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Bibliography on: Symbiosis

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ESP: PubMed Auto Bibliography 20 Oct 2018 at 01:42 Created: 

Symbiosis

Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2018-10-18

Resl P, Fernández-Mendoza F, Mayrhofer H, et al (2018)

The evolution of fungal substrate specificity in a widespread group of crustose lichens.

Proceedings. Biological sciences, 285(1889): pii:rspb.2018.0640.

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150-200 Mya clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, 'escape' from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.

RevDate: 2018-10-18

Xu Y, Zhu S, Liu F, et al (2018)

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize.

International journal of molecular sciences, 19(10): pii:ijms19103201.

Maize can form symbiotic relationships with arbuscular mycorrhiza (AM) fungus to increase productivity and resistance, but the miRNAs in maize responsible for this process have not been discovered. In this study, 155 known and 28 novel miRNAs were identified by performing high-throughput sequencing of sRNA in maize roots colonized by AM fungi. Similar to the profiles in other AM-capable plants, a large proportion of identified maize miRNAs were 24 nt in length. Fourteen and two miRNAs were significantly down- and up-regulated in response to AM fungus Glomus intraradices inoculation, respectively, suggesting potential roles of these miRNAs in AM symbiosis. Interestingly, 12 of 14 significantly down-regulated known maize miRNAs belong to the miR399 family, which was previously reported to be involved in the interaction between Medicagotruncatula and AM fungi. This result indicated that the miR399 family should regulate AM symbiosis conservatively across different plant lineages. Pathway and network analyses showed that the differentially expressed miRNAs might regulate lipid metabolism and phosphate starvation response in maize during the symbiosis process via their target genes. Several members of the miR399 family and the miR397 family should be involved in controlling the fatty acid metabolism and promoting lipid delivering from plants to AM fungi. To the best of our knowledge, this is the first report on miRNAs mediating fatty acids from plant to AM fungi. This study provides insight into the regulatory roles of miRNAs in the symbiosis between plants and AM fungi.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Thiem D, Złoch M, Gadzała-Kopciuch R, et al (2018)

Cadmium-induced changes in the production of siderophores by a plant growth promoting strain of Pseudomonas fulva.

Journal of basic microbiology, 58(7):623-632.

The impact of increasing Cd2+ exposure on the quality and quantity of siderophores produced by a plant growth promoting Pseudomonas fulva strain was tested to gain insight into the degree of change. P. fulva was cultured in the increasing concentrations of Cd2+ (0, 0.5, 1.0, 2.0 mM). The secreted siderophores were separated by HPLC and characterized by UHPLC-QTOF/MS. In the presence of 2 mM Cd2+ synthesis of siderophores (hydroxamates, catecholates, phenolates) was mitigated compared to the treatments with lower concentrations of Cd2+ (0.5 and 1 mM). Increased synthesis of catecholates in 0.5 and 1 mM Cd2+ and of phenolates in 0.5-2 mM Cd2+ was revealed compared to the variant without Cd2+ . Out of seven different hydroxamates, the secretion of ferrioxamine E was significantly decreased in the highest Cd2+ concentration. Two additional ferrioxamines, X2 and D2, were secreted independent of the presence or absence of Cd2+ . Exposure to Cd2+ change the composition of siderophores secreted by P. fulva with selective promotion of catecholates and phenolates at the expense of hydroxamates. Successful adaptation in a Cd-contaminated soil in the frame of practical applications to promote phytoremediation can be assumed.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Tang G, Li Q, Xing S, et al (2018)

The LsrB Protein Is Required for Agrobacterium tumefaciens Interaction with Host Plants.

Molecular plant-microbe interactions : MPMI, 31(9):951-961.

Agrobacterium tumefaciens infects and causes crown galls in dicot plants by transferring T-DNA from the Ti plasmid to the host plant via a type IV secretion system. This process requires appropriate environmental conditions, certain plant secretions, and bacterial regulators. In our previous work, a member of the LysR family of transcriptional regulators (LsrB) in Sinorhizobium meliloti was found to modulate its symbiotic interactions with the host plant alfalfa. However, the function of its homolog in A. tumefaciens remains unclear. In this study, we show that the LsrB protein of A. tumefaciens is required for efficient transformation of host plants. A lsrB deletion mutant of A. tumefaciens exhibits a number of defects, including in succinoglycan production, attachment, and resistance to oxidative stress and iron limitation. RNA-sequencing analysis indicated that 465 genes were significantly differentially expressed (upregulation of 162 genes and downregulation of 303 genes) in the mutant, compared with the wild-type strain, including those involved in succinoglycan production, iron transporter, and detoxification enzymes for oxidative stress. Moreover, expression of the lsrB gene from S. meliloti, Brucella abortus, or A. tumefaciens rescued the defects observed in the S. meliloti or A. tumefaciens lsrB deletion mutant. Our findings suggest that a conserved mechanism of LsrB function exists in symbiotic and pathogenic bacteria of the family Rhizobiaceae.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Rodrigues DR, Silva AFD, Cavalcanti MIP, et al (2018)

Phenotypic, genetic and symbiotic characterization of Erythrina velutina rhizobia from Caatinga dry forest.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 49(3):503-512.

Erythrina velutina ("mulungu") is a legume tree from Caatinga that associates with rhizobia but the diversity and symbiotic ability of "mulungu" rhizobia are poorly understood. The aim of this study was to characterize "mulungu" rhizobia from Caatinga. Bacteria were obteined from Serra Talhada and Caruaru in Caatinga under natural regeneration. The bacteria were evaluated to the amplification of nifH and nodC and to metabolic characteristics. Ten selected bacteria identified by 16S rRNA sequences. They were tested in vitro to NaCl and temperature tolerance, auxin production and calcium phosphate solubilization. The symbiotic ability were assessed in an greenhouse experiment. A total of 32 bacteria were obtained and 17 amplified both symbiotic genes. The bacteria showed a high variable metabolic profile. Bradyrhizobium (6), Rhizobium (3) and Paraburkholderia (1) were identified, differing from their geographic origin. The isolates grew up to 45°C to 0.51molL-1 of NaCl. Bacteria which produced more auxin in the medium with l-tryptophan and two Rhizobium and one Bradyrhizobium were phosphate solubilizers. All bacteria nodulated and ESA 90 (Rhizobium sp.) plus ESA 96 (Paraburkholderia sp.) were more efficient symbiotically. Diverse and efficient rhizobia inhabit the soils of Caatinga dry forests, with the bacterial differentiation by the sampling sites.

RevDate: 2018-10-19
CmpDate: 2018-10-18

Klasson L (2017)

The unpredictable road to reduction.

Nature ecology & evolution, 1(8):1062-1063.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Neave MJ, Michell CT, Apprill A, et al (2017)

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts.

Scientific reports, 7:40579 pii:srep40579.

Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60-76% and 81-90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Luo C, Luo K, Meng L, et al (2017)

Ecological impact of a secondary bacterial symbiont on the clones of Sitobion avenae (Fabricius) (Hemiptera: Aphididae).

Scientific reports, 7:40754 pii:srep40754.

Many insects harbor heritable endosymbionts, whether obligatory or facultative, and the role of facultative endosymbionts in shaping the phenotype of these species has become increasingly important. However, little is known about whether micro-injected endosymbionts can have any effects on aphid clones, which was measured using various ecological parameters. We examined the effects between symbiotic treatments and the vital life history traits generated by Regiella insecticola on the life table parameters of Sitobion avenae. The results showed that R. insecticola can decrease the intrinsic rate of increase (r), the finite rate of increase (λ) and birth rate and can increase the mean generation times (T) of S. avenae clones, suggesting that R. insecticola may decelerate the normal development of the hosts. No significant differences of these parameters were observed between the examined Sitobion avenae clones, and the symbiont treatment by genotype interaction affected only the net reproduction rate R0, pre-adult duration and total longevity but not the other parameters. Additionally, a population projection showed that R. insecticola decelerated the growth of the S. avenae clones. The evocable effects of R. insecticola on the S. avenae clones may have significant ramifications for the control of S. avenae populations under field/natural conditions.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Chung SH, Scully ED, Peiffer M, et al (2017)

Host plant species determines symbiotic bacterial community mediating suppression of plant defenses.

Scientific reports, 7:39690 pii:srep39690.

Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore's ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants.

RevDate: 2018-10-18
CmpDate: 2018-10-18

Herren CM, Webert KC, Drake MD, et al (2017)

Positive feedback between chironomids and algae creates net mutualism between benthic primary consumers and producers.

Ecology, 98(2):447-455.

The chironomids of Lake Mývatn show extreme population fluctuations that affect most aspects of the lake ecosystem. During periods of high chironomid densities, chironomid larvae comprise over 90% of aquatic secondary production. Here, we show that chironomid larvae substantially stimulate benthic gross primary production (GPP) and net primary production (NPP), despite consuming benthic algae. Benthic GPP in experimental mesocosms with 140,000 larvae/m2 was 71% higher than in mesocosms with no larvae. Similarly, chlorophyll a concentrations in mesocosms increased significantly over the range of larval densities. Furthermore, larvae showed increased growth rates at higher densities, possibly due to greater benthic algal availability in these treatments. We investigated the hypothesis that larvae promote benthic algal growth by alleviating nutrient limitation, and found that (1) larvae have the potential to cycle the entire yearly external loadings of nitrogen and phosphorus during the growing season, and (2) chlorophyll a concentrations were significantly greater in close proximity to larvae (on larval tubes). The positive feedback between chironomid larvae and benthic algae generated a net mutualism between the primary consumer and primary producer trophic levels in the benthic ecosystem. Thus, our results give an example in which unexpected positive feedbacks can lead to both high primary and high secondary production.

RevDate: 2018-10-17

Chang NN, Lin LH, Tu TH, et al (2018)

Trophic structure and energy flow in a shallow-water hydrothermal vent: Insights from a stable isotope approach.

PloS one, 13(10):e0204753 pii:PONE-D-18-06715.

Shallow-water hydrothermal vent ecosystems are distinct from the deep-sea counterparts, because they are in receipt of sustenance from both chemosynthetic and photosynthetic production and have a lack of symbiosis. The trophic linkage and energy flow in these ecosystems, however remain elusive, which allows us poor understanding of the whole spectrum of biological components distributed across such environmental gradients. In this study, a thorough isotopic survey was conducted on various biological specimens and suspended particulates collected along four transects across the venting features of a shallow-water hydrothermal field off Kueishan Island, Taiwan. The isotope data combined with a Bayesian-based mixing model indicate that the vent-associated particulate organic matter (vent POM), as primary contribution of chemoautotrophic populations, has a high δ13C value (-18.2 ± 1.1‰) and a low δ15N value (-1.7 ± 0.4‰). Zooplankton and epibenthic crustaceans, as the fundamental consumers, exhibit δ13C and δ15N values ranging from -21.3 to -19.8‰ and +5.1 to +7.5‰, respectively, and can utilize the vent POM for 38-53% of their diets. The vent-obligate crab Xenograpsus testudinatus shows a large variation in δ13C (from -18.8 to -13.9‰) and δ15N values (from 1.1 to 9.8‰), although an omnivorous trophic level (2.5) is identified for it using δ15N values of amino acids, and it can utilize the vent POM for 6-87% of its diet. The consistently low (< 10.0‰) and overlapping δ15N values for most of the analyzed macroinvertebrates suggest extensive ingestion of chemosynthetic production complementing the photosynthetic production, a weak prey-predator relationship and low trophic complexity possibly imposed by the extreme environmental contexts of shallow-water hydrothermal ecosystems.

RevDate: 2018-10-17

Isidra-Arellano MC, Reyero-Saavedra MDR, Sánchez-Correa MDS, et al (2018)

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia.

Genes, 9(10): pii:genes9100498.

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, which are genes controlling the nodulation process were significantly reduced in Pi-deficient common bean seedlings. In addition, whole-genome transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Moreover, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule numbers, was higher in Pi-deficient seedlings compared to control seedlings. The data presented in this study provides a mechanistic model to better understand how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia.

RevDate: 2018-10-16

Ma YY, Zhang HC, Xiang XJ, et al (2018)

Effects of long-term fertilization on arbuscular mycorrhizal fungal community in lime concretion black soil.

Ying yong sheng tai xue bao = The journal of applied ecology, 29(10):3398-3406.

In agroecosystem, arbuscular mycorrhizal fungi have mutually beneficial symbiosis with roots of many crops. Meanwhile, this special fungal community is also affected by agricultural mana-gements such as fertilization. The objective of this study was to investigate the effects of long-term fertilization managements (no fertilizer, chemical fertilizer, chemical fertilizer combined with straw, chemical fertilizer combined with manure) on arbuscular mycorrhizal fungal community (AM fungal community) in lime concretion black soil, and to identify the indicator species in each fertilization regime. The most dominant arbuscular mycorrhizal fungal phyla in lime concretion black soil were Archaeosporaceae, Diversisporaceae, Gigasporaceae, Claroideoglomeraceae, Glomeraceae and Paraglomeraceae. The genus Paraglomus was strongly and significantly associated with the application of chemical fertilizer and organic fertilizer. Compared with the control, long-term application of chemical fertilizer greatly changed AM fungal community structure and resulted in the decrease of AM fungal diversity, and the addition of wheat straw further decreased the diversity, while the addition of manure could alleviate diversity loss resulted from chemical fertilization. Soil pH and dissolved organic carbon (DOC) were the main factors affecting the changes of AM fungal community. In summary, long-term application of chemical fertilizer combined with different organic materials had different impacts on soil AM fungal community structure and diversity. The combination of chemical fertilizer and manure would be more conducive to the maintenance of AM fungal diversity.

RevDate: 2018-10-16

Guillermo Bueno C, Gerz M, Zobel M, et al (2018)

Conceptual differences lead to divergent trait estimates in empirical and taxonomic approaches to plant mycorrhizal trait assignment.

Mycorrhiza pii:10.1007/s00572-018-0869-1 [Epub ahead of print].

