amp; development/*microbiology/*parasitology ; Plasmodium/microbiology/pathogenicity ; Symbiosis ; }, abstract = {To study the interactive dynamics of wild mosquitoes and mosquitoes carrying genetically-modified bacteria, we formulate continuous-time homogeneous and stage-structured models in this study. With appropriate transformations, complete results of the existence and stability of all boundary and positive equilibria for the homogeneous model are established and complete results of the existence and local stability of all boundary and positive equilibria for the stage-structured model are obtained as well. The outcomes from the homogeneous and the stage-structured models are similar. Based on the homogeneous model, we particularly investigate how the horizontal transmission of the transgenic bacteria, via the uptake rate of the transgenic bacteria, affects the interactive dynamics.}, }
@article {pmid30045944, year = {2018}, author = {Macpherson, AJ and Ganal-Vonarburg, SC}, title = {IgA-about the unexpected.}, journal = {The Journal of experimental medicine}, volume = {215}, number = {8}, pages = {1965-1966}, pmid = {30045944}, issn = {1540-9538}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Immunoglobulin A ; Symbiosis ; }, abstract = {In this issue of JEM, Nakajima et al. (https://doi.org/10.1084/jem.20180427) demonstrate that glycan-dependent, epitope-independent IgA coating of intestinal bacteria alters bacterial gene expression and metabolism. This conferred coated bacteria with fitness within the mucus niche and contributed to intestinal homeostasis through cross-phylum interactions.}, }
@article {pmid30013237, year = {2018}, author = {Boldock, E and Surewaard, BGJ and Shamarina, D and Na, M and Fei, Y and Ali, A and Williams, A and Pollitt, EJG and Szkuta, P and Morris, P and Prajsnar, TK and McCoy, KD and Jin, T and Dockrell, DH and van Strijp, JAG and Kubes, P and Renshaw, SA and Foster, SJ}, title = {Human skin commensals augment Staphylococcus aureus pathogenesis.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {881-890}, pmid = {30013237}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; MR/K015753/1//Medical Research Council/United Kingdom ; MR/M004864/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; Disease Models, Animal ; Humans ; Inflammasomes/metabolism ; Kupffer Cells/cytology/immunology ; Macrophages/metabolism ; Mice ; Microbiota ; Peptidoglycan/metabolism/*pharmacology ; Reactive Oxygen Species/metabolism ; Sepsis/immunology/*microbiology ; Skin/*microbiology ; Staphylococcal Infections/immunology/*microbiology ; Staphylococcus aureus/growth &amp; development/*pathogenicity ; Symbiosis ; Virulence ; }, abstract = {All bacterial infections occur within a polymicrobial environment, from which a pathogen population emerges to establish disease within a host. Emphasis has been placed on prevention of pathogen dominance by competing microflora acting as probiotics1. Here we show that the virulence of the human pathogen Staphylococcus aureus is augmented by native, polymicrobial, commensal skin flora and individual species acting as 'proinfectious agents'. The outcome is pathogen proliferation, but not commensal. Pathogenesis augmentation can be mediated by particulate cell wall peptidoglycan, reducing the S. aureus infectious dose by over 1,000-fold. This phenomenon occurs using a range of S. aureus strains and infection models and is not mediated by established receptor-mediated pathways including Nod1, Nod2, Myd88 and the NLPR3 inflammasome. During mouse sepsis, augmentation depends on liver-resident macrophages (Kupffer cells) that capture and internalize both the pathogen and the proinfectious agent, leading to reduced production of reactive oxygen species, pathogen survival and subsequent multiple liver abscess formation. The augmented infection model more closely resembles the natural situation and establishes the role of resident environmental microflora in the initiation of disease by an invading pathogen. As the human microflora is ubiquitous2, its role in increasing susceptibility to infection by S. aureus highlights potential strategies for disease prevention.}, }
@article {pmid29922600, year = {2018}, author = {Fourie, R and Kuloyo, OO and Mochochoko, BM and Albertyn, J and Pohl, CH}, title = {Iron at the Centre of Candida albicans Interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {185}, pmid = {29922600}, issn = {2235-2988}, mesh = {Candida albicans/*metabolism/pathogenicity ; Candidiasis ; Gastrointestinal Tract ; Gene Expression Regulation, Fungal ; Homeostasis ; Host-Pathogen Interactions/*physiology ; Humans ; Immunity ; Iron/*metabolism ; Microbial Interactions/*physiology ; Symbiosis ; Virulence ; }, abstract = {Iron is an absolute requirement for both the host and most pathogens alike and is needed for normal cellular growth. The acquisition of iron by biological systems is regulated to circumvent toxicity of iron overload, as well as the growth deficits imposed by iron deficiency. In addition, hosts, such as humans, need to limit the availability of iron to pathogens. However, opportunistic pathogens such as Candida albicans are able to adapt to extremes of iron availability, such as the iron replete environment of the gastrointestinal tract and iron deficiency during systemic infection. C. albicans has developed a complex and effective regulatory circuit for iron acquisition and storage to circumvent iron limitation within the human host. As C. albicans can form complex interactions with both commensal and pathogenic co-inhabitants, it can be speculated that iron may play an important role in these interactions. In this review, we highlight host iron regulation as well as regulation of iron homeostasis in C. albicans. In addition, the review argues for the need for further research into the role of iron in polymicrobial interactions. Lastly, the role of iron in treatment of C. albicans infection is discussed.}, }
@article {pmid29792944, year = {2018}, author = {Stouthamer, CM and Kelly, S and Hunter, MS}, title = {Enrichment of low-density symbiont DNA from minute insects.}, journal = {Journal of microbiological methods}, volume = {151}, number = {}, pages = {16-19}, doi = {10.1016/j.mimet.2018.05.013}, pmid = {29792944}, issn = {1872-8359}, mesh = {Animals ; Arthropods/genetics/microbiology ; Bacteria/*genetics ; DNA, Bacterial/*isolation &amp; purification ; Host Microbial Interactions/*genetics ; Insecta/genetics/*microbiology ; Molecular Biology/*methods ; Sequence Analysis, DNA ; *Symbiosis ; Wasps/genetics/microbiology ; Wolbachia/genetics ; }, abstract = {Symbioses between bacteria and insects are often associated with changes in important biological traits that can significantly affect host fitness. To a large extent, studies of these interactions have been based on physiological changes or induced phenotypes in the host, and the genetic mechanisms by which symbionts interact with their hosts have only recently become better understood. Learning about symbionts has been challenging in part due to difficulties such as obtaining enough high quality genomic material for high throughput sequencing technology, especially for symbionts present in low titers, and in small or difficult to rear non-model hosts. Here we introduce a new method that substantially increases the yield of bacterial DNA in minute arthropod hosts, and requires less starting material relative to previous published methods.}, }
@article {pmid29725101, year = {2018}, author = {Toju, H and Peay, KG and Yamamichi, M and Narisawa, K and Hiruma, K and Naito, K and Fukuda, S and Ushio, M and Nakaoka, S and Onoda, Y and Yoshida, K and Schlaeppi, K and Bai, Y and Sugiura, R and Ichihashi, Y and Minamisawa, K and Kiers, ET}, title = {Core microbiomes for sustainable agroecosystems.}, journal = {Nature plants}, volume = {4}, number = {5}, pages = {247-257}, doi = {10.1038/s41477-018-0139-4}, pmid = {29725101}, issn = {2055-0278}, mesh = {*Agriculture/methods ; *Ecosystem ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.}, }
@article {pmid29659974, year = {2018}, author = {Chan, CX and Vaysberg, P and Price, DC and Pelletreau, KN and Rumpho, ME and Bhattacharya, D}, title = {Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica.}, journal = {Molecular biology and evolution}, volume = {35}, number = {7}, pages = {1706-1711}, doi = {10.1093/molbev/msy061}, pmid = {29659974}, issn = {1537-1719}, mesh = {Animals ; Down-Regulation ; Mollusca/*metabolism/*microbiology ; Stramenopiles/*physiology ; *Symbiosis ; Up-Regulation ; }, abstract = {Sacoglossan sea slugs offer fascinating systems to study the onset and persistence of algal-plastid symbioses. Elysia chlorotica is particularly noteworthy because it can survive for months, relying solely on energy produced by ingested plastids of the stramenopile alga Vaucheria litorea that are sequestered in cells lining its digestive diverticula. How this animal can maintain the actively photosynthesizing organelles without replenishment of proteins from the lost algal nucleus remains unknown. Here, we used RNA-Seq analysis to test the idea that plastid sequestration leaves a significant signature on host gene expression during E. chlorotica development. Our results support this hypothesis and show that upon exposure to and ingestion of V. litorea plastids, genes involved in microbe-associated molecular patterns and oxidative stress-response mechanisms are significantly up-regulated. Interestingly, our results with E. chlorotica mirror those found with corals that maintain dinoflagellates as intact cells in symbiosomes, suggesting parallels between these animal-algal symbiotic interactions.}, }
@article {pmid29659942, year = {2018}, author = {Vdacný, P}, title = {Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split.}, journal = {Molecular biology and evolution}, volume = {35}, number = {7}, pages = {1757-1769}, pmid = {29659942}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Ciliophora/*genetics ; Gastrointestinal Tract/*parasitology ; Marsupialia/*parasitology ; RNA, Ribosomal, 18S/genetics ; Symbiosis ; }, abstract = {Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.}, }
@article {pmid29610517, year = {2018}, author = {Leth, ML and Ejby, M and Workman, C and Ewald, DA and Pedersen, SS and Sternberg, C and Bahl, MI and Licht, TR and Aachmann, FL and Westereng, B and Abou Hachem, M}, title = {Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut.}, journal = {Nature microbiology}, volume = {3}, number = {5}, pages = {570-580}, doi = {10.1038/s41564-018-0132-8}, pmid = {29610517}, issn = {2058-5276}, mesh = {ATP-Binding Cassette Transporters/metabolism ; Bacterial Proteins/*metabolism ; Bacteroides/*growth &amp; development/metabolism ; Clostridiales/*growth &amp; development/metabolism ; Coculture Techniques ; Dietary Fiber/*metabolism ; Endo-1,4-beta Xylanases/metabolism ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Substrate Specificity ; Symbiosis ; Xylans/*metabolism ; }, abstract = {Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburia intestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R. intestinalis growth on different xylans. R. intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R. intestinalis prefers oligomers of 4-5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R. intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R. intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.}, }
@article {pmid29140081, year = {2018}, author = {Craft, KM and Townsend, SD}, title = {The Human Milk Glycome as a Defense Against Infectious Diseases: Rationale, Challenges, and Opportunities.}, journal = {ACS infectious diseases}, volume = {4}, number = {2}, pages = {77-83}, pmid = {29140081}, issn = {2373-8227}, support = {T32 GM065086/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Infections/immunology/metabolism/microbiology ; Communicable Diseases/etiology/*metabolism/microbiology ; *Disease Resistance/immunology ; Host-Pathogen Interactions ; Humans ; *Milk, Human/chemistry ; Oligosaccharides/chemistry/*metabolism ; Symbiosis ; }, abstract = {Each year over 3 million people die from infectious diseases with most of these deaths being poor and young children who live in low- and middle-income countries. Infectious diseases emerge for a multitude of reasons. On the social front, reasons include a breakdown of public health standards, international travel, and immigration (for financial, civil, and social reasons). At the molecular level, the modern rise of infectious diseases is tied to the juxtaposition of drug-resistant pathogens and a lack of new antimicrobials. The consequence is the possibility that humankind will return to the preantibiotic era wherein millions of people will perish from what should be trivial illnesses. Given the stakes, it is imperative that the chemistry community take leadership in delivering new antibiotic leads for clinical development. We believe this can happen through innovation in two areas. First is the development of novel chemical scaffolds to treat infections caused by multidrug-resistant pathogens. The second area, which is not exclusive to the first, is the generation of antibiotics that do not cause collateral damage to the host or the host's microbiome. Both can be enabled through advances in chemical synthesis. It is with this general philosophy in mind that we hypothesized human milk oligosaccharides (HMOs) could serve as novel chemical scaffolds for antibacterial development. We provide herein a personal account of our laboratory's progress toward the goal of using HMOs as a defense against infectious diseases.}, }
@article {pmid28860659, year = {2017}, author = {Chen, R and Wang, Z and Chen, J and Jiang, LY and Qiao, GX}, title = {Insect-bacteria parallel evolution in multiple-co-obligate-aphid association: a case in Lachninae (Hemiptera: Aphididae).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10204}, pmid = {28860659}, issn = {2045-2322}, mesh = {Animals ; Aphids/*classification/genetics/*microbiology ; Bacterial Proteins/genetics ; Buchnera/*classification/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Genome Size ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {Parallel phylogenies between aphid and its obligate symbiont Buchnera are hot topics which always focused on aphid lower taxonomic levels. Symbionts in the subfamily Lachninae are special. Buchnera in many lachnine species has undergone functional and genome size reduction that was replaced by other co-obligate symbionts. In this study, we constructed the phylogenetic relationships of Lachninae with a combined dataset of five genes sequenced from Buchnera to estimate the effects of a dual symbiotic system in the aphid-Buchnera cospeciation association. The phylogeny of Buchnera in Lachninae was well-resolved in the combined dataset. Each of the genera formed strongly supported monophyletic groups, with the exception of the genus Cinara. The phylogeny based on sequences from Buchnera was divided into five tribes according to the clades of the Lachninae hosts tree, with the phylogenies of Buchnera and Lachninae being generally congruent. These results first provided evidence of parallel evolution at the aphid subfamily level comprehensively and supported the view that topological congruence between the phylogenies of Buchnera and Lachninae would not be interfered with the other co-obligate symbionts, such as Sarretia, in aphid-entosymbiont association. These results also provided new insight in understanding host-plant coevolution in lachnine lineages.}, }
@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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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. ORS285 bclA mutant.}, journal = {Journal of bacteriology}, volume = {}, number = {}, 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 enforce 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. 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. The bclA nodule bacteria constitute thus 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 with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less 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 non-symbiotic 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.ImportanceThe legume-rhizobium symbiosis is a major ecological process fueling the biogeochemical nitrogen cycle with reduced nitrogen. It represents also a promising strategy to cut down 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}, 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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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, ET and de Anda, J and Wong, GCL and Newman, D}, 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 = {}, 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. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent consequences of extended hopanoid loss in the initiation of root nodule formation and in the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1264/jsme2.ME19011}, pmid = {31167992}, issn = {1347-4405}, 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 {pmid30624120, year = {2018}, author = {Shipway, JR and Altamia, MA and Haga, T and Velásquez, M and Albano, J and Dechavez, R and Concepcion, GP and Haygood, MG and Distel, DL}, title = {Observations on the Life History and Geographic Range of the Giant Chemosymbiotic Shipworm Kuphus polythalamius (Bivalvia: Teredinidae).}, journal = {The Biological bulletin}, volume = {235}, number = {3}, pages = {167-177}, doi = {10.1086/700278}, pmid = {30624120}, issn = {1939-8697}, support = {U19 TW008163/TW/FIC NIH HHS/United States ; }, mesh = {*Animal Distribution ; Animals ; Bivalvia/*physiology ; Chemoautotrophic Growth ; Pacific Ocean ; Symbiosis ; }, abstract = {Kuphus polythalamius (Teredinidae) is one of the world's largest, most rarely observed, and least understood bivalves. Kuphus polythalamius is also among the few shallow-water marine species and the only teredinid species determined to harbor sulfur-oxidizing chemoautotrophic (thioautotrophic) symbionts. Until the recent discovery of living specimens in the Philippines, this species was known only from calcareous hard parts, fossils, and the preserved soft tissues of a single large specimen. As a result, the anatomy, biology, life history, and geographic range of K. polythalamius remain obscure. Here we report the collection and description of the smallest living specimens of K. polythalamius yet discovered and confirm the species identity of these individuals by using sequences of three genetic markers. Unlike previously collected specimens, all of which have been reported to occur in marine sediments, these specimens were observed burrowing in wood, the same substrate utilized by all other members of the family. These observations suggest that K. polythalamius initially settles on wood and subsequently transitions into sediment, where this species may grow to enormous sizes. This discovery led us to search for and find previously unidentified and misidentified wood-boring specimens of this species within museum collections, and it allowed us to show that the recent geographic range (since 1933) of this species extends across a 3000-mile span from the Philippines to Papua New Guinea and the Solomon Islands.}, }
@article {pmid30624116, year = {2018}, author = {Dossi, FCA and da Silva, EP and Cônsoli, FL}, title = {Shifting the Balance: Heat Stress Challenges the Symbiotic Interactions of the Asian Citrus Psyllid, Diaphorina citri (Hemiptera, Liviidae).}, journal = {The Biological bulletin}, volume = {235}, number = {3}, pages = {195-203}, doi = {10.1086/699755}, pmid = {30624116}, issn = {1939-8697}, mesh = {Animals ; Hemiptera/*physiology ; *Hot Temperature ; Symbiosis/*physiology ; }, abstract = {Global warming may impact biodiversity by disrupting biological interactions, including long-term insect-microbe mutualistic associations. Symbiont-mediated insect tolerance to high temperatures is an ecologically important trait that significantly influences an insect's life history. Disruption of microbial symbionts that are required by insects would substantially impact their pest status. Diaphorina citri, a worldwide citrus pest, is associated with the mutualistic symbionts Candidatus Carsonella ruddii and Candidatus Profftella armatura. Wolbachia is also associated with D. citri, but its contribution to the host is unknown. Symbiont density is dependent on a range of factors, including the thermosensitivity of the host and/or symbiont to heat stress. Here, we predicted that short-term heat stress of D. citri would disrupt the host-symbiont phenological synchrony and differentially affect the growth and density of symbionts. We investigated the effects of exposing D. citri eggs to different temperatures for different periods of time on the growth dynamics of symbionts during the nymphal development of D. citri (first instar to fifth instar) by real-time polymerase chain reaction. Symbiont densities were assessed as the number of gene copies, using specific molecular markers: 16S rRNA for Carsonella and Profftella and ftsZ for Wolbachia. Statistical modeling of the copy numbers of symbionts revealed differences in their growth patterns, particularly in the early instars of heat-shocked insects. Wolbachia was the only symbiont to benefit from heat-shock treatment. Although the symbionts responded differently to heat stress, the lack of differences in symbiont densities between treated and control late nymphs suggests the existence of an adaptive genetic process to restore phenological synchrony during the development of immatures in preparation for adult life. Our findings contribute to the understanding of the potential deleterious effects of high temperatures on host-symbiont interactions. Our data also suggest that the effects of host exposure to high temperatures in symbiont growth are highly variable and dependent on the interactions among members of the community of symbionts harbored by a host. Such dependence points to unpredictable consequences for agroecosystems worldwide due to climate change-related effects on the ecological traits of symbiont-dependent insect pests.}, }
@article {pmid30542952, year = {2019}, author = {Dhaneesha, M and Hasin, O and Sivakumar, KC and Ravinesh, R and Naman, CB and Carmeli, S and Sajeevan, TP}, title = {DNA Binding and Molecular Dynamic Studies of Polycyclic Tetramate Macrolactams (PTM) with Potential Anticancer Activity Isolated from a Sponge-Associated Streptomyces zhaozhouensis subsp. mycale subsp. nov.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {1}, pages = {124-137}, doi = {10.1007/s10126-018-9866-9}, pmid = {30542952}, issn = {1436-2236}, support = {292/2016/KSCSTE dated 07.07.2016//Kerala State Council for Science, Technology and Environment/ ; }, mesh = {Animals ; Antineoplastic Agents/*chemistry/isolation &amp; purification/pharmacology ; Apoptosis/*drug effects/genetics ; Binding Sites ; Cell Line, Tumor ; Cell Survival/drug effects ; DNA/*chemistry ; Epithelial Cells/drug effects/metabolism/pathology ; G1 Phase Cell Cycle Checkpoints/drug effects/genetics ; Humans ; Inhibitory Concentration 50 ; Lactams/*chemistry/isolation &amp; purification/pharmacology ; Lactams, Macrocyclic/*chemistry/isolation &amp; purification/pharmacology ; Molecular Docking Simulation ; Nucleic Acid Conformation ; Phylogeny ; Porifera/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; S Phase Cell Cycle Checkpoints/drug effects/genetics ; Streptomyces/*chemistry/classification/metabolism ; Symbiosis/physiology ; }, abstract = {A sponge-associated actinomycete (strain MCCB267) was isolated from a marine sponge Mycale sp. collected in the Indian Ocean off the Southeast coast of India. Phylogenetic studies of this strain using 16S rRNA gene sequencing showed high sequence similarity to Streptomyces zhaozhouensis. However, strain MCCB267 showed distinct physiological and biochemical characteristic features and was thus designated as S. zhaozhouensis subsp. mycale. subsp. nov. A cytotoxicity-guided fractionation of the crude ethyl acetate extract of strain MCCB267 culture medium yielded four pure compounds belonging to the polycyclic tetramate macrolactam (PTM) family of natural products: ikarugamycin (IK) (1), clifednamide A (CF) (2), 30-oxo-28-N-methylikarugamycin (OI) (3), and 28-N-methylikarugamycin (MI) (4). The four compounds exhibited promising cytotoxic activity against NCI-H460 lung carcinoma cells in vitro, by inducing cell death via apoptosis. Flow cytometric analysis revealed that 1, 3, and 4 induced cell cycle arrest during G1 phase in the NCI-H460 cell line, whereas 2 induced cell arrest in the S phase. A concentration-dependent accumulation of cells in the sub-G1 phase was also detected upon treatment of the cancer cell line with compounds 1-4. The in vitro cytotoxicity studies were supported by molecular docking and molecular dynamic simulation analyses. An in silico study revealed that the PTMs can bind to the minor groove of DNA and subsequently induce the apoptotic stimuli leading to cell death. The characterization of the isolated actinomycete, the study of the mode of action of the four PTMs, 1-4, and the molecular docking and molecular dynamic simulations analyses are herein described.}, }
@article {pmid30540788, year = {2018}, author = {Pietri, JE and Tiffany, C and Liang, D}, title = {Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207985}, doi = {10.1371/journal.pone.0207985}, pmid = {30540788}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Blattellidae/drug effects/*microbiology/physiology ; Feces/microbiology ; Female ; Insecticide Resistance/drug effects ; Insecticides/*metabolism/pharmacology ; Male ; Microbiota/drug effects/*physiology ; Oxazines/*metabolism/pharmacology ; Symbiosis ; }, abstract = {The German cockroach, Blatella germanica, is a common pest in urban environments and is among the most resilient insects in the world. The remarkable ability of the German cockroach to develop resistance when exposed to toxic insecticides is a prime example of adaptive evolution and makes control of this insect an ongoing struggle. Like many other organisms, the German cockroach is host to a diverse community of symbiotic microbes that play important roles in its physiology. In some insect species, there is a strong correlation between the commensal microbial community and insecticide resistance. In particular, several bacteria have been implicated in the detoxification of xenobiotics, including synthetic insecticides. While multiple mechanisms that mediate insecticide resistance in cockroaches have been discovered, significant knowledge gaps still exist in this area of research. Here, we examine the effects of altering the microbiota on resistance to a common insecticide using antibiotic treatments. We describe an indoxacarb-resistant laboratory strain in which treatment with antibiotic increases susceptibility to orally administered insecticide. We further reveal that this strains harbors a gut microbial community that differs significantly from that of susceptible cockroaches in which insecticide resistance is unaffected by antibiotic. More importantly, we demonstrate that transfer of gut microbes from the resistant to the susceptible strain via fecal transplant increases its resistance. Lastly, our data show that antibiotic treatment adversely affects several reproductive life-history traits that may contribute to the dynamics of resistance at the population level. Together these results suggest that the microbiota contributes to both physiological and evolutionary aspects of insecticide resistance and that targeting this community may be an effective strategy to control the German cockroach.}, }
@article {pmid30297831, year = {2018}, author = {Lin, JS and Li, X and Luo, Z and Mysore, KS and Wen, J and Xie, F}, title = {NIN interacts with NLPs to mediate nitrate inhibition of nodulation in Medicago truncatula.}, journal = {Nature plants}, volume = {4}, number = {11}, pages = {942-952}, doi = {10.1038/s41477-018-0261-3}, pmid = {30297831}, issn = {2055-0278}, mesh = {Gene Expression Regulation, Plant ; Medicago truncatula/*metabolism ; Nitrates/*metabolism/physiology ; Plant Proteins/metabolism/*physiology ; Plant Root Nodulation/*physiology ; Rhizobium ; Symbiosis ; }, abstract = {Legume plants can assimilate inorganic nitrogen and have access to fixed nitrogen through symbiotic interaction with diazotrophic bacteria called rhizobia. Symbiotic nitrogen fixation is an energy-consuming process and is strongly inhibited when sufficient levels of fixed nitrogen are available, but the molecular mechanisms governing this regulation are largely unknown. The transcription factor nodule inception (NIN) is strictly required for nodulation and belongs to a family of NIN-like proteins (NLPs), which have been implicated in the regulation of nitrogen homeostasis in Arabidopsis. Here, we show that mutation or downregulation of NLP genes prevents nitrate inhibition of infection, nodule formation and nitrogen fixation. We find that NIN and NLPs physically interact through their carboxy-terminal PB1 domains. Furthermore, we find that NLP1 is required for the expression of nitrate-responsive genes and that nitrate triggers NLP1 re-localization from the cytosol to the nucleus. Finally, we show that NLP1 can suppress NIN activation of CRE1 expression in Nicotiana benthamiana and Medicago truncatula. Our findings highlight a central role for NLPs in the suppression of nodulation by nitrate.}, }
