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330 results for “symbiosis”
Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
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Dirt cheap: An experimental test of controls on resource exchange in an ectomycorrhizal symbiosis
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Data from: Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
<p class="western"><span>Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit, and symbiont fitness), we conducted comparative genomic and selection analyses of the full genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka:Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating variation in benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.</span></p>
Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis
Multipartite symbioses are complex symbiotic relationships involving multiple interacting partners. These types of partnerships provide excellent opportunities in which to apply a comparative approach to identify common historical patterns of population differentiation and species-specific life history traits. Using three symbiotic blue stain fungal species (Ophiostomatacea) associated with outbreaking populations of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western Canada, we applied phylogenetic, population genetic, and demographic approaches to clarify phylogeographic patterns among the three fungal species. Broadly, the three species showed significant population differentiation, forming northern and southern populations, despite dramatic differences in haplotype diversity. Finer scale structuring and population demographic patterns were less consistent, showing some interspecific incongruence. By contrasting these species simultaneously, we were able to identify differences in recombination rate and ecological traits that can explain the observed patterns of incongruence among the fungal species. By applying a comparative approach to partners of a multipartite symbiosis we were able to distinguish congruent population structuring and species-specific differences that help us to understand the complexity and evolution of this symbiotic system.
Data from: Breakdown of a defensive symbiosis, but not endogenous defenses, at elevated temperatures
Environmental factors, including temperature, can have large effects on species interactions, including mutualisms and antagonisms. Most insect species are infected with heritable bacterial symbionts with many protecting their hosts from natural enemies. However, many symbionts or their products are thermally sensitive hence their effectiveness may vary across a range of temperatures. In the pea aphid, Acyrthosiphon pisum, the bacterial symbiont Hamiltonella defensa, and its associated APSE bacteriophages confer resistance to this aphid's dominant parasitoid, Aphidius ervi. Here we investigate the effects of temperature on both endogenous and symbiont-based protection against this parasitoid. We also explored the defensive properties of the X-type symbiont, a bacterium hypothesized to shape aphid defense when co-occurring with H. defensa. We show that H. defensa protection fails at higher temperatures, although some aphid genotype and H. defensa strain combinations are more robust than others at moderately warmer temperatures. We also found that a single X-type strain neither defended against parasitism by A. ervi nor rescued lost H. defensa protection at higher temperatures. In contrast, endogenous aphid resistance was effective across temperatures, revealing that these distinct defensive modes are not equally robust to changing environments. Through a survey of field-collected pea aphids we found a negative correlation between H. defensa frequencies and average daily temperatures across North American locales, fitting expectations for reduced symbiont benefits under warm climates. Based on these findings, we propose that rising global temperatures could promote the widespread breakdown of defensive mutualisms, a prospect with implications for both human and ecosystem health.
Contrasting patterns in biomass allocation, root morphology and mycorrhizal symbiosis for phosphorus acquisition among 20 chickpea genotypes with different amounts of rhizosheath carboxylates