Empirical and taxonomic approaches are the two main methods used to assign plant mycorrhizal traits to species lists. While the empirical approach uses only available empirical information, the taxonomic approach extrapolates certain core information about plant mycorrhizal types and statuses to related species. Despite recent claims that the taxonomic approach is now almost definitive, with little benefit to be gained from further empirical data collection, it has not been thoroughly compared with the empirical approach. Using the most complete available plant mycorrhizal trait information for Europe and both assignment approaches, we calculate the proportion of species for each trait, and model environmental drivers of trait distribution across the continent. We found large degrees of mismatch between approaches, with consequences for biogeographical interpretation, among facultatively mycorrhizal (FM; 91% of species mismatched), non-mycorrhizal (NM; 45%), and to a lesser extent arbuscular mycorrhizal (AM; 16%) plant species. This can partly be attributed to the taxonomic precision of the taxonomic approach and the use of different AM, NM, and FM concepts. Our results showed that the extrapolations of the taxonomic approach do not consistently match with empirical information and indicate that more empirical data are needed, in particular for FM, NM, and AM plant species. Clarifying certain concepts underlying mycorrhizal traits and empirically describing NM, AM, and FM species within plant families can greatly improve our understanding of the biogeography of mycorrhizal symbiosis.

RevDate: 2018-10-16

Shukla SP, Plata C, Reichelt M, et al (2018)

Microbiome-assisted carrion preservation aids larval development in a burying beetle.

Proceedings of the National Academy of Sciences of the United States of America pii:1812808115 [Epub ahead of print].

The ability to feed on a wide range of diets has enabled insects to diversify and colonize specialized niches. Carrion, for example, is highly susceptible to microbial decomposers, but is kept palatable several days after an animal's death by carrion-feeding insects. Here we show that the burying beetle Nicrophorus vespilloides preserves carrion by preventing the microbial succession associated with carrion decomposition, thus ensuring a high-quality resource for their developing larvae. Beetle-tended carcasses showed no signs of degradation and hosted a microbial community containing the beetles' gut microbiota, including the yeast Yarrowia In contrast, untended carcasses showed visual and olfactory signs of putrefaction, and their microbial community consisted of endogenous and soil-originating microbial decomposers. This regulation of the carcass' bacterial and fungal community and transcriptomic profile was associated with lower concentrations of putrescine and cadaverine (toxic polyamines associated with carcass putrefaction) and altered levels of proteases, lipases, and free amino acids. Beetle-tended carcasses develop a biofilm-like matrix housing the yeast, which, when experimentally removed, leads to reduced larval growth. Thus, tended carcasses hosted a mutualistic microbial community that promotes optimal larval development, likely through symbiont-mediated extraintestinal digestion and detoxification of carrion nutrients. The adaptive preservation of carrion coordinated by the beetles and their symbionts demonstrates a specialized resource-management strategy through which insects modify their habitats to enhance fitness.

RevDate: 2018-10-16

Liao D, Wang S, Cui M, et al (2018)

Phytohormones Regulate the Development of Arbuscular Mycorrhizal Symbiosis.

International journal of molecular sciences, 19(10): pii:ijms19103146.

Most terrestrial plants are able to form a root symbiosis with arbuscular mycorrhizal (AM) fungi for enhancing the assimilation of mineral nutrients. AM fungi are obligate symbionts that depend on host plants as their sole carbon source. Development of an AM association requires a continuous signal exchange between the two symbionts, which triggers coordinated differentiation of both partners, to enable their interaction within the root cells. The control of the AM symbiosis involves a finely-tuned process, and an increasing number of studies have pointed to a pivotal role of several phytohormones, such as strigolactones (SLs), gibberellic acids (GAs), and auxin, in the modulation of AM symbiosis, through the early recognition of events up to the final arbuscular formation. SLs are involved in the presymbiotic growth of the fungus, while auxin is required for both the early steps of fungal growth and the differentiation of arbuscules. GAs modulate arbuscule formation in a dose-dependent manner, via DELLA proteins, a group of GRAS transcription factors that negatively control the GA signaling. Here, we summarize the recent findings on the roles of these plant hormones in AM symbiosis, and also explore the current understanding of how the DELLA proteins act as central regulators to coordinate plant hormone signaling, to regulate the AM symbiosis.

RevDate: 2018-10-15

Dos Santos Lima Fagotti D, Abrantes JLF, Cerezini P, et al (2018)

Quorum sensing communication: Bradyrhizobium-Azospirillum interaction via N-acyl-homoserine lactones in the promotion of soybean symbiosis.

Journal of basic microbiology [Epub ahead of print].

Quorum-sensing (QS) mechanisms are important in intra- and inter-specific communication among bacteria. We investigated QS mechanisms in Bradyrhizobium japonicum strain CPAC 15 and Azospirillum brasilense strains Ab-V5 and Ab-V6, used in commercial co-inoculants for the soybean crop in Brazil. A transconjugant of CPAC 15-QS with partial inactivation of N-acyl-homoserine lactones (AHLs) was obtained and several parameters were evaluated; in vitro, CPAC 15 and the transconjugant differed in growth, but not in biofilm formation, and no differences were observed in the symbiotic performance in vivo. The genome of CPAC 15 carries functional luxI and luxR genes and low amounts of three AHL molecules were detected: 3-OH-C12-AHL, 3-OH-C14-AHL, and 3-oxo-C14-AHL. Multiple copies of luxR-like genes, but not of luxI are present in the genomes of Ab-V5 and Ab-V6, and differences in gene expression were observed when the strains were co-cultured with B. japonicum; we may infer that the luxR-genes of A. brasilense may perceive the AHL molecules of B. japonicum. Soybean symbiotic performance was improved especially by co-inoculation with Ab-V6, which, contrarily to Ab-V5, did not respond to the AHLs of CPAC 15. We concluded that A. brasilense Ab-V5, but not Ab-V6, responded to the QS signals of CPAC 15, and that the synergistic interaction may be credited, at least partially, to the QS interaction. In addition, we confirmed inter- and intra-species QS communication between B. japonicum and A. brasilense and, for Azospirillum, at the strain level, impacting several steps of the symbiosis, from cell growth to plant nodulation and growth.

RevDate: 2018-10-17

Kremer N, Koch EJ, El Filali A, et al (2018)

Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis.

mSystems, 3(5): pii:mSystems00165-18.

In horizontally transmitted symbioses, structural, biochemical, and molecular features both facilitate host colonization by specific symbionts and mediate their persistent carriage. In the association between the squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri, the symbionts interact with two epithelial fields; they interact (i) transiently with the superficial ciliated field that potentiates colonization and regresses within days of colonization and (ii) persistently with the cells that line the internal crypts, whose ultrastructure changes in response to the symbionts. Development of the association creates conditions that promote the symbiotic partner over the lifetime of the host. To determine whether light organ maturation requires continuous interactions with V. fischeri or only the signaling that occurs during its initiation, we compared 4-week-old squid that were uncolonized with those colonized either persistently by wild-type V. fischeri or transiently by a V. fischeri mutant that triggers early events in morphogenesis but does not persist. Microscopic analysis of the light organs showed that, while morphogenesis of the superficial ciliated field is greatly accelerated by V. fischeri colonization, its eventual outcome is largely independent of colonization state. In contrast, the symbiont-induced changes in crypt cell shape require persistent host-symbiont interaction, reflected in the similarity between uncolonized and transiently colonized animals. Transcriptomic analyses reflected the microscopy results; host gene expression at 4 weeks was due primarily to the persistent interactions of host and symbiont cells. Further, the transcriptomic signature of specific pathways reflected the daily rhythm of symbiont release and regrowth and required the presence of the symbionts. IMPORTANCE A long-term relationship between symbiotic partners is often characterized by development and maturation of host structures that harbor the symbiont cells over the host's lifetime. To understand the mechanisms involved in symbiosis maintenance more fully, we studied the mature bobtail squid, whose light-emitting organ, under experimental conditions, can be transiently or persistently colonized by Vibrio fischeri or remain uncolonized. Superficial anatomical changes in the organ were largely independent of symbiosis. However, both the microanatomy of cells with which symbionts interact and the patterns of gene expression in the mature animal were due principally to the persistent interactions of host and symbiont cells rather than to a response to early colonization events. Further, the characteristic pronounced daily rhythm on the host transcriptome required persistent V. fischeri colonization of the organ. This experimental study provides a window into how persistent symbiotic colonization influences the form and function of host animal tissues.

RevDate: 2018-10-17

Buhian WP, S Bensmihen (2018)

Mini-Review: Nod Factor Regulation of Phytohormone Signaling and Homeostasis During Rhizobia-Legume Symbiosis.

Frontiers in plant science, 9:1247.

The rhizobia-legume symbiosis is a mutualistic association in which bacteria provide plants with nitrogen compounds and the plant provides bacteria with carbon sources. A successful symbiotic interaction relies on a molecular dialog between the plant and the bacteria, and generally involves rhizobial lipo-chitooligosaccharide signals called Nod factors (NFs). In most cases, specific NF perception is required for rhizobia to enter root cells through newly formed intracellular structures called infection threads (ITs). Concomitantly to IT formation in root hairs, root cortical cells start to divide to create a new root organ called the nodule, which will provide the bacteria with a specific micro-environment required for symbiotic nitrogen fixation. During all these steps of plant-bacteria interaction, new plant cellular compartments and developmental programs are activated. This interaction is costly for the plant that tightly controls symbiosis establishment and functioning. Phytohormones are key regulators of cellular and developmental plasticity in plants, and they are influential endogenous signals that rapidly control plant responses. Although early symbiotic responses were known for decades to be linked to phytohormone-related responses, new data reveal the molecular mechanisms involved and links between phytohormones and the control of early symbiotic events. Reciprocally, NF signaling also targets phytohormone signaling pathways. In this review, we will focus on the emerging notion of NF and phytohormone signaling crosstalk, and how it could contribute to the tight control of symbiosis establishment in legume host plants.

RevDate: 2018-10-17

Santos-Garcia D, Juravel K, Freilich S, et al (2018)

To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies.

Frontiers in microbiology, 9:2254.

Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.

RevDate: 2018-10-14

Fabiańska I, Gerlach N, Almario J, et al (2018)

Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana.

The New phytologist [Epub ahead of print].

Plants respond to phosphorus (P)-limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi)-starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomical marker ITS2 we examined the changes in root-associated fungal communities in the AM non-host species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison to their P-deprived counterparts, while bulk-soil communities remained unaltered. Moreover, plants carrying mutations in phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM non-host plant, as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-14

Chew SF, Koh CZY, Hiong KC, et al (2018)

Light-enhanced expression of Carbonic Anhydrase 4-like supports shell formation in the fluted giant clam Tridacna squamosa.

Gene pii:S0378-1119(18)31057-6 [Epub ahead of print].

Giant clams represent symbiotic associations between a host clam and its extracellular zooxanthellae. They are able to grow in nutrient-deficient tropical marine environments and conduct light-enhanced shell formation (calcification) with the aid of photosynthates donated by the symbiotic zooxanthellae. In light, there is a high demand for inorganic carbon (Ci) to support photosynthesis in the symbionts and light-enhanced calcification in the host. In this study, we cloned and characterized a host Carbonic Anhydrase 4 homolog (CA4-like) from the whitish inner mantle of the giant clam Tridacna squamosa. The full cDNA coding sequence of CA4-like consisted of 1002 bp, encoding for 334 amino acids of 38.5 kDa. The host CA4-like was phenogramically distinct from algal CAs. The transcript level of CA4-like in the inner mantle was ~3-fold higher than those in the colorful outer mantle and the ctenidium. In the inner mantle, CA4-like was immunolocalized in the apical membrane of the seawater-facing epithelial cells, but absent from the shell-facing epithelium. Hence, CA4-like was positioned to catalyze the conversion of HCO3- to CO2 in the ambient seawater which would facilitate CO2 uptake. The absorbed CO2 could be converted back to HCO3- by the cytoplasmic CA2-like. As the protein abundance of CA4-like increased in the inner mantle after 6 or 12 h of light exposure, there could be an augmentation of the total CA4-like activity to increase Ci uptake in light. It is plausible that the absorbed Ci was allocated preferentially for shell formation due to the close proximity of the seawater-facing epithelium to the shell-facing epithelium in the inner mantle that contains only few zooxanthellae.

RevDate: 2018-10-13

Zhou Z, Liu Z, Wang L, et al (2018)

Oxidative stress, apoptosis activation and symbiosis disruption in giant clam Tridacna crocea under high temperature.

Fish & shellfish immunology pii:S1050-4648(18)30666-1 [Epub ahead of print].

Giant clams are one of the most important animals in coral reef ecosystem, and its growth and reproduction are being threatened by acute heat stress due to global warming. In the present study, the symbiont density, the crucial enzymes to physiological activities and the transcriptome were investigated in the outer mantle of giant clam Tridacna crocea after the acute exposure of high temperature. The density of symbiotic zooxanthellae decreased significantly during 12-24 h, with the minimum level (7.75 × 105 cell cm-2, p < 0.05) at 12 h after heat stress. The activities of superoxide dismutase in the heat stress group was significantly lower than that in the control group at 24 h after heat stress, while no significant change in the activities of catalase was observed during the entire stress process. The activation level of caspase3 began to increase significantly at 12 h (1.22-fold, p < 0.05), and reached the highest level at 24 h (1.38-fold, p < 0.05) after heat stress. Six paired-end libraries were sequenced in two groups, including the heat stress and control group at 12 h after heat stress. Through the assembling of 187,116,632 paired-end reads with lengths of 2 × 150 bp, a total of 26,676 genes were obtained which derived from giant clam. Bioinformatics analysis revealed 47 significantly upregulated and 88 significantly downregulated genes at 12 h after the treatment. There were 12 overrepresented GO terms for significantly upregulated genes, mostly related to unfolded protein binding and ATP binding, whereas no GO term was overrepresented for significantly downregulated genes. These results collectively suggest high temperature could induce excessive oxidative stress through the repressed antioxidant ability, the apoptosis activated by the unfolded protein response, and further the collapse of the symbiosis between host and symbiont, which has been threatening the growth and reproduction of the giant clam T. crocea.

RevDate: 2018-10-13

Ribeiro-Barros AI, Catarino S, Moura I, et al (2018)

Actinorhizal trees and shrubs from Africa: distribution, conservation and uses.

Antonie van Leeuwenhoek pii:10.1007/s10482-018-1174-x [Epub ahead of print].