@article {pmid30194504, year = {2019}, author = {Miura, N and Motone, K and Takagi, T and Aburaya, S and Watanabe, S and Aoki, W and Ueda, M}, title = {Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {1}, pages = {1-8}, doi = {10.1007/s10126-018-9853-1}, pmid = {30194504}, issn = {1436-2236}, support = {17J07458//Japan Society for the Promotion of Science/ ; 16J08791//Japan Society for the Promotion of Science/ ; 17J05024//Japan Society for the Promotion of Science/ ; 18K14479//Japan Society for the Promotion of Science/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; Japan ; Microbiota/genetics ; Pacific Ocean ; RNA, Ribosomal, 16S/*genetics ; Rhodobacteraceae/classification/*genetics/isolation &amp; purification ; Symbiosis/physiology ; Vibrio/*growth &amp; development/pathogenicity ; }, abstract = {The coral microbiome has attracted increased attention because of its potential roles in host protection against deadly diseases. However, little is known about the role of coral-associated bacteria against the temperature-dependent opportunistic pathogen Vibrio coralliilyticus. In this study, we tested whether bacteria associated with the reef-building coral Galaxea fascicularis could inhibit the growth of V. coralliilyticus. Twenty-nine cultivable bacteria were successfully isolated from a healthy colony of G. fascicularis kept in an aquarium. Among the bacterial isolates, three Ruegeria sp. strains inhibited the growth of V. coralliilyticus P1 as a reference strain and Vibrio sp. isolated in this study. Ruegeria sp. strains were also detected from other G. fascicularis colonies in the aquarium and in previous field studies by 16S rRNA amplicon sequencing, suggesting that Ruegeria sp. strains are common among G. fascicularis colonies. These results illuminate the potential role of Ruegeria sp. in protecting corals against pathogenic Vibrio species.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003512}, pmid = {31166165}, issn = {1466-5034}, 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 = {}, number = {}, pages = {}, doi = {10.1002/ps.5507}, pmid = {31166074}, issn = {1526-4998}, 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 were strongly affected by agricultural practices, such as tillage and the use of pesticides and fertilizers, which strongly affected 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, attracting beneficial organisms and repelling harmful ones, including other plants. We review a number of fascinating cases like 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1007/s10265-019-01117-7}, pmid = {31165947}, issn = {1618-0860}, support = {23380042//Japan Society for the Promotion of Science/ ; }, 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 {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 {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 {pmid29643214, year = {2018}, author = {Norin, T and Mills, SC and Crespel, A and Cortese, D and Killen, SS and Beldade, R}, title = {Anemone bleaching increases the metabolic demands of symbiont anemonefish.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1876}, pages = {}, pmid = {29643214}, issn = {1471-2954}, mesh = {Animals ; Climate Change ; Locomotion/physiology ; Oxygen Consumption/physiology ; Perciformes/*metabolism/physiology ; Sea Anemones/*physiology ; Symbiosis/*physiology ; }, abstract = {Increased ocean temperatures are causing mass bleaching of anemones and corals in the tropics worldwide. While such heat-induced loss of algal symbionts (zooxanthellae) directly affects anemones and corals physiologically, this damage may also cascade on to other animal symbionts. Metabolic rate is an integrative physiological trait shown to relate to various aspects of organismal performance, behaviour and locomotor capacity, and also shows plasticity during exposure to acute and chronic stressors. As climate warming is expected to affect the physiology, behaviour and life history of animals, including ectotherms such as fish, we measured if residing in bleached versus unbleached sea anemones (Heteractis magnifica) affected the standard (i.e. baseline) metabolic rate and behaviour (activity) of juvenile orange-fin anemonefish (Amphiprion chrysopterus). Metabolic rate was estimated from rates of oxygen uptake [Formula: see text], and the standard metabolic rate [Formula: see text] of anemonefish from bleached anemones was significantly higher by 8.2% compared with that of fish residing in unbleached anemones, possibly due to increased stress levels. Activity levels did not differ between fish from bleached and unbleached anemones. As [Formula: see text] reflects the minimum cost of living, the increased metabolic demands may contribute to the negative impacts of bleaching on important anemonefish life history and fitness traits observed previously (e.g. reduced spawning frequency and lower fecundity).}, }
@article {pmid29618548, year = {2018}, author = {Jacobsen, RM and Sverdrup-Thygeson, A and Kauserud, H and Birkemoe, T}, title = {Revealing hidden insect-fungus interactions; moderately specialized, modular and anti-nested detritivore networks.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1876}, pages = {}, pmid = {29618548}, issn = {1471-2954}, mesh = {Animals ; *Biota ; Coleoptera/*microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/*analysis ; Ecosystem ; Fungi/*classification ; Norway ; Plant Diseases/microbiology ; Symbiosis ; Wood ; }, abstract = {Ecological networks are composed of interacting communities that influence ecosystem structure and function. Fungi are the driving force for ecosystem processes such as decomposition and carbon sequestration in terrestrial habitats, and are strongly influenced by interactions with invertebrates. Yet, interactions in detritivore communities have rarely been considered from a network perspective. In the present study, we analyse the interaction networks between three functional guilds of fungi and insects sampled from dead wood. Using DNA metabarcoding to identify fungi, we reveal a diversity of interactions differing in specificity in the detritivore networks, involving three guilds of fungi. Plant pathogenic fungi were relatively unspecialized in their interactions with insects inhabiting dead wood, while interactions between the insects and wood-decay fungi exhibited the highest degree of specialization, which was similar to estimates for animal-mediated seed dispersal networks in previous studies. The low degree of specialization for insect symbiont fungi was unexpected. In general, the pooled insect-fungus networks were significantly more specialized, more modular and less nested than randomized networks. Thus, the detritivore networks had an unusual anti-nested structure. Future studies might corroborate whether this is a common aspect of networks based on interactions with fungi, possibly owing to their often intense competition for substrate.}, }
@article {pmid29393559, year = {2018}, author = {Michalik, A and Schulz, F and Michalik, K and Wascher, F and Horn, M and Szklarzewicz, T}, title = {Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae).}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1148-1157}, doi = {10.1111/1462-2920.14057}, pmid = {29393559}, issn = {1462-2920}, mesh = {Animals ; Enterobacteriaceae/*classification/*genetics/growth &amp; development ; Hemiptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Symbiosis/genetics/*physiology ; }, abstract = {Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod-shaped bacteria. Phylogenetic analyses have revealed that the coccoid bacteria represent a sister group to the secondary symbiont of the mealybug Melanococcus albizziae, whereas the rod-shaped symbionts are close relatives of Arsenophonus symbionts in insects - to our knowledge, this is the first report of the presence of Arsenophonus bacterium in scale insects. As a comparison of 16S and 23S rRNA genes sequences of the G. brachypodii coccoid symbiont with other gammaprotebacterial sequences showed only low similarity (∼90%), we propose the name 'Candidatus Kotejella greeniscae' for its tentative classification. Both symbionts are transovarially transmitted from one generation to the next. The infection takes place in the neck region of the ovariole. The bacteria migrate between follicular cells, as well as through the cytoplasm of those cells to the perivitelline space, where they form a characteristic 'symbiont ball'. Our findings provide evidence for a polyphyletic origin of symbionts of Eriococcidae.}, }
@article {pmid29345102, year = {2018}, author = {Martin, E and Varotto Boccazzi, I and De Marco, L and Bongiorno, G and Montagna, M and Sacchi, L and Mensah, P and Ricci, I and Gradoni, L and Bandi, C and Epis, S}, title = {The mycobiota of the sand fly Phlebotomus perniciosus: Involvement of yeast symbionts in uric acid metabolism.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1064-1077}, doi = {10.1111/1462-2920.14044}, pmid = {29345102}, issn = {1462-2920}, mesh = {Animals ; Female ; Genome, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; Insect Vectors ; Larva/microbiology ; Male ; Malpighian Tubules/microbiology ; Microbiota/genetics ; Phlebotomus/*microbiology ; RNA, Ribosomal/genetics ; Saccharomycetales/*genetics/isolation &amp; purification/*metabolism ; Symbiosis/*physiology ; Uric Acid/*metabolism ; }, abstract = {The knowledge of the fungal mycobiota of arthropods, including the vectors of human and animal diseases, is still limited. Here, the mycobiota associated with the sand fly Phlebotomus perniciosus, the main vector of leishmaniasis in the western Mediterranean area, by a culture-dependent approach (microbiological analyses and sequencing of the 26S rRNA gene), internal transcribed spacer (ITS) rRNA amplicon-based next-generation sequencing, fluorescence in situ hybridisation (FISH), and genome sequencing of the dominant yeast species was investigated. The dominant species was Meyerozyma guilliermondii, known for its biotechnological applications. The focus was on this yeast and its prevalence in adults, pupae and larvae of reared sand flies (overall prevalence: 57.5%) and of field-collected individuals (overall prevalence: 9%) was investigated. Using whole-mount FISH and microscopic examination, it was further showed that M. guilliermondii colonizes the midgut of females, males and larvae and the distal part of Malpighian tubules of female sand flies, suggesting a possible role in urate degradation. Finally, the sequencing and analysis of the genome of M. guilliermondii allowed predicting the complete uric acid degradation pathway, suggesting that the yeast could contribute to the removal of the excess of nitrogenous wastes after the blood meal of the insect host.}, }
@article {pmid29144582, year = {2017}, author = {Wood, CW and Stinchcombe, JR}, title = {A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism.}, journal = {Molecular ecology}, volume = {26}, number = {21}, pages = {5869-5871}, doi = {10.1111/mec.14370}, pmid = {29144582}, issn = {1365-294X}, mesh = {Biological Evolution ; *Fabaceae ; Genotype ; *Rhizobium ; Symbiosis ; }, abstract = {The maintenance of genetic variation in the benefits provided by mutualists is an evolutionary puzzle (Heath &amp; Stinchcombe,). Over time, natural selection should favour the benefit strategy that confers the highest fitness, eroding genetic variation in partner quality. Yet abundant genetic variation in partner quality exists in many systems (Heath &amp; Stinchcombe,). One possible resolution to this puzzle is that the genetic identity of both a host and its partner affects the benefits each mutualist provides to the other, a pattern known as a genotype-by-genotype interaction (Figure). Mounting evidence suggests that genotype-by-genotype interactions between partners are pervasive at the phenotypic level (Barrett, Zee, Bever, Miller, &amp; Thrall, ; Heath, ; Hoeksema &amp; Thompson,). Ultimately, however, to link these phenotypic patterns to the maintenance of genetic variation in mutualisms we need to answer two questions: How much variation in mutualism phenotypes is attributable to genotype-by-genotype interactions, and what mutualistic functions are influenced by each partner and by the interaction between their genomes? In this issue of Molecular Ecology, Burghardt et al. (2017) use transcriptomics to address both questions in the legume-rhizobia mutualism.}, }
@article {pmid28607345, year = {2017}, author = {Chen, HK and Wang, LH and Chen, WU and Mayfield, AB and Levy, O and Lin, CS and Chen, CS}, title = {Coral lipid bodies as the relay center interconnecting diel-dependent lipidomic changes in different cellular compartments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3244}, pmid = {28607345}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/cytology/*microbiology/*physiology ; Circadian Rhythm ; Dinoflagellida/physiology ; Lipid Droplets ; Lipid Metabolism/*physiology ; Symbiosis/physiology ; }, abstract = {Lipid bodies (LBs) in the coral gastrodermal tissues are key organelles in the regulation of endosymbiosis and exhibit a diel rhythmicity. Using the scleractinian Euphyllia glabrescens collected across the diel cycle, we observed temporally dynamic lipid profiles in three cellular compartments: host coral gastrodermal cells, LBs, and in hospite Symbiodinium. Particularly, the lipidome varied over time, demonstrating the temporally variable nature of the coral-Symbiodinium endosymbiosis. The lipidome-scale data highlight the dynamic, light-driven metabolism of such associations and reveal that LBs are not only lipid storage organelles but also act as a relay center in metabolic trafficking. Furthermore, lipogenesis in LBs is significantly regulated by coral hosts and the lipid metabolites within holobionts featured predominantly triacylglycerols, sterol esters, and free fatty acids. Given these findings through a time-varied lipidome status, the present study provided valuable insights likely to be crucial to understand the cellular biology of the coral-Symbiodinium endosymbiosis.}, }
@article {pmid28091933, year = {2017}, author = {Givaudan, A and Lanois, A}, title = {Flagellar Regulation and Virulence in the Entomopathogenic Bacteria-Xenorhabdus nematophila and Photorhabdus luminescens.}, journal = {Current topics in microbiology and immunology}, volume = {402}, number = {}, pages = {39-51}, doi = {10.1007/82_2016_53}, pmid = {28091933}, issn = {0070-217X}, mesh = {*Flagella/physiology ; *Photorhabdus ; Symbiosis ; Virulence ; *Xenorhabdus ; }, abstract = {There is a complex interplay between the regulation of flagellar motility and the expression of virulence factors in many bacterial pathogens. Here, we review the literature on the direct and indirect roles of flagellar motility in mediating the tripartite interaction between entomopathogenic bacteria (Photorhabdus and Xenorhabdus), their nematode hosts, and their insect targets. First, we describe the swimming and swarming motility of insect pathogenic bacteria and its impact on insect colonization. Then, we describe the coupling between the expression of flagellar and virulence genes and the dynamic of expression of the flagellar regulon during invertebrate infection. We show that the flagellar type 3 secretion system (T3SS) is also an export apparatus for virulence proteins in X. nematophila. Finally, we demonstrate that phenotypic variation, a common property of the bacterial symbionts of nematodes, also alters flagellar motility in Photorhabdus and Xenorhabdus. Finally, the so-called phenotypic heterogeneity phenomenon in the flagellar gene expression network will be also discussed. As the main molecular studies were performed in X. nematophila, future perspectives for the study of the interplay between flagellum and invertebrate interactions in Photorhabdus will be discussed.}, }
@article {pmid27995342, year = {2017}, author = {Eleftherianos, I and Shokal, U and Yadav, S and Kenney, E and Maldonado, T}, title = {Insect Immunity to Entomopathogenic Nematodes and Their Mutualistic Bacteria.}, journal = {Current topics in microbiology and immunology}, volume = {402}, number = {}, pages = {123-156}, doi = {10.1007/82_2016_52}, pmid = {27995342}, issn = {0070-217X}, support = {R01 AI110675/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Bacteria ; Biological Control Agents ; Humans ; *Insecta/immunology ; *Nematoda/parasitology ; Symbiosis ; }, abstract = {Entomopathogenic nematodes are important organisms for the biological control of insect pests and excellent models for dissecting the molecular basis of the insect immune response against both the nematode parasites and their mutualistic bacteria. Previous research involving the use of various insects has found distinct differences in the number and nature of immune mechanisms that are activated in response to entomopathogenic nematode parasites containing or lacking their associated bacteria. Recent studies using model insects have started to reveal the identity of certain molecules with potential anti-nematode or antibacterial activity as well as the molecular components that nematodes and their bacteria employ to evade or defeat the insect immune system. Identification and characterization of the genes that regulate the insect immune response to nematode-bacteria complexes will contribute significantly to the development of improved practices to control insects of agricultural and medical importance, and potentially nematode parasites that infect mammals, perhaps even humans.}, }
@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}, 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}, 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}, 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 = {}, number = {}, pages = {}, 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 {pmid30832430, year = {2019}, author = {Alaswad, AA and Oehrle, NW and Krishnan, HB}, title = {Classical Soybean (Glycine max (L.) Merr) Symbionts, Sinorhizobium fredii USDA191 and Bradyrhizobium diazoefficiens USDA110, Reveal Contrasting Symbiotic Phenotype on Pigeon Pea (Cajanus cajan (L.) Millsp).}, journal = {International journal of molecular sciences}, volume = {20}, number = {5}, pages = {}, doi = {10.3390/ijms20051091}, pmid = {30832430}, issn = {1422-0067}, mesh = {Bradyrhizobium/genetics/metabolism/*pathogenicity ; Cajanus/metabolism/*microbiology ; Host Specificity ; Nitrogen Fixation ; *Phenotype ; Root Nodules, Plant/metabolism/microbiology/ultrastructure ; Sinorhizobium fredii/genetics/metabolism/*pathogenicity ; Soybeans/microbiology ; *Symbiosis ; Type III Secretion Systems/genetics ; }, abstract = {Pigeon pea (Cajanus cajan (L.) Millspaugh) is cultivated widely in semiarid agricultural regions in over 90 countries around the world. This important legume can enter into symbiotic associations with a wide range of rhizobia including Bradyrhizobium and fast-growing rhizobia. In comparison with other major legumes such as soybean and common bean, only limited information is available on the symbiotic interaction of pigeon pea with rhizobia. In this study, we investigated the ability of two classical soybean symbionts-S. fredii USDA191 and B. diazoefficiens USDA110-and their type 3 secretion system (T3SS) mutants, to nodulate pigeon pea. Both S. fredii USDA191 and a T3SS mutant S. fredii RCB26 formed nitrogen-fixing nodules on pigeon pea. Inoculation of pigeon pea roots with B. diazoefficiens USDA110 and B. diazoefficiens Δ136 (a T3SS mutant) resulted in the formation of Fix- and Fix+ nodules, respectively. Light and transmission electron microscopy of Fix- nodules initiated by B. diazoefficiens USDA110 revealed the complete absence of rhizobia within these nodules. In contrast, Fix+ nodules formed by B. diazoefficiens Δ136 revealed a central region that was completely filled with rhizobia. Ultrastructural investigation revealed the presence of numerous bacteroids surrounded by peribacteroid membranes in the infected cells. Analysis of nodule proteins by one- and two-dimensional gel electrophoresis revealed that leghemoglobin was absent in B. diazoefficiens USDA110 nodules, while it was abundantly present in B. diazoefficiens Δ136 nodules. Results of competitive nodulation assays indicated that B. diazoefficiens Δ136 had greater competitiveness for nodulation on pigeon pea than did the wild type strain. Our results suggest that this T3SS mutant of B. diazoefficiens, due to its greater competitiveness and ability to form Fix+ nodules, could be exploited as a potential inoculant to boost pigeon pea productivity.}, }
@article {pmid30773714, year = {2019}, author = {Estellé, J}, title = {Benefits from the joint analysis of host genomes and metagenomes: Select the holobiont.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {136}, number = {2}, pages = {75-76}, doi = {10.1111/jbg.12383}, pmid = {30773714}, issn = {1439-0388}, mesh = {Animals ; Genetic Variation ; *Genome ; Genotyping Techniques ; *Metagenome ; Symbiosis/*genetics ; }, }
@article {pmid30241612, year = {2018}, author = {Cadwell, K}, title = {Sugar Turns Bacteria Sweet: A Peace Offering in the Gut.}, journal = {Cell}, volume = {175}, number = {1}, pages = {36-37}, doi = {10.1016/j.cell.2018.08.053}, pmid = {30241612}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Asymptomatic Infections ; Bacteria ; Humans ; *Sugars ; Symbiosis ; Virulence ; }, abstract = {Following an infection, a subset of individuals can remain disease free despite harboring a pathogen for a prolonged period. In this issue of Cell, Sanchez et al. demonstrate that a metabolically favorable host response can drive an otherwise lethal bacterial pathogen to abandon virulence and become a commensal microorganism.}, }
@article {pmid30127409, year = {2018}, author = {Taylor, BN and Menge, DNL}, title = {Light regulates tropical symbiotic nitrogen fixation more strongly than soil nitrogen.}, journal = {Nature plants}, volume = {4}, number = {9}, pages = {655-661}, doi = {10.1038/s41477-018-0231-9}, pmid = {30127409}, issn = {2055-0278}, mesh = {Fabaceae/growth &amp; development/metabolism/physiology ; Light ; Nitrogen/*metabolism ; Nitrogen Fixation/*radiation effects ; Rhizobiaceae/metabolism ; Seedlings/growth &amp; development ; Soil ; Symbiosis/*radiation effects ; Trees/growth &amp; development/metabolism/physiology ; Tropical Climate ; }, abstract = {Nitrogen limits primary production in almost every biome on Earth1,2. Symbiotic nitrogen fixation, conducted by certain angiosperms and their endosymbiotic bacteria, is the largest potential natural source of new nitrogen into the biosphere3, influencing global primary production, carbon sequestration and element cycling. Because symbiotic nitrogen fixation represents an alternative to soil nitrogen uptake, much of the work on symbiotic nitrogen fixation regulation has focused on soil nitrogen availability4-8. However, because symbiotic nitrogen fixation is an energetically expensive process9, light availability to the plant may also regulate symbiotic nitrogen fixation rates10,11. Despite the importance of symbiotic nitrogen fixation to biosphere functioning, the environmental factors that most strongly regulate this process remain unresolved. Here we show that light regulates symbiotic nitrogen fixation more strongly than does soil nitrogen and that light mediates the response of symbiotic nitrogen fixation to soil nitrogen availability. In a shadehouse experiment, low light levels (comparable with forest understories) completely shut down symbiotic nitrogen fixation, whereas soil nitrogen levels that far exceeded plant demand did not fully downregulate symbiotic nitrogen fixation at high light. For in situ forest seedlings, light was a notable predictor of symbiotic nitrogen fixation activity, but soil-extractable nitrogen was not. Light as a primary regulator of symbiotic nitrogen fixation is a departure from decades of focus on soil nitrogen availability. This shift in our understanding of symbiotic nitrogen fixation regulation can resolve a long-standing biogeochemical paradox12, and it will improve our ability to predict how symbiotic nitrogen fixation will fuel the global forest carbon sink and respond to human alteration of the global nitrogen cycle.}, }
@article {pmid29245006, year = {2017}, author = {Douglas, AE}, title = {Big Role for a Tiny Genome.}, journal = {Cell}, volume = {171}, number = {7}, pages = {1472-1473}, doi = {10.1016/j.cell.2017.11.038}, pmid = {29245006}, issn = {1097-4172}, mesh = {Animals ; Bacteria ; *Coleoptera ; *Herbivory ; Insecta ; Symbiosis ; }, abstract = {In this issue of Cell, Salem et al. demonstrate a remarkable instance of herbivory dependent on a co-evolved mutualism with specialized bacteria. Despite having a tiny genome and limited metabolic repertoire, the bacteria in Cassida beetles produce pectinases predicted to mediate degradation of plant cell walls in the insect diet.}, }
@article {pmid28855622, year = {2017}, author = {Fan, W and Guo, W and Van Etten, JL and Mower, JP}, title = {Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10101}, pmid = {28855622}, issn = {2045-2322}, support = {P30 GM103509/GM/NIGMS NIH HHS/United States ; }, mesh = {Chlorella/genetics ; Chlorophyta/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Introns ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Ancient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix). The mitogenomes and plastomes of the three newly sequenced endosymbionts have a standard set of genes compared with free-living trebouxiophytes, providing no evidence for functional genomic reduction. Instead, their organellar genomes are generally larger and more intron rich. Intron content is highly variable among the members of Chlorella, suggesting very high rates of gain and/or loss of introns during evolution. Phylogenetic analysis of plastid and mitochondrial genes demonstrated that the three endosymbionts do not form a monophyletic group, indicating that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae. In addition, M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.}, }
@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 = {}, 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 = {}, number = {}, pages = {}, 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}, 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 {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.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00957-19}, pmid = {31152017}, issn = {1098-5336}, abstract = {A stable and efficient plasmid transfer system was developed for the nitrogen-fixing symbiotic actinobacteria 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, the plasmid pHKT1 that expresses the green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 X 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 the passage in a plant host. As a proof of concept, a salt-tolerance candidate gene from the high salt-tolerance Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. End-point 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, overcoming a major hurdle in the field. This is a step in developing genetic tools in Frankia will open up new avenues for research for actinorhizal symbiosis.ImportanceThe 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 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 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 = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b01618}, pmid = {31150238}, issn = {1520-5118}, abstract = {This study investigated effects of seed aging and imbibition on sugar metabolite levels in Epichloë endophyte-infected and endophyte-free seed of tall fescue (Festuca arundinacea Schreb.). Gas chromatography with flame ionization detection was employed for analysis of sugar metabolites within the seed tissues, with embryo and endosperm tissues analyzed separately. Mannitol, ribitol and trehalose were more abundant in embryo than endosperm tissues and were identified at consistently higher levels 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 {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 {pmid30834947, year = {2019}, author = {Pandey, PK and Samanta, R and Yadav, RNS}, title = {Inside the plant: addressing bacterial endophytes in biotic stress alleviation.}, journal = {Archives of microbiology}, volume = {201}, number = {4}, pages = {415-429}, doi = {10.1007/s00203-019-01642-y}, pmid = {30834947}, issn = {1432-072X}, support = {Grant no. BT/04/NE/2009//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {*Bacterial Physiological Phenomena ; Endophytes/*physiology ; Plants/microbiology ; Stress, Physiological ; Symbiosis ; }, abstract = {Bacterial endophytes are the internal association of bacteria with the plants, cherished whole or any part of their life cycle inside the plant. They are reported to improve plant health against the biotic stresses via de novo synthesis of structural compounds and stimulation of plant immunity. They are found to be vital in development of host resistance against phytopathogens and capable in reducing and elimination of deleterious effects of plant pathogens. Fungal-, bacterial-, viral-, insect- and nematode-associated negative effect can be reduced by the bacterial endophytes. They are also reported to control plant pathogens through several defense mechanisms such as by producing antimicrobial compounds and antibiotics, de novo synthesis of structural compounds, keeping out of pathogens by niche competition and induction of plant immunity or induced systemic resistance. In this review, an effort is made to summarize the exploitation of endophytic bacteria as a biological substitute to control biotic stresses in agricultural practices.}, }
@article {pmid30639767, year = {2019}, author = {Davis, WJ and Amses, KR and Benny, GL and Carter-House, D and Chang, Y and Grigoriev, I and Smith, ME and Spatafora, JW and Stajich, JE and James, TY}, title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {152-163}, doi = {10.1016/j.ympev.2019.01.006}, pmid = {30639767}, issn = {1095-9513}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Fungal Proteins/genetics ; Fungi/*classification/*genetics ; Gene Library ; *Genome, Fungal ; Genomics ; Likelihood Functions ; *Phylogeny ; Symbiosis/genetics ; }, abstract = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.}, }
@article {pmid30621755, year = {2018}, author = {Osmanovic, D and Kessler, DA and Rabin, Y and Soen, Y}, title = {Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {24}, doi = {10.1186/s13062-018-0224-7}, pmid = {30621755}, issn = {1745-6150}, mesh = {*Adaptation, Biological ; Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; *Host-Pathogen Interactions ; *Microbiota ; Models, Genetic ; *Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.<br><br>RESULTS: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (&quot;detox&quot;). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host's offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).<br><br>CONCLUSIONS: These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.<br><br>REVIEWERS: This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.}, }
@article {pmid30329064, year = {2019}, author = {Kashkouli, M and Fathipour, Y and Mehrabadi, M}, title = {Potential Management Tactics for Pistachio Stink Bugs, Brachynema germari, Acrosternum heegeri and Acrosternum arabicum (Hemiptera: Pentatomidae): High Temperature and Chemical Surface Sterilants Leading to Symbiont Suppression.}, journal = {Journal of economic entomology}, volume = {112}, number = {1}, pages = {244-254}, doi = {10.1093/jee/toy324}, pmid = {30329064}, issn = {1938-291X}, mesh = {Animals ; Fertility ; *Hemiptera/microbiology ; Hot Temperature ; Insect Control/*methods ; Longevity ; Ovum ; Sterilization ; Symbiosis ; }, abstract = {Insect symbionts offer an opportunity to deal with the anticipated elevated demand for novel pest management strategies. One approach is the disruption of essential symbionts required by the pests. In the present study, we examined the effects of symbiont elimination strategies, high temperature and sterilization agents, on the fitness of three stink bugs, Brachynema germari Kolenati, Acrosternum heegeri Fieber, and Acrosternum arabicum Wagner by using demographic approach. In the high-temperature experiments, almost all insects exhibited severe fitness defects, including elevated nymphal mortality and reduced population growth parameters (especially intrinsic rate of increase, r), as well as significant reductions in the gut symbiont titers. In the egg surface sterilization assays, we experimentally assessed the effects of sterilization agents on the bugs and their symbionts and observed similar fitness defects to those observed under the high-temperature condition. According to the results, we concluded that the host's defective phenotypes are attributable not to the heat stress itself but to the suppression of the symbiont titer, which highlights the possibility that global warming and elevated temperature may negatively affect this mutualism. Together, the results suggest the biological importance of the bacterial symbiont for the host that might help us for better management of these important pests in the future.}, }