<p>1. Adjustments in root biomass allocation, root morphology, carboxylate exudation and mycorrhizal symbiosis are well-known strategies for plants to cope with phosphorus (P) deficiency. Large genotypic variation in these functional traits has been demonstrated within numerous species. Yet, whether these functional traits are coordinated differently among genotypes of a species to enhance P acquisition remains unknown.</p> <p>2. We characterised 11 root functional traits associated with P acquisition in 20 chickpea genotypes with contrasting amounts of rhizosheath carboxylates, grown in a glasshouse with severely limiting insoluble (10 mg kg<sup>–1</sup> FePO<sub>4</sub>), moderately limiting soluble (10 mg kg<sup>–1</sup> KH<sub>2</sub>PO<sub>4</sub>), and adequate (50 mg kg<sup>–1</sup> KH<sub>2</sub>PO<sub>4</sub>) P supply.</p> <p>3. Substantial variation was found among genotypes in root functional traits associated with P acquisition. Genotypes with a large amount of carboxylates (HRC) had thinner roots, and a lower root mass fraction and root mass density, but higher specific root length and colonisation by arbuscular mycorrhizal fungi (AMF) than genotypes with a small amount of rhizosheath carboxylates.</p> <p>4. In response to soil P availability, chickpea genotypes showed large plasticity in root biomass allocation, rhizosheath pH, carboxylate amount, and colonisation by AMF, but a limited response in most root morphological traits (i.e. mean root diameter, root mass density and specific root length). Shoot P content was strongly correlated with different root functional traits in the three P treatments.</p> <p>5. Our findings suggest a range of predictable relationships between root functional traits among chickpea genotypes; those with HRC tended to have relatively thinner roots with lower cost of root construction, while allocating more resources to carboxylate exudation and colonisation by AMF. The shift in the relationships between shoot P content and root functional traits indicates that <span class="fontstyle01"><span>root traits and/or trait combinations in chickpea vary in a manner that enhances P acquisition under specific soil P conditions (i.e. P sources/ levels)</span></span>. Such knowledge provides valuable information for chickpea genotype breeding and our understanding of evolution of traits with improved root/rhizosphere functioning.</p> <p> </p>
SYMBA project Industrial Symbiosis mapping
<p>The dataset includes the infomation collected during the elaboration of the Industrial Symbiosis (IS) mapping carried out in the framework of the SYMBA project (101135562). Concretely, it compiles the data included in the deliverable D3.1 Report on current Industrial Symbiosis solutions in Europe.</p> <p>The updated v3.0 of the dataset includes the prioritisation of IS solutions, resulting from the application of the Multicriteria Decision Analysis (MCDA) methodology developed under the SYMBA project. This prioritisation, detailed in Deliverable D3.3: Evaluation of IS Prioritised Solutions, applies weighted scoring factors across five readiness dimensions: Symbiosis, Environmental, Societal, Organisational, and Legal/Ethical. The weighting factors used for prioritisation are presented in the adjacent table. For more in-depth insight into the evaluation and prioritisation approach, consult Deliverable D3.3.</p>
Data for mycorrhizal C/N ratio determines plant-derived carbon and nitrogen allocation to symbiosis
<p><span><span>Nutrient cycling in temperate forests is driven by carbon allocation of trees to soil via ectomycorrhizas (EM). The sink activities of different fungal taxa for host resources are unknown. Aboveground dual </span><span>labeling of young beech<span> with <sup>15</sup>N and <sup>13</sup>C was used to trace resource transport to ectomycorrhizal root tips. Isotope enrichment in EM correlated with that in the corresponding EM-attached lateral root, supporting that EM drive taxon-specific N- and C-fluxes. The enrichments with <sup>13</sup>C and <sup>15</sup>N in EM increased with decreasing C/N ratio of the symbiotic association. Abundances of EM species were positively correlated with <sup>13</sup>C enrichment, demonstrating higher fitness of stronger than of less C-demanding symbioses. Overall, our results imply that differences among the resource traits of EM species regulate the supply of the symbioses with host-derived C and N.</span></span></span></p> <p><span><span><span>Here we provide the data sets containing information on the identities of fungal species colonizing roots tips of European beech and for N, C, 15N and 13C contents in bark, coarse roots, fine roots, very fine lateral roots, ectomycorrhizal species and rhizosphere soil and for biomass of the different compartments. The data were collected 5 and 20 days after labelling.</span></span></span></p>
Formations of mycorrhizal symbiosis alter the phenolic heteropolymers in roots and leaves of four temperate woody species