Actinorhizal plants are a group of perennial dicotyledonous angiosperms, comprised of more than 200 species, most of which can establish root-nodule symbiosis with the nitrogen fixing actinobacteria of the genus Frankia. They are key providers of fundamental goods and services and can give a major contribution to mitigate the combined effects of climate changes, human population growth and loss of biodiversity. This aspect is particularly relevant for the developing economies of many African countries, which are highly exposed to climate and anthropogenic disturbances. In this work we have analyzed the distribution, conservation and uses of actinorhizal species native to or introduced in Africa. A total of 42 taxa distributed over six botanical families (Betulaceae, Casuarinaceae, Myricaceae, Elaeagnaceae, Rhamnaceae and Coriariaceae) were identified. The vast majority is able to thrive under a range of diverse environments and has multiple ecological and economic potential. More than half of the identified species belong to the genus Morella (Myricaceae), most of them native to Middle, Eastern and Southern Africa. Although the information about the conservation status and uses of Morella spp. is largely incomplete, the available data is indicative of their potential in e.g. forestry and agroforestry, food and medicine. Therefore, efforts should be made to upgrade actinorhizal research in Africa towards the sustainable use of biodiversity at the service of local (bio)economies.

RevDate: 2018-10-13

ŠobÁŇovÁ A, Z ĎuriŠ (2018)

Kaviengella jeffkinchi, a new genus and species of symbiotic shrimp (Crustacea: Decapoda: Palaemonidae) from Papua New Guinea.

Zootaxa, 4415(1):118-134 pii:zootaxa.4415.1.5.

A very small adult specimen of symbiotic palaemonid shrimp collected from Kavieng Lagoon, N.W. New Ireland Island, Papua New Guinea, is described as a new genus and species. Due to the slender subcylindrical body, reduced rostrum, elongated eyes and distolaterally produced uropodal exopods, the new species is somewhat similar to shrimps of the endosymbiotic sponge genus Nippontonia. Both second pereiopods are lost, but the specimen is unique by its bidentate scaphocerites, an apical corona of spiniform teeth on the mandibular molar process, five posterior telson cuspidate setae from which the median and intermediate ones are long, hooked, and the broadly spoon-like dactyli of the first pereiopods chelae with marginal pectination. Based on those characters, the new genus is without parallel among all symbiotic palaemonid shrimps. Its close phylogenetic relationship to the spongobiotic genera Nippontonia, Onycocaridella, and Thaumastocaris, is also confirmed by molecular comparison.

RevDate: 2018-10-13

Osawa M, Naruse T, PKL Ng (2018)

New records of species of the Polyonyx sinensis group (Crustacea: Decapoda: Anomura: Porcellanidae) from Japan, the Philippines, Singapore, and Malaysia, with descriptions of two new species.

Zootaxa, 4429(2):303-323 pii:zootaxa.4429.2.6.

Five species of the genus Polyonyx Stimpson, 1858 are reported from southern Japan, the Philippines, Singapore, and Peninsular Malaysia. All of them belong to the P. sinensis group, which is morphologically defined by having the dactyli of the ambulatory legs each with the dorsal claw being much smaller than the ventral claw. Two species are described as new to science, one each from Peninsular Malaysia and the Ryukyu Islands in Japan, and their affinities are discussed. Polyonyx boucheti Osawa, 2007, P. heok Osawa Ng, 2016, and P. thai Werding, 2001, are also newly reported from southern Japan, the Philippines, and Singapore. A key to the Indo-West Pacific species of the P. sinensis group is provided.

RevDate: 2018-10-12

An J, Sun M, van Velzen R, et al (2018)

Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis.

Journal of experimental botany, 69(21):5255-5264.

The perennial woody plants of citrus are one of the most important fruit crops in the world and largely depends on arbuscular mycorrhizal symbiosis (AMS) to obtain essential nutrients from soil. However, the molecular aspects of AMS in citrus and perennial woody plants in general have largely been understudied. We used RNA-sequencing to identify differentially expressed genes in roots of Poncirus trifoliata upon mycorrhization by the AM fungus Glomus versiforme and evaluated their conservation by comparative transcriptome analyses with four herbaceous model plants. We identified 282 differentially expressed genes in P. trifoliata, including orthologs of 21 genes with characterized roles in AMS and 83 genes that are considered to be conserved in AM-host plants. Comparative transcriptome analysis revealed a 'core set' of 156 genes from P. trifoliata whose orthologous genes from at least three of the five species also exhibited similar transcriptional changes during AMS. Functional analysis of one of these conserved AM-induced genes, a 3-keto-acyl-ACP reductase (FatG) involved in fatty acid biosynthesis, confirmed its involvement in AMS in Medicago truncatula. Our results identify a core transcriptional program for AMS that is largely conserved between P. trifoliata and other plants. The comparative transcriptomics approach adds to previous phylogenomics studies to identify conserved genes required for AMS.

RevDate: 2018-10-12

Van Geel M, Yu K, Ceulemans T, et al (2018)

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas.

FEMS microbiology ecology pii:5128480 [Epub ahead of print].

Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.

RevDate: 2018-10-12

Navrátilová D, Tláskalová P, Kohout P, et al (2018)

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil.

FEMS microbiology ecology pii:5128479 [Epub ahead of print].

Microbial communities in roots and shoots of plants and in soil are important for plant growth and health and take part in important ecosystem processes. Therefore, understanding the factors that affect their diversity is important. We have analysed fungal and bacterial communities associated with plant shoots, roots and soil over a 1 km2 area in a semi-natural temperate grassland with 1-43 plant species per 0.1 m2, to describe the relationships between plant and microbial diversity and to identify the drivers of bacterial and fungal community composition. Microbial community composition differed between shoots, roots and soil. While both fungal and bacterial species richness in shoots increased with plant species richness, no correlation was found between plant and microbial diversity in roots and soil. Chemistry was a significant predictor of bacterial and fungal community composition in soil as was also the spatial location of the sampled site. In this species rich grassland, the effects of plants on the microbiome composition seemed to be restricted to the shoot-associated taxa; in contrast, the microbiomes of roots or soil were not affected. The results support our hypothesis that the effect of plants on the microbiome composition decreases from shoots to roots and soil.

RevDate: 2018-10-12

Leftwich PT, Hutchings MI, T Chapman (2018)

Diet, Gut Microbes and Host Mate Choice: Understanding the significance of microbiome effects on host mate choice requires a case by case evaluation.

BioEssays : news and reviews in molecular, cellular and developmental biology [Epub ahead of print].

All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Recent reports that assortative mating of hosts by diet can be mediated by commensal gut microbes have attracted interest as a potential route to host reproductive isolation (RI). Here, the authors discuss logical problems with this line of argument. The authors briefly review how microbes can affect host mating preferences and evaluate recent findings from fruitflies. Endosymbionts can potentially influence host RI given stable and recurrent co-association of hosts and microbes over evolutionary time. However, observations of co-occurrence of microbes and hosts are ripe for misinterpretation and such associations will rarely represent a meaningful holobiont. A framework in which hosts and their microbes are independent evolutionary units provides the only satisfactory explanation for the observed range of effects and associations.

RevDate: 2018-10-12

Hasid R, Jaya Arma M, A Nurmas (2018)

Existence Arbuscula Mycorrhiza and Its Application Effect to Several Variety of Corn Plant (<I>Zeal mays </I> L.) in Marginal Dry Land.

Pakistan journal of biological sciences : PJBS, 21(4):199-204.

BACKGROUND AND OBJECTIVE: Arbuscula mycorrhiza (AM) have a very large function in symbiosis with plant roots, it's very important to be studied further because AM utilization is an alternative solution to improve the yield of corn plant in poor land. Until now the productivity of corn plant, especially in Southeast Sulawesi, Indonesia is lower than it's genetic potential, one of the causes is the cultivation of many plant done in sub optimal land with low technology applications especially the use of organic and biological fertilizer very low. This study aimed to observe the presence of AM and evaluate the growth and productivity of corn plant that AM inoculated.

MATERIALS AND METHODS: The study consisted two series of experiments, namely (1) Existence arbuscula mycorrhiza in rhizosphere of dominant weed (bladygrass) in dry land in Kendari, Southeast Sulawesi, Indonesia, was observed descriptively, (2) Effect of arbuscula mycorrhiza to several variety of corn plant (Zea mays L.) in Marginal dry land. The experiment was arranged based Randomized Block Design (RBD) consisted of eight treatments corn variety.

RESULTS: The results showed that spore populations were found in rhizosphere of dominant weed was 792-901 spores 100 g-1 soil, 70-90% roots infection. Some genera found are Glomus, Gigasphora, Acaulospora, Entrophospora, Scutellospora. Symbiosis effect of arbuscula mycorrhiza with plant growth indicates that Phosphorus uptake was highest in Batu Putih variety. However the highest in yield was show in Dana variety. Compared with the lowest production, the production difference was higher in Dana 47.70%.

CONCLUSION: Existence of arbuscula mycorrhiza in dominant weed rhizosphere in dry land is very high. The response of various varieties of maize plants to arbuscula mycorrhiza indicates that local varieties have a higher adaptability compared with introduction varieties.

RevDate: 2018-10-11

Hocher V, Ngom M, Carré-Mlouka A, et al (2018)

Signalling in actinorhizal root nodule symbioses.

Antonie van Leeuwenhoek pii:10.1007/s10482-018-1182-x [Epub ahead of print].

Plants able to establish a nitrogen-fixing root nodule symbiosis with the actinobacterium Frankia are called actinorhizal. These interactions lead to the formation of new root organs, called actinorhizal nodules, where the bacteria are hosted intracellularly and fix atmospheric nitrogen thus providing the plant with an almost unlimited source of nitrogen for its nutrition. Like other symbiotic interactions, actinorhizal nodulation involves elaborate signalling between both partners of the symbiosis, leading to specific recognition between the plant and its compatible microbial partner, its accommodation inside plant cells and the development of functional root nodules. Actinorhizal nodulation shares many features with rhizobial nodulation but our knowledge on the molecular mechanisms involved in actinorhizal nodulation remains very scarce. However recent technical achievements for several actinorhizal species are allowing major discoveries in this field. In this review, we provide an outline on signalling molecules involved at different stages of actinorhizal nodule formation and the corresponding signalling pathways and gene networks.

RevDate: 2018-10-11

Rimington WR, Pressel S, Duckett JG, et al (2018)

Ancient plants with ancient fungi: liverworts associate with early-diverging arbuscular mycorrhizal fungi.

Proceedings. Biological sciences, 285(1888): pii:rspb.2018.1600.

Arbuscular mycorrhizas are widespread in land plants including liverworts, some of the closest living relatives of the first plants to colonize land 500 million years ago (MYA). Previous investigations reported near-exclusive colonization of liverworts by the most recently evolved arbuscular mycorrhizal fungi, the Glomeraceae, indicating a recent acquisition from flowering plants at odds with the widely held notion that arbuscular mycorrhizal-like associations in liverworts represent the ancestral symbiotic condition in land plants. We performed an analysis of symbiotic fungi in 674 globally collected liverworts using molecular phylogenetics and electron microscopy. Here, we show every order of arbuscular mycorrhizal fungi colonizes early-diverging liverworts, with non-Glomeraceae being at least 10 times more common than in flowering plants. Arbuscular mycorrhizal fungi in liverworts and other ancient plant lineages (hornworts, lycopods, and ferns) were delimited into 58 taxa and 36 singletons, of which at least 43 are novel and specific to liverworts. The discovery that early plant lineages are colonized by early-diverging fungi supports the hypothesis that arbuscular mycorrhizas are an ancestral symbiosis for all land plants.

RevDate: 2018-10-14

Lang C, Barnett MJ, Fisher RF, et al (2018)

Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions.

mSphere, 3(5): pii:3/5/e00454-18.

Bacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF σs) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti carries genes for 11 ECF-like σs (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entire S. meliloti cohort of ECF σs. We discovered new targets for individual σs, confirmed others by overexpressing individual ECF σs, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF σ gene and its demonstrated or putative anti-σ gene and also a strain in which all 11 ECF σ and anti-σ genes were deleted. This all-ECF σ deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF σs were required for symbiosis on the host plants Medicago sativa and Medicago truncatula: the strain deleted for all ECF σ and anti-σ genes was symbiotically normal.IMPORTANCE Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.

RevDate: 2018-10-11

Guyomar C, Legeai F, Jousselin E, et al (2018)

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.

Microbiome, 6(1):181 pii:10.1186/s40168-018-0562-9.

BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.

RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.

CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.

RevDate: 2018-10-11

Osti JF, A Rodrigues (2018)

Escovopsioides as a fungal antagonist of the fungus cultivated by leafcutter ants.

BMC microbiology, 18(1):130 pii:10.1186/s12866-018-1265-x.

BACKGROUND: Fungus gardens of fungus-growing (attine) ants harbor complex microbiomes in addition to the mutualistic fungus they cultivate for food. Fungi in the genus Escovopsioides were recently described as members of this microbiome but their role in the ant-fungus symbiosis is poorly known. In this study, we assessed the phylogenetic diversity of 21 Escovopsioides isolates obtained from fungus gardens of leafcutter ants (genera Atta and Acromyrmex) and non-leafcutter ants (genera Trachymyrmex and Apterostigma) sampled from several regions in Brazil.

RESULTS: Regardless of the sample locality or ant genera, phylogenetic analysis showed low genetic diversity among the 20 Escovopsisoides isolates examined, which prompted the identification as Escovopsioides nivea (the only described species in the genus). In contrast, one Escovopsioides isolate obtained from a fungus garden of Apterostigma megacephala was considered a new phylogenetic species. Dual-culture plate assays showed that Escovopsioides isolates inhibited the mycelium growth of Leucoagaricus gongylophorus, the mutualistic fungus cultivated by somes species of leafcutter ants. In addition, Escovopsioides growth experiments in fungus gardens with and without ant workers showed this fungus is detrimental to the ant-fungus symbiosis.

CONCLUSIONS: Here, we provide clues for the antagonism of Escovopsioides towards the mutualistic fungus of leafcutter ants.

RevDate: 2018-10-10

Santiago R, Martins MCB, Vilaça MD, et al (2018)

Phytochemical and biological evaluation of metabolites produced by alginate-immobilized Bionts isolated from the lichen Cladonia substellata vain.

Fitoterapia pii:S0367-326X(18)31047-5 [Epub ahead of print].

In this work, new biotechnological procedures have been optimized on the basis of immobilization in alginate of bionts isolated from the lichen C. substellata. From these immobilizates, soluble and biologically active phenolics can be obtained. During bionts-immobilization, stictic, norstictic and usnic acids were secreted to the medium. The amount produced of each of them differed depending on the immobilization time, the precursor supplied and the type of biont used. Greater amounts of stictic acid were detected and maintained over time in all bioreactors. The opposite occurs in non-immobilized thallus. Virtually, all plant phenols exhibit antioxidant activity to a greater or lesser degree, so that the antioxidant capacity of stictic acid (82.13% oxidation inhibition) was tested. The soluble extract of immobilized algae co-incubated in sodium acetate with fungal hyphae contained carbohydrates and exhibited a potent antioxidant capacity after 13 days of immobilization (94.87%). Therefore, attempts have been made to relate both parameters. On the other hand, the growth of Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae was inhibited by phenolic compounds produced by immobilizates, although the organic extract of the whole lichen showed the highest activity due to a possible synergy with other indeterminate compounds. Thus, C. substellata immobilized bionts are a potential source of different natural antioxidant and antimicrobial compounds.