@article {pmid30071013, year = {2018}, author = {Ma, D and Leulier, F}, title = {The importance of being persistent: The first true resident gut symbiont in Drosophila.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e2006945}, pmid = {30071013}, issn = {1545-7885}, mesh = {Acetobacter ; Animals ; Drosophila/*microbiology/physiology ; Drosophila melanogaster/microbiology/physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract ; Microbiota ; Symbiosis/physiology ; }, abstract = {In the animal kingdom, nutritional mutualism is a perpetual and intimate dialogue carried out between the host and its associated gut community members. This dialogue affects many aspects of the host's development and physiology. Some constituents of the animal gut microbiota can stably reside within the host for years, and such long-term persistence might be a prerequisite for these microbes to assert their beneficial impact. How long-term persistence is established and maintained is an interesting question, and several classic model organisms associated with cultivable resident strains are used to address this question. However, in Drosophila, this model has long eluded fly geneticists. In this issue of PLOS Biology, Pais and colleagues present the most rigorous and comprehensive demonstration to date that persistence and gut residency do take place in the digestive tract of Drosophila melanogaster. This natural gut isolate of Acetobacter thailandicus stably colonizes the adult fly foregut, accelerates larval maturation, and boosts host fecundity and fertility as efficiently as the known laboratory strains. The discovery of such stable association will be a boon for the Drosophila community interested in host-microbiota interaction, as it not only provides a novel model to unravel the molecular underpinnings of persistence but also opens a new arena for using Drosophila to study the implications of gut persistence in evolution and ecology.}, }
@article {pmid30037568, year = {2018}, author = {Mostowy, RJ and Holt, KE}, title = {Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {1008-1021}, pmid = {30037568}, issn = {1878-4380}, mesh = {Animals ; Antigens, Bacterial/chemistry/genetics/physiology ; Bacteria/*genetics/*metabolism/pathogenicity ; Bacterial Capsules/*chemistry/*genetics/immunology/*physiology ; *Biodiversity ; Cell Communication ; Ecology ; Evolution, Molecular ; Genetic Loci ; Humans ; Immunity ; Lipopolysaccharides/classification/genetics/immunology/physiology ; Phage Therapy ; Polysaccharides ; Polysaccharides, Bacterial/chemistry/genetics/immunology/physiology ; Serotyping ; Symbiosis ; Vaccines, Conjugate ; }, abstract = {Bacterial pathogens and commensals are surrounded by diverse surface polysaccharides which include capsules and lipopolysaccharides. These carbohydrates play a vital role in bacterial ecology and interactions with the environment. Here, we review recent rapid advancements in this field, which have improved our understanding of the roles, structures, and genetics of bacterial polysaccharide antigens. Genetic loci encoding the biosynthesis of these antigens may have evolved as bacterial diversity-generating machines, driven by selection from a variety of forces, including host immunity, bacteriophages, and cell-cell interactions. We argue that the high adaptive potential of polysaccharide antigens should be taken into account in the design of polysaccharide-targeting medical interventions like conjugate vaccines and phage-based therapies.}, }
@article {pmid29563264, year = {2018}, author = {Madden, AA and Epps, MJ and Fukami, T and Irwin, RE and Sheppard, J and Sorger, DM and Dunn, RR}, title = {The ecology of insect-yeast relationships and its relevance to human industry.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1875}, pages = {}, pmid = {29563264}, issn = {1471-2954}, mesh = {Animals ; Ascomycota/*physiology ; Biological Evolution ; Ecosystem ; *Food Industry ; Humans ; Insecta/*microbiology ; Plant Nectar/metabolism ; Symbiosis ; }, abstract = {Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.}, }
@article {pmid31089666, year = {2018}, author = {Cazzolla Gatti, R}, title = {endogenosymbiosis: from hypothesis to empirical evidence towards a Unified Symbiogenetic Theory (UST).}, journal = {Theoretical biology forum}, volume = {111}, number = {1-2}, pages = {13-26}, doi = {10.19272/201811402002}, pmid = {31089666}, issn = {0035-6050}, mesh = {*Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {In 1967 Lynn (Sagan) Margulis proposed that mitochondria, photosynthetic plastids and cilia were acquired prokaryotes and evolved symbiotically to form anaerobic bacteria, photosynthetic bacteria and eventually algae. Although most of this theory is well-accepted now, the hypothesis that endosymbiotic spirochaetes developed into eukaryotic flagella and cilia, and the following proposals of an endosymbiotic origin of other eukaryotic organelles such as peroxisomes, glyoxysomes, etc. have not received much acceptance, since evidence suggests they lack a genome and do not show ultrastructural similarities to bacteria or archaea. Nevertheless, the idea that over millennia mitochondria, plastids, prokaryotic and eukaryotic cells and even flagella and peroxisomes, as either primary or secondary endosymbionts, transferred some or all of their own DNA to the host cell’s nucleus through a process called «endogenosymbiosis» (i.e. a symbiotic gene transfer, such as the internalisation of the endosymbiont’s DNA with lateral transfer) has been recently suggested. This endogenosymbiosis could take place during the evolutionary transition from the symbiotic interacting community, invoked by Margulis, to a fully-integrated (either prokaryotic or eukaryotic) cell. This process could explain the missing evidence of the presence of DNA in flagella and peroxisomes whose ancestor endosymbionts, during the long endogenosymbiotic evolution, could have transferred their whole genome to the host cell that subsequently integrated it in its own genome, directly controlling its expression. Furthermore, the endogenosymbiosis hypothesis could be the explanation of the transition between an RNA to a DNA world and of some cases of true sympatric evolution of species, apparently inexplicable by the canonical speciation processes. Here, after an introduction to the theoretical basis of endogenosymbiosis and a discussion of the empirical confirming evidence, I show a graphical summary of the integration between this and the former endosymbiosis theories. The Serial Endosymbiosis Theory and the Secondary Endosymbiosis are merged with the Endogenosymbiosis Theory in a Unified Symbiogenetic Theory (UST).}, }
@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 iPSC lines in the presence of valproic acid.}, journal = {Journal of tissue engineering and regenerative medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/term.2904}, pmid = {31148385}, issn = {1932-7005}, 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 4 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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15975}, pmid = {31148173}, issn = {1469-8137}, 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. This article is protected by copyright. All rights reserved.}, }
@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 {pmid30804519, year = {2019}, author = {Delavaux, CS and Weigelt, P and Dawson, W and Duchicela, J and Essl, F and van Kleunen, M and König, C and Pergl, J and Pyšek, P and Stein, A and Winter, M and Schultz, P and Kreft, H and Bever, JD}, title = {Mycorrhizal fungi influence global plant biogeography.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {3}, pages = {424-429}, doi = {10.1038/s41559-019-0823-4}, pmid = {30804519}, issn = {2397-334X}, mesh = {Biodiversity ; Islands ; Mycorrhizae/*physiology ; *Plant Dispersal ; Plants/*microbiology ; *Symbiosis ; }, abstract = {Island biogeography has traditionally focused primarily on abiotic drivers of colonization, extinction and speciation. However, establishment on islands could also be limited by biotic drivers, such as the absence of symbionts. Most plants, for example, form symbioses with mycorrhizal fungi, whose limited dispersal to islands could act as a colonization filter for plants. We tested this hypothesis using global-scale analyses of ~1.4 million plant occurrences, including ~200,000 plant species across ~1,100 regions. We find evidence for a mycorrhizal filter (that is, the filtering out of mycorrhizal plants on islands), with mycorrhizal associations less common among native island plants than native mainland plants. Furthermore, the proportion of native mycorrhizal plants in island floras decreased with isolation, possibly as a consequence of a decline in symbiont establishment. We also show that mycorrhizal plants contribute disproportionately to the classic latitudinal gradient of plant species diversity, with the proportion of mycorrhizal plants being highest near the equator and decreasing towards the poles. Anthropogenic pressure and land use alter these plant biogeographical patterns. Naturalized floras show a greater proportion of mycorrhizal plant species on islands than in mainland regions, as expected from the anthropogenic co-introduction of plants with their symbionts to islands and anthropogenic disturbance of symbionts in mainland regions. We identify the mycorrhizal association as an overlooked driver of global plant biogeographical patterns with implications for contemporary island biogeography and our understanding of plant invasions.}, }
@article {pmid30742105, year = {2019}, author = {Davies, NG and Flasche, S and Jit, M and Atkins, KE}, title = {Within-host dynamics shape antibiotic resistance in commensal bacteria.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {3}, pages = {440-449}, doi = {10.1038/s41559-018-0786-x}, pmid = {30742105}, issn = {2397-334X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Physiological Phenomena/drug effects ; Biological Evolution ; Drug Resistance, Microbial/*physiology ; Escherichia coli/*drug effects/physiology ; Europe ; *Host-Pathogen Interactions ; *Microbial Interactions ; Streptococcus pneumoniae/*drug effects/physiology ; Symbiosis ; }, abstract = {The spread of antibiotic resistance, a major threat to human health, is poorly understood. Simple population-level models of bacterial transmission predict that above a certain rate of antibiotic consumption in a population, resistant bacteria should completely eliminate non-resistant strains, while below this threshold they should be unable to persist at all. This prediction stands at odds with empirical evidence showing that resistant and non-resistant strains coexist stably over a wide range of antibiotic consumption rates. Not knowing what drives this long-term coexistence is a barrier to developing evidence-based strategies for managing the spread of resistance. Here, we argue that competition between resistant and sensitive pathogens within individual hosts gives resistant pathogens a relative fitness benefit when they are rare, promoting coexistence between strains at the population level. To test this hypothesis, we embed mechanistically explicit within-host dynamics in a structurally neutral pathogen transmission model. Doing so allows us to reproduce patterns of resistance observed in the opportunistic pathogens Escherichia coli and Streptococcus pneumoniae across European countries and to identify factors that may shape resistance evolution in bacteria by modulating the intensity and outcomes of within-host competition.}, }
@article {pmid30570692, year = {2019}, author = {Olanrewaju, OS and Ayangbenro, AS and Glick, BR and Babalola, OO}, title = {Plant health: feedback effect of root exudates-rhizobiome interactions.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {3}, pages = {1155-1166}, doi = {10.1007/s00253-018-9556-6}, pmid = {30570692}, issn = {1432-0614}, support = {UID81192//National Research Foundation/ ; }, mesh = {Bacteria/metabolism ; Fungi/metabolism ; Microbiota/*physiology ; Plant Development/*physiology ; Plant Exudates ; Plant Roots/*metabolism/*microbiology ; Plants/metabolism/*microbiology ; Quorum Sensing/physiology ; Rhizosphere ; Symbiosis/*physiology ; }, abstract = {The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.}, }
@article {pmid30426159, year = {2019}, author = {Mohanty, I and Rath, A and Swain, SP and Pradhan, N and Hazra, RK}, title = {Wolbachia Population in Vectors and Non-vectors: A Sustainable Approach Towards Dengue Control.}, journal = {Current microbiology}, volume = {76}, number = {2}, pages = {133-143}, doi = {10.1007/s00284-018-1596-8}, pmid = {30426159}, issn = {1432-0991}, support = {0//Lady Tata Memorial Trust/ ; }, mesh = {Aedes/microbiology ; Animals ; Biological Control Agents ; Communicable Disease Control/*methods ; Dengue/*prevention &amp; control/transmission ; Female ; India ; Male ; Mosquito Vectors/classification/*microbiology ; Ovary/microbiology ; Polymerase Chain Reaction ; Prevalence ; Salivary Glands/microbiology ; Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia is gram negative obligate endosymbiont known for reproductive manipulation in the host. It is important to study the presence of natural Wolbachia in mosquitoes which can later help in understanding the effect of transfected strain on indigenous strain. With this view, the present study is undertaken to focus on the prevalence, diversity, infection frequencies, phylogeny and density of indigenous Wolbachia strains in wild mosquito species of Odisha. Our study confirms Wolbachia presence in Ae. albopictus, Cx. quinquefasciatus, Cx. vishnui, Cx. gelidus, Ar. subalbatus, Mn. uniformis, and Mn. indiana. Wolbachia in the above mosquitoes were separated into two supergroups (A and B). Ae. albopictus, the major vector of dengue and chikungungunya had both super-infection and mono-infection. The ovaries of Ae. albopictus were highest in density of Wolbachia as compared to midguts or salivary glands. wAlBA and wAlbB density were variable in mosquitoes of F1 generation for both the sex and at different age. We also found that Wolbachia super-infection in females tends to increase whereas wAlbA density reduced completely as compared to wAlbB in males when they grew old. Giemsa stained squashed ovaries revealed pink pleomorphic Wolbachia cells with different shapes and forms. This study is unique in its kind covering the major aspects of the endosymbiont Wolbachia and focusing on its potential as a biocontrol agent in arboviral outbreaks. Knowledge on potential of the indigenous strain and interactions between Wolbachia and viruses can be utilized further to reduce the global burden of vector borne diseases.}, }
@article {pmid30013162, year = {2018}, author = {Lin, XB and Wang, T and Stothard, P and Corander, J and Wang, J and Baines, JF and Knowles, SCL and Baltrūnaitė, L and Tasseva, G and Schmaltz, R and Tollenaar, S and Cody, LA and Grenier, T and Wu, W and Ramer-Tait, AE and Walter, J}, title = {The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2770-2784}, pmid = {30013162}, issn = {1751-7370}, mesh = {Animals ; Biofilms/*growth &amp; development ; Biological Evolution ; *Gastrointestinal Microbiome ; Genomics ; Lactobacillus/genetics/isolation &amp; purification/*physiology ; Lactobacillus reuteri/genetics/isolation &amp; purification/*physiology ; Mice/*microbiology ; Symbiosis/genetics ; }, abstract = {The eco-evolutionary interactions among members of the vertebrate gut microbiota that ultimately result in host-specific communities are poorly understood. Here we show that Lactobacillus reuteri coexists with species that belong to the Lactobacillus johnsonii cluster (L. johnsonii, L. gasseri, and L taiwanensis) in a taxonomically wide range of rodents, suggesting cohabitation over evolutionary times. The two dominant Lactobacillus species found in wild mice establish a commensalistic relationship in gastric biofilms when introduced together into germ-free mice in which L. reuteri facilitates colonization of L. taiwanensis. Genomic analysis revealed allopatric diversification in strains of both species that originated from geographically separated locations (Scotland and France). Allopatry of the strains resulted in reduced formation of mixed biofilms in vitro, indicating that interspecies interactions in gastric Lactobacillus-biofilms are the result of an adaptive evolutionary process that occurred in a biogeographical context. In summary, these findings suggest that members within the vertebrate gut microbiota can evolve inter-dependencies through ecological facilitation, which could represent one mechanism by which host-specific bacterial communities assemble across vertebrate species and an explanation for their spatial and biogeographic patterns.}, }
@article {pmid29977009, year = {2018}, author = {Røder, HL and Herschend, J and Russel, J and Andersen, MF and Madsen, JS and Sørensen, SJ and Burmølle, M}, title = {Enhanced bacterial mutualism through an evolved biofilm phenotype.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2608-2618}, pmid = {29977009}, issn = {1751-7370}, mesh = {Biofilms/*growth &amp; development ; Cyclic GMP/analogs &amp; derivatives/biosynthesis ; Escherichia coli Proteins/genetics ; Paenibacillus/genetics/*physiology ; Phenotype ; Phosphorus-Oxygen Lyases/genetics ; *Symbiosis ; Xanthomonas/genetics/*physiology ; }, abstract = {Microbial communities primarily consist of multiple species that affect one another's fitness both directly and indirectly. This study showed that the cocultivation of Paenibacillus amylolyticus and Xanthomonas retroflexus exhibited facultative mutualistic interactions in a static environment, during the course of which a new adapted phenotypic variant of X. retroflexus appeared. Although the emergence of this variant was not directly linked to the presence of P. amylolyticus, its establishment in the coculture enhanced the productivity of both species due to mutations that stimulated biofilm formation. The mutations were detected in genes encoding a diguanylate cyclase predicted to synthesise cyclic-di-GMP. Examinations of the biofilm formed in cocultures of P. amylolyticus and the new variant of X. retroflexus revealed a distinct spatial organisation: P. amylolyticus only resided in biofilms in association with X. retroflexus and occupied the outer layers. The X. retroflexus variant therefore facilitated increased P. amylolyticus growth as it produced more biofilm biomass. The increase in X. retroflexus biomass was thus not at the expense of P. amylolyticus, demonstrating that interspecies interactions can shape diversification in a mutualistic coculture and reinforce these interactions, ultimately resulting in enhanced communal performance.}, }
@article {pmid29358683, year = {2018}, author = {Mullineaux-Sanders, C and Suez, J and Elinav, E and Frankel, G}, title = {Sieving through gut models of colonization resistance.}, journal = {Nature microbiology}, volume = {3}, number = {2}, pages = {132-140}, doi = {10.1038/s41564-017-0095-1}, pmid = {29358683}, issn = {2058-5276}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Enterobacteriaceae/growth &amp; development/pathogenicity ; Enterobacteriaceae Infections/drug therapy/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Germ-Free Life ; Host-Pathogen Interactions/drug effects/*physiology ; Humans ; Mice ; Models, Animal ; Symbiosis ; }, abstract = {The development of innovative high-throughput genomics and metabolomics technologies has considerably expanded our understanding of the commensal microorganisms residing within the human body, collectively termed the microbiota. In recent years, the microbiota has been reported to have important roles in multiple aspects of human health, pathology and host-pathogen interactions. One function of commensals that has attracted particular interest is their role in protection against pathogens and pathobionts, a concept known as colonization resistance. However, pathogens are also able to sense and exploit the microbiota during infection. Therefore, obtaining a holistic understanding of colonization resistance mechanisms is essential for the development of microbiome-based and microbiome-targeting therapies for humans and animals. Achieving this is dependent on utilizing physiologically relevant animal models. In this Perspective, we discuss the colonization resistance functions of the gut microbiota and sieve through the advantages and limitations of murine models commonly used to study such mechanisms within the context of enteric bacterial infection.}, }
@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 = {}, number = {}, pages = {}, 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 oberseved 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 {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 = {}, number = {}, pages = {}, doi = {10.1101/gr.245001.118}, pmid = {31138619}, issn = {1549-5469}, 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 'genomic symbiosis'. However, these telomere-specialized, jockey family retrotransposons may actually evolve to 'selfishly' over-replicate 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-million-year-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 D. 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 'selfish' machinery shapes telomere elongation across Drosophila rather than completely domesticated, symbiotic mobile elements.}, }
@article {pmid30912174, year = {2019}, author = {Bing, XL and Zhao, DS and Hong, XY}, title = {Bacterial reproductive manipulators in rice planthoppers.}, journal = {Archives of insect biochemistry and physiology}, volume = {101}, number = {2}, pages = {e21548}, doi = {10.1002/arch.21548}, pmid = {30912174}, issn = {1520-6327}, support = {31672035//National Natural Science Foundation of China/ ; 31871976//National Natural Science Foundation of China/ ; 804015//the startup grant from Nanjing Agricultural University/ ; }, mesh = {Animals ; *Bacterial Physiological Phenomena ; Female ; Hemiptera/*microbiology/physiology ; Male ; Reproduction/*physiology ; Symbiosis ; }, abstract = {Rice planthoppers (Hemiptera: Delphacidae) are notorious pests for rice (Oryza sativa) in Asia, posing a serious threat to rice production and grain security. Rice planthoppers harbor diverse bacterial symbionts, including Wolbachia, Cardinium, Spiroplasma, and Arsenophonus, which are known to manipulate reproduction in arthropod hosts. This microreview is to introduce current knowledge of bacterial reproductive manipulators in rice planthoppers, including their diversity, population dynamics, localization, transmission, and biological functions.}, }
@article {pmid30762095, year = {2019}, author = {Martínez-Rodríguez, P and Rolán-Alvarez, E and Del Mar Pérez-Ruiz, M and Arroyo-Yebras, F and Carpena-Catoira, C and Carvajal-Rodríguez, A and Bella, JL}, title = {Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1036-1047}, doi = {10.1007/s00248-019-01338-2}, pmid = {30762095}, issn = {1432-184X}, support = {CGL2016-75482-P//Ministerio de Ciencia y Tecnolog?a/ ; BFU2013-44635//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, mesh = {Animals ; Biological Coevolution ; Computer Simulation ; Geography ; Grasshoppers/*microbiology ; Linear Models ; *Polymorphism, Genetic ; Seasons ; *Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia is an intracellular endosymbiont that can produce a range of effects on host fitness, but the temporal dynamics of Wolbachia strains have rarely been experimentally evaluated. We compare interannual strain frequencies along a geographical region for understanding the forces that shape Wolbachia strain frequency in natural populations of its host, Chorthippus parallelus (Orthoptera, Acrididae). General linear models show that strain frequency changes significantly across geographical and temporal scales. Computer simulation allows to reject the compatibility of the observed patterns with either genetic drift or sampling errors. We use consecutive years to estimate total Wolbachia strain fitness. Our estimation of Wolbachia fitness is significant in most cases, within locality and between consecutive years, following a negatively frequency-dependent trend. Wolbachia spp. B and F strains show a temporal pattern of variation that is compatible with a negative frequency-dependent natural selection mechanism. Our results suggest that such a mechanism should be at least considered in future experimental and theoretical research strategies that attempt to understand Wolbachia biodiversity.}, }
@article {pmid30664701, year = {2019}, author = {Lu, M and Hedin, LO}, title = {Global plant-symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {2}, pages = {239-250}, doi = {10.1038/s41559-018-0759-0}, pmid = {30664701}, issn = {2397-334X}, mesh = {*Bacterial Physiological Phenomena ; Biological Evolution ; Fungi/*physiology ; Game Theory ; Life History Traits ; Models, Biological ; Plants/*microbiology ; *Symbiosis ; }, abstract = {One of the most distinct but unresolved global patterns is the apparent variation in plant-symbiont nutrient strategies across biomes. This pattern is central to our understanding of plant-soil-nutrient feedbacks in the land biosphere, which, in turn, are essential for our ability to predict the future dynamics of the Earth system. Here, we present an evolution-based trait-modelling approach for resolving (1) the organization of plant-symbiont relationships across biomes worldwide and (2) the emergent consequences for plant community composition and land biogeochemical cycles. Using game theory, we allow plants to use different belowground strategies to acquire nutrients and compete within local plant-soil-nutrient cycles in boreal, temperate and tropical biomes. The evolutionarily stable strategies that emerge from this analysis allow us to predict the distribution of belowground symbioses worldwide, the sequence and timing of plant succession, the bistability of ecto- versus arbuscular mycorrhizae in temperate and tropical forests, and major differences in the land carbon and nutrient cycles across biomes. Our findings imply that belowground symbioses have been central to the evolutionary assembly of plant communities and plant-nutrient feedbacks at the scale of land biomes. We conclude that complex global patterns emerge from local between-organism interactions in the context of Darwinian natural selection and evolution, and that the underlying dynamics can be mechanistically probed by our low-dimensional modelling approach.}, }
@article {pmid30397795, year = {2019}, author = {Palacios, OA and Lopez, BR and Bashan, Y and de-Bashan, LE}, title = {Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {980-992}, doi = {10.1007/s00248-018-1282-1}, pmid = {30397795}, issn = {1432-184X}, support = {251102//Consejo Nacional de Ciencia y Tecnología/ ; 284562//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Azospirillum brasilense/*physiology ; Chlorella/*physiology ; Indoleacetic Acids/metabolism ; Microalgae/physiology ; Population Growth ; Starch/metabolism ; *Symbiosis ; Tryptophan/metabolism ; }, abstract = {The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media. Overall, populations of bacteria and microalgae were larger when co-immobilized. However, the highest starch production was measured in C. sorokiniana immobilized alone and growing continuously in a C-free mineral medium. In this interaction, the initial nutritional condition influenced the time at which the highest accumulation of starch occurred in Chlorella, where the N-free medium induced faster starch production and the richer medium delayed its accumulation. Formation of aggregates made of microalgae and bacteria occurred in all nutritional conditions, with maximum at 83 h in mineral medium, and coincided with declining starch content. This study demonstrates that synthetic mutualism between C. sorokiniana and A. brasilense can be modulated by the initial nutritional condition, mainly by the presence or absence of nitrogen and carbon in the medium in which they are interacting.}, }
@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 = {}, number = {}, 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. By studying microbially independent animals, we will gain a more complete picture 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}, 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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15953}, pmid = {31125438}, issn = {1469-8137}, 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 roots with the root-knot nematode Meloidogyne graminicola. •Genetic approaches and chemical sprays were used to manipulate SL signaling in rice prior to 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. While the application of low dose of the SL analog 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 to 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15958}, pmid = {31125425}, issn = {1469-8137}, 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 to 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 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/mmi.14312}, pmid = {31124196}, issn = {1365-2958}, 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. This article is protected by copyright. All rights reserved.}, }
@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}, support = {31872129//National Natural Science Foundation of China/ ; 162300410107 and 162300410346//Natural Science Foundation of Henan Province/ ; 172102110169, 182102110067, 182102110289 and 192102110001//Foundation of Henan Science and Technology Committee/ ; 18A180009//Foundation of Henan Educational Committee/ ; 2017GGJS146//Training Program of Youth Backbone Teacher of Henan Province/ ; }, 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 {pmid30566883, year = {2018}, author = {Grizotte-Lake, M and Zhong, G and Duncan, K and Kirkwood, J and Iyer, N and Smolenski, I and Isoherranen, N and Vaishnava, S}, title = {Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis.}, journal = {Immunity}, volume = {49}, number = {6}, pages = {1103-1115.e6}, doi = {10.1016/j.immuni.2018.11.018}, pmid = {30566883}, issn = {1097-4180}, support = {R01 DK113265/DK/NIDDK NIH HHS/United States ; R01 GM111772/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol Oxidoreductases/genetics/metabolism ; Animals ; Bacteria/classification/genetics ; Dysbiosis/*metabolism/microbiology ; Epithelial Cells/*metabolism/microbiology ; Host Microbial Interactions ; Interleukins/*metabolism ; Intestinal Mucosa/cytology/*metabolism/microbiology ; Lymphocytes/metabolism/microbiology ; Mice, Inbred C57BL ; Mice, Knockout ; Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Salmonella typhimurium/genetics/physiology ; Symbiosis ; Tretinoin/*metabolism ; }, abstract = {Retinoic acid (RA), a vitamin A metabolite, regulates transcriptional programs that drive protective or pathogenic immune responses in the intestine, in a manner dependent on RA concentration. Vitamin A is obtained from diet and is metabolized by intestinal epithelial cells (IECs), which operate in intimate association with microbes and immune cells. Here we found that commensal bacteria belonging to class Clostridia modulate RA concentration in the gut by suppressing the expression of retinol dehydrogenase 7 (Rdh7) in IECs. Rdh7 expression and associated RA amounts were lower in the intestinal tissue of conventional mice, as compared to germ-free mice. Deletion of Rdh7 in IECs diminished RA signaling in immune cells, reduced the IL-22-dependent antimicrobial response, and enhanced resistance to colonization by Salmonella Typhimurium. Our findings define a regulatory circuit wherein bacterial regulation of IEC-intrinsic RA synthesis protects microbial communities in the gut from excessive immune activity, achieving a balance that prevents colonization by enteric pathogens.}, }
@article {pmid30374168, year = {2018}, author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA}, title = {Microbial nitrogen limitation in the mammalian large intestine.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1441-1450}, pmid = {30374168}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Diet ; Dietary Proteins ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Intestine, Large/*metabolism/*microbiology ; Mammals/*microbiology ; Mice ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.}, }