<p>The decomposition rates of senesced tissues from plants associated with ectomycorrhizal (EcM) fungi tend to differ from that associated with arbuscular mycorrhizal (AM) fungi. However, the chemical underpinnings that could drive the observed differences in decomposition are less explored.</p> <p>Here, we characterized the content, composition, and spatial organization of phenolic heteropolymers in roots and leaves of four temperate tree species across eight plant-fungus combinations, forming either AM or EcM associations.</p> <p>Colonization by either AM or EcM fungi tended to decrease the abundance of lignin, condensed tannins, and ratios of lignin and nitrogen in roots and/or leaves, which would lead to lower chemical recalcitrance of tissues. The decrease in root lignin abundance by either mycorrhizal type was associated with an expanded cortex, potentially facilitating symbiosis. Additionally, changes in lignin molecular composition by mycorrhizal symbiosis differed between plant phylogenetic lineages irrespective of mycorrhizal type.</p> <p>Our results suggest that the mycorrhiza-associated changes in plant chemical traits that regulate litter decomposition may not be unique to AM or EcM associations; rather, both associations can reduce root and leaf chemical recalcitrance. Further, the differential modification in lignin composition by mycorrhizal symbiosis between plant phylogenetic groups highlights the influence of plant evolutionary history in plant-mycorrhizal interactions.</p>
Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
<p class="Standard">The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: <i>Berndtia</i> and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.</p> <p class="Standard"> </p> <p class="Standard"><i>Key words: </i>adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny</p>
No disruption of rhizobial symbiosis during early stages of cowpea domestication
<p>Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen fixing symbiosis between cowpea and root-nodulating <i>Bradyrhizobium.</i> We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and symbiosis trait variation among wild and early-domesticated cowpea genotypes<i>. </i>Cowpeas experienced modest decreases in genome-wide diversity during early domestication. Nonetheless, domesticated cowpeas responded efficiently to variation in symbiotic effectiveness, by forming more root nodules with nitrogen-fixing rhizobia and sanctioning non-fixing strains. Domesticated populations invested a larger proportion of host tissues into root nodules than wild cowpeas. Unlike soybean and wheat, cowpea showed no compelling evidence for degradation of symbiosis during domestication. Domesticated cowpeas experienced a less severe bottleneck than these crops and the low nutrient conditions in Africa where cowpea landraces were developed likely favored plant genotypes that gain substantial benefits from symbiosis. Breeders have largely neglected symbiosis traits, but artificial selection for improved plant responses to microbiota could increase plant performance and sustainability.</p>
Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi
<p>Ectomycorrhiza (ECM) is a symbiotic relation between plant and fungi that is essential for nutrient uptake of many stand forming trees. There are two conflicting views about the evolution of ECM in fungi suggesting (1) relatively few transitions to ECM followed by reversals to non-ECM, or (2) many independent origins of ECM and no reversals. In this study, we compare these, and other, hypotheses and test the impact of different models on inference. We assembled a dataset of five marker gene sequences (nuc58, nucLSU, nucSSU, rpb1, and rpb2) and 2,174 fungal taxa covering the three subphyla: Agaricomycotina, Mucoromycotina and Pezizomycotina. The fit of different models, including models with variable rates in clades or through time, to the pattern of ECM fungal taxa was tested in a Bayesian framework, and using AIC and simulations. We find that models implementing variable rates are a better fit than models without rate shift, and that the conclusion about the relative rate between ECM and non-ECM depend largely on whether rate shifts are allowed or not. We conclude that standard constant-rate ancestral state reconstruction models are not adequate for the analysis of the evolution of ECM fungi, and may give contradictory results to more extensive analyses. </p>
Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)
<p>For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant <i>Trachymyrmex septentrionalis</i> using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.</p>
Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
<p>The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host <em>Medicago truncatula</em> with a community of 88 <em>Ensifer meliloti</em> strains. Multi-strain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, <em>i.e.</em>, genotype-by-genotype, effects on rhizobia fitness and some annotated rhizobia genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multi-strain contexts.</p>
Data from: Experimental evidence that phosphorus fertilization and arbuscular mycorrhizal symbiosis can reduce the carbon cost of phosphorus uptake