RevDate: 2018-10-16

Li Y, Ruan Y, Kasson MT, et al (2018)

Structure of the Ambrosia Beetle (Coleoptera: Curculionidae) Mycangia Revealed Through Micro-Computed Tomography.

Journal of insect science (Online), 18(5): pii:5125956.

Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) rely on a symbiosis with fungi for their nutrition. Symbiotic fungi are preserved and transported in specialized storage structures called mycangia. Although pivotal in the symbiosis, mycangia have been notoriously difficult to study, given their minute size and membranous structure. We compared the application of novel visualization methods for the study of mycangia, namely micro-computed tomography (micro-CT) and laser ablation tomography (LATscan) with traditional paraffin sectioning. Micro-CT scanning has shown the greatest promise in new organ discovery, while sectioning remains the only method with sufficient resolution for cellular visualization. All three common types of mycangia (oral, mesonotal, and pronotal) were successfully visualized and presented for different species of ambrosia beetles: Ambrosiodmus minor (Stebbing) 1909, Euplatypus compositus (Say) 1823, Premnobius cavipennis Eichhoff 1878, Scolytoplatypus raja Blandford 1893, Xylosandrus crassiusculus (Motschulsky) 1866 and X. amputatus (Blandford) 1894. A reconstruction of the mycangium and the surrounding musculature in X. amputatus is also presented. The advantages of micro-CT compared to the previously commonly used microtome sectioning include the easy visualization and recording of three-dimensional structures, their position in reference to other internal structures, the ability to distinguish natural aberrations from technical artifacts, and the unprecedented visualizations of the anatomic context of mycangia enabled by the integrated software.

RevDate: 2018-10-14

Wiles TJ, Wall ES, Schlomann BH, et al (2018)

Modernized Tools for Streamlined Genetic Manipulation and Comparative Study of Wild and Diverse Proteobacterial Lineages.

mBio, 9(5): pii:mBio.01877-18.

Correlating the presence of bacteria and the genes they carry with aspects of plant and animal biology is rapidly outpacing the functional characterization of naturally occurring symbioses. A major barrier to mechanistic studies is the lack of tools for the efficient genetic manipulation of wild and diverse bacterial isolates. To address the need for improved molecular tools, we used a collection of proteobacterial isolates native to the zebrafish intestinal microbiota as a testbed to construct a series of modernized vectors that expedite genetic knock-in and knockout procedures across lineages. The innovations that we introduce enhance the flexibility of conventional genetic techniques, making it easier to manipulate many different bacterial isolates with a single set of tools. We developed alternative strategies for domestication-free conjugation, designed plasmids with customizable features, and streamlined allelic exchange using visual markers of homologous recombination. We demonstrate the potential of these tools through a comparative study of bacterial behavior within the zebrafish intestine. Live imaging of fluorescently tagged isolates revealed a spectrum of distinct population structures that differ in their biogeography and dominant growth mode (i.e., planktonic versus aggregated). Most striking, we observed divergent genotype-phenotype relationships: several isolates that are predicted by genomic analysis and in vitro assays to be capable of flagellar motility do not display this trait within living hosts. Together, the tools generated in this work provide a new resource for the functional characterization of wild and diverse bacterial lineages that will help speed the research pipeline from sequencing-based correlations to mechanistic underpinnings.IMPORTANCE A great challenge in microbiota research is the immense diversity of symbiotic bacteria with the capacity to impact the lives of plants and animals. Moving beyond correlative DNA sequencing-based studies to define the cellular and molecular mechanisms by which symbiotic bacteria influence the biology of their hosts is stalling because genetic manipulation of new and uncharacterized bacterial isolates remains slow and difficult with current genetic tools. Moreover, developing tools de novo is an arduous and time-consuming task and thus represents a significant barrier to progress. To address this problem, we developed a suite of engineering vectors that streamline conventional genetic techniques by improving postconjugation counterselection, modularity, and allelic exchange. Our modernized tools and step-by-step protocols will empower researchers to investigate the inner workings of both established and newly emerging models of bacterial symbiosis.

RevDate: 2018-10-17

Hernandez-Agreda A, Leggat W, Bongaerts P, et al (2018)

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere.

mBio, 9(5): pii:mBio.00812-18.

Studies of the coral microbiome predominantly characterize the microbial community of the host species as a collective, rather than that of the individual. This ecological perspective on the coral microbiome has led to the conclusion that the coral holobiont is the most diverse microbial biosphere studied thus far. However, investigating the microbiome of the individual, rather than that of the species, highlights common and conserved community attributes which can provide insights into the significance of microbial associations to the host. Here, we show there are consistent characteristics between individuals in the proposed three components of the coral microbiome (i.e., "environmentally responsive community," "resident or individual microbiome," and "core microbiome"). We found that the resident microbiome of a photoendosymbiotic coral harbored <3% (∼605 phylotypes) of the 16S rRNA phylotypes associated with all investigated individuals of that species ("species-specific microbiome") (∼21,654 phylotypes; individuals from Pachyseris speciosa [n = 123], Mycedium elephantotus [n = 95], and Acropora aculeus [n = 91] from 10 reef locations). The remaining bacterial phylotypes (>96%) (environmentally responsive community) of the species-specific microbiome were in fact not found in association with the majority of individuals of the species. Only 0.1% (∼21 phylotypes) of the species-specific microbiome of each species was shared among all individuals of the species (core microbiome), equating to ∼3.4% of the resident microbiome. We found taxonomic redundancy and consistent patterns of composition, structure, and taxonomic breadth across individual microbiomes from the three coral species. Our results demonstrate that the coral microbiome is structured at the individual level.IMPORTANCE We propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an important baseline from which the functional roles and the functional niches within which microbes reside can be deciphered.

RevDate: 2018-10-10

Okubo N, Takahashi S, Y Nakano (2018)

Microplastics disturb the anthozoan-algae symbiotic relationship.

Marine pollution bulletin, 135:83-89.

World production of plastic has dramatically increased from the 1950's and now it reaches approximately 311 million tons per year. The resulting accumulation of small plastic detritus less than 5 mm in size, termed "microplastics", has started threatening the life cycles of marine organisms. Here we show the first evidence that microplastics disturb the initiation of symbiotic relationships in anthozoan-algae symbiosis. We found in both the aposymbiotic sea-anemone Aiptasia sp. and the coral Favites chinensis that the infectivity of symbiotic algae into the host is severely suppressed by microspheres fed either directly or indirectly through microsphere-fed Artemia sp. Similar trends were seen when microplastics collected from commercial facewash were used instead of microspheres. Therefore, ongoing accumulation of microplastics in the ocean might disturb the healthy anthozoan-algae symbiotic relationships, which are cornerstones of the biologically enriched coral reef ecosystem.

RevDate: 2018-10-09

Dovrat G, E Sheffer (2018)

Symbiotic dinitrogen fixation is seasonal and strongly regulated in water-limited environments.

The New phytologist [Epub ahead of print].

1.Plants, especially perennials, growing in drylands and seasonally dry ecosystems are uniquely adapted to dry conditions. Legume shrubs and trees, capable of symbiotic dinitrogen (N2) fixation, often dominate in drylands. However, the strategies that allow symbiotic fixation in these ecosystems, and their influence on the nitrogen cycle, are largely unresolved. We evaluated the climatic, biogeochemical and ontogenetic factors influencing nitrogen fixation in an abundant Mediterranean legume shrub, Calicotome villosa. 2.We measured nodulation, fixation rate, nitrogen allocation, and soil biogeochemistry, in three field sites over a full year. A controlled experiment evaluated differences in plant regulation of fixation as a function of soil nutrient availability and seedling and adult developmental stages. 3.We found a strong seasonal pattern, shifting between high fixation rates during the rainy season at flowering and seed-set times to almost none in the rainless season. Under controlled conditions plants downregulated fixation in response to soil nitrogen availability, but this response was stronger in seedlings compared to adult shrubs. Finally, we did not find elevated soil nitrogen under N2 -fixing shrubs. 4.We conclude that seasonal nitrogen fixation, regulation of fixation, and nitrogen conservation, are key adaptations influencing the dominance of dryland legumes in the community, with broader consequences on the ecosystem nitrogen cycle. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-11

Palmer AG, Senechal AC, Haire TC, et al (2018)

Selection of appropriate autoinducer analogs for the modulation of quorum sensing at the host-bacteria interface.

ACS chemical biology [Epub ahead of print].

Bacteria regulate a variety of phenotypes in response to their population density using quorum sensing (QS). This phenomenon is regulated by small molecule or peptide signals, the best characterized of which are the N-acyl L-homoserine lactones (AHLs) utilized by Gram-negative bacteria. As many QS-controlled phenotypes, notably pathogenic-ity and symbiosis, can profoundly impact host eukaryotes, there is significant interest in developing methods to modulate QS signaling and either ameliorate or augment these phenotypes. One strategy has been the use of non-native AHL ana-logues to agonize or antagonize specific AHL receptors. This approach is complicated, however, by the potential for pro-spective hosts to respond to both native AHLs as well as synthetic analogues. Accordingly, identifying AHL analogues with little or no activity towards eukaryotes is important in developing QS modulation as a strategy for the regulation of prokaryotic behaviors. Herein, we utilize the model plant Arabidopsis thaliana to characterize eukaryotic responses to a variety of synthetic AHL analogues to identify structural elements of existing scaffolds that may elicit responses in pro-spective hosts. Our results indicate that, while many of these compounds have no discernable effect on A. thaliana, some elicit strong phenotypes similar to those produced by auxin, a hormone involved in almost all aspects of plant develop-ment. We outline concentrations and chemical scaffolds ideal for deployment on plant hosts for the regulation of QS. This approach should be exportable to other eukaryotes for the selection of optimal AHL tools for the study of QS at the host-microbe interface.

RevDate: 2018-10-10

Kalra S, Jena BN, R Yeravdekar (2018)

Emotional and Psychological Needs of People with Diabetes.

Indian journal of endocrinology and metabolism, 22(5):696-704.

Diabetes is a chronic metabolic disorder that impacts physical, social and mental including psychological well-being of people living with it. Additionally, psychosocial problems that are most common in diabetes patients often result in serious negative impact on patient's well-being and social life, if left un-addressed. Addressing such psychosocial aspects including cognitive, emotional, behavioral and social factors in the treatment interventions would help overcome the psychological barriers, associated with adherence and self-care for diabetes; the latter being the ultimate goal of management of patients with diabetes. While ample literature on self-management and psychological interventions for diabetes is available, there is limited information on the impact of psychological response and unmanaged emotional distresses on overall health. The current review therefore examines the emotional, psychological needs of the patients with diabetes and emphasizes the role of diabetologist, mental health professionals including clinical psychologists to mitigate the problems faced by these patients. Search was performed using a combination of keywords that cover all relevant terminology for diabetes and associated emotional distress. The psychological reactions experienced by the patient upon diagnosis of diabetes have been reviewed in this article with a focus on typical emotional distress at different levels. Identifying and supporting patients with psychosocial problems early in the course of diabetes may promote psychosocial well-being and improve their ability to adjust or take adequate responsibility in diabetes self-management - the utopian state dreamt of by all diabetologists !.

RevDate: 2018-10-07

Jiang Y, Xie Q, Wang W, et al (2018)

Medicago AP2-domain Transcription Factor WRI5a Is a Master Regulator of Lipid Biosynthesis and Transfer During Mycorrhizal Symbiosis.

Molecular plant pii:S1674-2052(18)30301-0 [Epub ahead of print].

Most land plants evolve a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi to improve nutrient acquisition from the soil. In return, up to 20% of host plant photosynthate is transferred to the mycorrhizal fungus in the form of lipids and sugar. Nutrient exchange must be regulated by both partners in order to maintain a reliable symbiotic relationship. However, the mechanisms underlying the regulation of lipid transfer from plant to AM fungus remain elusive. Here, we show that Medicago truncatula AP2/EREBP transcription factor WRI5a, and likely its two homologs WRI5b/Erf1 and WRI5c, are master regulators of AM symbiosis by controlling lipid transfer and periarbuscular membrane formation. We found that WRI5a binds the AW-box cis-regulatory elements in the promoters of STR and MtPT4 in M. truncatula, which encodes a periarbuscular membrane-localized ABC transporter required for lipid transfer from the plant to AM fungi-and a phosphate transporter required for phosphate transfer from AM fungi to the plant, respectively. The M. truncatula wri5a mutant and RNAi composite plants hairy roots displayed impaired arbuscule formation, whereas overexpression of WRI5a resulted in enhanced expression of STR and MtPT4, suggesting that WRI5a regulates bidirectional symbiotic nutrient exchange. Moreover, we found that WRI5a and RAM1 (Required for Arbuscular Mycorrhization symbiosis 1) encoding a GRAS-domain transcription factor regulate each other at the transcriptional level, forming a positive feedback loop for regulating AM symbiosis. Our data suggest a role for WRI5a in controlling lipid transfer and periarbuscular membrane formation via the regulation of genes for the biosynthesis and supply of fatty acids and phosphate uptake in arbuscule-containing cells.

RevDate: 2018-10-05

Becquer A, Garcia K, C Plassard (2018)

HcPT1.2 participates in Pi acquisition in Hebeloma cylindrosporum external hyphae of ectomycorrhizas under high and low phosphate conditions.

Plant signaling & behavior [Epub ahead of print].

Ectomycorrhizal fungi improve tree phosphorus nutrition through transporters specifically localized at soil-hyphae and symbiotic interfaces. In the model symbiosis between the fungus Hebeloma cylindrosporum and the maritime pine (Pinus pinaster), several transporters possibly involved in phosphate fluxes were identified, including three H+:Pi transporters. Among these three, we recently unraveled the function of one of them, named HcPT2, in both pure culture and symbiotic interaction with P. pinaster. Here we investigated the transporter named HcPT1.2, by analyzing inorganic phosphate transport ability in a yeast complementation assay, assessing its expression in the fungus associated or not with the plant, and immunolocalizing the proteins in ectomycorrhizas. We also evaluated the effect of external Pi concentration on expression and localization of HcPT1.2. Our results revealed that HcPT1.2 is involved in Pi acquisition by H. cylindrosporum mycelium, irrespective of the external Pi concentrations.