@article {pmid30297742, year = {2018}, author = {Ahrendt, SR and Quandt, CA and Ciobanu, D and Clum, A and Salamov, A and Andreopoulos, B and Cheng, JF and Woyke, T and Pelin, A and Henrissat, B and Reynolds, NK and Benny, GL and Smith, ME and James, TY and Grigoriev, IV}, title = {Leveraging single-cell genomics to expand the fungal tree of life.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1417-1428}, doi = {10.1038/s41564-018-0261-0}, pmid = {30297742}, issn = {2058-5276}, mesh = {Biodiversity ; DNA, Ribosomal/genetics ; Fungi/classification/enzymology/*genetics/*metabolism ; Genetic Variation ; *Genome, Fungal ; *Genomics ; Heterozygote ; Life Cycle Stages ; Metabolic Networks and Pathways/genetics/physiology ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Secondary Metabolism/genetics/physiology ; Sequence Analysis, DNA ; Symbiosis/genetics/physiology ; }, abstract = {Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.}, }
@article {pmid30027485, year = {2019}, author = {Gabaldón, T and Fairhead, C}, title = {Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal.}, journal = {Current genetics}, volume = {65}, number = {1}, pages = {93-98}, doi = {10.1007/s00294-018-0867-z}, pmid = {30027485}, issn = {1432-0983}, support = {BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {Candida glabrata/classification/*genetics/physiology ; Candidiasis/microbiology ; Genes, Mating Type, Fungal/*genetics ; Genome, Fungal/*genetics ; Genomics/*methods ; Host-Pathogen Interactions ; Humans ; Phylogeny ; Reproduction/genetics ; Symbiosis ; }, abstract = {Candida glabrata is an opportunistic yeast pathogen, whose incidence has increased over the last decades. Despite its genus name, this species is actually more closely related to the budding yeast Saccharomyces cerevisiae than to other Candida pathogens, such as Candida albicans. Hence, C. glabrata and C. albicans must have acquired the ability to infect humans independently, which is reflected in the use of different mechanism for virulence, and survival in the host. Yet, research on C. glabrata suffers from assumptions carried over from the more studied C. albicans. Regarding the adaptation of C. glabrata to the human host, the prejudice was that, just as C. albicans, C. glabrata is a natural human commensal that turns deadly when immune defenses weaken. It was also considered asexual, as no one has observed mating, diploids, or spores, despite great efforts. However, the recent analysis of whole genomes from globally distributed C. glabrata isolates have shaken these assumptions. C. glabrata seems to be only secondarily associated to humans, as indicated by a lack of co-evolution with its host, and genomic footprints of recombination shows compelling evidence that this yeast is able to have sex. Here, we discuss the implications of this and other recent findings and highlight the new questions opened by this change in paradigm.}, }
@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 = {}, number = {}, pages = {}, 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 {pmid29379208, year = {2018}, author = {Probst, AJ and Ladd, B and Jarett, JK and Geller-McGrath, DE and Sieber, CMK and Emerson, JB and Anantharaman, K and Thomas, BC and Malmstrom, RR and Stieglmeier, M and Klingl, A and Woyke, T and Ryan, MC and Banfield, JF}, title = {Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {328-336}, doi = {10.1038/s41564-017-0098-y}, pmid = {29379208}, issn = {2058-5276}, mesh = {Archaea/*classification/growth &amp; development ; Autotrophic Processes ; Bacteria/*classification/growth &amp; development ; Carbon Cycle ; Geologic Sediments/*microbiology ; Groundwater/*microbiology ; Metagenomics ; Phylogeny ; *Symbiosis ; }, abstract = {An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus &quot;Altiarchaeum sp.&quot; and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. &quot;Altiarchaeum&quot;. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.}, }
@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 {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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, 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 {pmid30107045, year = {2018}, author = {Yadav, S and Eleftherianos, I}, title = {The Imaginal Disc Growth Factors 2 and 3 participate in the Drosophila response to nematode infection.}, journal = {Parasite immunology}, volume = {40}, number = {10}, pages = {e12581}, doi = {10.1111/pim.12581}, pmid = {30107045}, issn = {1365-3024}, support = {1R01AI110675-01A1//National Institute of Allergy and Infectious Diseases/ ; //Columbian College of Arts and Sciences at GWU/ ; //Department of Biological Sciences at GWU/ ; //Cosmos Club Foundation/ ; }, mesh = {Animals ; Drosophila/*immunology/*parasitology ; Drosophila Proteins/biosynthesis/genetics/*immunology/metabolism ; Glycoproteins/biosynthesis/genetics/*immunology/metabolism ; Imaginal Discs/metabolism ; Larva/immunology/parasitology ; Nematode Infections/*immunology ; Species Specificity ; Strongyloidea/*immunology/microbiology ; Symbiosis ; Xenorhabdus/growth &amp; development ; }, abstract = {The Drosophila imaginal disc growth factors (IDGFs) induce the proliferation of imaginal disc cells and terminate cell proliferation at the end of larval development. However, the participation of Idgf-encoding genes in other physiological processes of Drosophila including the immune response to infection is not fully understood. Here, we show the contribution of Idgf2 and Idgf3 in the Drosophila response to infection with Steinernema carpocapsae nematodes carrying or lacking their mutualistic Xenorhabdus nematophila bacteria (symbiotic or axenic nematodes, respectively). We find that Idgf2 and Idgf3 are upregulated in Drosophila larvae infected with symbiotic or axenic Steinernema and inactivation of Idgf2 confers a survival advantage to Drosophila larvae against axenic nematodes. Inactivation of Idgf2 induces the Imd and Jak/Stat pathways, whereas inactivation of Idgf3 induces the Imd, Toll and Jak/Stat pathways. We also show that inactivation of the Imd pathway receptor PGRP-LE upregulates Idgf2 against Steinernema nematode infection. Finally, we demonstrate that inactivation of Idgf3 induces the recruitment of larval haemocytes in response to Steinernema. Our results indicate that Idgf2 and Idgf3 might be involved in different yet crucial immune functions in the Drosophila antinematode immune response. Similar findings will promote the development of new targets for species-specific pest control strategies.}, }
@article {pmid29410379, year = {2018}, author = {Shi, B and Leung, DYM and Taylor, PA and Li, H}, title = {Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {138}, number = {7}, pages = {1668-1671}, pmid = {29410379}, issn = {1523-1747}, support = {R01 GM099530/GM/NIGMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; UL1 RR025780/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Carrier State/microbiology ; Child ; Child, Preschool ; Dermatitis, Atopic/*microbiology/pathology ; Female ; Humans ; Male ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification/*pathogenicity ; *Microbiota ; Middle Aged ; Skin/*microbiology/pathology ; Staphylococcal Skin Infections/*microbiology/pathology ; Symbiosis ; Young Adult ; }, }
@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 {pmid28397362, year = {2017}, author = {Roy, M and Vasco-Palacios, A and Geml, J and Buyck, B and Delgat, L and Giachini, A and Grebenc, T and Harrower, E and Kuhar, F and Magnago, A and Rinaldi, AC and Schimann, H and Selosse, MA and Sulzbacher, MA and Wartchow, F and Neves, MA}, title = {The (re)discovery of ectomycorrhizal symbioses in Neotropical ecosystems sketched in Florianópolis.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {920-923}, doi = {10.1111/nph.14531}, pmid = {28397362}, issn = {1469-8137}, mesh = {Brazil ; Congresses as Topic ; DNA Barcoding, Taxonomic ; *Ecosystem ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; *Symbiosis ; }, }
@article {pmid28272801, year = {2017}, author = {Truong, C and Mujic, AB and Healy, R and Kuhar, F and Furci, G and Torres, D and Niskanen, T and Sandoval-Leiva, PA and Fernández, N and Escobar, JM and Moretto, A and Palfner, G and Pfister, D and Nouhra, E and Swenie, R and Sánchez-García, M and Matheny, PB and Smith, ME}, title = {How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {913-919}, doi = {10.1111/nph.14509}, pmid = {28272801}, issn = {1469-8137}, mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification ; Plants/microbiology ; South America ; Symbiosis ; }, }
@article {pmid28079936, year = {2017}, author = {Wurzburger, N and Brookshire, EN and McCormack, ML and Lankau, RA}, title = {Mycorrhizal fungi as drivers and modulators of terrestrial ecosystem processes.}, journal = {The New phytologist}, volume = {213}, number = {3}, pages = {996-999}, doi = {10.1111/nph.14409}, pmid = {28079936}, issn = {1469-8137}, mesh = {Congresses as Topic ; *Ecosystem ; Mycorrhizae/*physiology ; Symbiosis ; }, }
@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}, }
@article {pmid30727958, year = {2019}, author = {Kampfraath, AA and Klasson, L and Anvar, SY and Vossen, RHAM and Roelofs, D and Kraaijeveld, K and Ellers, J}, title = {Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {106}, doi = {10.1186/s12864-019-5492-9}, pmid = {30727958}, issn = {1471-2164}, support = {865.12.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 15494//Stichting voor de Technische Wetenschappen/ ; }, mesh = {Animals ; Arthropods/*microbiology/physiology ; DNA Repair ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Parthenogenesis ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics/physiology ; }, abstract = {BACKGROUND: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).<br><br>RESULTS: Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.<br><br>CONCLUSIONS: The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.}, }
@article {pmid30681888, year = {2019}, author = {Marczak, M and Żebracki, K and Koper, P and Turska-Szewczuk, A and Mazur, A and Wydrych, J and Wójcik, M and Skorupska, A}, title = {Mgl2 Is a Hypothetical Methyltransferase Involved in Exopolysaccharide Production, Biofilm Formation, and Motility in Rhizobium leguminosarum bv. trifolii.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI01190026R}, doi = {10.1094/MPMI-01-19-0026-R}, pmid = {30681888}, issn = {0894-0282}, abstract = {In this study, functional characterization of the mgl2 gene located near the Pss-I exopolysaccharide biosynthesis region in Rhizobium leguminosarum bv. trifolii TA1 is described. The hypothetical protein encoded by the mgl2 gene was found to be similar to methyltransferases (MTases). Protein homology and template-based modeling facilitated prediction of the Mgl2 structure, which greatly resembled class I MTases with a S-adenosyl-L-methionine-binding cleft. The Mgl2 protein was engaged in exopolysaccharide, but not lipopolysaccharide, synthesis. The mgl2 deletion mutant produced exopolysaccharide comprised of only low molecular weight fractions, while overexpression of mgl2 caused overproduction of exopolysaccharide with a normal low to high molecular weight ratio. The deletion of the mgl2 gene resulted in disturbances in biofilm formation and a slight increase in motility in minimal medium. Red clover (Trifolium pratense) inoculated with the mgl2 mutant formed effective nodules, and the appearance of the plants indicated active nitrogen fixation. The mgl2 gene was preceded by an active and strong promoter. Mgl2 was defined as an integral membrane protein and formed homodimers in vivo; however, it did not interact with Pss proteins encoded within the Pss-I region. The results are discussed in the context of the possible involvement of the newly described potential MTase in various metabolic traits, such as the exopolysaccharide synthesis and motility that are important for rhizobial saprophytic and symbiotic relationships.}, }
@article {pmid30356215, year = {2018}, author = {Schretter, CE and Vielmetter, J and Bartos, I and Marka, Z and Marka, S and Argade, S and Mazmanian, SK}, title = {A gut microbial factor modulates locomotor behaviour in Drosophila.}, journal = {Nature}, volume = {563}, number = {7731}, pages = {402-406}, pmid = {30356215}, issn = {1476-4687}, support = {R01 NS085910/NS/NINDS NIH HHS/United States ; }, mesh = {Aldose-Ketose Isomerases/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; *Carbohydrate Metabolism/drug effects ; Drosophila melanogaster/drug effects/metabolism/*microbiology/*physiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Germ-Free Life ; Lactobacillus brevis/*enzymology/isolation &amp; purification/*metabolism ; Locomotion/drug effects/*physiology ; Motor Activity/drug effects/physiology ; Neural Pathways ; Neurons/drug effects/metabolism ; Octopamine/metabolism/pharmacology ; Symbiosis ; }, abstract = {While research into the biology of animal behaviour has primarily focused on the central nervous system, cues from peripheral tissues and the environment have been implicated in brain development and function1. There is emerging evidence that bidirectional communication between the gut and the brain affects behaviours including anxiety, cognition, nociception and social interaction1-9. Coordinated locomotor behaviour is critical for the survival and propagation of animals, and is regulated by internal and external sensory inputs10,11. However, little is known about how the gut microbiome influences host locomotion, or the molecular and cellular mechanisms involved. Here we report that germ-free status or antibiotic treatment results in hyperactive locomotor behaviour in the fruit fly Drosophila melanogaster. Increased walking speed and daily activity in the absence of a gut microbiome are rescued by mono-colonization with specific bacteria, including the fly commensal Lactobacillus brevis. The bacterial enzyme xylose isomerase from L. brevis recapitulates the locomotor effects of microbial colonization by modulating sugar metabolism in flies. Notably, thermogenetic activation of octopaminergic neurons or exogenous administration of octopamine, the invertebrate counterpart of noradrenaline, abrogates the effects of xylose isomerase on Drosophila locomotion. These findings reveal a previously unappreciated role for the gut microbiome in modulating locomotion, and identify octopaminergic neurons as mediators of peripheral microbial cues that regulate motor behaviour in animals.}, }
@article {pmid29868500, year = {2018}, author = {Ma, ZP and Song, Y and Cai, ZH and Lin, ZJ and Lin, GH and Wang, Y and Zhou, J}, title = {Anti-quorum Sensing Activities of Selected Coral Symbiotic Bacterial Extracts From the South China Sea.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {144}, pmid = {29868500}, issn = {2235-2988}, mesh = {Acyl-Butyrolactones/isolation &amp; purification/pharmacology ; Animals ; Anthozoa/*microbiology ; Anti-Bacterial Agents/*isolation &amp; purification/*pharmacology ; Bacteria/genetics/*isolation &amp; purification/*metabolism ; Bacterial Adhesion/drug effects ; Bacterial Proteins/genetics ; Biofilms/drug effects/growth &amp; development ; China ; Chromobacterium ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gram-Positive Bacteria/isolation &amp; purification/metabolism ; Ligases/genetics ; Metalloendopeptidases/genetics ; Microbial Consortia ; Pseudomonas aeruginosa/drug effects/genetics ; Quorum Sensing/*drug effects/genetics ; Seawater/microbiology ; Staphylococcus hominis/genetics/isolation &amp; purification/metabolism ; Symbiosis ; Trans-Activators/genetics ; Transcription Factors/genetics ; Virulence/genetics ; Whole Genome Sequencing ; }, abstract = {The worldwide increase in antibiotic-resistant pathogens means that identification of alternative antibacterial drug targets and the subsequent development of new treatment strategies are urgently required. One such new target is the quorum sensing (QS) system. Coral microbial consortia harbor an enormous diversity of microbes, and are thus rich sources for isolating novel bioactive and pharmacologically valuable natural products. However, to date, the versatility of their bioactive compounds has not been broadly explored. In this study, about two hundred bacterial colonies were isolated from a coral species (Pocillopora damicornis) and screened for their ability to inhibit QS using the bioreporter strain Chromobacterium violaceum ATCC 12472. Approximately 15% (30 isolates) exhibited anti-QS activity, against the indicator strain. Among them, a typical Gram-positive bacterium, D11 (Staphylococcus hominis) was identified and its anti-QS activity was investigated. Confocal microscopy observations showed that the bacterial extract inhibited the biofilm formation of clinical isolates of wild-type P. aeruginosa PAO1 in a dose-dependent pattern. Chromatographic separation led to the isolation of a potent QS inhibitor that was identified by high-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy as DL-homocysteine thiolactone. Gene expression analyses using RT-PCR showed that strain D11 led to a significant down-regulation of QS regulatory genes (lasI, lasR, rhlI, and rhlR), as well as a virulence-related gene (lasB). From the chemical structure, the target compound (DL-homocysteine thiolactone) is an analog of the acyl-homoserine lactones (AHLs), and we presume that DL-homocysteine thiolactone outcompetes AHL in occupying the receptor and thereby inhibiting QS. Whole-genome sequence analysis of S. hominis D11 revealed the presence of predicted genes involved in the biosynthesis of homocysteine thiolactone. This study indicates that coral microbes are a resource bank for developing QS inhibitors and they will facilitate the discovery of new biotechnologically relevant compounds that could be used instead of traditional antibiotics.}, }
@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}, 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 = {}, number = {}, pages = {}, 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 = {}, number = {}, 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 = {}, number = {}, 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 poSSPs 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 regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analyses was performed during the trophophase, 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, OEssp1 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 at a higher amount in the OEssp1 and was absent from KDssp1. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in initiation of fruiting body formation as well as earlier aging. It is proposed that Ssp1 might function as a part of the fungal communication network and regulating the pattern of fungal development and metabolism in P. ostreatusImportanceSmall 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 as 'effectors'. It is proposed 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 = {P50GM098911 and P01GM125576.//National Institute of General Medical Sciences of the National Institutes of Health/ ; P01GM125576//National Institute of General Medical Sciences of the National Institutes of Health/ ; P50GM098911//National Institute of General Medical Sciences of the National Institutes of Health/ ; Collaborative Research Centre (CRC) 1182 &quot;Origin//Deutsche Forschungsgemeinschaft/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 5R37AI050661-16//National Institutes of Health/ ; }, 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 = {}, number = {}, pages = {}, 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 {pmid30592732, year = {2018}, author = {Sen, A and Duperron, S and Hourdez, S and Piquet, B and Léger, N and Gebruk, A and Le Port, AS and Svenning, MM and Andersen, AC}, title = {Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209273}, doi = {10.1371/journal.pone.0209273}, pmid = {30592732}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; *Bacteria/genetics ; Cold Temperature ; DNA, Mitochondrial ; Norway ; Oceans and Seas ; Phylogeny ; Polychaeta/anatomy &amp; histology/*microbiology/ultrastructure ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {We provide the first detailed identification of Barents Sea cold seep frenulate hosts and their symbionts. Mitochondrial COI sequence analysis, in combination with detailed morphological investigations through both light and electron microscopy was used for identifying frenulate hosts, and comparing them to Oligobrachia haakonmosbiensis and Oligobrachia webbi, two morphologically similar species known from the Norwegian Sea. Specimens from sites previously assumed to host O. haakonmosbiensis were included in our molecular analysis, which allowed us to provide new insight on the debate regarding species identity of these Oligobrachia worms. Our results indicate that high Arctic seeps are inhabited by a species that though closely related to Oligobrachia haakonmosbiensis, is nonetheless distinct. We refer to this group as the Oligobrachia sp. CPL-clade, based on the colloquial names of the sites they are currently known to inhabit. Since members of the Oligobrachia sp. CPL-clade cannot be distinguished from O. haakonmosbiensis or O. webbi based on morphology, we suggest that a complex of cryptic Oligobrachia species inhabit seeps in the Norwegian Sea and the Arctic. The symbionts of the Oligobrachia sp. CPL-clade were also found to be closely related to O. haakonmosbiensis symbionts, but genetically distinct. Fluorescent in situ hybridization and transmission electron micrographs revealed extremely dense populations of bacteria within the trophosome of members of the Oligobrachia sp. CPL-clade, which is unusual for frenulates. Bacterial genes for sulfur oxidation were detected and small rod shaped bacteria (round in cross section), typical of siboglinid-associated sulfur-oxidizing bacteria, were seen on electron micrographs of trophosome bacteriocytes, suggesting that sulfide constitutes the main energy source. We hypothesize that specific, local geochemical conditions, in particular, high sulfide fluxes and concentrations could account for the unusually high symbiont densities in members of the Oligrobrachia sp. CPL-clade.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz067}, pmid = {31095296}, issn = {1574-6941}, abstract = {The legume host and soil environment play a major role to establish effective symbiosis with diverse rhizobia for growth promotion and nodule formation. Aim of this study was to access morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that isolate were highly diverse in their appearance on yeast mannitol agar plates. The test isolates 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 (CCA) showed that soil pH and mineral nutrients could significantly influence bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient with resulted 45 unique BOX-types. Isolates' 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 genes' phylogenies suggested that the isolates' sym loci probably relate to 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, G 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 {pmid30810852, year = {2019}, author = {Vissa, S and Hofstetter, RW and Bonifácio, L and Khaustov, A and Knee, W and Uhey, DA}, title = {Phoretic mite communities associated with bark beetles in the maritime and stone pine forests of Setúbal, Portugal.}, journal = {Experimental &amp; applied acarology}, volume = {77}, number = {2}, pages = {117-131}, doi = {10.1007/s10493-019-00348-6}, pmid = {30810852}, issn = {1572-9702}, mesh = {Animals ; *Forests ; Mites/*physiology ; Pinus/growth &amp; development ; Portugal ; *Symbiosis ; Trees/growth &amp; development ; Weevils/*physiology ; }, abstract = {The phoretic mite communities of prominent bark beetle pests associated with pine stands of southern Portugal were sampled to determine whether they vary across bark beetle species and stand type. Bark beetles were sampled for mites from two primary (aggressive) bark beetle species (Ips sexdentatus and Orthotomicus erosus) and the most common secondary species (Hylurgus ligniperda) in maritime pine (Pinus pinaster) and stone pine (Pinus pinea) in the Setúbal province of Portugal. Twelve mite species, spanning diverse ecological roles, are found associated with these bark beetle systems. The relative abundances of the 12 species that make up the phoretic mite communities of maritime and stone pine varied significantly between host beetle species as well as between stand type, indicating that the phoretic host and dominant tree type are important drivers of mite community composition. The functional roles of these mites are outlined and their ecological significance in pine forest ecosystems is discussed.}, }
@article {pmid30596699, year = {2018}, author = {Xie, L and Lehvävirta, S and Timonen, S and Kasurinen, J and Niemikapee, J and Valkonen, JPT}, title = {Species-specific synergistic effects of two plant growth-promoting microbes on green roof plant biomass and photosynthetic efficiency.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209432}, doi = {10.1371/journal.pone.0209432}, pmid = {30596699}, issn = {1932-6203}, mesh = {Biomass ; Phosphorus/metabolism ; Photosynthesis/*genetics ; Plant Development/*genetics ; Species Specificity ; Symbiosis/*genetics ; Viridiplantae/genetics/growth &amp; development ; }, abstract = {Rhizophagus irregularis, an arbuscular mycorrhizal fungus, and Bacillus amyloliquefaciens, a bacterium, are microorganisms that promote plant growth. They associate with plant roots and facilitate nutrient absorption by their hosts, increase resistance against pathogens and pests, and regulate plant growth through phytohormones. In this study, eight local plant species in Finland (Antennaria dioica, Campanula rotundifolia, Fragaria vesca, Geranium sanguineum, Lotus corniculatus, Thymus serpyllum, Trifolium repens, and Viola tricolor) were inoculated with R. irregularis and/or B. amyloliquefaciens in autoclaved substrates to evaluate the plant growth-promoting effects of different plant/microbe combinations under controlled conditions. The eight plant species were inoculated with R. irregularis, B. amyloliquefaciens, or both microbes or were not inoculated as a control. The impact of the microbes on the plants was evaluated by measuring dry shoot weight, colonization rate by the arbuscular mycorrhizal fungus, bacterial population density, and chlorophyll fluorescence using a plant phenotyping facility. Under dual inoculation conditions, B. amyloliquefaciens acted as a &quot;mycorrhiza helper bacterium&quot; to facilitate arbuscular mycorrhizal fungus colonization in all tested plants. In contrast, R. irregularis did not demonstrate reciprocal facilitation of the population density of B. amyloliquefaciens. Dual inoculation with B. amyloliquefaciens and R. irregularis resulted in the greatest increase in shoot weight and photosynthetic efficiency in T. repens and F. vesca.}, }
@article {pmid30596693, year = {2018}, author = {Newton, AC and Boscolo, D and Ferreira, PA and Lopes, LE and Evans, P}, title = {Impacts of deforestation on plant-pollinator networks assessed using an agent based model.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209406}, doi = {10.1371/journal.pone.0209406}, pmid = {30596693}, issn = {1932-6203}, mesh = {Animals ; Bees/physiology ; Conservation of Natural Resources ; *Ecosystem ; *Forests ; Humans ; *Plant Physiological Phenomena ; Pollination/physiology ; Symbiosis/physiology ; Systems Analysis ; }, abstract = {Plant-pollinator networks have been widely used to understand the ecology of mutualistic interactions between plants and animals. While a number of general patterns have been identified, the mechanisms underlying the structure of plant-pollinator networks are poorly understood. Here we present an agent based model (ABM) that simulates the movement of bees over heterogeneous landscapes and captures pollination events, enabling the influence of landscape pattern on pollination networks to be explored. Using the model, we conducted a series of experiments using virtual landscapes representing a gradient of forest loss and fragmentation. The ABM was able to produce expected trends in network structure, from simulations of interactions between individual plants and pollinators. For example, results indicated an increase in the index of complementary specialization (H2') and a decline in network connectance with increasing forest cover. Furthermore, network nestedness was not associated with the degree of forest cover, but was positively related to forest patch size, further supporting results obtained in the field. This illustrates the potential value of ABMs for exploring the structure and dynamics of plant-pollinator networks, and for understanding the mechanisms that underlie them. We attribute the results obtained primarily to a shift from specialist to generalist pollinators with increasing forest loss, a trend that has been observed in some field situations.}, }
@article {pmid29878200, year = {2018}, author = {Lee, FJ and Miller, KI and McKinlay, JB and Newton, ILG}, title = {Differential carbohydrate utilization and organic acid production by honey bee symbionts.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {8}, pages = {}, doi = {10.1093/femsec/fiy113}, pmid = {29878200}, issn = {1574-6941}, mesh = {Acetates/metabolism ; Animals ; Bacteria/genetics/*metabolism ; Bees/*microbiology ; Carbohydrate Metabolism/*physiology ; Carbohydrates ; Fatty Acids, Volatile/biosynthesis/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Lactic Acid/metabolism ; Metagenome ; Symbiosis/physiology ; }, abstract = {The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.}, }
@article {pmid31064586, year = {2018}, author = {Marie, A}, title = {&quot;Self-sacrifice&quot; as an accidental outcome of extreme within-group mutualism.}, journal = {The Behavioral and brain sciences}, volume = {41}, number = {}, pages = {e210}, doi = {10.1017/S0140525X1800167X}, pmid = {31064586}, issn = {1469-1825}, mesh = {*Biological Evolution ; Marriage ; Morals ; *Symbiosis ; Warfare ; }, abstract = {Whitehouse makes no room for evolutionary approaches to extreme behaviors based on partner choice and mutualism, which have been convincingly invoked to make sense of ordinary morality. Extended to intergroup warfare, these evolutionary mechanisms may play a pivotal role in explaining the existence of extreme - though not functionally sacrificial - behaviors, benefiting non-kin fellow fighters, together with the distinctive phenomenology those behaviors display.}, }
@article {pmid29194919, year = {2018}, author = {Lavy, A and Keren, R and Yu, K and Thomas, BC and Alvarez-Cohen, L and Banfield, JF and Ilan, M}, title = {A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {800-814}, pmid = {29194919}, issn = {1462-2920}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/classification/genetics/metabolism ; Genome, Bacterial/genetics ; Indian Ocean ; Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Sulfur/*metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.}, }