<p>Data from "Experimental evidence that phosphorus fertilization and arbuscular mycorrhizal symbiosis can reduce the carbon cost of phosphorus uptake". Functional Ecology</p>
Shared evolutionary origin and clade-specific signatures of symbiosis in lifestyle distinctive fungi
<p>Data repository established for the appendix dataset documented in Scarlet M. Au’s MPhil in Biological Science (Plant Sciences) thesis, submitted to the University of Cambridge, UK. </p> <p><strong>Appendix A.</strong> List of 182 species from the Mucoromycota subphylum</p> <p><strong>Appendix B.</strong> List of 535 BUSCO single copy genes identified for single copy phylogenies. </p> <p>1) Appendix B-1 contains BUSCO genes mostly annotated relative to the <em>Rhizophagus irregularis </em>DAOM_181602_v1.0. For genes that were missing, annotations were drawn from the Lyc-1 and the <em>Thamnidium elegans</em> genomes. </p> <p>2) Appendix B-2 contains BUSCO genes annotated relative to the <em>Rhizophagus irregularis </em>DAOM_181602_v1.0 genome. </p> <p>3) Appendix B-3 contains BUSCO genes annotated relative to the Lyc-1 genome.</p> <p>4) Appendix B-4 contains BUSCO genes annotated relative to the <em>Thamnidium elegans</em> genome. </p> <p><strong>Appendix C.</strong> Hierarchical clustering by orthogroup absence/presence and abundance. </p> <p>1) Full hierarchical clustering by row (species) and columns (orthogroups) for binary matrix. </p> <p>2) Full hierarchical clustering by row (species) and columns (orthogroups) for normalised matrix. </p> <p>3) Full hierarchical clustering by row (species) only for binary matrix. </p> <p>4) Full hierarchical clustering by row (species only) for normalised matrix.</p> <p><strong>Appendix D. </strong>36 out of 72 orthogroups shared between MFRE and AM fungal genomes contain known functional annotations. </p> <p> </p>
Convergent evolution of NFP-facilitated root nodule symbiosis
<p># NFP</p> <p>Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."</p> <p>## 00_sequences<br>This directory contains NFP/LYR homologs and annotations.</p> <p>## 02_alignments<br>This directory contains NFP alignments</p> <p>## 03_trees<br>This directory contains gene trees and species tree guides for the analyses.</p> <p>## 04_reconciliation<br>This directory contains notung files and figures for the gene tree reconciliation analysis</p> <p>## 05_synteny<br>This directory contains files for the synteny analyses. The base directory contains circos plots and a subdirectory `Synteny.2.2020` containing scripts and summary output as well as the following:<br>### Results_Apr01.zip<br>Summary of synteny results<br>### csvs.zip<br>An archive containing all csvs in the analysis.<br>### fastas.zip<br>synteny analysis - chr 5 v 8.zip<br>### tsvs.zip<br>An archive containing all csvs in the analysis.<br>### blasts.zip<br>An archive containing blast results.<br>### coords.zip<br>An archive containing genome coordinate files.<br>### gffs.zip<br>An archive containing GFF annotations.<br>### gff3s.zip<br>An archive containing GFF annotations.<br>### imgs.zip<br>An archive containing figure files used for preparing the manuscript.<br> <br>## figs<br>This directory contains figure files used for preparing the manuscript.</p> <p>## Scripts_used_CF<br>This directory contains submission and shell scripts used to conduct the analyses.</p>
Figure 3 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 3. Pupae containing the exoskeletons of adults. (a) Female; (b) male.
Fig. 2 in Acropyga and Azteca Ants (Hymenoptera: Formicidae) with Scale Insects (Sternorrhyncha: Coccoidea): 20 Million Years of Intimate Symbiosis
Fig. 2. Acropyga from Saül, French Guiana. An alate gyne carrying a mealybug while in copula.
Data from: Symbiont-specific responses to environmental cues in a threesome lichen symbiosis
<p><span>Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We investigated differential gene expression in photosymbiodemes of the lichen <em>Peltigera</em> <em>britannica</em> at different temperatures representing mild and putatively stressful conditions and compared gene expression of thallus sectors containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts. Firstly, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Secondly, we quantified photobiont-mediated differences in fungal gene expression. High temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data. As expected, the expression of genes involved in photosynthesis was increased in both photobiont types at 15 and 25°C. The green algae exhibited thermal stress responses mainly at 25°C, and the fungus and the cyanobacteria already by 15°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima. Furthermore, photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression.</span></p>
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