RevDate: 2018-10-16

Mancini MV, Damiani C, Accoti A, et al (2018)

Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.

BMC microbiology, 18(1):126 pii:10.1186/s12866-018-1266-9.

BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.

RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.

CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.

RevDate: 2018-10-17

Higuchi R, Song C, Hoshina R, et al (2018)

Endosymbiosis-related changes in ultrastructure and chemical composition of Chlorella variabilis (Archaeplastida, Chlorophyta) cell wall in Paramecium bursaria (Ciliophora, Oligohymenophorea).

European journal of protistology, 66:149-155 pii:S0932-4739(18)30081-6 [Epub ahead of print].

Chlorella variabilis, a symbiotic alga, is usually present in the cytoplasm of Paramecium bursaria, although it can be cultured in host-free conditions. Morphological and chemical properties of its cell wall were compared between its free-living and symbiotic states. Transmission electron microscopy (quick-freezing and freeze-substitution methods) revealed that the cell wall thickness of symbiotic C. variabilis was reduced to about half that of the free-living one. Chemical properties of the cell wall were examined by treatment with three fluorescent reagents (calcofluor white M2R, FITC-WGA, and FITC-LFA) having specific binding affinities to different polysaccharides. When the algae were re-introduced into Paramecium host cells, calcofluor fluorescence intensity reduced by about 50%. Calcofluor stains β-d-glucopyranose polysaccharides such as cellulose, N-acetylglucosamine, sialic acid, and glycosaminoglycans. Because treatment with cellulase showed no effect on calcofluor fluorescence intensity, we consider that cellulose is not majorly responsible for the stainability of calcofluor. Staining intensities of FITC-WGA and FITC-LFA were similar in the free-living and symbiotic conditions, suggesting that N-acetylglucosamine and sialic acid are also not responsible for the reduction in the stainability of calcofluor associated with intracellular symbiosis. The amount of glycosaminoglycans on the cell wall may decrease in C. variabilis present in the cytoplasm of P. bursaria.

RevDate: 2018-10-11

Tsikou D, Ramirez EE, Psarrakou IS, et al (2018)

A Lotus japonicus E3 ligase interacts with the Nod Factor Receptor 5 and positively regulates nodulation.

BMC plant biology, 18(1):217 pii:10.1186/s12870-018-1425-z.

BACKGROUND: Post-translational modification of receptor proteins is involved in activation and de-activation of signalling systems in plants. Both ubiquitination and deubiquitination have been implicated in plant interactions with pathogens and symbionts.

RESULTS: Here we present LjPUB13, a PUB-ARMADILLO repeat E3 ligase that specifically ubiquitinates the kinase domain of the Nod Factor receptor NFR5 and has a direct role in nodule organogenesis events in Lotus japonicus. Phenotypic analyses of three LORE1 retroelement insertion plant lines revealed that pub13 plants display delayed and reduced nodulation capacity and retarded growth. LjPUB13 expression is spatially regulated during symbiosis with Mesorhizobium loti, with increased levels in young developing nodules.

CONCLUSION: LjPUB13 is an E3 ligase with a positive regulatory role during the initial stages of nodulation in L. japonicus.

RevDate: 2018-10-17

Malolepszy A, Kelly S, Sørensen KK, et al (2018)

A plant chitinase controls cortical infection thread progression and nitrogen-fixing symbiosis.

eLife, 7: pii:38874.

Morphogens provide positional information and their concentration is key to the organized development of multicellular organisms. Nitrogen-fixing root nodules are unique organs induced by Nod factor-producing bacteria. Localized production of Nod factors establishes a developmental field within the root where plant cells are reprogrammed to form infection threads and primordia. We found that regulation of Nod factor levels by Lotus japonicus is required for the formation of nitrogen-fixing organs, determining the fate of this induced developmental program. Our analysis of plant and bacterial mutants shows that a host chitinase modulates Nod factor levels possibly in a structure-dependent manner. In Lotus, this is required for maintaining Nod factor signalling in parallel with the elongation of infection threads within the nodule cortex, while root hair infection and primordia formation are not influenced. Our study shows that infected nodules require balanced levels of Nod factors for completing their transition to functional, nitrogen-fixing organs.

RevDate: 2018-10-07

Zhu X, Cao Q, Sun L, et al (2018)

Stomatal Conductance and Morphology of Arbuscular Mycorrhizal Wheat Plants Response to Elevated CO2 and NaCl Stress.

Frontiers in plant science, 9:1363.

RevDate: 2018-10-17

Li H, Sosa-Calvo J, Horn HA, et al (2018)

Convergent evolution of complex structures for ant-bacterial defensive symbiosis in fungus-farming ants.

Proceedings of the National Academy of Sciences of the United States of America, 115(42):10720-10725.

Evolutionary adaptations for maintaining beneficial microbes are hallmarks of mutualistic evolution. Fungus-farming "attine" ant species have complex cuticular modifications and specialized glands that house and nourish antibiotic-producing Actinobacteria symbionts, which in turn protect their hosts' fungus gardens from pathogens. Here we reconstruct ant-Actinobacteria evolutionary history across the full range of variation within subtribe Attina by combining dated phylogenomic and ultramorphological analyses. Ancestral-state analyses indicate the ant-Actinobacteria symbiosis arose early in attine-ant evolution, a conclusion consistent with direct observations of Actinobacteria on fossil ants in Oligo-Miocene amber. qPCR indicates that the dominant ant-associated Actinobacteria belong to the genus Pseudonocardia Tracing the evolutionary trajectories of Pseudonocardia-maintaining mechanisms across attine ants reveals a continuum of adaptations. In Myrmicocrypta species, which retain many ancestral morphological and behavioral traits, Pseudonocardia occur in specific locations on the legs and antennae, unassociated with any specialized structures. In contrast, specialized cuticular structures, including crypts and tubercles, evolved at least three times in derived attine-ant lineages. Conspicuous caste differences in Pseudonocardia-maintaining structures, in which specialized structures are present in worker ants and queens but reduced or lost in males, are consistent with vertical Pseudonocardia transmission. Although the majority of attine ants are associated with Pseudonocardia, there have been multiple losses of bacterial symbionts and bacteria-maintaining structures in different lineages over evolutionary time. The early origin of ant-Pseudonocardia mutualism and the multiple evolutionary convergences on strikingly similar anatomical adaptations for maintaining bacterial symbionts indicate that Pseudonocardia have played a critical role in the evolution of ant fungiculture.

RevDate: 2018-10-04

Hecht LBB, Thompson PC, BM Rosenthal (2018)

Comparative demography elucidates the longevity of parasitic and symbiotic relationships.

Proceedings. Biological sciences, 285(1888): pii:rspb.2018.1032.

Parasitic and symbiotic relationships govern vast nutrient and energy flows, yet controversy surrounds their longevity. Enduring relationships may engender parallel phylogenies among hosts and parasites, but so may ephemeral relationships when parasites colonize related hosts. An understanding of whether symbiont and host populations have grown and contracted in concert would be useful when considering the temporal durability of these relationships. Here, we devised methods to compare demographic histories derived from genomic data. We compared the historical growth of the agent of severe human malaria, Plasmodium falciparum, and its mosquito vector, Anopheles gambiae, to human and primate histories, thereby discerning long-term parallels and anthropogenic population explosions. The growth history of Trichinella spiralis, a zoonotic parasite disseminated by swine, proved regionally specific, paralleling distinctive growth histories for wild boar in Asia and Europe. Parallel histories were inferred for an anemone and its algal symbiont (Exaiptasia pallida and Symbiodinium minutum). Concerted growth in potatoes and the agent of potato blight (Solanum tuberosum and Phytophthora infestans) did not commence until the age of potato domestication. Through these examples, we illustrate the utility of comparative historical demography as a new exploratory tool by which to interrogate the origins and durability of myriad ecological relationships. To facilitate future use of this approach, we introduce a tool called C-PSMC to align and evaluate the similarity of demographic history curves.

RevDate: 2018-10-02

Giauque H, Connor EW, CV Hawkes (2018)

Endophyte traits relevant to stress tolerance, resource use, and habitat of origin predict effects on host plants.

The New phytologist [Epub ahead of print].

All terrestrial plants are colonized by foliar endophytic fungi that can affect plant growth and physiology, but predicting those effects on the plant host remains a challenge. Here, we examined three paradigms that potentially control how endophytes affect plant hosts: habitat adaptation, evolutionary history, and functional traits. We screened 35 plant-endophyte pairings in a microcosm experiment under well-watered and drought conditions with Panicum virgatum as the host. We related measured plant responses to fungal phylogenetic relatedness, characteristics of fungal habitats across a rainfall gradient, and functional traits of the fungi related to stress tolerance and resource use. Functional traits and habitat characteristics of the fungi predicted 26-53% of endophyte-mediated effects on measures of plant growth, physiology, and survival. Overall, survival was higher for plants grown with more stress-tolerant fungi and aboveground biomass was enhanced by fungi from warmer and drier habitats. Plant growth and physiology were also dependent on fungal resource use indicators; however, specific predictors depended on water availability. Simple ecological traits of foliar endophytic fungi observed in culture can translate to symbiotic lifestyles. These findings offer new insight and key testable predictions for likely pathways by which endophytes benefit the plant host. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-17

Ledón-Rettig CC, Moczek AP, EJ Ragsdale (2018)

Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host.

Proceedings of the National Academy of Sciences of the United States of America, 115(42):10696-10701.

A recent accumulation of studies has demonstrated that nongenetic, maternally transmitted factors are often critical to the health and development of offspring and can therefore play a role in ecological and evolutionary processes. In particular, microorganisms such as bacteria have been championed as heritable, symbiotic partners capable of conferring fitness benefits to their hosts. At the same time, parents may also pass various nonmicrobial organisms to their offspring, yet the roles of such organisms in shaping the developmental environment of their hosts remain largely unexplored. Here, we show that the nematode Diplogastrellus monhysteroides is transgenerationally inherited and sexually transmitted by the dung beetle Onthophagus taurus By manipulating artificial chambers in which beetle offspring develop, we demonstrate that the presence of D. monhysteroides nematodes enhances the growth of beetle offspring, empirically challenging the paradigm that nematodes are merely commensal or even detrimental to their insect hosts. Finally, our research presents a compelling mechanism whereby the nematodes influence the health of beetle larvae: D. monhysteroides nematodes engineer the bacterial and fungal communities that also inhabit the beetle developmental chambers, including specific taxa known to be involved in biomass degradation, possibly allowing larval beetles better access to their otherwise recalcitrant, plant-based diet. Thus, our findings illustrate that nongenetic inheritance can include intermediately sized organisms that live and proliferate in close association with, and in certain cases enhance, the development of their hosts' offspring.

RevDate: 2018-10-01

Liu H, Stephens TG, González-Pech RA, et al (2018)

Erratum: Publisher Correction: Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis.

Communications biology, 1:126 pii:117.

[This corrects the article DOI: 10.1038/s42003-018-0098-3.].

RevDate: 2018-10-03

Hoeksema JD, Bever JD, Chakraborty S, et al (2018)

Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism.

Communications biology, 1:116 pii:120.

Most plants engage in symbioses with mycorrhizal fungi in soils and net consequences for plants vary widely from mutualism to parasitism. However, we lack a synthetic understanding of the evolutionary and ecological forces driving such variation for this or any other nutritional symbiosis. We used meta-analysis across 646 combinations of plants and fungi to show that evolutionary history explains substantially more variation in plant responses to mycorrhizal fungi than the ecological factors included in this study, such as nutrient fertilization and additional microbes. Evolutionary history also has a different influence on outcomes of ectomycorrhizal versus arbuscular mycorrhizal symbioses; the former are best explained by the multiple evolutionary origins of ectomycorrhizal lifestyle in plants, while the latter are best explained by recent diversification in plants; both are also explained by evolution of specificity between plants and fungi. These results provide the foundation for a synthetic framework to predict the outcomes of nutritional mutualisms.

RevDate: 2018-10-03

Liu H, Stephens TG, González-Pech RA, et al (2018)

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis.

Communications biology, 1:95 pii:98.

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

RevDate: 2018-10-03

Birnbaum C, Morald TK, Tibbett M, et al (2018)

Effect of plant root symbionts on performance of native woody species in competition with an invasive grass in multispecies microcosms.

Ecology and evolution, 8(17):8652-8664 pii:ECE34397.

The majority of terrestrial plants form mutualistic associations with arbuscular mycorrhizal fungi (AMF) and rhizobia (i.e., nitrogen-fixing bacteria). Understanding these associations has important implications for ecological theory and for restoration practice. Here, we tested whether the presence of AMF and rhizobia influences the performance of native woody plants invaded by a non-native grass in experimental microcosms. We planted eight plant species (i.e., Acacia acuminata, A. microbotrya, Eucalyptus loxophleba subsp. loxophleba, E. astringens, Calothamnus quadrifidus, Callistemon phoeniceus, Hakea lissocarpha and H. prostrata) in microcosms of field-conditioned soil with and without addition of AMF and rhizobia in a fully factorial experimental design. After seedling establishment, we seeded half the microcosms with an invasive grass Bromus diandrus. We measured shoot and root biomass of native plants and Bromus, and on roots, the percentage colonization by AMF, number of rhizobia-forming nodules and number of proteaceous root clusters. We found no effect of plant root symbionts or Bromus addition on performance of myrtaceous, and as predicted, proteaceous species as they rely little or not at all on AMF and rhizobia. Soil treatments with AMF and rhizobia had a strong positive effect (i.e., larger biomass) on native legumes (A. microbotrya and A. acuminata). However, the beneficial effect of root symbionts on legumes became negative (i.e., lower biomass and less nodules) if Bromus was present, especially for one legume, i.e., A. acuminata, suggesting a disruptive effect of the invader on the mutualism. We also found a stimulating effect of Bromus on root nodule production in A. microbotrya and AMF colonization in A. acuminata which could be indicative of legumes' increased resource acquisition requirement, i.e., for nitrogen and phosphorus, respectively, in response to the Bromus addition. We have demonstrated the importance of measuring belowground effects because the aboveground effects gave limited indication of the effects occurring belowground.