@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}, 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}, 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 {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 Jingquan, Y}, title = {A novel CO2 -responsive systemic signaling pathway controlling plant mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15917}, pmid = {31087385}, issn = {1469-8137}, abstract = {Rising atmospheric carbon dioxide concentrations (eCO2) 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, 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 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, 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}, 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 {pmid30327531, year = {2019}, author = {Bennek, E and Mandić, AD and Verdier, J and Roubrocks, S and Pabst, O and Van Best, N and Benz, I and Kufer, T and Trautwein, C and Sellge, G}, title = {Subcellular antigen localization in commensal E. coli is critical for T cell activation and induction of specific tolerance.}, journal = {Mucosal immunology}, volume = {12}, number = {1}, pages = {97-107}, doi = {10.1038/s41385-018-0061-0}, pmid = {30327531}, issn = {1935-3456}, mesh = {Administration, Oral ; Animals ; Antigens, Bacterial/genetics/immunology ; Cells, Cultured ; Escherichia coli/*physiology ; Female ; Forkhead Transcription Factors/metabolism ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Immune Tolerance ; Intracellular Space ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microorganisms, Genetically-Modified ; Ovalbumin/genetics/immunology ; Peptides/genetics/immunology ; Symbiosis ; T-Lymphocytes, Regulatory/*immunology ; }, abstract = {Oral tolerance to soluble antigens is critically important for the maintenance of immunological homeostasis in the gut. The mechanisms of tolerance induction to antigens of the gut microbiota are still less well understood. Here, we investigate whether the subcellular localization of antigens within non-pathogenic E. coli has a role for its ability to induce antigen-specific tolerance. E. coli that express an ovalbumin (OVA) peptide in the cytoplasm, at the outer membrane or as secreted protein were generated. Intestinal colonization of mice with non-pathogenic E. coli expressing OVA at the membrane induced the expansion of antigen-specific Foxp3+ Tregs and mediated systemic immune tolerance. In contrast, cytoplasmic OVA was ignored by antigen-specific CD4+ T cells and failed to induce tolerance. In vitro experiments revealed that surface-displayed OVA of viable E. coli was about two times of magnitude more efficient to activate antigen-specific CD4+ T cells than soluble antigens, surface-displayed antigens of heat-killed E. coli or cytoplasmic antigen of viable or heat-killed E. coli. This effect was independent of the antigen uptake efficiency in dendritic cells. In summary, our results show that subcellular antigen localization in viable E. coli strongly influences antigen-specific CD4+ cell expansion and tolerance induction upon intestinal colonization.}, }
@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 = {}, number = {}, pages = {}, 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}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.ijmm.2019.04.004}, pmid = {31079999}, issn = {1618-0607}, 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 {pmid30716462, year = {2019}, author = {Odeniran, PO and Macleod, ET and Ademola, IO and Welburn, SC}, title = {Endosymbionts interaction with trypanosomes in Palpalis group of Glossina captured in southwest Nigeria.}, journal = {Parasitology international}, volume = {70}, number = {}, pages = {64-69}, doi = {10.1016/j.parint.2019.01.011}, pmid = {30716462}, issn = {1873-0329}, mesh = {Animals ; Enterobacteriaceae/*isolation &amp; purification/physiology ; Insect Vectors/microbiology/parasitology ; Nigeria ; Polymerase Chain Reaction ; Prevalence ; *Symbiosis ; Trypanosoma/microbiology/*physiology ; Tsetse Flies/*microbiology/*parasitology ; Wolbachia ; }, abstract = {Glossina species epidemiological studies were conducted in &quot;fly-belt&quot; endemic zone of southwest Nigeria. Two major study areas were identified and four Nzi traps were set in each site for tsetse collection. This study was conducted to determine the prevalence of endosymbionts (Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia) in natural field-trapped populations of G. p. palpalis and G. tachinoides and investigate the corresponding interactions with African trypanosomes. A total of 64 tsetse flies were collected, these included G. p. palpalis (n = 28) and G. tachinoides (n = 36). Trypanosome infection and endosymbionts of these flies were determined using polymerase chain reaction (PCR) amplification. The infection rates of W. glossinidia was 100.0% in both species, no flies were positive for Wolbachia. Sodalis glossinidius prevalence was similar between the two-tsetse species, with G. p. palpalis and G. tachinoides showing prevalence of 35.7% (95%CI: 20.7-54.2) and 27.8% (95%CI: 15.9-44.0) respectively. No relationship was found between the endosymbionts and trypanosomes in trapped tsetse flies. More studies are needed to enhance the potential control interventions mediated by endosymbionts to reduce parasitic infections.}, }
@article {pmid30684037, year = {2019}, author = {Kumar, U and Nayak, AK and Panneerselvam, P and Kumar, A and Mohanty, S and Shahid, M and Sahoo, A and Kaviraj, M and Priya, H and Jambhulkar, NN and Dash, PK and Mohapatra, SD and Nayak, PK}, title = {Cyanobiont diversity in six Azolla spp. and relation to Azolla-nutrient profiling.}, journal = {Planta}, volume = {249}, number = {5}, pages = {1435-1447}, doi = {10.1007/s00425-019-03093-7}, pmid = {30684037}, issn = {1432-2048}, mesh = {Anabaena/metabolism ; Antioxidants/metabolism ; Aspergillus/*metabolism ; Cyanobacteria/metabolism ; RNA, Ribosomal, 16S/metabolism ; Symbiosis/physiology ; }, abstract = {MAIN CONCLUSION: Illumina-Miseq®-based cyanobiont diversity and biomass were analyzed in six Azolla spp. Results revealed that 93-98% of total operational taxonomic units (OTUs) belong to Nostacaceae followed by Cylindrospermopsis with about 1-6% OTUs. The taxonomy of Azolla-cyanobiont is a long-term debate within the scientific community. Morphological and biochemical-based reports indicated the presence of Anabaena, Nostoc and/or Trichormus azollae as abundant Azolla-cyanobionts, however, molecular data did not support the abundance of Anabaena and/or Nostoc. To understand furthermore, the cyanobiont diversity in six species of Azolla (A. microphylla, A. mexicana, A. filiculoides, A. caroliniana, A. pinnata and A. rubra) was analyzed based on 16S rRNA Illumina-MiSeq sequencing. Additionally, biomass and nutrient profiling of Azolla spp. were analyzed and correlated with cyanobiont diversity. Illumina-MiSeq data revealed that 99.6-99.9% of total operational taxonomic units (OTUs) belonged to Nostocophycideae (class), Nostocales (order) and Nostacaceae (family). At genus level, the unassigned affiliation (93.4-97.9%) under Nostacaceae family was abundant followed by Cylindrospermopsis OTUs (1.1-6.0%). Interestingly, A. pinnata harboured maximum Cylindrospermopsis OTUs and also recorded higher biomass (40.67 g m-2 day-1), whereas crude protein (25.9%) and antioxidants (76.9%) were recorded to be higher in A. microphylla. Biplot analysis revealed that A. pinnata and its cyanobiont abundance were positively correlated with neutral and acid detergent fibers. Overall, the present findings deepened the understanding about cyanobiont in Azolla and its relations with Azolla nutrient profiling.}, }
@article {pmid30672456, year = {2019}, author = {Angers, A and Ouimet, P and Tsyvian-Dzyabko, A and Nock, T and Breton, S}, title = {[The underestimated coding potential of mitochondrial DNA].}, journal = {Medecine sciences : M/S}, volume = {35}, number = {1}, pages = {46-54}, doi = {10.1051/medsci/2018308}, pmid = {30672456}, issn = {1958-5381}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Bacteria/genetics ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/*genetics ; Female ; Humans ; Insulin Resistance/genetics ; Intracellular Signaling Peptides and Proteins/genetics ; Male ; Mitochondrial Proteins/*genetics ; Open Reading Frames/genetics ; Peptides/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Mitochondria are ancient organelles that emerged from the endosymbiosis of free-living proto-bacteria. They still retain a semi-autonomous genetic system with a small genome. Mitochondrial DNA (mtDNA) codes for 13 essential proteins for the production of ATP, the sequences of which are relatively conserved across Metazoans. The discovery of additional mitochondria-derived peptides (MDPs) indicates an underestimated coding potential. Humanin, an anti-apoptotic peptide, is likely independently transcribed from within the 16S rRNA gene, as are recently described SHLPs. MOTS-c, discovered in silico, has been demonstrated to be involved in metabolism and insulin sensitivity. Gau, is a positionally conserved open reading frame (ORF) sequence found in the antisense strand of the COX1 gene and its corresponding peptide is strictly colocalized with mitochondrial markers. In bivalves with doubly uniparental inheritance of mtDNA, male and female mtDNAs each carry a separate additional gene possibly involved in sex determination. Other MDPs likely exist and their investigation will shed light on the underestimated functional repertoire of mitochondria.}, }
@article {pmid30315353, year = {2019}, author = {Enebe, MC and Babalola, OO}, title = {The impact of microbes in the orchestration of plants' resistance to biotic stress: a disease management approach.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {9-25}, doi = {10.1007/s00253-018-9433-3}, pmid = {30315353}, issn = {1432-0614}, support = {Grants Ref: UID81192, UID95111//National Research Foundation/ ; }, mesh = {Biological Control Agents ; Disease Resistance ; Endophytes/physiology ; Food Preservation/methods ; Fruit ; Host-Pathogen Interactions/*physiology ; Plant Immunity ; Plant Physiological Phenomena ; Plants/immunology/*microbiology ; Soil Microbiology ; Stress, Physiological/*physiology ; Symbiosis ; }, abstract = {The struggle for survival is a natural and a continuous process. Microbes are struggling to survive by depending on plants for their nutrition while plants on the other hand are resisting the attack of microbes in order to survive. This interaction is a tug of war and the knowledge of microbe-plant relationship will enable farmers/agriculturists improve crop health, yield, sustain regular food supply, and minimize the use of agrochemicals such as fungicides and pesticides in the fight against plant pathogens. Although, these chemicals are capable of inhibiting pathogens, they also constitute an environmental hazard. However, certain microbes known as plant growth-promoting microbes (PGPM) aid in the sensitization and priming of the plant immune defense arsenal for it to conquer invading pathogens. PGPM perform this function by the production of elicitors such as volatile organic compounds, antimicrobials, and/or through competition. These elicitors are capable of inducing the expression of pathogenesis-related genes in plants through induced systemic resistance or acquired systemic resistance channels. This review discusses the current findings on the influence and participation of microbes in plants' resistance to biotic stress and to suggest integrative approach as a better practice in disease management and control for the achievement of sustainable environment, agriculture, and increasing food production.}, }
@article {pmid30241736, year = {2018}, author = {Ferlian, O and Biere, A and Bonfante, P and Buscot, F and Eisenhauer, N and Fernandez, I and Hause, B and Herrmann, S and Krajinski-Barth, F and Meier, IC and Pozo, MJ and Rasmann, S and Rillig, MC and Tarkka, MT and van Dam, NM and Wagg, C and Martinez-Medina, A}, title = {Growing Research Networks on Mycorrhizae for Mutual Benefits.}, journal = {Trends in plant science}, volume = {23}, number = {11}, pages = {975-984}, doi = {10.1016/j.tplants.2018.08.008}, pmid = {30241736}, issn = {1878-4372}, mesh = {Mycorrhizae/*physiology ; Plant Roots/microbiology ; Symbiosis ; }, abstract = {Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations.}, }
@article {pmid29967516, year = {2018}, author = {Banks, JA}, title = {Fern genomes finally here.}, journal = {Nature plants}, volume = {4}, number = {7}, pages = {404-405}, doi = {10.1038/s41477-018-0202-1}, pmid = {29967516}, issn = {2055-0278}, mesh = {*Cyanobacteria ; *Embryophyta ; *Ferns ; Phylogeny ; Symbiosis ; }, }
@article {pmid29570981, year = {2018}, author = {Kust, A and Mareš, J and Jokela, J and Urajová, P and Hájek, J and Saurav, K and Voráčová, K and Fewer, DP and Haapaniemi, E and Permi, P and Řeháková, K and Sivonen, K and Hrouzek, P}, title = {Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium.}, journal = {ACS chemical biology}, volume = {13}, number = {5}, pages = {1123-1129}, doi = {10.1021/acschembio.7b01048}, pmid = {29570981}, issn = {1554-8937}, mesh = {Cyanobacteria/genetics/*metabolism ; Genes, Bacterial ; Magnetic Resonance Spectroscopy ; Multigene Family ; Peptide Synthases/metabolism ; Polyketide Synthases/metabolism ; Polyketides/*isolation &amp; purification/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {The pederin family includes a number of bioactive compounds isolated from symbiotic organisms of diverse evolutionary origin. Pederin is linked to beetle-induced dermatitis in humans, and pederin family members possess potent antitumor activity caused by selective inhibition of the eukaryotic ribosome. Their biosynthesis is accomplished by a polyketide/nonribosomal peptide synthetase machinery employing an unusual trans-acyltransferase mechanism. Here, we report a novel pederin type compound, cusperin, from the free-living cyanobacterium Cuspidothrix issatschenkoi (earlier Aphanizomenon). The chemical structure of cusperin is similar to that of nosperin recently isolated from the lichen cyanobiont Nostoc sharing the tehrahydropyran moiety and major part of the linear backbone. However, the cusperin molecule is extended by a glycine residue and lacks one hydroxyl substituent. Pederins were previously thought to be exclusive to symbiotic relationships. However, C. issatschenkoi is a nonsymbiotic planktonic organism and a frequent component of toxic water blooms. Cusperin is devoid of the cytotoxic activity reported for other pederin family members. Hence, our findings raise questions about the role of pederin analogues in cyanobacteria and broaden the knowledge of ecological distribution of this group of polyketides.}, }
@article {pmid29524256, year = {2018}, author = {Tatu, AL and Nwabudike, LC}, title = {Reply to: Kubiak K et al. Endosymbiosis and its significance in dermatology.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {32}, number = {9}, pages = {e346-e347}, doi = {10.1111/jdv.14921}, pmid = {29524256}, issn = {1468-3083}, mesh = {*Dermatology ; Humans ; *Prostatic Neoplasms ; Symbiosis ; }, }
@article {pmid31078557, year = {2019}, author = {Wiles, TJ and Guillemin, K}, title = {The Other Side of the Coin: What Beneficial Microbes Can Teach us about Pathogenic Potential.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmb.2019.05.001}, pmid = {31078557}, issn = {1089-8638}, abstract = {Koch's postulates and molecular Koch's postulates have made an indelible mark on how we study and classify microbes, particularly pathogens. However, rigid adherence to these historic postulates constrains our view of not only microbial pathogenesis, but host-microbe relationships in general. Collectively the postulates imply that a 'microbial pathogen' is a clearly identifiable organism with the exclusive capacity to elicit disease through an arsenal of pathogen-specific 'virulence factors'. This narrow definition has been repeatedly contradicted. Advances in DNA sequencing technologies and new experimental systems have revealed that the outcomes of host-microbe interactions are highly contextual and dynamic, especially those involving resident microbiota and variable aspects of host biology. Clarifying what differentiates pathogenic from non-pathogenic microbes, including their paradoxical ability to masquerade as one another, is critical to developing targeted diagnostics and treatments for infectious disease. Such endeavors will also inform the design of therapeutic strategies based on microbiome engineering by providing insights into how manipulating entire host-microbe systems may directly or indirectly alter the pathogenic potential of microbial communities. With these goals in mind, we discuss the need to develop experimental models that better capture the contexts that determine the nature of host-microbe relationships. To demonstrate the potential of one such model-the zebrafish and its resident microbiota-we describe recent work that has revealed the thin line between pathogenic and mutualistic relationships, how the intestine physically shapes bacterial populations and inflammation, and the ability of microbial transmission to override the host's innate immune system.}, }
@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 = {}, 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}, 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 harbors 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 A. indica and A. 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 harbors 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcz081}, pmid = {31076773}, issn = {1471-9053}, 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. Strigolactones 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 wildtype 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 = {}, number = {}, pages = {}, 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 co-culture through basic and advanced microscopic techniques.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.201900138}, pmid = {31074496}, issn = {1521-4028}, abstract = {Detailed information on structural changes that occur during ontogenesis of Rhizophagus irregularis in axenically developed co-cultures 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 amongst these to identify the suitable technique for rapid and detailed analysis of mycorrhizal structures. Three stages were identified in mycorrhizal ontogenesis from initiation (pre-infection stage of hyphae; its branching, infection and appressoria formation; epidermal opening; hyphal entry), progression (arbuscular development; hyphal coils and vesicles) to maturity (extra-radical spores). Scanning electron microscopy was found to be an efficient tool for studying spatial three-dimensional progression. Adding to the advantages of advanced microscopy, the potential of autofluorescence to explore the stages of symbiosis non-destructively was established. We also report imaging of ultrathin sections by bright field microscopy to provide finer details at subcellular interface. Owing to the merits of non-destructive 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. This article is protected by copyright. All rights reserved.}, }
@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 {pmid30693447, year = {2019}, author = {Saadani, O and Jebara, SH and Fatnassi, IC and Chiboub, M and Mannai, K and Zarrad, I and Jebara, M}, title = {Effect of Vicia faba L. var. minor and Sulla coronaria (L.) Medik associated with plant growth-promoting bacteria on lettuce cropping system and heavy metal phytoremediation under field conditions.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {8}, pages = {8125-8135}, doi = {10.1007/s11356-019-04302-2}, pmid = {30693447}, issn = {1614-7499}, support = {MOBIDOC//PASRI, Tunisia funded by European Union/ ; }, mesh = {Agricultural Inoculants/*growth &amp; development/metabolism ; Biodegradation, Environmental ; Crop Production/methods ; Fabaceae/growth &amp; development/metabolism/microbiology ; Lettuce/*growth &amp; development/metabolism ; Metals, Heavy/*analysis/metabolism ; Plant Development/drug effects ; Rhizobium/*growth &amp; development/metabolism ; Soil/chemistry ; Soil Pollutants/*analysis/metabolism ; Symbiosis ; Vicia faba/*growth &amp; development/metabolism/microbiology ; }, abstract = {Researches involving the use of association between legumes and PGPBs (plant growth-promoting bacteria) in heavy metal phytoremediation process were mainly performed for soils highly contaminated. However, even in agriculture soils, with moderate or low contamination levels, plants can accumulate high rates of heavy metals. So, food chain contamination by these metals presents a real threat to animal and human health. This work aimed to evaluate the use of two legumes/PGPB symbioses; Vicia faba var. minor and Sulla coronaria have been inoculated with specific heavy metal-resistant inocula in a crop rotation system with Lactuca sativa as a following crop, in order to assess their effects on soil fertility, lettuce yield, and heavy metal content. Our results showed that legume inoculation significantly enhanced their biomass production, nitrogen and phosphorus content. The use of our symbioses as green manure before lettuce cultivation, as a rotation cropping system, affected positively soil fertility. In fact, we recorded a higher organic matter content, with rapid decomposition in the soil of inoculated plots. Besides, results demonstrated a greater nitrogen and phosphorus content in this soil, especially in the plot cultivated with inoculated V. faba var. minor. The improvement of soil fertility enhanced lettuce yield and its nitrogen and phosphorus content. Moreover, inoculated legumes extracted and accumulated more heavy metals than non-inoculated legumes. Our symbioses play the role of organic trap for heavy metals, making them unavailable for following crops. These facts were supported by lettuce heavy metal content, showing a significant decrease in metal accumulation, mainly zinc and cadmium, in edible parts. Results showed the usefulness of the studied symbioses, as a main part of a rotation system with lettuce. Our symbioses can be suggested for agriculture soil phytoremediation, aiming to enhance non-legume crop yield and limit heavy metal translocation to food chain.}, }
@article {pmid30520104, year = {2018}, author = {Foyer, CH and Nguyen, HT and Lam, HM}, title = {A seed change in our understanding of legume biology from genomics to the efficient cooperation between nodulation and arbuscular mycorrhizal fungi.}, journal = {Plant, cell &amp; environment}, volume = {41}, number = {9}, pages = {1949-1954}, doi = {10.1111/pce.13419}, pmid = {30520104}, issn = {1365-3040}, support = {//Worldwide University Network (WUN)/International ; }, mesh = {Fabaceae/genetics/*physiology ; Genome, Plant ; Genomics ; Mycorrhizae/*physiology ; Nitrogen Fixation ; Plant Roots/microbiology ; Seeds/*physiology ; *Soil Microbiology ; Stress, Physiological ; Symbiosis ; }, abstract = {Grain legumes play a significant role in global food security. They have an advantage over cereals in that they can form symbiotic associations with nitrogen-fixing bacteria, making them self-sufficient in terms of nitrogen acquisition. In addition to this superior agronomic trait, grain legumes have excellent nutritional properties and are thus widely used as animal feed as well as in human nutrition. Current global trends towards increased legume consumption and availability of value-added products, as well as legume production in developing countries require the provision of improved cultivars with better productivity and adaptability. Intensive efforts are thus underway to elaborate genomic resources and gain an improved knowledge base in a number of legume crops. There is also an emerging understanding of the beneficial interactions between legume-associated organisms, particularly rhizobia and arbuscular mycorrhizal fungi, which result in improved nodulation and nutrient acquisition. The emerging focus on legume breeding for high sustainable yields as well as improved biotic and abiotic stress tolerance traits will serve to close the current gap between grain legume production and demand. With the support from policymakers, this increase in knowledge can be readily translated into increased crop production to meet the demands of an increasing global population.}, }
@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 = {}, number = {}, pages = {}, 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}, 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, AM and Harrison, M}, title = {A phosphate-dependent requirement for the transcription factors IPD3 and IPD3L during AM symbiosis in Medicago truncatula.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, 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 ipd3 ipd3l, hyphal entry through the epidermis and overall colonization levels are reduced relative to wild type but fully developed arbuscules are present in the cortex. In comparison with 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 (DMI3) induces the expression of transcriptional regulators REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1) and REQUIRED for ARBUSCULE DEVELOPMENT 1 (RAD1), providing a possible avenue for arbuscule development even 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-P environments, while IPD3 and IPD3L maintain signaling in higher-P environments. The latter may buffer the pathway from short-term variation in P levels encountered by roots during growth in heterogeneous soil environments.}, }
@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 ; }, 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 {pmid30420746, year = {2018}, author = {Murat, C and Payen, T and Noel, B and Kuo, A and Morin, E and Chen, J and Kohler, A and Krizsán, K and Balestrini, R and Da Silva, C and Montanini, B and Hainaut, M and Levati, E and Barry, KW and Belfiori, B and Cichocki, N and Clum, A and Dockter, RB and Fauchery, L and Guy, J and Iotti, M and Le Tacon, F and Lindquist, EA and Lipzen, A and Malagnac, F and Mello, A and Molinier, V and Miyauchi, S and Poulain, J and Riccioni, C and Rubini, A and Sitrit, Y and Splivallo, R and Traeger, S and Wang, M and Žifčáková, L and Wipf, D and Zambonelli, A and Paolocci, F and Nowrousian, M and Ottonello, S and Baldrian, P and Spatafora, JW and Henrissat, B and Nagy, LG and Aury, JM and Wincker, P and Grigoriev, IV and Bonfante, P and Martin, FM}, title = {Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {12}, pages = {1956-1965}, doi = {10.1038/s41559-018-0710-4}, pmid = {30420746}, issn = {2397-334X}, mesh = {Ascomycota/*genetics/physiology ; DNA, Fungal/analysis ; *Genome, Fungal ; *Life History Traits ; Mycorrhizae/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.}, }
@article {pmid29124861, year = {2018}, author = {Certner, RH and Vollmer, SV}, title = {Inhibiting bacterial quorum sensing arrests coral disease development and disease-associated microbes.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {645-657}, doi = {10.1111/1462-2920.13991}, pmid = {29124861}, issn = {1462-2920}, mesh = {4-Butyrolactone/analogs &amp; derivatives/antagonists &amp; inhibitors ; Animals ; Anthozoa/*microbiology ; Caribbean Region ; Coral Reefs ; Flavobacteriaceae/drug effects ; Gammaproteobacteria/growth &amp; development ; Microbiota/*drug effects ; Quorum Sensing/*drug effects ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Among the greatest threats to coral reefs are coral epizootics, which are increasing in frequency and severity across many reef ecosystems. In particular, white band disease (WBD) has devastated Caribbean acroporid populations since its initial outbreak in 1979. However, despite its widespread and damaging effects, the aetiology of WBD remains largely unresolved. Here, we examine the role of quorum sensing within bacterial communities associated with WBD-infected Acropora cervicornis. Microbial communities isolated from WBD-infected corals were exposed to quorum sensing inhibitor (QSI) - a N-acyl homoserine lactone autoinducer antagonist - and then dosed onto healthy test corals. WBD-associated bacteria supplemented with QSI lost the ability to establish disease, while healthy corals exposed to uninhibited WBD bacterial communities became infected within two days. Microbial 16S rRNA metagenomic sequencing analyses were then used to identify shifts in bacterial communities due to QSI exposure on WBD-associated bacterial communities. Our results demonstrated that Vibrionaceae and Flavobacteriaceae abundances were strongly inhibited by the addition of QSI to WBD-infected corals, whereas putative coral symbiont Endozoicomonas and Halomonadaceae abundances decrease dramatically in diseased corals.}, }
@article {pmid29098761, year = {2018}, author = {Astudillo-García, C and Slaby, BM and Waite, DW and Bayer, K and Hentschel, U and Taylor, MW}, title = {Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {561-576}, doi = {10.1111/1462-2920.13965}, pmid = {29098761}, issn = {1462-2920}, mesh = {Animals ; Bacteria, Aerobic/*classification/genetics ; Molecular Typing ; Phylogeny ; Porifera/*microbiology ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Many marine sponges contain dense and diverse communities of associated microorganisms. Members of the 'sponge-associated unclassified lineage' (SAUL) are frequently recorded from sponges, yet little is known about these bacteria. Here we investigated the distribution and phylogenetic status of SAUL. A meta-analysis of the available literature revealed the widespread distribution of this clade and its association with taxonomically varied sponge hosts. Phylogenetic analyses, conducted using both 16S rRNA gene-based phylogeny and concatenated marker protein sequences, revealed that SAUL is a sister clade of the candidate phylum 'Latescibacteria'. Furthermore, we conducted a comprehensive analysis of two draft genomes assembled from sponge metagenomes, revealing novel insights into the physiology of this symbiont. Metabolic reconstruction suggested that SAUL members are aerobic bacteria with facultative anaerobic metabolism, with the capacity to degrade multiple sponge- and algae-derived carbohydrates. We described for the first time in a sponge symbiont the putative genomic capacity to transport phosphate into the cell and to produce and store polyphosphate granules, presumably constituting a phosphate reservoir for the sponge host in deprivation periods. Our findings suggest that the lifestyle of SAUL is symbiotic with the host sponge, and identify symbiont factors which may facilitate the establishment and maintenance of this relationship.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/mec.15122}, pmid = {31066947}, issn = {1365-294X}, 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, 21 °C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified 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 abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. Post 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 unravels 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. This article is protected by copyright. All rights reserved.}, }
@article {pmid31066909, year = {2019}, author = {Martinez-Medina, A and Pescador, L and Fernandez, 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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15898}, pmid = {31066909}, issn = {1469-8137}, 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 on 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. This article is protected by copyright. All rights reserved.}, }
@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 {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 {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 {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 {pmid31062009, year = {2019}, author = {Dhanjal, NI and Sharma, S and Skalny, AV and Skalnaya, MG and Ajsuvakova, OP and Tinkov, AA and Zhang, F and Guo, X and Prabhu, KS and Tejo Prakash, N}, title = {Selenium-rich maize modulates the expression of prostaglandin genes in lipopolysaccharide-stimulated RAW264.7 macrophages.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9fo00186g}, pmid = {31062009}, issn = {2042-650X}, abstract = {Cell signaling is necessary for the organs to co-ordinate with the whole body and it includes response to external stimuli, inflammation, hormonal secretions and other various metabolic functions. In the present study, we have focused on the inflammatory signals modulated by the reactive oxygen and nitrogen species (RONS). Under homeostatic conditions, these species turn on the COX-1-dependent arachidonic acid (AA) pathway towards the release of anti-inflammatory enzymes. However, the excess release of these ions induces negative effects in the form of inflammation by turning on the COX-2-dependent AA pathway to release pro-inflammatory enzymes. In the present study, we observed the shunting of the COX-2-dependent AA pathway towards the release of anti-inflammatory enzymes with the supplementation of organic dietary selenium in the form of seleniferous maize extracts. We observed that 500 nM selenium concentration in Se-maize extracts downregulated the COX-2 and mPGES-1 expressions by 3.8- and 3.2-fold and upregulated the GPx-1 and H-PGDS expressions by 5.0- and 5.4-fold, respectively. To facilitate more availability of Se from the dietary matrices, Se-maize extracts were incubated with rMETase. It was observed that the enzyme-treated cells increased the downregulation of COX-2 and mPGES-1 expressions by 24.8- and 21.0-fold and the upregulation of GPx-1 and H-PGDS expressions by 13.2- and 16.5-fold, respectively.}, }
@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 = {}, number = {}, pages = {}, 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 over one hundred nodulation and nitrogen fixation mutants from a population of Tnt1-insertion mutants of Medigaco truncatula (Pislariu et al., 2011). Using Tnt1 as a tag to identify genetic lesions in these mutants, we discovered that insertions in a nodule-specific PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) 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 four days post-inoculation (DPI), 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 co-localized with vacuoles and the endoplasmic reticulum. MtNPD1 belongs to a cluster of 5 nodule-specific single PLAT domain-encoding genes, with apparent non-redundant functions.}, }
@article {pmid30744948, year = {2019}, author = {Binetruy, F and Bailly, X and Chevillon, C and Martin, OY and Bernasconi, MV and Duron, O}, title = {Phylogenetics of the Spiroplasma ixodetis endosymbiont reveals past transfers between ticks and other arthropods.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {3}, pages = {575-584}, doi = {10.1016/j.ttbdis.2019.02.001}, pmid = {30744948}, issn = {1877-9603}, mesh = {Animals ; Arthropods/*microbiology ; Bacterial Typing Techniques ; Disease Transmission, Infectious ; Female ; Genetic Variation ; Gram-Negative Bacterial Infections/*transmission ; Infectious Disease Transmission, Vertical ; Male ; Multilocus Sequence Typing ; *Phylogeny ; Spiroplasma/classification/*genetics ; *Symbiosis ; Ticks/*microbiology ; }, abstract = {The bacterium Spiroplasma ixodetis is a maternally inherited endosymbiont primarily described from ticks but also found widespread across other arthropods. While it has been identified as a male-killing agent in some insect species, the consequences of infection with S. ixodetis in ticks are entirely unknown, and it is unclear how this endosymbiont spreads across tick species. Here, we have investigated this aspect through the examination of the diversity and evolutionary history of S. ixodetis infections in 12 tick species and 12 other arthropod species. Using a multi-locus typing approach, we identified that ticks harbor a substantial diversity of divergent S. ixodetis strains. Phylogenetic investigations revealed that these S. ixodetis strains do not cluster within a tick-specific subclade but rather exhibit distinct evolutionary origins. In their past, these strains have undergone repeated horizontal transfers between ticks and other arthropods, including aphids and flies. This diversity pattern strongly suggests that maternal inheritance and horizontal transfers are key drivers of S. ixodetis spread, dictating global incidence of infections across tick communities. We do not, however, detect evidence of S. ixodetis-based male-killing since we observed that infections were widely present in both males and females across populations of the African blue tick Rhipicephalus decoloratus.}, }
@article {pmid30269177, year = {2019}, author = {Chevrette, MG and Currie, CR}, title = {Emerging evolutionary paradigms in antibiotic discovery.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {46}, number = {3-4}, pages = {257-271}, doi = {10.1007/s10295-018-2085-6}, pmid = {30269177}, issn = {1476-5535}, support = {T32 GM008505/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 A1109673//National Institutes of Health/ ; T32 GM008505//National Institute of General Medical Sciences/ ; }, mesh = {Actinobacteria/metabolism ; Anti-Bacterial Agents/*chemistry ; Bacteria/metabolism ; Biological Products/*chemistry ; Biosynthetic Pathways ; *Drug Discovery ; Drug-Related Side Effects and Adverse Reactions ; Evolution, Molecular ; Fungi/metabolism ; Symbiosis ; }, abstract = {Antibiotics revolutionized medicine and remain its cornerstone. Despite their global importance and the continuous threat of resistant pathogens, few antibiotics have been discovered in recent years. Natural products, especially the secondary metabolites of Actinobacteria, have been the traditional discovery source of antibiotics. In nature, the chemistry of antibiotic natural products is shaped by the unique evolution and ecology of their producing organisms, yet these influences remain largely unknown. Here, we highlight the ecology of antibiotics employed by microbes in defensive symbioses and review the evolutionary processes underlying the chemical diversity and activity of microbe-derived antibiotics, including the dynamics of vertical and lateral transmission of biosynthetic pathways and the evolution of efficacy, targeting specificity, and toxicity. We argue that a deeper understanding of the ecology and evolution of microbial interactions and the metabolites that mediate them will allow for an alternative, rational approach to discover new antibiotics.}, }
@article {pmid30265339, year = {2018}, author = {Zhao, D and Hoffmann, AA and Zhang, Z and Niu, H and Guo, H}, title = {Interactions Between Facultative Symbionts Hamiltonella and Cardinium in Bemisia tabaci (Hemiptera: Aleyrodoidea): Cooperation or Conflict?.}, journal = {Journal of economic entomology}, volume = {111}, number = {6}, pages = {2660-2666}, doi = {10.1093/jee/toy261}, pmid = {30265339}, issn = {1938-291X}, mesh = {Animals ; Bacteroidaceae/*physiology ; Enterobacteriaceae/*physiology ; Fertility ; Hemiptera/*microbiology ; Reproductive Isolation ; Symbiosis ; }, abstract = {Maternally-inherited facultative symbionts are widespread in most insect species, and it is common that several symbionts coexist in the same host individual. Hence, the symbionts may compete or share for the limited resources and space in the host. The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodoidea), harbors a diverse array of facultative symbionts, among which Hamiltonella sp. and Cardinium sp. are abundant species. Hamiltonella alone increases host fitness, while Cardinium alone confers lower fitness. Locking those different partners together creates ideal situations for the evolution of interactions between symbionts. In this study, we compared the fitness effects of whiteflies infected with only Hamiltonella to Hamiltonella-Cardnium co-infected whiteflies and measured the density of Hamiltonella and Cardinium during host aging, aiming to explore Hamiltonella-Cardinium interactions in B. tabaci. Our results illustrated that Hamiltonella-Cardinium coinfection induced lower fecundity, egg hatchability and number of female offspring, leading to a male-biased sex ratio in offspring, while there is no evidence for reproductive incompatibility between the infections. We also found an antagonistic interaction between Hamiltonella and Cardinium given that the density of the latter increased across time and led to a decrease of Hamiltonella density, which may be the underlying causes of the fitness cost in double-infected B. tabaci. Exploring the ecological consequences of co-infections of these different symbionts helps us to understand the nature of host-symbiont interactions in this species and potential for evolutionary conflict.}, }
@article {pmid31059742, year = {2019}, author = {Chaubey, MG and Patel, SNK 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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15883}, pmid = {31059123}, issn = {1469-8137}, 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 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15888}, pmid = {31059122}, issn = {1469-8137}, 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. 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 pull-down 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/nph.15891}, pmid = {31058335}, issn = {1469-8137}, 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 is scarce data about CO production by pathogens, especially non-fungal 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 to wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. In contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. A. 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. This article is protected by copyright. All rights reserved.}, }
@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/ ; }, 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 = {}, number = {}, pages = {}, 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}, 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 {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}, 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}, 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 {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 {pmid30909122, year = {2019}, author = {Cooper, D and Wuebbolt, C and Heryanto, C and Eleftherianos, I}, title = {The prophenoloxidase system in Drosophila participates in the anti-nematode immune response.}, journal = {Molecular immunology}, volume = {109}, number = {}, pages = {88-98}, doi = {10.1016/j.molimm.2019.03.008}, pmid = {30909122}, issn = {1872-9142}, mesh = {Animals ; Catechol Oxidase/genetics/*metabolism ; Cell Differentiation ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/enzymology/genetics/*immunology/*parasitology ; Enzyme Precursors/genetics/*metabolism ; Gene Expression Regulation ; Genes, Insect ; Hemocytes/metabolism ; *Immunity ; Larva ; Nematoda/*physiology ; Survival Analysis ; Symbiosis ; }, abstract = {Drosophila melanogaster relies on an evolutionarily conserved innate immune system to protect itself from potentially deadly pathogens. One of the earliest pathways activated after injury or infection is the melanization pathway, which is responsible for synthesizing and depositing melanin at the site of injury, or onto invading microbes. Three genes, PPO1-3, encoding prophenoloxidase (PPO), an inactive precursor of phenoloxidase (PO), are responsible for the production of melanin after their activation via immune challenge. One pathogen capable of infecting D. melanogaster are entomopathogenic nematodes. Steinernema carpocapsae nematodes exist in a mutualistic relationship with Xenorhabdus nematophila bacteria and are an important biological control agent for controlling insect pests. The nematode-bacteria complex (symbiotic nematodes) can be separated, creating &quot;axenic&quot; nematodes, devoid of their associated bacteria, which are still capable of infecting and killing D. melanogaster. In order to investigate how the D. melanogaster melanization pathway contributes to the anti-nematode immune response, symbiotic and axenic S. carpocapsae were used to study D. melanogaster survival, PPO gene expression, and activation of PPO to PO. Our research suggests that the expression of all three D. melanogaster PPO genes contributes to survival, however only PPO1 or PPO3 appear to be up-regulated during axenic or symbiotic nematode infection. Additionally, we present data suggesting that a complex regulatory system exists between PPOs, potentially allowing for the compensation of PPOs by one another. Further, we found that axenic nematode infection leads to higher levels of PO, suggesting that X. nematophila suppresses this activation. We also report for the first time the differentiation of lamellocytes, a specialized type of hemocytes in D. melanogaster, in response to symbiotic S. carpocapsae nematode infection. Our results suggest an important role played by the melanization pathway in response to nematode infection, and demonstrate how this response can be manipulated by S. carpocapsae nematodes and their mutualistic X. nematophila bacteria.}, }
@article {pmid30668658, year = {2019}, author = {Moreira, M and Aguiar, AMF and Bourtzis, K and Latorre, A and Khadem, M}, title = {Wolbachia (Alphaproteobacteria: Rickettsiales) Infections in Isolated Aphid Populations from Oceanic Islands of the Azores Archipelago: Revisiting the Supergroups M and N.}, journal = {Environmental entomology}, volume = {48}, number = {2}, pages = {326-334}, doi = {10.1093/ee/nvy189}, pmid = {30668658}, issn = {1938-2936}, mesh = {Animals ; Aphids/genetics/*microbiology ; Azores ; Symbiosis ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {Aphids (Hemiptera: Aphididae) have provided a suitable model to study endosymbionts, their community, and dynamics since the discovery of the obligate endosymbiont Buchnera aphidicola in these organisms. In previous studies, Wolbachia was found in some aphid species. In the present study, we report the prevalence of Wolbachia in aphids sampled from a geographically isolated region (Azores Islands), aiming at a better understanding and characterization of the two newly reported supergroups, M and N. The description of the supergroup M was based on 16S rRNA as well as some protein-coding genes. However, the assignment of the supergroup N was according to 16S rRNA gene sequences of a very few samples. We collected aphid samples and performed phylogenetic analysis of 16S rRNA gene as well as four protein-coding genes (gatB, ftsZ, coxA, and hcpA). The results demonstrate that the 16S rRNA gene data can unambiguously assign the strain supergroup and that the two supergroups, N and M, are equally prevalent in Azorean aphids. The available sequence data for the protein-coding markers can identify supergroup M but the status of supergroup N is inconclusive, requiring further studies. The data suggest that horizontal transmission of Wolbachia (Hertig and Wolbach) between two phylogenetically distant aphid species cohabiting the same plant host.}, }
@article {pmid30550591, year = {2018}, author = {Chase, TJ and Pratchett, MS and Frank, GE and Hoogenboom, MO}, title = {Coral-dwelling fish moderate bleaching susceptibility of coral hosts.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208545}, doi = {10.1371/journal.pone.0208545}, pmid = {30550591}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/growth &amp; development/*metabolism ; Chlorophyll/analysis ; *Coral Reefs ; Fishes/*physiology ; Photosynthesis ; Symbiosis ; Temperature ; }, abstract = {Global environmental change has the potential to disrupt well established species interactions, with impacts on nutrient cycling and ecosystem function. On coral reefs, fish living within the branches of coral colonies can promote coral performance, and it has been hypothesized that the enhanced water flow and nutrients provided by fish to corals could ameliorate coral bleaching. The aim of this study was to evaluate the influence of small, aggregating damselfish on the health of their host corals (physiology, recovery, and survival) before, during, and after a thermal-bleaching event. When comparing coral colonies with and without fish, those with resident fish exhibited higher Symbiodinium densities and chlorophyll in both field and experimentally-induced bleaching conditions, and higher protein concentrations in field colonies. Additionally, colonies with damselfish in aquaria exhibited both higher photosynthetic efficiency (FV/FM) during bleaching stress and post-bleaching recovery, compared to uninhabited colonies. These results demonstrate that symbiotic damselfishes, and the services they provide, translate into measureable impacts on coral tissue, and can influence coral bleaching susceptibility/resilience and recovery. By mediating how external abiotic stressors influence coral colony health, damselfish can affect the functional responses of these interspecific interactions in a warming ocean.}, }
@article {pmid30496253, year = {2018}, author = {Ikram, M and Ali, N and Jan, G and Jan, FG and Rahman, IU and Iqbal, A and Hamayun, M}, title = {IAA producing fungal endophyte Penicillium roqueforti Thom., enhances stress tolerance and nutrients uptake in wheat plants grown on heavy metal contaminated soils.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0208150}, doi = {10.1371/journal.pone.0208150}, pmid = {30496253}, issn = {1932-6203}, mesh = {Biodegradation, Environmental ; Endophytes/*physiology ; Indoleacetic Acids/*metabolism ; Metals, Heavy/*metabolism ; Nutrients/metabolism ; Penicillium/*physiology ; Seedlings/microbiology/physiology ; Soil Pollutants/*metabolism ; Stress, Physiological ; Symbiosis ; Triticum/*microbiology/physiology ; }, abstract = {Heavy metals contaminated soil is a serious environmental concern that has a negative impact on agriculture and ecosystem. Economical and efficient ways are needed to address this problem worldwide. In this regard, exploration and application of proficient microbial strains that can help the crop plants to thrive in agricultural soils that are greatly contaminated with heavy metals. The present study mainly focused on the effect of IAA producing endophytic fungi Penicillium ruqueforti Thom., on wheat plants cultivated in soil rich in heavy metals (Ni, Cd, Cu, Zn, and Pb). P. ruqueforti has induced great resistance in wheat inoculated plants grown in heavy metal contaminated soil. Application of the isolated strain of P. ruqueforti restricted the transfer of heavy metals from soil to the plants by secreting indole acetic acid (IAA). Furthermore, P. ruqueforti inoculated wheat seedlings watered with waste water had higher plant growth, nutrient uptake and low concentrations of heavy metals in shoot and roots. On the contrary, non-inoculated wheat plants under heavy metal stress had stunted growth with symptoms of chlorosis. From the results, it is concluded that P. ruqueforti inoculation can establish a symbiotic relationship with host plants, which is useful for phytostabilization of heavy metals or in other words helping the host crops to flourish through soil that are highly contaminated with heavy metals.}, }
@article {pmid30392387, year = {2019}, author = {Al-Kandari, F and Woodward, MJ}, title = {Genotypic and phenotypic diversity differences of presumptive commensal and avian pathogenic E. coli.}, journal = {British poultry science}, volume = {60}, number = {1}, pages = {79-86}, doi = {10.1080/00071668.2018.1544415}, pmid = {30392387}, issn = {1466-1799}, mesh = {Animals ; *Chickens ; England/epidemiology ; Escherichia coli/*genetics/*pathogenicity/physiology ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; *Genetic Variation ; Genotype ; Phenotype ; Poultry Diseases/*epidemiology/microbiology ; Symbiosis/genetics ; *Turkeys ; Virulence/genetics ; }, abstract = {1. The objective of the experiment was to characterise the genotypic and phenotypic differences between presumptive commensal E. coli and avian pathogenic E. coli (APEC) of poultry. 2. DNA was extracted from 65 confirmed APEC E. coli from chicken, 100 presumptive commensal E. coli from healthy turkey and 35 from healthy chicken. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and virulence factors genotyping was performed to characterise genetic features. 3. Carbon source utilisation and antimicrobial susceptibility tests were performed to characterise phenotypic features of isolates. 4. The genetic divergence between E. coli strains tested by ERIC-PCR profiles and virulence-associated genes showed a clear genetic separation between E. coli APEC and turkey E. coli strains. 5. The carbon utilisation profile of turkey isolates was different from chicken and APEC strains; whereas antimicrobial susceptibility was highest for turkey isolates (53%), and lowest for APEC strains (33.8%). 6. The study showed a significant negative correlation between utilisation of arabitol and adonitol with different virulence determinants tested, which suggests that the ability to utilise some uncommon carbon sources may be used to discriminate between presumptive commensal E. coli and APEC.}, }
@article {pmid29975680, year = {2018}, author = {Pais, IS and Valente, RS and Sporniak, M and Teixeira, L}, title = {Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.}, journal = {PLoS biology}, volume = {16}, number = {7}, pages = {e2005710}, pmid = {29975680}, issn = {1545-7885}, mesh = {Animals ; Bacteria/growth &amp; development/*metabolism ; Biodiversity ; Drosophila melanogaster/*microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Models, Biological ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {Animals live together with diverse bacteria that can impact their biology. In Drosophila melanogaster, gut-associated bacterial communities are relatively simple in composition but also have a strong impact on host development and physiology. It is generally assumed that gut bacteria in D. melanogaster are transient and their constant ingestion with food is required to maintain their presence in the gut. Here, we identify bacterial species from wild-caught D. melanogaster that stably associate with the host independently of continuous inoculation. Moreover, we show that specific Acetobacter wild isolates can proliferate in the gut. We further demonstrate that the interaction between D. melanogaster and the wild isolated Acetobacter thailandicus is mutually beneficial and that the stability of the gut association is key to this mutualism. The stable population in the gut of D. melanogaster allows continuous bacterial spreading into the environment, which is advantageous to the bacterium itself. The bacterial dissemination is in turn advantageous to the host because the next generation of flies develops in the presence of this particularly beneficial bacterium. A. thailandicus leads to a faster host development and higher fertility of emerging adults when compared to other bacteria isolated from wild-caught flies. Furthermore, A. thailandicus is sufficient and advantageous when D. melanogaster develops in axenic or freshly collected figs, respectively. This isolate of A. thailandicus colonizes several genotypes of D. melanogaster but not the closely related D. simulans, indicating that the stable association is host specific. This work establishes a new conceptual model to understand D. melanogaster-gut microbiota interactions in an ecological context; stable interactions can be mutualistic through microbial farming, a common strategy in insects. Moreover, these results develop the use of D. melanogaster as a model to study gut microbiota proliferation and colonization.}, }
@article {pmid29852240, year = {2018}, author = {Cording, S and Medvedovic, J and Lecuyer, E and Aychek, T and Eberl, G}, title = {Control of pathogens and microbiota by innate lymphoid cells.}, journal = {Microbes and infection}, volume = {20}, number = {6}, pages = {317-322}, doi = {10.1016/j.micinf.2018.05.003}, pmid = {29852240}, issn = {1769-714X}, mesh = {Animals ; Cytokines/immunology ; Homeostasis/immunology ; Host-Pathogen Interactions/*immunology ; Humans ; *Immunity, Innate ; Intestinal Mucosa/immunology ; Lymphocytes/cytology/*immunology ; Microbiota/*immunology ; Respiratory Mucosa/immunology ; Symbiosis/immunology ; }, abstract = {Innate lymphoid cells (ILCs) are the innate counterpart of T cells. Upon infection or injury, ILCs react promptly to direct the developing immune response to the one most adapted to the threat facing the organism. Therefore, ILCs play an important role early in resistance to infection, but also to maintain homeostasis with the symbiotic microbiota following perturbations induced by diet and pathogens. Such roles of ILCs have been best characterized in the intestine and lung, mucosal sites that are exposed to the environment and are therefore colonized with diverse but specific types of microbes. Understanding the dialogue between pathogens, microbiota and ILCs may lead to new strategies to re-inforce immunity for prevention, vaccination and therapy.}, }
@article {pmid29291350, year = {2018}, author = {Smith, TE and Pond, CD and Pierce, E and Harmer, ZP and Kwan, J and Zachariah, MM and Harper, MK and Wyche, TP and Matainaho, TK and Bugni, TS and Barrows, LR and Ireland, CM and Schmidt, EW}, title = {Accessing chemical diversity from the uncultivated symbionts of small marine animals.}, journal = {Nature chemical biology}, volume = {14}, number = {2}, pages = {179-185}, pmid = {29291350}, issn = {1552-4469}, support = {R01 GM102602/GM/NIGMS NIH HHS/United States ; R01 GM107557/GM/NIGMS NIH HHS/United States ; U01 TW006671/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Anti-HIV Agents/*pharmacology ; Bacteria ; Biological Products/*pharmacology ; DNA/analysis ; *Drug Discovery ; Drug Evaluation, Preclinical ; Genomics ; HIV Infections/*drug therapy ; Humans ; Lysinoalanine/chemistry ; Metagenome ; Metagenomics ; *Microbiota ; Multigene Family ; Peptides/pharmacology ; Structure-Activity Relationship ; *Symbiosis ; Synthetic Biology ; T-Lymphocytes/drug effects ; Urochordata ; }, abstract = {Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within. We solved this problem by combining chemistry, metagenomics, and synthetic biology to directly identify and synthesize the natural products. We show that these anti-HIV compounds, the divamides, are a novel family of lanthipeptides produced by symbiotic bacteria living in the tunicate. Neighboring animal colonies contain structurally related divamides that differ starkly in their biological properties, suggesting a role for biosynthetic plasticity in a native context wherein biological interactions take place.}, }
@article {pmid29255283, year = {2018}, author = {Stappenbeck, TS}, title = {Assigning function to symbionts.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {6-7}, doi = {10.1038/s41564-017-0088-0}, pmid = {29255283}, issn = {2058-5276}, mesh = {Animals ; Bacterial Infections/etiology/*microbiology ; Computational Biology/*methods/trends ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Microbiological Techniques/*methods/trends ; *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 = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuz011}, pmid = {31049565}, issn = {1574-6976}, 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 {pmid30658519, year = {2019}, author = {Milosevic, I and Vujovic, A and Barac, A and Djelic, M and Korac, M and Radovanovic Spurnic, A and Gmizic, I and Stevanovic, O and Djordjevic, V and Lekic, N and Russo, E and Amedei, A}, title = {Gut-Liver Axis, Gut Microbiota, and Its Modulation in the Management of Liver Diseases: A Review of the Literature.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020395}, pmid = {30658519}, issn = {1422-0067}, mesh = {Animals ; *Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/*metabolism/*microbiology ; Humans ; Liver/immunology/*metabolism/pathology ; Liver Diseases/*etiology/*metabolism/pathology/therapy ; Prebiotics ; Probiotics ; Symbiosis ; }, abstract = {The rapid scientific interest in gut microbiota (GM) has coincided with a global increase in the prevalence of infectious and non-infectivous liver diseases. GM, which is also called &quot;the new virtual metabolic organ&quot;, makes axis with a number of extraintestinal organs, such as kidneys, brain, cardiovascular, and the bone system. The gut-liver axis has attracted greater attention in recent years. GM communication is bi-directional and involves endocrine and immunological mechanisms. In this way, gut-dysbiosis and composition of &quot;ancient&quot; microbiota could be linked to pathogenesis of numerous chronic liver diseases such as chronic hepatitis B (CHB), chronic hepatitis C (CHC), alcoholic liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), development of liver cirrhosis, and hepatocellular carcinoma (HCC). In this paper, we discuss the current evidence supporting a GM role in the management of different chronic liver diseases and potential new therapeutic GM targets, like fecal transplantation, antibiotics, probiotics, prebiotics, and symbiotics. We conclude that population-level shifts in GM could play a regulatory role in the gut-liver axis and, consequently, etiopathogenesis of chronic liver diseases. This could have a positive impact on future therapeutic strategies.}, }
@article {pmid30546098, year = {2019}, author = {Wright, AT}, title = {Gut commensals make choline too.}, journal = {Nature microbiology}, volume = {4}, number = {1}, pages = {4-5}, doi = {10.1038/s41564-018-0325-1}, pmid = {30546098}, issn = {2058-5276}, mesh = {Choline ; *Gastrointestinal Microbiome ; *Phospholipase D ; Phospholipases ; Symbiosis ; }, }
@article {pmid30224553, year = {2018}, author = {Chakraborty, R and Lam, V and Kommineni, S and Stromich, J and Hayward, M and Kristich, CJ and Salzman, NH}, title = {Ceftriaxone Administration Disrupts Intestinal Homeostasis, Mediating Noninflammatory Proliferation and Dissemination of Commensal Enterococci.}, journal = {Infection and immunity}, volume = {86}, number = {12}, pages = {}, pmid = {30224553}, issn = {1098-5522}, support = {R01 GM099526/GM/NIGMS NIH HHS/United States ; R01 AI081692/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacterial Translocation ; Ceftriaxone/*adverse effects ; Enterococcus faecalis ; Gastrointestinal Microbiome ; Gram-Positive Bacterial Infections ; Homeostasis/*drug effects ; Intestines/*drug effects/microbiology/physiopathology ; Male ; Mice ; Mice, Inbred C57BL ; Symbiosis/*drug effects ; }, abstract = {Enterococci are Gram-positive commensals of the mammalian intestinal tract and harbor intrinsic resistance to broad-spectrum cephalosporins. Disruption of colonization resistance in humans by antibiotics allows enterococci to proliferate in the gut and cause disseminated infections. In this study, we used Enterococcus faecalis (EF)-colonized mice to study the dynamics of enterococci, commensal microbiota, and the host in response to systemic ceftriaxone administration. We found that the mouse model recapitulates intestinal proliferation and dissemination of enterococci seen in humans. Employing a ceftriaxone-sensitive strain of enterococci (E. faecalis JL308), we showed that increased intestinal abundance is critical for the systemic dissemination of enterococci. Investigation of the impact of ceftriaxone on the mucosal barrier defenses and integrity suggested that translocation of enterococci across the intestinal mucosa was not associated with intestinal pathology or increased permeability. Ceftriaxone-induced alteration of intestinal microbial composition was associated with transient increase in the abundance of multiple bacterial operational taxonomic units (OTUs) in addition to enterococci, for example, lactobacilli, which also disseminated to the extraintestinal organs. Collectively, these results emphasize that ceftriaxone-induced disruption of colonization resistance and alteration of mucosal homeostasis facilitate increased intestinal abundance of a limited number of commensals along with enterococci, allowing their translocation and systemic dissemination in a healthy host.}, }