RevDate: 2018-10-03

Mohammed M, Jaiswal SK, Sowley ENK, et al (2018)

Symbiotic N2 Fixation and Grain Yield of Endangered Kersting's Groundnut Landraces in Response to Soil and Plant Associated Bradyrhizobium Inoculation to Promote Ecological Resource-Use Efficiency.

Frontiers in microbiology, 9:2105.

Kersting's groundnut (Macrotyloma geocarpum Harms) is a neglected, endangered food and medicinal legume in Africa. Efforts to harness the benefits of the legume-rhizobia symbiosis have focused on few major legumes to the neglect of underutilized ones such as Kersting's groundnut. This study assessed plant growth, N-fixed and grain yield of five Kersting's groundnut landraces in response to inoculation with Bradyrhizobium strain CB756 at two locations in the Northern Region of Ghana. The transferability of cowpea-derived Simple Sequence Repeat (SSR) markers to Kersting's groundnut was also assessed. The symbiotic results revealed significant variation in nodulation, shoot biomass, δ15N, percent N derived from fixation, amount of N-fixed and soil N uptake. The cross-taxa SSR primers revealed monomorphic bands with sizes within the expected range in all the Kersting's groundnut landraces. The results of the aligned nucleotide sequences revealed marked genetic variability among the landraces. Kersting's groundnut was found to be a low N2-fixer, with 28-45% of its N derived from fixation at Nyankpala and 15-29% at Savelugu. Nitrogen contribution was 28-50 kg N-fixed·ha-1 at Nyankpala, and 12-32 kg N-fixed·ha-1 at Savelugu. Uninoculated plants of the Kersting's groundnut landraces Puffeun, Dowie, Sigiri and Boli, respectively, contributed 22, 16, 13, and 15 kg N-fixed·ha-1 from symbiosis at Savelugu as opposed to 89, 82, 69, and 89 kg N·ha-1 from soil. Landrace Puffeun was highly compatible with the introduced strain CB756 if based on δ15N and %Ndfa values, while Dowie, Funsi and Boli showed greater compatibility with native rhizobia in Ghanaian soils. The unimproved Kersting's groundnut in association with soil microsymbionts could produce grain yield of 1,137-1,556 kg ha-1 at Nyankpala, and 921-1,192 kg ha-1 at Savelugu. These findings suggest the need for further work to improve the efficiency of the Kersting's groundnut-rhizobia symbiosis for increased grain yield and resource-use efficiency in cropping systems.

RevDate: 2018-10-14

Mansfield KM, TD Gilmore (2018)

Innate immunity and cnidarian-Symbiodiniaceae mutualism.

Developmental and comparative immunology, 90:199-209 pii:S0145-305X(18)30381-1 [Epub ahead of print].

The phylum Cnidaria (sea anemones, corals, hydra, jellyfish) is one the most distantly related animal phyla to humans, and yet cnidarians harbor many of the same cellular pathways involved in innate immunity in mammals. In addition to its role in pathogen recognition, the innate immune system has a role in managing beneficial microbes and supporting mutualistic microbial symbioses. Some corals and sea anemones undergo mutualistic symbioses with photosynthetic algae in the family Symbiodiniaceae. These symbioses can be disrupted by anthropogenic disturbances of ocean environments, which can have devastating consequences for the health of coral reef ecosystems. Several studies of cnidarian-Symbiodiniaceae symbiosis have implicated proteins in the host immune system as playing a role in both symbiont tolerance and loss of symbiosis (i.e., bleaching). In this review, we critically evaluate current knowledge about the role of host immunity in the regulation of symbiosis in cnidarians.

RevDate: 2018-09-29

Prasad S, Rastogi B, Shah A, et al (2018)

DTI in essential tremor with and without rest tremor: Two sides of the same coin?.

RevDate: 2018-09-29

Li X, Zheng J, Yang Y, et al (2018)

INCREASING NODULE SIZE1 expression is required for normal rhizobial symbiosis and nodule development.

Plant physiology pii:pp.18.01018 [Epub ahead of print].

Nodulation is crucial for biological nitrogen fixation (BNF) in legumes, but the molecular mechanisms underlying BNF have remained elusive. Here, we cloned a candidate gene underlying a major nodulation QTL in soybean (Glycine max), INCREASING NODULE SIZE1 (GmINS1). GmINS1 encodes a cell wall a β-expansin, and is primarily expressed in vascular bundles, along with cortical and parenchyma cells of nodules. Four SNPs distinguishing the two parents were found in the GmINS1 promoter region. Among them, SNP A/C has a significant effect on GmINS1 expression in the parental genotype P2, based on GUS activity and promoter deletion analysis. The expression of GmINS1 and the P2 genotype promoter were strongly associated with nodule development, not only in the parents but also in 40 progeny lines and 40 genotypes selected from a soybean core collection. Overexpression of GmINS1 resulted in increases in the number, biomass, infection cell abundance, and nitrogenase activity of large nodules, and subsequently changed the N content and biomass of soybean plants. GmINS1 suppression via RNAi had the opposite effect. Double suppression of GmEXPB2 and GmINS1 dramatically inhibited soybean nodulation. Our results reveal that GmINS1 is a critical gene in nodule development, and that GmEXPB2 and GmINS1 synergistically control nodulation in soybean. Our findings shed light on the genetic basis of soybean nodulation, and provide a candidate gene for optimizing BNF capacity through molecular breeding in soybean.

RevDate: 2018-10-02

Pouncey AL, Scott AJ, Alexander JL, et al (2018)

Gut microbiota, chemotherapy and the host: the influence of the gut microbiota on cancer treatment.

Ecancermedicalscience, 12:868 pii:can-12-868.

The gut microbiota exists in a dynamic balance between symbiosis and pathogenesis and can influence almost any aspect of host physiology. Growing evidence suggests that the gut microbiota not only plays a key role in carcinogenesis but also influences the efficacy and toxicity of anticancer therapy. The microbiota modulates the host response to chemotherapy via numerous mechanisms, including immunomodulation, xenometabolism and alteration of community structure. Furthermore, exploitation of the microbiota offers opportunities for the personalisation of chemotherapeutic regimens and the development of novel therapies. In this article, we explore the host-chemotherapeutic microbiota axis, from basic science to clinical research, and describe how it may change the face of cancer treatment.

RevDate: 2018-09-27

Hinzke T, Kleiner M, S Markert (2018)

Centrifugation-Based Enrichment of Bacterial Cell Populations for Metaproteomic Studies on Bacteria-Invertebrate Symbioses.

Methods in molecular biology (Clifton, N.J.), 1841:319-334.

Owing to high sample complexity, metaproteomic investigations on bacteria-animal symbioses with two or more uncultured partners can be challenging. A selective isolation or enrichment of distinct (sub-)populations within those consortia can solve this problem. Subsequent discrete proteomic analyses benefit from increased sample purity and higher proteome coverage for each of the individual organisms. Here, we describe centrifugation-based methods that allow for a separation of the host and its bacterial symbiont population(s), or even for an enrichment of distinct symbiotic cell cycle stages in the deep-sea mussels Bathymodiolus azoricus and B. thermophilus, the gutless oligochaete Olavius algarvensis and the deep-sea tube worm Riftia pachyptila, respectively.

RevDate: 2018-10-02

Lorite MJ, Estrella MJ, Escaray FJ, et al (2018)

The Rhizobia-Lotus Symbioses: Deeply Specific and Widely Diverse.

Frontiers in microbiology, 9:2055.

The symbiosis between Lotus and rhizobia has been long considered very specific and only two bacterial species were recognized as the microsymbionts of Lotus: Mesorhizobium loti was considered the typical rhizobia for the L. corniculatus complex, whereas Bradyrhizobium sp. (Lotus) was the symbiont for L. uliginosus and related species. As discussed in this review, this situation has dramatically changed during the last 15 years, with the characterization of nodule bacteria from worldwide geographical locations and from previously unexplored Lotus spp. Current data support that the Lotus rhizobia are dispersed amongst nearly 20 species in five genera (Mesorhizobium, Bradyrhizobium, Rhizobium, Ensifer, and Aminobacter). As a consequence, M. loti could be regarded an infrequent symbiont of Lotus, and several plant-bacteria compatibility groups can be envisaged. Despite the great progress achieved with the model L. japonicus in understanding the establishment and functionality of the symbiosis, the genetic and biochemical bases governing the stringent host-bacteria compatibility pairships within the genus Lotus await to be uncovered. Several Lotus spp. are grown for forage, and inoculation with rhizobia is a common practice in various countries. However, the great diversity of the Lotus rhizobia is likely squandered, as only few bacterial strains are used as inoculants for Lotus pastures in very different geographical locations, with a great variety of edaphic and climatic conditions. The agroecological potential of the genus Lotus can not be fully harnessed without acknowledging the great diversity of rhizobia-Lotus interactions, along with a better understanding of the specific plant and bacterial requirements for optimal symbiotic nitrogen fixation under increasingly constrained environmental conditions.

RevDate: 2018-10-01

Meng F, Seredych M, Chen C, et al (2018)

MXene Sorbents for Removal of Urea from Dialysate: A Step toward the Wearable Artificial Kidney.

ACS nano [Epub ahead of print].

The wearable artificial kidney can deliver continuous ambulatory dialysis for more than 3 million patients with end-stage renal disease. However, the efficient removal of urea is a key challenge in miniaturizing the device and making it light and small enough for practical use. Here, we show that two-dimensional titanium carbide (MXene) with the composition of Ti3C2T x, where T x represents surface termination groups such as -OH, -O-, and -F, can adsorb urea, reaching 99% removal efficiency from aqueous solution and 94% from dialysate at the initial urea concentration of 30 mg/dL, with the maximum urea adsorption capacity of 10.4 mg/g at room temperature. When tested at 37 °C, we achieved a 2-fold increase in urea removal efficiency from dialysate, with the maximum urea adsorption capacity of 21.7 mg/g. Ti3C2T x showed good hemocompatibility; it did not induce cell apoptosis or reduce the metabolizing cell fraction, indicating no impact on cell viability at concentrations of up to 200 μg/mL. The biocompatibility of Ti3C2T x and its selectivity for urea adsorption from dialysate open a new opportunity in designing a miniaturized dialysate regeneration system for a wearable artificial kidney.

RevDate: 2018-09-26

Hage-Ahmed K, Rosner K, S Steinkellner (2018)

Arbuscular mycorrhizal fungi and their response to pesticides.

Pest management science [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of plant species and can provide multiple benefits to the host plant. In agro-ecosystems, the abundance and community structure of AMF are affected by agricultural management practices. This review describes and discusses the current knowledge on the effects of inorganic and organic chemical pesticides on AMF in the conflicting area between agricultural use and environmental concerns. Variable effects have been reported following chemical pesticide use, ranging from neutral to positive and negative. Moreover, a species-specific reaction has been documented. The reported effects of pesticides on arbuscular mycorrhizal symbiosis are very diverse, and even when the same substance is investigated, the results are often contradictory. These effects depend on many parameters, such as the active substance, the mode of action, the mode of application and the dosage. In the field, determinants such as the physico-chemical behavior of the active substances, the soil type and other soil microorganisms contribute to the fate of pesticides and thus the amount of active substances to which AMF are exposed. This review highlights that the fate of AMF following pesticide use needs to be addressed in a broader agro-ecosystem context. This article is protected by copyright. All rights reserved.

RevDate: 2018-09-26

Cornejo-Castillo FM, Del Carmen Muñoz-Marin M, Turk-Kubo KA, et al (2018)

UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa.

Environmental microbiology [Epub ahead of print].

The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2)-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts. This article is protected by copyright. All rights reserved.

RevDate: 2018-10-02

Ankrah NYD, Chouaia B, AE Douglas (2018)

The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes.

mBio, 9(5): pii:mBio.01433-18.

Various intracellular bacterial symbionts that provide their host with essential nutrients have much-reduced genomes, attributed largely to genomic decay and relaxed selection. To obtain quantitative estimates of the metabolic function of these bacteria, we reconstructed genome- and transcriptome-informed metabolic models of three xylem-feeding insects that bear two bacterial symbionts with complementary metabolic functions: a primary symbiont, Sulcia, that has codiversified with the insects, and a coprimary symbiont of distinct taxonomic origin and with different degrees of genome reduction in each insect species (Hodgkinia in a cicada, Baumannia in a sharpshooter, and Sodalis in a spittlebug). Our simulations reveal extensive bidirectional flux of multiple metabolites between each symbiont and the host, but near-complete metabolic segregation (i.e., near absence of metabolic cross-feeding) between the two symbionts, a likely mode of host control over symbiont metabolism. Genome reduction of the symbionts is associated with an increased number of host metabolic inputs to the symbiont and also reduced metabolic cost to the host. In particular, Sulcia and Hodgkinia with genomes of ≤0.3 Mb are calculated to recycle ∼30 to 80% of host-derived nitrogen to essential amino acids returned to the host, while Baumannia and Sodalis with genomes of ≥0.6 Mb recycle 10 to 15% of host nitrogen. We hypothesize that genome reduction of symbionts may be driven by selection for increased host control and reduced host costs, as well as by the stochastic process of genomic decay and relaxed selection.IMPORTANCE Current understanding of many animal-microbial symbioses involving unculturable bacterial symbionts with much-reduced genomes derives almost entirely from nonquantitative inferences from genome data. To overcome this limitation, we reconstructed multipartner metabolic models that quantify both the metabolic fluxes within and between three xylem-feeding insects and their bacterial symbionts. This revealed near-complete metabolic segregation between cooccurring bacterial symbionts, despite extensive metabolite exchange between each symbiont and the host, suggestive of strict host controls over the metabolism of its symbionts. We extended the model analysis to investigate metabolic costs. The positive relationship between symbiont genome size and the metabolic cost incurred by the host points to fitness benefits to the host of bearing symbionts with small genomes. The multicompartment metabolic models developed here can be applied to other symbioses that are not readily tractable to experimental approaches.

RevDate: 2018-10-15

Varga S, CD Soulsbury (2018)

Arbuscular mycorrhizal fungi change host plant DNA methylation systemically.

Plant biology (Stuttgart, Germany) [Epub ahead of print].