@article {pmid30182224, year = {2018}, author = {Baltrus, DA and Spraker, J and Arnold, AE}, title = {Quantifying Re-association of a Facultative Endohyphal Bacterium with a Filamentous Fungus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1848}, number = {}, pages = {1-11}, doi = {10.1007/978-1-4939-8724-5_1}, pmid = {30182224}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacterial Physiological Phenomena/drug effects ; Coculture Techniques ; Fungi/drug effects/*physiology ; Gentamicins/pharmacology ; Phenotype ; *Symbiosis ; }, abstract = {We present here a method to quantify reassociation between facultative endohyphal bacteria and filamentous fungal hosts. Our method takes advantage of the capabilities of fungal cell walls to selectively protect internal bacteria from gentamicin treatment, an assay adapted from studies of internalized bacterial pathogens in cell culture. We report the efficacy of gentamicin to kill planktonic bacteria treated during fungal coculture, and also describe and characterize a sampling scheme to recover and quantify culturable bacteria from the growing edge of fungal mycelium in vitro. This assay enables qualitative and quantitative tests of reassociation capabilities for facultative endohyphal bacteria with host fungi and provides a means to investigate the genetic basis for these associations in a repeatable way.}, }
@article {pmid29764656, year = {2018}, author = {Simon, JC and Peccoud, J}, title = {Rapid evolution of aphid pests in agricultural environments.}, journal = {Current opinion in insect science}, volume = {26}, number = {}, pages = {17-24}, doi = {10.1016/j.cois.2017.12.009}, pmid = {29764656}, issn = {2214-5753}, mesh = {*Adaptation, Biological ; Alkenes ; Animals ; Aphids/*genetics/microbiology/physiology ; *Biological Evolution ; Crops, Agricultural ; Insect Control/methods ; Phenotype ; Pyrans ; Symbiosis ; }, abstract = {Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids. We outline the peculiar mode of reproduction, the polyphenism for biologically important traits and the diverse and flexible associations with microbial symbionts as key determinants of adaptive potential and pest status of aphids.}, }
@article {pmid29411455, year = {2018}, author = {Ivens, ABF and Gadau, A and Kiers, ET and Kronauer, DJC}, title = {Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1898-1914}, pmid = {29411455}, issn = {1365-294X}, support = {335542//European Research Council/International ; UL1 TR000043/TR/NCATS NIH HHS/United States ; }, mesh = {Acetobacteraceae/genetics/physiology ; Animals ; Ants/genetics/*microbiology ; Aphids/genetics/*microbiology ; Behavior, Animal ; Buchnera/genetics ; Microbiota/*genetics ; Phylogeny ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host-microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew-producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species-specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants' microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar-processing Acetobacteraceae bacteria, known from other honeydew-feeding ants and which likely reside extracellularly in the ants' guts. These ant-microbe associations are arguably more &quot;open&quot; and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.}, }
@article {pmid29411448, year = {2018}, author = {Prest, TL and Kimball, AK and Kueneman, JG and McKenzie, VJ}, title = {Host-associated bacterial community succession during amphibian development.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1992-2006}, doi = {10.1111/mec.14507}, pmid = {29411448}, issn = {1365-294X}, mesh = {Animals ; Bufonidae/genetics/growth &amp; development/*microbiology ; Host Microbial Interactions/*genetics ; Larva/genetics/growth &amp; development/microbiology ; Metamorphosis, Biological/*genetics ; Symbiosis/*genetics ; }, abstract = {Amphibians undergo significant developmental changes during their life cycle, as they typically move from a primarily aquatic environment to a more terrestrial one. Amphibian skin is a mucosal tissue that assembles communities of symbiotic microbiota. However, it is currently not well understood as to where amphibians acquire their skin symbionts, and whether the sources of microbial symbionts change throughout development. In this study, we utilized data collected from four wild boreal toad populations (Anaxyrus boreas); specifically, we sampled the skin bacterial communities during toad development, including eggs, tadpoles, subadults and adults as well as environmental sources of bacteria (water, aquatic sediment and soil). Using 16S rRNA marker gene profiling coupled with SourceTracker, we show that while primary environmental sources remained constant throughout the life cycle, secondary sources of boreal toad symbionts significantly changed with development. We found that toad skin communities changed predictably across development and that two developmental disturbance events (egg hatching and metamorphosis) dictated major changes. Toad skin communities assembled to alternative stable states following each of these developmental disturbances. Using the predicted average rRNA operon copy number of the communities at each life stage, we showed how the skin bacterial communities undergo a successional pattern whereby &quot;fast-growing&quot; (copiotroph) generalist bacteria dominate first before &quot;slow-growing&quot; (oligotroph) specialized bacteria take over. Our study highlights how host-associated bacterial community assembly is tightly coupled to host development and that host-associated communities demonstrate successional patterns akin to those observed in free-living bacteria as well as macrofaunal communities.}, }
@article {pmid29290092, year = {2018}, author = {Kessler, RW and Weiss, A and Kuegler, S and Hermes, C and Wichard, T}, title = {Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta).}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1808-1819}, doi = {10.1111/mec.14472}, pmid = {29290092}, issn = {1365-294X}, mesh = {Culture Media/chemistry/metabolism ; Host-Pathogen Interactions/*genetics ; Morphogenesis/drug effects/genetics ; Rhodobacteraceae/*genetics/metabolism ; Sulfhydryl Compounds/metabolism ; Sulfides/metabolism ; Sulfonium Compounds/chemistry/metabolism ; Symbiosis/*genetics ; Ulva/*genetics/growth &amp; development/metabolism/microbiology ; }, abstract = {The marine macroalga Ulva mutabilis (Chlorophyta) develops into callus-like colonies consisting of undifferentiated cells and abnormal cell walls under axenic conditions. Ulva mutabilis is routinely cultured with two bacteria, the Roseovarius sp. MS2 strain and the Maribacter sp. MS6 strain, which release morphogenetic compounds and ensure proper algal morphogenesis. Using this tripartite community as an emerging model system, we tested the hypothesis that the bacterial-algal interactions evolved as a result of mutually taking advantage of signals in the environment. Our study aimed to determine whether cross-kingdom crosstalk is mediated by the attraction of bacteria through algal chemotactic signals. Roseovarius sp. MS2 senses the known osmolyte dimethylsulfoniopropionate (DMSP) released by Ulva into the growth medium. Roseovarius sp. is attracted by DMSP and takes it up rapidly such that DMSP can only be determined in axenic growth media. As DMSP did not promote bacterial growth under the tested conditions, Roseovarius benefited solely from glycerol as the carbon source provided by Ulva. Roseovarius quickly catabolized DMSP into methanethiol (MeSH) and dimethylsulphide (DMS). We conclude that many bacteria can use DMSP as a reliable signal indicating a food source and promote the subsequent development and morphogenesis in Ulva.}, }
@article {pmid29230893, year = {2018}, author = {Kohl, KD and Dearing, MD and Bordenstein, SR}, title = {Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1874-1883}, pmid = {29230893}, issn = {1365-294X}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; T32 DK007673/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Ecology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/genetics/microbiology ; Ruminococcus/*genetics ; Symbiosis/genetics ; }, abstract = {Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.}, }
@article {pmid29164717, year = {2018}, author = {Raymann, K and Bobay, LM and Moran, NA}, title = {Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {2057-2066}, pmid = {29164717}, issn = {1365-294X}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bees/drug effects/genetics/*microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gastrointestinal Tract/drug effects/microbiology ; Genetic Variation/genetics ; Host Microbial Interactions/drug effects/genetics ; Neisseriaceae/drug effects/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated. To address this gap, we used amplicon sequencing of protein-coding genes to assess effects of antibiotics on fine-scale genetic diversity of the honeybee gut microbiota. We followed the population dynamics of alleles within two dominant core species of the bee gut community, Gilliamella apicola and Snodgrassella alvi, following antibiotic perturbation. Whereas we observed a large reduction in genetic diversity in G. apicola, S. alvi diversity was mostly unaffected. The reduction in G. apicola diversity accompanied an increase in the frequency of several alleles, suggesting resistance to antibiotic treatment. We find that antibiotic perturbation can cause major shifts in diversity and that the extent of these shifts can vary substantially across species. Thus, antibiotics impact not only species composition, but also allelic diversity within species, potentially affecting hosts if variants with particular functions are reduced or eliminated. Overall, we show that amplicon sequencing of protein-coding genes, without clustering into operational taxonomic units, provides an accurate picture of the fine-scale dynamics of microbial communities over time.}, }
@article {pmid29134727, year = {2018}, author = {Thairu, MW and Cheng, S and Hansen, AK}, title = {A sRNA in a reduced mutualistic symbiont genome regulates its own gene expression.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1766-1776}, doi = {10.1111/mec.14424}, pmid = {29134727}, issn = {1365-294X}, mesh = {Animals ; Aphids/genetics/microbiology ; Buchnera/*genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome, Bacterial/genetics ; *Proteomics ; RNA/genetics ; RNA, Messenger/genetics ; Symbiosis/*genetics ; }, abstract = {Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa. In this study, we investigate whether differential protein regulation in Buchnera is the result of post-transcriptional gene regulation via sRNAs. We characterize the sRNA profile of two Buchnera life stages: (i) when Buchnera is transitioning from an extracellular proliferating state in aphid embryos and (ii) when Buchnera is in an intracellular nonproliferating state in aphid bacteriocytes (specialized symbiont cells). Overall, we identified 90 differentially expressed sRNAs, 97% of which were upregulated in aphid embryos. Of these sRNAs, the majority were predicted to be involved in the regulation of various metabolic processes, including arginine biosynthesis. Using a heterologous dual expression vector, we reveal for the first time that a Buchnera antisense sRNA can post-transcriptionally interact with its cognate Buchnera coding sequence, carB, a gene involved in arginine biosynthesis. These results corroborate our in vivo RNAseq and proteomic data, where the candidate antisense sRNA carB and the protein CarB are significantly upregulated in aphid embryos. Overall, we demonstrate that Buchnera may regulate gene expression independently from its host by utilizing sRNAs.}, }
@article {pmid29124895, year = {2018}, author = {Lawson, CA and Raina, JB and Kahlke, T and Seymour, JR and Suggett, DJ}, title = {Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {7-11}, doi = {10.1111/1758-2229.12599}, pmid = {29124895}, issn = {1758-2229}, mesh = {Animals ; Anthozoa/parasitology ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; Dinoflagellida/*microbiology ; Genome, Bacterial/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.}, }
@article {pmid29113026, year = {2018}, author = {Bost, A and Franzenburg, S and Adair, KL and Martinson, VG and Loeb, G and Douglas, AE}, title = {How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1848-1859}, doi = {10.1111/mec.14413}, pmid = {29113026}, issn = {1365-294X}, mesh = {Acetobacteraceae/genetics ; Animals ; Biodiversity ; Drosophila melanogaster/*genetics/microbiology ; Enterobacteriaceae/genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; *Transcription, Genetic ; }, abstract = {Despite evidence from laboratory experiments that perturbation of the gut microbiota affects many traits of the animal host, our understanding of the effect of variation in microbiota composition on animals in natural populations is very limited. The core purpose of this study on the fruit fly Drosophila melanogaster was to identify the impact of natural variation in the taxonomic composition of gut bacterial communities on host traits, with the gut transcriptome as a molecular index of microbiota-responsive host traits. Use of the gut transcriptome was validated by demonstrating significant transcriptional differences between the guts of laboratory flies colonized with bacteria and maintained under axenic conditions. Wild Drosophila from six field collections made over two years had gut bacterial communities of diverse composition, dominated to varying extents by Acetobacteraceae and Enterobacteriaceae. The gut transcriptomes also varied among collections and differed markedly from those of laboratory flies. However, no overall relationship between variation in the wild fly transcriptome and taxonomic composition of the gut microbiota was evident at all taxonomic scales of bacteria tested for both individual fly genes and functional categories in Gene Ontology. We conclude that the interaction between microbiota composition and host functional traits may be confounded by uncontrolled variation in both ecological circumstance and host traits (e.g., genotype, age physiological condition) under natural conditions, and that microbiota effects on host traits identified in the laboratory should, therefore, be extrapolated to field population with great caution.}, }
@article {pmid31038750, year = {2019}, author = {Gomes, SI and van Bodegom, PM and Merckx, VS and Soudzilovskaia, NA}, title = {Environmental drivers for cheaters of arbuscular mycorrhizal symbiosis in tropical rainforests.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15876}, pmid = {31038750}, issn = {1469-8137}, abstract = {Hundreds of non-photosynthetic 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 to 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 favor a weak mutualism between plants and arbuscular mycorrhizal fungi according to the trade balance model. Our study points out which soil properties favor 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, 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 {pmid30459180, year = {2019}, author = {Singh, ND}, title = {Wolbachia Infection Associated with Increased Recombination in Drosophila.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {1}, pages = {229-237}, doi = {10.1534/g3.118.200827}, pmid = {30459180}, issn = {2160-1836}, mesh = {Animals ; Drosophila melanogaster/*genetics/microbiology ; Fertility/genetics ; Genome, Insect/genetics ; Reproduction/*genetics ; Symbiosis/*genetics ; Wolbachia/*genetics/pathogenicity ; }, abstract = {Wolbachia is a maternally-transmitted endosymbiotic bacteria that infects a large diversity of arthropod and nematode hosts. Some strains of Wolbachia are parasitic, manipulating host reproduction to benefit themselves, while other strains of Wolbachia exhibit obligate or facultative mutualisms with their host. The effects of Wolbachia on its host are many, though primarily relate to host immune and reproductive function. Here we test the hypothesis that Wolbachia infection alters the frequency of homologous recombination during meiosis. We use D. melanogaster as a model system, and survey recombination in eight wild-derived Wolbachia-infected (strain wMel) and Wolbachia-uninfected strains, controlling for genotype. We measure recombination in two intervals of the genome. Our results indicate that Wolbachia infection is associated with increased recombination in one genomic interval and not the other. The effect of Wolbachia infection on recombination is thus heterogenous across the genome. Our data also indicate a reproductive benefit of Wolbachia infection; infected females show higher fecundity than their uninfected genotypic controls. Given the prevalence of Wolbachia infection in natural populations, our findings suggest that Wolbachia infection is likely to contribute to recombination rate and fecundity variation among individuals in nature.}, }
@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}, 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2019.04.002}, pmid = {31031015}, issn = {1618-0984}, 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 {pmid30883545, year = {2019}, author = {Valdano, E and Manrubia, S and Gómez, S and Arenas, A}, title = {Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission.}, journal = {PLoS computational biology}, volume = {15}, number = {3}, pages = {e1006876}, doi = {10.1371/journal.pcbi.1006876}, pmid = {30883545}, issn = {1553-7358}, mesh = {Animals ; Biological Evolution ; *Host-Pathogen Interactions ; Humans ; Models, Theoretical ; Prevalence ; Symbiosis ; Virus Diseases/*transmission ; Virus Replication ; }, abstract = {Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle, however, requires the full genome, so that a systemic infection of a host requires the concurrent presence of several particles. This represents an apparent evolutionary drawback of multipartitism, while its advantages remain unclear. A transition from monopartite to multipartite viral forms has been described in vitro under conditions of high multiplicity of infection, suggesting that cooperation between defective mutants is a plausible evolutionary pathway towards multipartitism. However, it is unknown how the putative advantages that multipartitism might enjoy at the microscopic level affect its epidemiology, or if an explicit advantange is needed to explain its ecological persistence. In order to disentangle which mechanisms might contribute to the rise and fixation of multipartitism, we here investigate the interaction between viral spreading dynamics and host population structure. We set up a compartmental model of the spread of a virus in its different forms and explore its epidemiology using both analytical and numerical techniques. We uncover that the impact of host contact structure on spreading dynamics entails a rich phenomenology of ecological relationships that includes cooperation, competition, and commensality. Furthermore, we find out that multipartitism might rise to fixation even in the absence of explicit microscopic advantages. Multipartitism allows the virus to colonize environments that could not be invaded by the monopartite form, while homogeneous contacts between hosts facilitate its spread. We conjecture that these features might have led to an increase in the diversity and prevalence of multipartite viral forms concomitantly with the expansion of agricultural practices.}, }
@article {pmid30873932, year = {2019}, author = {Malke, H}, title = {Genetics and Pathogenicity Factors of Group C and G Streptococci.}, journal = {Microbiology spectrum}, volume = {7}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.GPP3-0002-2017}, pmid = {30873932}, issn = {2165-0497}, mesh = {Animals ; Antigens, Bacterial/classification/genetics ; Antigens, Surface/classification ; Bacterial Proteins/classification/genetics ; Cell Membrane ; Cell Wall ; DNA, Bacterial ; Exotoxins/classification/genetics ; Genes, Bacterial ; Host Specificity ; Humans ; *Phylogeny ; Streptococcal Infections/microbiology ; Streptococcus/*classification/*genetics/pathogenicity ; Streptokinase/genetics ; Symbiosis ; Virulence Factors/*genetics ; }, abstract = {Of the eight phylogenetic groups comprising the genus Streptococcus, Lancefield group C and G streptococci (GCS and GGS, resp.) occupy four of them, including the Pyogenic, Anginosus, and Mitis groups, and one Unnamed group so far. These organisms thrive as opportunistic commensals in both humans and animals but may also be associated with clinically serious infections, often resembling those due to their closest genetic relatives, the group A streptoccci (GAS). Advances in molecular genetics, taxonomic approaches and phylogenomic studies have led to the establishment of at least 12 species, several of which being subdivided into subspecies. This review summarizes these advances, citing 264 early and recent references. It focuses on the molecular structure and genetic regulation of clinically important proteins associated with the cell wall, cytoplasmic membrane and extracellular environment. The article also addresses the question of how, based on the current knowledge, basic research and translational medicine might proceed to further advance our understanding of these multifaceted organisms. Particular emphasis in this respect is placed on streptokinase as the protein determining the host specificity of infection and the Rsh-mediated stringent response with its potential for supporting bacterial survival under nutritional stress conditions.}, }
@article {pmid30193959, year = {2018}, author = {Porter, NT and Luis, AS and Martens, EC}, title = {Bacteroides thetaiotaomicron.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {966-967}, doi = {10.1016/j.tim.2018.08.005}, pmid = {30193959}, issn = {1878-4380}, mesh = {Bacteroides thetaiotaomicron/*physiology ; Dietary Fiber/metabolism ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Host Microbial Interactions/*physiology ; Humans ; Microbial Interactions/physiology ; Plant Cells ; Polysaccharides/metabolism ; Symbiosis ; }, abstract = {This infographic on Bacteroides thetaiotaomicron (Bt) explores the ability of this microbe to digest a broad array of complex carbohydrates, alter its surface features, and its emerging role in gastrointestinal diseases. The infographic of Bacteroides thetaiotaomicron (Bt) illustrates two key facets of its symbiotic lifestyle in the human gut: a broad ability to digest dietary fiber polysaccharides and host glycans, and a dynamic cell-surface architecture that promotes both interactions with and evasion of the host immune system. The starch-utilization system (Sus) is a cell-surface and periplasmic system involved in starch cleavage and transport. Over 80 additional Sus-like systems utilize substrates ranging from host glycans to plant cell wall pectins. Bt has evolved intricate strategies to interact with other microbes or its host, including modification of its surface. Some nutrient utilization pathways select for or directly trigger changes in capsular polysaccharide (CPS) expression. Like other fermentative members of the gut microbiome, Bt produces host absorbable short-chain and organic acids, which can all be absorbed by the host as a source of energy.}, }
@article {pmid30120872, year = {2019}, author = {Dello Jacovo, E and Valentine, TA and Maluk, M and Toorop, P and Lopez Del Egido, L and Frachon, N and Kenicer, G and Park, L and Goff, M and Ferro, VA and Bonomi, C and James, EK and Iannetta, PPM}, title = {Towards a characterisation of the wild legume bitter vetch (Lathyrus linifolius L. (Reichard) Bässler): heteromorphic seed germination, root nodule structure and N-fixing rhizobial symbionts.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {21}, number = {3}, pages = {523-532}, doi = {10.1111/plb.12902}, pmid = {30120872}, issn = {1438-8677}, support = {FP7/2007-2013///People Programme (Marie Curie Actions) of the European Union Seventh Framework Programme/ ; //Rural and Environment Science and Analytical Services Division/ ; }, mesh = {Fabaceae/*metabolism/*microbiology ; Germination/*physiology ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*physiology ; Root Nodules, Plant/metabolism/microbiology ; Seeds/metabolism/microbiology ; Symbiosis/physiology ; }, abstract = {Lathyrus linifolius L. (Reichard) Bässler (Fabiaceae, bitter vetch) is a nitrogen (N) fixing species. A coloniser of low nutrient (N) soils, it supports biodiversity such as key moth and butterfly species, and its roots are known for their organoleptic and claimed therapeutic properties. Thus, the species has high potential for restoration, conservation, novel cropping and as a model species. The last because of its genetic synteny with important pulse crops. However, regeneration and functional attributes of L. linifolius remain to be characterised. Seeds of L. linifolius were characterised using physical, colorimetric and chemical data. Ultrastructural and functional characterisation of the N-fixing root nodules included immunolabelling with nifH protein antibodies (recognising the N-fixing enzyme, nitrogenase). Endosymbiotic bacteria were isolated from root nodules and characterised phylogenetically using 16S rRNA, nodA and nodD gene sequences. L. linifolius yielded heteromorphic seed of distinct colour classes: green and brown. Seed morphotypes had similar C:N ratios and were equally germinable (ca. 90%) after scarification at differing optimal temperatures (16 and 20 °C). Brown seeds were larger and comprised a larger proportion of the seed batch (69%). L. linifolius root nodules appeared indeterminate in structure, effective (capable of fixing atmospheric N) and having strains very similar to Rhizobium leguminosarum biovar viciae. The findings and rhizobial isolates have potential application for ecological restoration and horticulture using native seeds. Also, the data and rhizobial resources have potential applications in comparative and functional studies with related and socio-economically important crops such as Pisum, Lens and Vicia.}, }
@article {pmid30067212, year = {2018}, author = {Barthole, G}, title = {[Never alone. Microorganism, ecology, evolution].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {6-7}, pages = {604-607}, doi = {10.1051/medsci/20183406023}, pmid = {30067212}, issn = {1958-5381}, mesh = {Animals ; *Biological Evolution ; Civilization ; *Ecosystem ; Endophytes/*physiology ; Host Microbial Interactions/physiology ; Humans ; Microbial Interactions/physiology ; Mitochondria/physiology ; Plants/microbiology ; Symbiosis/*physiology ; }, }
@article {pmid29909042, year = {2018}, author = {Keen, EC and Dantas, G}, title = {Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {943-954}, doi = {10.1016/j.tim.2018.05.009}, pmid = {29909042}, issn = {1878-4380}, support = {R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/*virology ; Bacterial Physiological Phenomena ; Bacteriophages/*physiology ; Host Microbial Interactions/immunology/physiology ; Humans ; Lysogeny ; Microbial Interactions/*immunology/*physiology ; Microbiota/*immunology ; Models, Animal ; Phenotype ; Prophages ; Symbiosis ; }, abstract = {Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.}, }
@article {pmid29880910, year = {2018}, author = {Yurchenko, T and Ševčíková, T and Přibyl, P and El Karkouri, K and Klimeš, V and Amaral, R and Zbránková, V and Kim, E and Raoult, D and Santos, LMA and Eliáš, M}, title = {A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2163-2175}, pmid = {29880910}, issn = {1751-7370}, mesh = {*Gene Transfer, Horizontal ; Genomics ; Operon ; Rickettsiaceae/*genetics ; Stramenopiles/*microbiology ; Symbiosis ; }, abstract = {Rickettsiales are obligate intracellular bacteria originally found in metazoans, but more recently recognized as widespread endosymbionts of various protists. One genus was detected also in several green algae, but reports on rickettsialean endosymbionts in other algal groups are lacking. Here we show that several distantly related eustigmatophytes (coccoid algae belonging to Ochrophyta, Stramenopiles) are infected by Candidatus Phycorickettsia gen. nov., a new member of the family Rickettsiaceae. The genome sequence of Ca. Phycorickettsia trachydisci sp. nov., an endosymbiont of Trachydiscus minutus CCALA 838, revealed genomic features (size, GC content, number of genes) typical for other Rickettsiales, but some unusual aspects of the gene content were noted. Specifically, Phycorickettsia lacks genes for several components of the respiration chain, haem biosynthesis pathway, or c-di-GMP-based signalling. On the other hand, it uniquely harbours a six-gene operon of enigmatic function that we recently reported from plastid genomes of two distantly related eustigmatophytes and from various non-rickettsialean bacteria. Strikingly, the eustigmatophyte operon is closely related to the one from Phycorickettsia, suggesting a gene transfer event between the endosymbiont and host lineages in early eustigmatophyte evolution. We hypothesize an important role of the operon in the physiology of Phycorickettsia infection and a long-term eustigmatophyte-Phycorickettsia coexistence.}, }
@article {pmid29871873, year = {2018}, author = {Hunter, P}, title = {The revival of the extended phenotype: After more than 30 years, Dawkins' Extended Phenotype hypothesis is enriching evolutionary biology and inspiring potential applications.}, journal = {EMBO reports}, volume = {19}, number = {7}, pages = {}, pmid = {29871873}, issn = {1469-3178}, mesh = {*Biological Evolution ; Coral Reefs ; Host-Parasite Interactions/*genetics ; *Phenotype ; Symbiosis/*genetics ; }, }
@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 = {}, number = {}, pages = {}, 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, AJ 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 = {}, number = {}, pages = {}, doi = {10.1094/MPMI-11-18-0304-R}, pmid = {31025899}, issn = {0894-0282}, abstract = {Plants encounter beneficial and detrimental microorganisms both above- and below ground and the health status of the plant depends on the composition of this pan-microbiome. Beneficial microorganisms contribute to plant nutrition and/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 above ground resistance against necrotrophic pathogens and is mediated by jasmonic acid/ethylene- signaling. By contrast, systemic acquired resistance relies on salicylic acid (SA) 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 pre-established 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 = {}, number = {}, pages = {}, doi = {10.2217/fmb-2018-0317}, pmid = {31025880}, issn = {1746-0921}, 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}, 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}, 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 determine distinct autoactivation states of Symbiosis Receptor Kinase.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.9b00071}, pmid = {31021099}, issn = {1520-4995}, abstract = {Plant receptor-like kinases (RLKs) have Tyr in 'gatekeeper' position adjacent to hinge region. Gatekeeper is phosphorylated in several RLKs including symbiosis receptor kinase (SYMRK) but the significance remains unknown. Gatekeeper substitution did not inactivate Arachis hypogaea SYMRK but affected autophosphorylation on selected sites. Herein we show that nonphosphorylatable gatekeepers (Y670F/A) restrict SYMRK to be a Ser/Thr kinase with a basal level of phosphorylation (~5 P/polypeptide, referred as State-I) whereas phosphorylatable gatekeepers (Y670, Y670T) allowed SYMRK to be dual specific (Ser/Thr/Tyr) with a maximal level of phosphorylation (~10 P/polypeptide, referred as State-II). State-II SYMRKs were phosphorylated on gatekeeper residue 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 State-I SYMRKs. To identify other determinants of State-I features we mutagenized all the nine sites where phosphorylation was affected by nonphosphorylatable gatekeepers (Y670F/A). Only two such mutants S754A and S757A located on the activation loop failed to phosphorylate on 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 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 auto 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 = {}, number = {}, pages = {}, 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/ ; }, 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 {pmid30893296, year = {2019}, author = {Fattouh, N and Cazevieille, C and Landmann, F}, title = {Wolbachia endosymbionts subvert the endoplasmic reticulum to acquire host membranes without triggering ER stress.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {3}, pages = {e0007218}, doi = {10.1371/journal.pntd.0007218}, pmid = {30893296}, issn = {1935-2735}, mesh = {Animals ; Cell Line ; Drosophila melanogaster/cytology/*microbiology ; Endoplasmic Reticulum/metabolism/*microbiology ; Gene Expression Profiling ; Golgi Apparatus/metabolism/microbiology ; Host-Pathogen Interactions ; Intracellular Membranes/metabolism/*microbiology ; Stress, Physiological/genetics/*physiology ; Symbiosis/genetics/*physiology ; Vacuoles/microbiology ; Wolbachia/pathogenicity/*physiology ; }, abstract = {The reproductive parasites Wolbachia are the most common endosymbionts on earth, present in a plethora of arthropod species. They have been introduced into mosquitos to successfully prevent the spread of vector-borne diseases, yet the strategies of host cell subversion underlying their obligate intracellular lifestyle remain to be explored in depth in order to gain insights into the mechanisms of pathogen-blocking. Like some other intracellular bacteria, Wolbachia reside in a host-derived vacuole in order to replicate and escape the immune surveillance. Using here the pathogen-blocking Wolbachia strain from Drosophila melanogaster, introduced into two different Drosophila cell lines, we show that Wolbachia subvert the endoplasmic reticulum to acquire their vacuolar membrane and colonize the host cell at high density. Wolbachia redistribute the endoplasmic reticulum, and time lapse experiments reveal tight coupled dynamics suggesting important signalling events or nutrient uptake. Wolbachia infection however does not affect the tubular or cisternal morphologies. A fraction of endoplasmic reticulum becomes clustered, allowing the endosymbionts to reside in between the endoplasmic reticulum and the Golgi apparatus, possibly modulating the traffic between these two organelles. Gene expression analyses and immunostaining studies suggest that Wolbachia achieve persistent infections at very high titers without triggering endoplasmic reticulum stress or enhanced ERAD-driven proteolysis, suggesting that amino acid salvage is achieved through modulation of other signalling pathways.}, }
@article {pmid30070649, year = {2019}, author = {Schierstaedt, J and Bziuk, N and Kuzmanović, N and Blau, K and Smalla, K and Jechalke, S}, title = {Role of Plasmids in Plant-Bacteria Interactions.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {17-38}, doi = {10.21775/cimb.030.017}, pmid = {30070649}, issn = {1467-3045}, mesh = {*Bacterial Physiological Phenomena ; Endophytes ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; Plasmids/*genetics ; Rhizosphere ; *Symbiosis ; }, abstract = {Plants are colonized by diverse microorganisms, which may positively or negatively influence the plant fitness. The positive impact includes nutrient acquisition, enhancement of resistance to biotic and abiotic stresses, both important factors for plant growth and survival, while plant pathogenic bacteria can cause diseases. Plant pathogens are adapted to negate or evade plant defense mechanisms, e.g. by the injection of effector proteins into the host cells or by avoiding the recognition by the host. Plasmids play an important role in the rapid bacterial adaptation to stresses and changing environmental conditions. In the plant environment, plasmids can further provide a selective advantage for the host bacteria, e.g. by carrying genes encoding metabolic pathways, metal and antibiotic resistances, or pathogenicity-related genes. However, we are only beginning to understand the role of mobile genetic elements and horizontal gene transfer for plant-associated bacteria. In this review, we aim to provide a short update on what is known about plasmids and horizontal gene transfer of plant associated bacteria and their role in plant-bacteria interactions. Furthermore, we discuss tools available to study the plant-associated mobilome, its transferability, and its bacterial hosts.}, }
@article {pmid30070648, year = {2019}, author = {Holden, N}, title = {You Are What You Can Find to Eat: Bacterial Metabolism in the Rhizosphere.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {1-16}, doi = {10.21775/cimb.030.001}, pmid = {30070648}, issn = {1467-3045}, mesh = {Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; *Energy Metabolism ; Metabolic Networks and Pathways ; *Plant Physiological Phenomena ; Plant Roots/*microbiology ; *Rhizosphere ; Symbiosis ; }, abstract = {Metabolism is the underpinning force that sustains life. Within the rhizosphere it is a cyclic process, with substrates flowing between different compartments of the complete soil-plant-microbe system. The physiochemical and structural environment of the rhizosphere is shaped by a combination of plant genotype and soil type, both of which strongly impact the microbial community structure. External influences such as seasonality, the degree of water saturation and anthropomorphic inputs also play a role. Together these factors influence the flux of metabolites through the rhizosphere community, which in turn impacts on plant growth, development and disease. In this review, the focus is on metabolism within the bacterial population of the rhizosphere, since this group covers every type of plant-microbe interaction: from obligately symbiotic to destructively pathogenic, and includes those have little or no direct impact on plant hosts. The focus of the review is on metabolic functions that occur in the rhizosphere either during bacteria-plant interactions or bacteria-bacteria interactions and mainly covers heterotrophic metabolism of organic substrates. As such, many of the autotrophic (and phototrophic) reactions of inorganic compounds are not included.}, }
@article {pmid29925618, year = {2018}, author = {Caves, EM and Green, PA and Johnsen, S}, title = {Mutual visual signalling between the cleaner shrimp Ancylomenes pedersoni and its client fish.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {29925618}, issn = {1471-2954}, mesh = {*Animal Communication ; Animals ; Cues ; Curacao ; Fishes/*physiology ; Palaemonidae/*physiology ; Photic Stimulation ; *Symbiosis ; *Visual Perception ; }, abstract = {Cleaner shrimp and their reef fish clients are an interspecific mutualistic interaction that is thought to be mediated by signals, and a useful system for studying the dynamics of interspecific signalling. To demonstrate signalling, one must show that purported signals at minimum (a) result in a consistent state change in the receiver and (b) contain reliable information about the sender's intrinsic state or future behaviour. Additionally, signals must be perceptible by receivers. Here, we document fundamental attributes of the signalling system between the cleaner shrimp Ancylomenes pedersoni and its clients. First, we use sequential analysis of in situ behavioural interactions to show that cleaner antenna whipping reliably predicts subsequent cleaning. If shrimp do not signal via antenna whipping, clients triple their likelihood of being cleaned by adopting darker coloration over a matter of seconds, consistent with dark colour change signalling that clients want cleaning. Using experimental manipulations, we found that visual stimuli are sufficient to elicit antenna whipping, and that shrimp are more likely to 'clean' dark than light visual stimuli. Lastly, we show that antenna whipping and colour change are perceptible when accounting for the intended receiver's visual acuity and spectral sensitivity, which differ markedly between cleaners and clients. Our results show that signalling by both cleaners and clients can initiate and mediate their mutualistic interaction.}, }
@article {pmid31018159, year = {2019}, author = {Bethencourt, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.resmic.2019.04.002}, pmid = {31018159}, issn = {1769-7123}, 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 {pmid30627568, year = {2018}, author = {Ismail,  and Hamayun, M and Hussain, A and Iqbal, A and Khan, SA and Lee, IJ}, title = {Endophytic Fungus Aspergillus japonicus Mediates Host Plant Growth under Normal and Heat Stress Conditions.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {7696831}, doi = {10.1155/2018/7696831}, pmid = {30627568}, issn = {2314-6141}, mesh = {Aspergillus/metabolism/*physiology ; DNA, Ribosomal/genetics ; Endophytes/metabolism/*physiology ; Flavonoids/metabolism ; Heat-Shock Response/*physiology ; Helianthus/metabolism/physiology ; Indoleacetic Acids/metabolism ; Phenol/metabolism ; Phylogeny ; Plant Growth Regulators/*metabolism ; Salicylic Acid/metabolism ; Soybeans/metabolism/physiology ; Stress, Physiological/*physiology ; Symbiosis/*physiology ; }, abstract = {We have isolated an endophytic fungus with heat stress alleviation potential from wild plant Euphorbia indica L. The phylogenetic analysis and 18S rDNA sequence homology revealed that the designated isolate was Aspergillus japonicus EuR-26. Analysis of A. japonicus culture filtrate displayed higher concentrations of salicylic acid (SA), indoleacetic acid (IAA), flavonoids, and phenolics. Furthermore, A. japonicus association with soybean and sunflower had improved plant biomass and other growth features under high temperature stress (40°C) in comparison to endophyte-free plants. In fact, endophytic association mitigated heat stress by negotiating the activities of abscisic acid, catalase, and ascorbic acid oxidase in both soybean and sunflower. The nutritional quality (phenolic, flavonoids, soluble sugars, proteins, and lipids) of the A. japonicus-associated seedlings has also improved under heat stress in comparison to endophyte-free plants. From the results, it is concluded that A. japonicus can modulate host plants growth under heat stress and can be used as thermal stress alleviator in arid and semiarid regions of the globe (where mean summer temperature exceeds 40°C) to sustain agriculture.}, }
@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 = {}, number = {}, pages = {}, 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}, 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 {pmid30446385, year = {2018}, author = {Iatsenko, I and Boquete, JP and Lemaitre, B}, title = {Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan.}, journal = {Immunity}, volume = {49}, number = {5}, pages = {929-942.e5}, doi = {10.1016/j.immuni.2018.09.017}, pmid = {30446385}, issn = {1097-4180}, mesh = {Animals ; Carrier Proteins/genetics/metabolism ; Drosophila/*physiology ; Dysbiosis ; Gene Expression ; Intestinal Mucosa/immunology/metabolism/microbiology ; L-Lactate Dehydrogenase/genetics/metabolism ; Lactic Acid/*metabolism ; *Longevity ; *Microbiota ; Mutation ; NADPH Oxidases/genetics/*metabolism ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; Symbiosis ; }, abstract = {Commensal microbes colonize the gut epithelia of virtually all animals and provide several benefits to their hosts. Changes in commensal populations can lead to dysbiosis, which is associated with numerous pathologies and decreased lifespan. Peptidoglycan recognition proteins (PGRPs) are important regulators of the commensal microbiota and intestinal homeostasis. Here, we found that a null mutation in Drosophila PGRP-SD was associated with overgrowth of Lactobacillus plantarum in the fly gut and a shortened lifespan. L. plantarum-derived lactic acid triggered the activation of the intestinal NADPH oxidase Nox and the generation of reactive oxygen species (ROS). In turn, ROS production promoted intestinal damage, increased proliferation of intestinal stem cells, and dysplasia. Nox-mediated ROS production required lactate oxidation by the host intestinal lactate dehydrogenase, revealing a host-commensal metabolic crosstalk that is probably broadly conserved. Our findings outline a mechanism whereby host immune dysfunction leads to commensal dysbiosis that in turn promotes age-related pathologies.}, }
@article {pmid29970413, year = {2018}, author = {Matamoros, MA and Kim, A and Peñuelas, M and Ihling, C and Griesser, E and Hoffmann, R and Fedorova, M and Frolov, A and Becana, M}, title = {Protein Carbonylation and Glycation in Legume Nodules.}, journal = {Plant physiology}, volume = {177}, number = {4}, pages = {1510-1528}, pmid = {29970413}, issn = {1532-2548}, mesh = {Amino Acids/metabolism ; Chromatography, Liquid/methods ; Leghemoglobin/metabolism ; Malate Dehydrogenase/genetics/metabolism ; Nuclear Proteins/metabolism ; Phaseolus/*metabolism ; Plant Proteins/analysis/genetics/*metabolism ; Protein Carbonylation ; Root Nodules, Plant/*metabolism/microbiology ; Symbiosis ; Tandem Mass Spectrometry/methods ; }, abstract = {Nitrogen fixation is an agronomically and environmentally important process catalyzed by bacterial nitrogenase within legume root nodules. These unique symbiotic organs have high metabolic rates and produce large amounts of reactive oxygen species that may modify proteins irreversibly. Here, we examined two types of oxidative posttranslational modifications of nodule proteins: carbonylation, which occurs by direct oxidation of certain amino acids or by interaction with reactive aldehydes arising from cell membrane lipid peroxides; and glycation, which results from the reaction of lysine and arginine residues with reducing sugars or their autooxidation products. We used a strategy based on the enrichment of carbonylated peptides by affinity chromatography followed by liquid chromatography-tandem mass spectrometry to identify 369 oxidized proteins in bean (Phaseolus vulgaris) nodules. Of these, 238 corresponded to plant proteins and 131 to bacterial proteins. Lipid peroxidation products induced most carbonylation sites. This study also revealed that carbonylation has major effects on two key nodule proteins. Metal-catalyzed oxidation caused the inactivation of malate dehydrogenase and the aggregation of leghemoglobin. In addition, numerous glycated proteins were identified in vivo, including three key nodule proteins: sucrose synthase, glutamine synthetase, and glutamate synthase. Label-free quantification identified 10 plant proteins and 18 bacterial proteins as age-specifically glycated. Overall, our results suggest that the selective carbonylation or glycation of crucial proteins involved in nitrogen metabolism, transcriptional regulation, and signaling may constitute a mechanism to control cell metabolism and nodule senescence.}, }
@article {pmid29182785, year = {2018}, author = {Fjalstad, JW and Esaiassen, E and Juvet, LK and van den Anker, JN and Klingenberg, C}, title = {Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {3}, pages = {569-580}, doi = {10.1093/jac/dkx426}, pmid = {29182785}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/adverse effects/*therapeutic use ; *Drug Resistance, Multiple, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gram-Negative Bacteria/drug effects ; Gram-Negative Bacterial Infections/drug therapy ; Humans ; Infant, Newborn ; Observational Studies as Topic ; Randomized Controlled Trials as Topic ; Symbiosis/drug effects ; }, abstract = {Objectives: To systematically review the impact of antibiotic therapy in the neonatal period on changes in the gut microbiota and/or antibiotic resistance development.<br><br>Methods: Data sources were PubMed, Embase, Medline and the Cochrane Database, supplemented by manual searches of reference lists. Randomized controlled trials (RCTs) and observational studies were included if they provided data on different categories of antibiotic treatment (yes versus no, long versus short duration and/or broad- versus narrow-spectrum regimens) and subsequent changes in the gut microbiota and/or antibiotic resistance development. We evaluated risk of bias using the Cochrane Handbook, adapted to include observational studies. When appropriate, we used the vote-counting method to perform semi-quantitative meta-analyses. We applied the Grades of Recommendation, Assessment, Development and Evaluation approach to rate the quality of evidence (QoE). Study protocol registration: PROSPERO CRD42015026743.<br><br>Results: We included 48 studies, comprising 3 RCTs and 45 observational studies. Prolonged antibiotic treatment was associated with reduced gut microbial diversity in all three studies investigating this outcome (very low QoE). Antibiotic treatment was associated with reduced colonization rates of protective commensal anaerobic bacteria in four of five studies (very low QoE). However, all three categories of antibiotic treatment were associated with an increased risk of antibiotic resistance development, in particular MDR in Gram-negative bacteria, and we graded the QoE for these outcomes as moderate.<br><br>Conclusions: We are moderately confident that antibiotic treatment leads to antibiotic resistance development in neonates and it may also induce potentially disease-promoting gut microbiota alterations. Our findings emphasize the need to reduce unnecessary antibiotic treatment in neonates.}, }
@article {pmid28855618, year = {2017}, author = {Smith, H and Epstein, H and Torda, G}, title = {The molecular basis of differential morphology and bleaching thresholds in two morphs of the coral Pocillopora acuta.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10066}, pmid = {28855618}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/classification/*genetics ; Coral Reefs ; DNA, Intergenic/genetics ; Dinoflagellida/physiology ; *Genetic Speciation ; Genetics, Population ; *Genome ; Pacific Ocean ; *Phylogeny ; Symbiosis/physiology ; Whole Genome Sequencing ; }, abstract = {Processes of cnidarian evolution, including hybridization and phenotypic plasticity, have complicated the clear diagnosis of species boundaries within the phylum. Pocillopora acuta, a species of scleractinian coral that was recently split from the widespread Pocillopora damicornis species complex, occurs in at least two distinct morphs on the Great Barrier Reef. Contrasting morphology combined with evidence of differential bleaching thresholds among sympatrically distributed colonies suggest that the taxonomy of this recently described species is not fully resolved and may represent its own species complex. To examine the basis of sympatric differentiation between the two morphs, we combined analyses of micro- and macro-skeletal morphology with genome wide sequencing of the coral host, as well as ITS2 genotyping of the associated Symbiodinium communities. We found consistent differences between morphs on both the macro- and micro-skeletal scale. In addition, we identified 18 candidate functional genes that relate to skeletal formation and morphology that may explain how the two morphs regulate growth to achieve their distinct growth forms. With inconclusive results in endosymbiotic algal community diversity between the two morphs, we propose that colony morphology may be linked to bleaching susceptibility. We conclude that cryptic speciation may be in the early stages within the species P. acuta.}, }
@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 = {}, number = {}, pages = {}, 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 {pmid30902623, year = {2019}, author = {Maal-Bared, R and Dixon, B and Axelsson-Olsson, D}, title = {Fate of internalized Campylobacter jejuni and Mycobacterium avium from encysted and excysted Acanthamoeba polyphaga.}, journal = {Experimental parasitology}, volume = {199}, number = {}, pages = {104-110}, doi = {10.1016/j.exppara.2019.03.011}, pmid = {30902623}, issn = {1090-2449}, mesh = {Acanthamoeba/genetics/growth &amp; development/*microbiology ; Bacterial Load ; Campylobacter jejuni/*physiology ; Coculture Techniques ; Culture Media/chemistry ; DNA, Protozoan/isolation &amp; purification ; Mycobacterium avium/*physiology ; Nucleic Acid Amplification Techniques ; Refrigeration ; Symbiosis ; Trophozoites ; }, abstract = {Association of the water- and foodborne pathogen Campylobacter jejuni with free-living Acanthamoeba spp. trophozoites enhances C. jejuni survival and resistance to biocides and starvation. When facing less than optimal environmental conditions, however, the Acanthamoeba spp. host can temporarily transform from trophozoite to cyst and back to trophozoite, calling the survival of the internalized symbiont and resulting public health risk into question. Studies investigating internalized C. jejuni survival after A. castellanii trophozoite transformation have neither been able to detect its presence inside the Acanthamoeba cyst after encystation nor to confirm its presence upon excystation of trophozoites through culture-based techniques. The purpose of this study was to detect C. jejuni and Mycobacterium avium recovered from A. polyphaga trophozoites after co-culture and induction of trophozoite encystation using three different encystation methods (Neff's medium, McMillen's medium and refrigeration), as well as after cyst excystation. Internalized M. avium was used as a positive control, since studies have consistently detected the organism after co-culture and after host excystation. Concentrations of C. jejuni in A. polyphaga trophozoites were 4.5 × 105 CFU/ml, but it was not detected by PCR or culture post-encystation. This supports the hypothesis that C. jejuni may be digested during encystation of the amoebae. M. avium was recovered at a mean concentration of 1.9 × 104 from co-cultured trophozoites and 4.4 × 101 CFU/ml after excystation. The results also suggest that M. avium recovery post-excystation was statistically significantly different based on which encystation method was used, ranging from 1.3 × 101 for Neff's medium to 5.4 × 101 CFU/ml for refrigeration. No M. avium was recovered from A. polyphaga cysts when trophozoites were encysted by McMillen's medium. Since C. jejuni internalized in cysts would be more likely to survive harsh environmental conditions and disinfection, a better understanding of potential symbioses between free-living amoebae and campylobacters in drinking water distribution systems and food processing environments is needed to protect public health. Future co-culture experiments examining survival of internalized C. jejuni should carefully consider the encystation media used, and include molecular detection tools to falsify the hypothesis that C. jejuni may be present in a viable but not culturable state.}, }
@article {pmid30773514, year = {2019}, author = {Ramírez, MDA and España, M and Aguirre, C and Kojima, K and Ohkama-Ohtsu, N and Sekimoto, H and Yokoyama, T}, title = {Burkholderia and Paraburkholderia are Predominant Soybean Rhizobial Genera in Venezuelan Soils in Different Climatic and Topographical Regions.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {43-58}, doi = {10.1264/jsme2.ME18076}, pmid = {30773514}, issn = {1347-4405}, mesh = {Aluminum Compounds/metabolism ; Bradyrhizobium/classification/genetics/isolation &amp; purification/physiology ; Burkholderia/classification/genetics/isolation &amp; purification/physiology ; Burkholderiaceae/*classification/genetics/*isolation &amp; purification/physiology ; Climate ; Genes, Bacterial/genetics ; Geography ; Multilocus Sequence Typing ; Nitrogen Fixation/genetics ; *Phylogeny ; Plant Root Nodulation ; Rhizobium/classification/genetics/isolation &amp; purification/physiology ; Root Nodules, Plant/microbiology ; Sodium Chloride/metabolism ; *Soil Microbiology ; Soybeans/*microbiology ; Stress, Physiological ; Symbiosis ; Venezuela ; }, abstract = {The climate, topography, fauna, and flora of Venezuela are highly diverse. However, limited information is currently available on the characterization of soybean rhizobia in Venezuela. To clarify the physiological and genetic diversities of soybean rhizobia in Venezuela, soybean root nodules were collected from 11 soil types located in different topographical regions. A total of 395 root nodules were collected and 120 isolates were obtained. All isolates were classified in terms of stress tolerance under different concentrations of NaCl and Al3+. The tolerance levels of isolates to NaCl and Al3+ varied. Based on sampling origins and stress tolerance levels, 44 isolates were selected for further characterization. An inoculation test indicated that all isolates showed the capacity for root nodulation on soybean. Based on multilocus sequence typing (MLST), 20 isolates were classified into the genera Rhizobium and Bradyrhizobium. The remaining 24 isolates were classified into the genus Burkholderia or Paraburkholderia. There is currently no evidence to demonstrate that the genera Burkholderia and Paraburkholderia are the predominant soybean rhizobia in agricultural fields. Of the 24 isolates classified in (Para) Burkholderia, the nodD-nodB intergenic spacer regions of 10 isolates and the nifH gene sequences of 17 isolates were closely related to the genera Rhizobium and Bradyrhizobium, respectively. The root nodulation numbers of five (Para) Burkholderia isolates were higher than those of the 20 α-rhizobia. Furthermore, among the 44 isolates tested, one Paraburkholderia isolate exhibited the highest nitrogen-fixation activity in root nodules.}, }
@article {pmid30760664, year = {2019}, author = {Girard, L and Blanchet, E and Stien, D and Baudart, J and Suzuki, M and Lami, R}, title = {Evidence of a Large Diversity of N-acyl-Homoserine Lactones in Symbiotic Vibrio fischeri Strains Associated with the Squid Euprymna scolopes.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {99-103}, doi = {10.1264/jsme2.ME18145}, pmid = {30760664}, issn = {1347-4405}, mesh = {Acyl-Butyrolactones/*chemistry/metabolism ; Aliivibrio fischeri/*chemistry/genetics ; Animals ; Bacterial Proteins/genetics/metabolism ; Decapodiformes/*microbiology ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Phenotype ; *Quorum Sensing ; Species Specificity ; Symbiosis ; }, abstract = {Vibrio fischeri possesses a complex AHL-mediated Quorum-sensing (QS) system including two pathways, LuxI/R (3-oxo-C6-HSL and C6-HSL) and AinS/R (C8-HSL), which are important for the regulation of physiological traits. Diverse QS-dependent functional phenotypes have been described in V. fischeri; however, AHL diversity is still underestimated. In the present study, we investigated AHL diversity in five symbiotic V. fischeri strains with distinct phenotypic properties using UHPLC-HRMS/MS. The results obtained (1) revealed an unexpectedly high diversity of signaling molecules, (2) emphasized the complexity of QS in V. fischeri, and (3) highlight the importance of understanding the specificity of AHL-mediated QS.}, }
@article {pmid30584188, year = {2019}, author = {Akyol, TY and Niwa, R and Hirakawa, H and Maruyama, H and Sato, T and Suzuki, T and Fukunaga, A and Sato, T and Yoshida, S and Tawaraya, K and Saito, M and Ezawa, T and Sato, S}, title = {Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {23-32}, doi = {10.1264/jsme2.ME18109}, pmid = {30584188}, issn = {1347-4405}, mesh = {*Agriculture ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Fungi/classification/genetics/growth &amp; development/isolation &amp; purification ; *Microbiota ; Mycorrhizae/classification/*physiology ; Onions/growth &amp; development/microbiology ; Phosphorus/chemistry ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.}, }
@article {pmid29255260, year = {2017}, author = {Levy, A and Salas Gonzalez, I and Mittelviefhaus, M and Clingenpeel, S and Herrera Paredes, S and Miao, J and Wang, K and Devescovi, G and Stillman, K and Monteiro, F and Rangel Alvarez, B and Lundberg, DS and Lu, TY and Lebeis, S and Jin, Z and McDonald, M and Klein, AP and Feltcher, ME and Rio, TG and Grant, SR and Doty, SL and Ley, RE and Zhao, B and Venturi, V and Pelletier, DA and Vorholt, JA and Tringe, SG and Woyke, T and Dangl, JL}, title = {Genomic features of bacterial adaptation to plants.}, journal = {Nature genetics}, volume = {50}, number = {1}, pages = {138-150}, pmid = {29255260}, issn = {1546-1718}, support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM112345/GM/NIGMS NIH HHS/United States ; T32 GM007092/GM/NIGMS NIH HHS/United States ; T32 GM067553/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Bacteria/*genetics/growth &amp; development ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions/*genetics ; Plant Roots/genetics/microbiology ; Plants/*microbiology ; Symbiosis ; }, abstract = {Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.}, }
@article {pmid28805645, year = {2017}, author = {Biedermann, PH and Rohlfs, M}, title = {Evolutionary feedbacks between insect sociality and microbial management.}, journal = {Current opinion in insect science}, volume = {22}, number = {}, pages = {92-100}, doi = {10.1016/j.cois.2017.06.003}, pmid = {28805645}, issn = {2214-5753}, mesh = {Animals ; Behavior, Animal/physiology ; *Biological Evolution ; Ecosystem ; Feeding Behavior ; Insecta/*microbiology ; Microbiota ; Social Behavior ; Symbiosis ; }, abstract = {Fitness-determining interactions with microbes-in particular fungi-have often been considered a by-product of social evolution in insects. Here, we take the view that both beneficial and harmful microbial consortia are major drivers of social behaviours in many insect systems-ranging from aggregation to eusociality. We propose evolutionary feedbacks between the insect sociality and microbial communities that strengthen mutualistic interactions with beneficial (dietary or defensive) microbes and simultaneously increase the capacity to defend against pathogens (i.e. social immunity). We identified variation in habitat stability-as determined by breeding site predictability and ephemerality-as a main ecological factor that constrains these feedbacks. To test this hypothesis we suggest following the evolution of insect social traits upon experimental manipulation of habitat stability and microbial consortia.}, }
@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 = {}, number = {}, 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 years of experimental warming. Root- and leaf-associated fungi, which can mediate plants' climate sensitivity, responded divergently to elevation versus 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, 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 = {}, number = {}, pages = {}, doi = {10.1128/AEM.00512-19}, pmid = {31003984}, issn = {1098-5336}, abstract = {Microbial ecosystems tightly associated with a eukaryotic host are wide-spread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have co-evolved 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 towards Serratia plymuthica, while expressing a non-ribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms out-competed S. plymuthica for a successful colonization of the host. Strikingly, the plant host could 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 a mechanistic light on how multicellular biofilm units compete and 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 non-ribosomal 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 a first evidence to a mechanism by which the host can indirectly select