DNA methylation is an important epigenetic mechanism regulating gene expression in plants. DNA methylation has been shown to vary among species and also among plant tissues. However, no study has evaluated whether arbuscular mycorrhizal (AM) fungi affect DNA methylation levels in a tissue-specific manner. We investigated whether symbiosis with AM fungi affects DNA methylation in the host, focusing on different plant tissues (roots versus leaves) and across time. We carried out a 6-month pot experiment using Geranium robertianum in symbiosis with the AM fungus Funneliformis mosseae. Our results show that the pattern of total DNA methylation differed between leaves and roots and was related to when plants were harvested, confirming that DNA methylation is a process that occurs dynamically throughout an organism's lifetime. More importantly, the presence of AM fungus in roots of our experimental plants had a positive effect on total DNA methylation in both tissues. This study shows that colonisation by AM fungi can affect DNA methylation levels in their hosts and that plant DNA methylation varies in an age- and tissue-specific manner.

RevDate: 2018-09-25

Berrabah F, Ratet P, B Gourion (2018)

Legume nodule: massive infection in the absence of defense induction.

Molecular plant-microbe interactions : MPMI [Epub ahead of print].

Plants of the legume family host massive intracellular bacterial populations in the tissues of specialized organs: the nodules. In these organs, the bacteria, named rhizobia, can fix atmospheric nitrogen and transfer it to the plant. This special metabolic skill provides to the legumes an advantage when they grow on nitrogen scarce substrates. While packed with rhizobia, the nodule cells remain alive, metabolically active and do not develop defense reactions. Here we review our knowledge on the control of plant immunity during the rhizobia-legume symbiosis. We present the results of an evolutionary process that selected both divergence of microbial associated molecular motifs and active suppressors of immunity on the rhizobial side and, on the legume side, active mechanisms that contribute to suppression of immunity.

RevDate: 2018-09-25

Li M, Wang R, Tian H, et al (2018)

Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis.

Mycorrhiza pii:10.1007/s00572-018-0868-2 [Epub ahead of print].

The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AM fungi, and 108 genes were only expressed in non-mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AM colonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AM fungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for understanding the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.

RevDate: 2018-09-28

Linden CV, C Corbet (2018)

Killing two birds with one stone: Blocking the mitochondrial pyruvate carrier to inhibit lactate uptake by cancer cells and radiosensitize tumors.

Molecular & cellular oncology, 5(4):e1465016 pii:1465016.

Lactate-based metabolic symbiosis between glycolytic and oxidative cancer cells is known to facilitate tumor growth. We have recently demonstrated that 7ACC2 blocks extracellular lactate uptake via the inhibition of mitochondrial pyruvate carrier. 7ACC2 also prevents compensatory glucose oxidation, induces tumor reoxygenation and potentiates radiotherapy, making it a promising anticancer drug.

RevDate: 2018-09-28

Wang X, Luo Y, Liu D, et al (2018)

Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123.

Standards in genomic sciences, 13:18 pii:321.

Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province, China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete genome sequence information and genome annotation. The 7,374,589 bp long genome which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one chromosome and four plasmids. Moreover, a chromosome with no gaps was assembled.

RevDate: 2018-10-17

Duc NH, Csintalan Z, K Posta (2018)

Arbuscular mycorrhizal fungi mitigate negative effects of combined drought and heat stress on tomato plants.

Plant physiology and biochemistry : PPB, 132:297-307 pii:S0981-9428(18)30410-8 [Epub ahead of print].

Arbuscular mycorrhizal (AM) symbiosis can alleviate drought and temperature stresses in plants, but it is unknown whether the benefits can be maintained when the plants are exposed to combined drought and heat stress. In this study, the impacts of AM fungi, Septoglomus deserticola and Septoglomus constrictum on tomato plant tolerance to combined drought and heat stress were investigated. No substantial differences in physiological parameters were found in all plants under non-stress conditions, except a higher expression of SlLOXD and SlPIP2.7 in plants + S. constrictum. Under drought, heat and drought + heat stress, both fungal symbionts could moderate oxidative stress by decreasing the lipid peroxidation, hydrogen peroxide level and improving leaf and root antioxidant enzyme activities, however better performance in plants + S. constrictum. Under drought and the combined stress, inoculation with S. constrictum enhanced stomatal conductance, leaf water potential and relative water content, elevated Fv/Fm and biomass production of the hosts as compared to non-inoculated plants whilst these improvements in plants + S. deserticola were not obvious. Under the combined stress inoculation of S. constrictum did not change the expression of SlNCED and SlPIP2.7 in roots as under heat stress. Expression of SlLOXD in root were upregulated in plants + S. contrictum under drought + heat stress as in mycorrhizal roots under drought stress. Altogether, our results indicated that AM inoculation, particularly with S. constrictum had a positive influence on the tomato plant tolerance to drought + heat stress. Further studies are essential to add some light on molecular mechanisms of mycorrhizal plant tolerance to this combined stress.

RevDate: 2018-09-21

Hess J, Skrede I, De Mares MC, et al (2018)

Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita.

Molecular biology and evolution pii:5100885 [Epub ahead of print].

Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.

RevDate: 2018-10-16

Frare R, Ayub N, Alleva K, et al (2018)

The Ammonium Channel NOD26 is the Evolutionary Innovation that Drives the Emergence, Consolidation, and Dissemination of Nitrogen-Fixing Symbiosis in Angiosperms.

Journal of molecular evolution, 86(8):554-565.

Increasing evidence indicates that N-fixing symbiosis has evolved several times in the N-fixing clade of angiosperms and that this evolution is driven by a single evolutionary innovation. However, the genetics of this ancestral predisposition to N-fixing symbiosis remains unclear. A natural candidate for such molecular innovation is the ammonium channel NOD26, the main protein component of the symbiosome membrane, which facilitates the plant uptake of the nitrogen fixed by symbiotic bacteria. Here, in concordance with the emergence of N-fixing symbiosis in angiosperms but not in ancestral plants, phylogenetic analysis showed that NOD26 belongs to an angiosperm-exclusive subgroup of aquaporins. Integrated genomic, phylogenetic, and gene expression analyses supported NOD26 occurrence in the N-fixing clade, the increase in the NOD26 copy number by block and tandem duplications in legumes, and the low-copy number or even the loss of NOD26 in non-legume species of the N-fixing clade, which correlated with the possibility to lose N-fixing symbiosis in legume and non-legume lineages. Metabolic reconstructions showed that retention of NOD26 in N-fixing precursor could represent an adaptive mechanism to bypass energy crisis during anaerobic stress by ammonium detoxification. Finally, we discuss the potential use of NOD26 to transfer N-fixation to non-N-fixing crops as cereals.

RevDate: 2018-09-23

Bilal S, Shahzad R, Khan AL, et al (2018)

Endophytic Microbial Consortia of Phytohormones-Producing Fungus Paecilomyces formosus LHL10 and Bacteria Sphingomonas sp. LK11 to Glycine max L. Regulates Physio-hormonal Changes to Attenuate Aluminum and Zinc Stresses.

Frontiers in plant science, 9:1273.

The compatible microbial consortia containing fungal and bacterial symbionts acting synergistically are applied to improve plant growth and eco-physiological responses in extreme crop growth conditions. However, the interactive effects of phytohormones-producing endophytic fungal and bacterial symbionts plant growth and stress tolerance under heavy metal stress have been least known. In the current study, the phytohormones-producing endophytic Paecilomyces formosus LHL10 and Sphingomonas sp. LK11 revealed potent growth and tolerance during their initial screening against combined Al and Zn (2.5 mM each) stress. This was followed with their co-inoculation in the Al- and Zn-stressed Glycine max L. plants, showing significantly higher plant growth attributes (shoot/root length, fresh/dry weight, and chlorophyll content) than the plants solely inoculated with LHL10 or LK11 and the non-inoculated (control) plants under metal stresses. Interestingly, under metal stress, the consortia exhibited lower metal uptake and inhibited metal transport in roots. Metal-induced oxidative stresses were modulated in co-inoculated plants through reduced hydrogen peroxide, lipid peroxidation, and antioxidant enzymes (catalase and superoxide dismutase) in comparison to the non-inoculated plants. In addition, endophytic co-inoculation enhanced plant macronutrient uptake (P, K, S, and N) and modulated soil enzymatic activities under stress conditions. It significantly downregulated the expression of heavy metal ATPase genes GmHMA13, GmHMA18, GmHMA19, and GmPHA1 and upregulated the expression of an ariadne-like ubiquitin ligase gene GmARI1 under heavy metals stress. Furthermore, the endogenous phytohormonal contents of co-inoculated plants revealed significantly enhanced gibberellins and reduced abscisic acid and jasmonic acid contents, suggesting that this endophytic interaction mitigated the adverse effect of metal stresses in host plants. In conclusion, the co-inoculation of the endophytic fungus LHL10 and bacteria LK11 actively contributed to the tripartite mutualistic symbiosis in G. max under heavy metal stresses; this could be used an excellent strategy for sustainable agriculture in the heavy metal-contaminated fields.

RevDate: 2018-09-23

Chen M, Arato M, Borghi L, et al (2018)

Beneficial Services of Arbuscular Mycorrhizal Fungi - From Ecology to Application.

Frontiers in plant science, 9:1270.

Arbuscular mycorrhiza (AM) is the most common symbiotic association of plants with microbes. AM fungi occur in the majority of natural habitats and they provide a range of important ecological services, in particular by improving plant nutrition, stress resistance and tolerance, soil structure and fertility. AM fungi also interact with most crop plants including cereals, vegetables, and fruit trees, therefore, they receive increasing attention for their potential use in sustainable agriculture. Basic research of the past decade has revealed the existence of a dedicated recognition and signaling pathway that is required for AM. Furthermore, recent evidence provided new insight into the exchange of nutritional benefits between the symbiotic partners. The great potential for application of AM has given rise to a thriving industry for AM-related products for agriculture, horticulture, and landscaping. Here, we discuss new developments in these fields, and we highlight future potential and limits toward the use of AM fungi for plant production.

RevDate: 2018-09-23

Voß S, Betz R, Heidt S, et al (2018)

RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development.

Frontiers in microbiology, 9:2068.

Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant-microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.

RevDate: 2018-09-23

Clerissi C, Brunet S, Vidal-Dupiol J, et al (2018)

Protists Within Corals: The Hidden Diversity.

Frontiers in microbiology, 9:2043.

Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.

RevDate: 2018-09-20

Gtari M, Nouioui I, Sarkar I, et al (2018)

An update on the taxonomy of the genus Frankia Brunchorst, 1886, 174AL.

Antonie van Leeuwenhoek pii:10.1007/s10482-018-1165-y [Epub ahead of print].

Since the recognition of the name Frankia in the Approved Lists of bacterial names (1980), few amendments have been given to the genus description. Successive editions of Bergey's Manual of Systematics of Archaea and Bacteria have broadly conflicting suprageneric treatments of the genus without any advances for subgeneric classification. This review focuses on recent results from taxongenomics and phenoarray approaches to the positioning and the structuring of the genus Frankia. Based on phylogenomic analyses, Frankia should be considered the single member of the family Frankiaceae within the monophyletic order, Frankiales. A polyphasic strategy incorporating genome to genome data and omniLog® phenoarrays, together with classical approaches, has allowed the designation and an amended description of a type strain of the type species Frankia alni, and the recognition of at least 10 novel species covering symbiotic and non symbiotic taxa within the genus. Genome to phenome data will be shortly incorporated in the scheme for proposing novel species including those recalcitrant to isolation in axenic culture.

RevDate: 2018-09-19

Little MS, Ervin SM, Walton WG, et al (2018)

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β-Glucuronidase from the Human Gut Microbiome.

Protein science : a publication of the Protein Society [Epub ahead of print].

β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo- and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs. This article is protected by copyright. All rights reserved.

RevDate: 2018-09-21

Bharudin I, Abdul Rahim SN, Abu Bakar MF, et al (2018)

De novo transcriptome resources of the lichens, Dirinaria sp. UKM-J1 and UKM-K1 collected from Jerantut and Klang, Malaysia.

Data in brief, 19:2416-2419 pii:S2352-3409(18)30793-5.

Lichen is a symbiotic organism that exists as a single composite body consisting of a mycobiont (fungus) and a photobiont (algae or a cyanobacterium). Many lichen species are considered as extremophiles due to their tolerance to radiation, desiccation, temperature and pollution. However, not all lichen species are tolerant to harsh environmental conditions as several species are sensitive for example to nitrogen, sulphur, acidity, heavy metals, halogens (e.g. fluoride) and ozone. Thus, to better understand why some lichens can withstand exposure to pollutants as opposed to those that are susceptible, we focused on the lichen species of Dirinaria known for their wide distribution in the tropics, subtropics and pantropical, and moderate tolerance to air pollution. Their moderate tolerance to air pollution affords them to thrive in good air quality environments as well as polluted air environments. Lichen samples of Dirinaria sp., UKM-J1 and UKM-K1, were respectively collected from two areas with different levels of air quality based on Air Pollutant Index or API (with index pollutant criteria of PM10, carbon monoxide, ozone, nitrogen dioxide and sulfur dioxide) in the outskirt of Jerantut (UKM-J1), a rural area in the middle of Peninsular Malaysia and the township of Klang (UKM-K1), in a busy area of the Klang Valley, Malaysia. API was monitored throughout 2012-2013 whereby the sample collection site in Klang showed markedly higher concentrations of pollutants in all the index pollutant criteria as compared to that of Jerantut. We performed transcriptome sequencing using Illumina RNA-seq technology and de novo assembly of the transcripts from the lichen samples. Raw reads from both libraries were deposited in the NCBI database with the accession number SRP138994.

RevDate: 2018-10-11

White JF, Kingsley KL, Verma SK, et al (2018)

Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes.

Microorganisms, 6(3): pii:microorganisms6030095.

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the 'rhizophagy cycle.' In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells-locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes-effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.

RevDate: 2018-09-23

Jarett JK, Nayfach S, Podar M, et al (2018)

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.

Microbiome, 6(1):161 pii:10.1186/s40168-018-0539-8.

BACKGROUND: Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity.

RESULTS: From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs.

CONCLUSIONS: This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.

RevDate: 2018-10-03

Checcucci A, diCenzo GC, Ghini V, et al (2018)

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.

ACS synthetic biology [Epub ahead of print].

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

RevDate: 2018-10-13

Montero H, Choi J, U Paszkowski (2018)

Arbuscular mycorrhizal phenotyping: the dos and don'ts.

RevDate: 2018-10-15

Cremon C, Barbaro MR, Ventura M, et al (2018)

Pre- and probiotic overview.

Current opinion in pharmacology, 43:87-92 pii:S1471-4892(18)30083-3 [Epub ahead of print].

The dynamic relationship between gut microbiota and its human host is also known as a trophic association that might range from commensalism, where only the microbe enjoys a positive effect from the relationship, to intestinal symbiosis where both host and microbe benefit from their interaction. In the last years, we have started to understand how alterations of the gut microbiota composition leading to the disruption of host-microbial interactions are associated and/or predispose individuals to disease conditions ranging from inflammatory bowel diseases to allergy and functional gastrointestinal disorders, such as irritable bowel syndrome. While we await important insights in this field, the microbiota is already a therapeutic target. Based on the actual definitions, prebiotics are defined as substrates that are selectively utilized by host microorganisms conferring a health benefit, while probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Although their health promoting activities encompasses numerous effects, including immunostimulation, competitive exclusion of pathogens, and gut barrier enhancement, the exact mechanism of action by which these compounds exert their beneficial actions in humans is only partially known. In this review, we highlight the current insights into the clinical applications of prebiotics and probiotics in gastroenterology.

RevDate: 2018-09-15

Porter SS, Faber-Hammond J, Montoya AP, et al (2018)

Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium.

The ISME journal pii:10.1038/s41396-018-0266-y [Epub ahead of print].

Research on mutualism seeks to explain how cooperation can be maintained when uncooperative mutants co-occur with cooperative kin. Gains and losses of the gene modules required for cooperation punctuate symbiont phylogenies and drive lifestyle transitions between cooperative symbionts and uncooperative free-living lineages over evolutionary time. Yet whether uncooperative symbionts commonly evolve from within cooperative symbiont populations or from within distantly related lineages with antagonistic or free-living lifestyles (i.e., third-party mutualism exploiters or parasites), remains controversial. We use genomic data to show that genotypes that differ in the presence or absence of large islands of symbiosis genes are common within a single wild recombining population of Mesorhizobium symbionts isolated from host tissues and are an important source of standing heritable variation in cooperation in this population. In a focal population of Mesorhizobium, uncooperative variants that lack a symbiosis island segregate at 16% frequency in nodules, and genome size and symbiosis gene number are positively correlated with cooperation. This finding contrasts with the genomic architecture of variation in cooperation in other symbiont populations isolated from host tissues in which the islands of genes underlying cooperation are ubiquitous and variation in cooperation is primarily driven by allelic substitution and individual gene gain and loss events. Our study demonstrates that uncooperative mutants within mutualist populations can comprise a significant component of genetic variation in nature, providing biological rationale for models and experiments that seek to explain the maintenance of mutualism in the face of non-cooperators.

RevDate: 2018-09-15

Schwob G, Roy M, Pozzi CA, et al (2018)

In planta sporulation of Frankia as a determinant of alder-symbionts interactions.

Applied and environmental microbiology pii:AEM.01737-18 [Epub ahead of print].

Alnus genus forms symbiosis with the actinobacteria Frankia and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta. Spore-positive (Sp+) strains are predominant on Alnus incana (Ai) and Alnus viridis (Av) in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa (Ag) in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, and the effect of the sporulation genotype on the ECM communities. Trapping experiments were conducted using Ag, Ai and Av plantlets on 6 soils, differing in the alder species and the frequency of Sp+ nodules in the field. Higher diversity of Frankia and variation in Sp+ frequencies were observed in the trapping compared to the fields. Both indigenous and trapping species shape Frankia community structure in trapped nodules. Nodulation impediments were observed on several trapping conditions in Sp+ soils supporting a narrower host-range of Sp+ FrankiaAi and Av were able to associate equally with compatible Sp+ and Sp- in the greenhouse. Additionally, no host shift was observed for Alnus-specific ECM, and the sporulation genotype of Frankia defined the ECM communities on the host roots. The symbiotic association is likely determined by the host-range, the soil history and the type of in planta Frankia These results provide an insight into the biogeographical drivers of alder symbionts in the Holarctic region.Importance Most Frankia-actinorhizal plant symbioses are capable of high rates of nitrogen fixation comparable to those found on legumes. Yet our understanding of the ecology and distribution of Frankia is still very limited. Several studies have focused on the distribution patterns of Frankia, demonstrating a combination of host and pedoclimatic parameters in their biogeography. However, very few have considered the in planta sporulation form of the strain, although it is a unique feature among all symbiotic plant-associated microbes. Compared with Sp- Frankia strains, Sp+ would be obligate symbionts, highly dependent on the presence of a compatible host-species and with lower efficiency in nitrogen fixation. Understanding the biogeographical drivers of Sp+ Frankia strains might help to elucidate the ecological role of in planta sporulation, and the extent to which this trait mediates host-partner interactions in the alder-Frankia-ECM fungi symbiosis.

RevDate: 2018-10-14

Benndorf R, Guo H, Sommerwerk E, et al (2018)

Natural Products from Actinobacteria Associated with Fungus-Growing Termites.

Antibiotics (Basel, Switzerland), 7(3): pii:antibiotics7030083.

The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.

RevDate: 2018-09-14

Tsuji K, T Fukami (2018)

Community-wide consequences of sexual dimorphism: evidence from nectar microbes in dioecious plants.

Ecology [Epub ahead of print].

Intraspecific trait variation is receiving renewed interest as a factor affecting the structure of multi-species communities within and across trophic levels. One pervasive form of intraspecific trait variation is sexual dimorphism in animals and plants, which might exert large effects particularly on the communities of host-associated organisms, but the extent of these effects is not well understood. We investigated whether host-associated microbial communities developed differently in the floral nectar of female and male individuals of the dioecious shrubs, Eurya emarginata and E. japonica. We found that nectar-colonizing microbes such as bacteria and fungi were more than twice as prevalent and, overall, more than 10 times as abundant in male flowers as in female flowers. Microbial species composition also differed between flower sexes. To examine potential mechanisms behind these differences, we manipulated the frequency of flower visitation by animals and the order of arrival of microbial species to nectar. Animal visitation frequency affected microbial communities more greatly in male flowers, while arrival order affected them more in female flowers. These sex-specific effects appeared attributable to differences in how animals and microbes altered the chemical characteristics of nectar that limited microbial growth. Taken together, our results provide evidence that sexual dimorphism can have large effects on the structure of host-associated communities.

RevDate: 2018-09-14

Vasilchenko AS, Gritsenko VA, Kosyan DB, et al (2018)

A Low-Molecular-Weight Compound Derived from Human Leukocytes Determines a Bactericidal Activity of the Interferon Preparation.

Probiotics and antimicrobial proteins pii:10.1007/s12602-018-9463-2 [Epub ahead of print].

The aim of this study was to characterize the structure and mode of action of antimicrobials derived from a commercial preparation of alfa-interferon. By combination of semi-preparative/analytical reversed-phase high-performance liquid chromatography, we isolated and purified a novel active substance based on carbohydrate with a complex of amino acids, which determines antimicrobial property of commercial preparation of interferon. A size-exclusion chromatography was performed and LC/ESI-MS revealed molecular masses of active substance were in the range of 180-249 Da. Edman sequencing identified phenylthiohydantoin (PTH) derivatives which consisted a set of preliminary (Asp, Glu, Gly, and Ala) and minor amino acids (Leu and Thr) at equimolar ratio. Thus, the purified active substance is a compound containing the complex of amino acids connected with carbohydrate background and called leucidin. Leucidin demonstrated antimicrobial activity against the model Escherichia coli (E. coli) K12 strain at a minimal inhibitory concentration of 20 μg mL-1. The revealed antimicrobial mechanism of action is associated with violation of the bacterial cell wall leading to a SOS response and bacterial autolysis. Despite the preliminary nature of the results, obtained data allowed us to discover the previously unknown leukocyte-derived antimicrobial molecules.

RevDate: 2018-09-16

Saramago M, Robledo M, Matos RG, et al (2018)

Sinorhizobium meliloti RNase III: Catalytic Features and Impact on Symbiosis.

Frontiers in genetics, 9:350.

Members of the ribonuclease (RNase) III family of enzymes are metal-dependent double-strand specific endoribonucleases. They are ubiquitously found and eukaryotic RNase III-like enzymes include Dicer and Drosha, involved in RNA processing and RNA interference. In this work, we have addressed the primary characterization of RNase III from the symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti. The S. meliloti rnc gene does encode an RNase III-like protein (SmRNase III), with recognizable catalytic and double-stranded RNA (dsRNA)-binding domains that clusters in a branch with its α-proteobacterial counterparts. Purified SmRNase III dimerizes, is active at neutral to alkaline pH and behaves as a strict metal cofactor-dependent double-strand endoribonuclease, with catalytic features distinguishable from those of the prototypical member of the family, the Escherichia coli ortholog (EcRNase III). SmRNase III prefers Mn2+ rather than Mg2+ as metal cofactor, cleaves the generic structured R1.1 substrate at a site atypical for RNase III cleavage, and requires higher cofactor concentrations and longer dsRNA substrates than EcRNase III for optimal activity. Furthermore, the ultraconserved E125 amino acid was shown to play a major role in the metal-dependent catalysis of SmRNase III. SmRNase III degrades endogenous RNA substrates of diverse biogenesis with different efficiency, and is involved in the maturation of the 23S rRNA. SmRNase III loss-of-function neither compromises viability nor alters morphology of S. meliloti cells, but influences growth, nodulation kinetics, the onset of nitrogen fixation and the overall symbiotic efficiency of this bacterium on the roots of its legume host, alfalfa, which ultimately affects plant growth. Our results support an impact of SmRNase III on nodulation and symbiotic nitrogen fixation in plants.

RevDate: 2018-09-16

Mars Brisbin M, Mesrop LY, Grossmann MM, et al (2018)

Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F).

Frontiers in microbiology, 9:1998.

Photosymbiotic protists contribute to surface primary production in low-nutrient, open-ocean ecosystems and constitute model systems for studying plastid acquisition via endosymbiosis. Little is known, however, about host-symbiont dynamics in these important relationships, and whether these symbioses are mutualistic is debated. In this study, we applied single-cell sequencing methods and advanced fluorescent microscopy to investigate host-symbiont dynamics in clade F acantharians, a major group of photosymbiotic protists in oligotrophic subtropical gyres. We amplified the 18S rRNA gene from single acantharian hosts and environmental samples to assess intra-host symbiont diversity and to determine whether intra-host symbiont community composition directly reflects the available symbiont community in the surrounding environment. Our results demonstrate that clade F acantharians simultaneously host multiple species from the haptophyte genera Phaeocystis and Chrysochromulina. The intra-host symbiont community composition was distinct from the external free-living symbiont community, suggesting that these acantharians maintain symbionts for extended periods of time. After selectively staining digestive organelles, fluorescent confocal microscopy showed that symbionts were not being systematically digested, which is consistent with extended symbiont maintenance within hosts. Extended maintenance within hosts may benefit symbionts through protection from grazing or viral lysis, and therefore could enhance dispersal, provided that symbionts retain reproductive capacity. The evidence for extended symbiont maintenance therefore allows that Phaeocystis could glean some advantage from the symbiosis and leaves the possibility of mutualism.

RevDate: 2018-09-26

Niehs SP, Scherlach K, C Hertweck (2018)

Genomics-driven discovery of a linear lipopeptide promoting host colonization by endofungal bacteria.

Organic & biomolecular chemistry, 16(37):6967-6974.

The rice seedling blight fungus Rhizopus microsporus weakens or kills plants by means of a potent toxin produced by endobacteria (Burkholderia rhizoxinica) that live within the fungal hyphae. The success of the highly attuned microbial interaction is partly based on the bacteria's ability to roam and re-colonize the fungal host. Yet, apart from the toxin, chemical mediators of the symbiosis have remained elusive. By genome mining and comparison we identified a cryptic NRPS gene cluster that is conserved among all sequenced Rhizopus endosymbionts. Metabolic profiling and targeted gene inactivation led to the discovery of a novel linear lipopeptide, holrhizin A, which was fully characterized. Through in vitro and in vivo assays we found that holrhizin acts (A) as a biosurfactant to reduce surface tension, (B) influences the formation of mature biofilms and thus cell motility behavior that ultimately supports the bacterial cells to (C) colonize and invade the fungal host, consequently supporting the re-establishment of the exceptional Burkholderia-Rhizopus symbiosis. We not only unveil structure and function of an linear lipopeptide from endofungal bacteria but also provide a functional link between the symbiont's orphan NRPS genes and a chemical mediator that promotes bacterial invasion into the fungal host.

RevDate: 2018-10-03

Xue L, Klinnawee L, Zhou Y, et al (2018)

AP2 transcription factor CBX1 with a specific function in symbiotic exchange of nutrients in mycorrhizal Lotus japonicus.

Proceedings of the National Academy of Sciences of the United States of America, 115(39):E9239-E9246.

The arbuscular mycorrhizal (AM) symbiosis, a widespread mutualistic association between land plants and fungi, depends on reciprocal exchange of phosphorus driven by proton-coupled phosphate uptake into host plants and carbon supplied to AM fungi by host-dependent sugar and lipid biosynthesis. The molecular mechanisms and cis-regulatory modules underlying the control of phosphate uptake and de novo fatty acid synthesis in AM symbiosis are poorly understood. Here, we show that the AP2 family transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), a WRINKLED1 (WRI1) homolog, directly binds the evolutionary conserved CTTC motif that is enriched in mycorrhiza-regulated genes and activates Lotus japonicus phosphate transporter 4 (LjPT4) in vivo and in vitro. Moreover, the mycorrhiza-inducible gene encoding H+-ATPase (LjHA1), implicated in energizing nutrient uptake at the symbiotic interface across the periarbuscular membrane, is coregulated with LjPT4 by CBX1. Accordingly, CBX1-defective mutants show reduced mycorrhizal colonization. Furthermore, genome-wide-binding profiles, DNA-binding studies, and heterologous expression reveal additional binding of CBX1 to AW box, the consensus DNA-binding motif for WRI1, that is enriched in promoters of glycolysis and fatty acid biosynthesis genes. We show that CBX1 activates expression of lipid metabolic genes including glycerol-3-phosphate acyltransferase RAM2 implicated in acylglycerol biosynthesis. Our finding defines the role of CBX1 as a regulator of host genes involved in phosphate uptake and lipid synthesis through binding to the CTTC/AW molecular module, and supports a model underlying bidirectional exchange of phosphorus and carbon, a fundamental trait in the mutualistic AM symbiosis.

RevDate: 2018-09-11

diCenzo GC, Zamani M, Checcucci A, et al (2018)

Multi-disciplinary approaches for studying rhizobium - legume symbioses.

Canadian journal of microbiology [Epub ahead of print].

The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multi-disciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.

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In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

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In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

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