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38 results for “Symbioses”
Fig. 2 in Living Together in the Plankton: A Survey of Marine Protist Symbioses
Fig. 2. Transmission electron microscopic ultrathin section images of symbionts in some open ocean protists. a – free-living open ocean amoeba with two kinds of intracytoplasmic bacteroids (arrows): round to oval within double membranes, and curved dense rod within a single-membrane vacuole; b – dinoflagellate symbionts as found in planktonic foraminiferans and radiolarians; c – putative prymnesiid symbiont from a radiolarian; d – prasinomonad symbiont from a large spongiose skeletal radiolarian. Figs. b–d: N – nucleus, V – vacuole, arrows – light absorbing plastids (adapted from Anderson 1983). All scale bars: 2 µm.
Fig. 1 in Living Together in the Plankton: A Survey of Marine Protist Symbioses
Fig. 1. Light microscopic images of living symbiont-bearing open ocean protists. a – radiolarian showing the central capsule (Cp) containing the nucleus and surrounding cytoplasm, and external to it, long-tapered, radiating pseudopodia known as axopodia (Ax) appearing as a bright halo, including numerous golden-hued algal symbionts on the axopodia (arrows). Scale bar: 500 µm; b – planktonic foraminiferan bearing a calcitic shell (Sh) and peripherally radiating calcite spines that are covered by pseudopodial cytoplasm bearing scattered algal symbionts (arrows). The small greenish, rounded shell chamber contains dense clusters of symbionts within the intrashell cytoplasm. Scale bar: 100 µm; c – composite image of a portion of a colonial radiolarian with numerous central capsules containing dinoflagellate symbionts (arrows) in the peripheral cytoplasm of the central capsules. The entire colony is enclosed within a optically clear spherical gelatinous sheath. This portion of the colony is illuminated from the lower right-hand side. Scale bar: 500 µm; d – the dinoflagellate Noctiluca scintillans (green form) with numerous living prasinomonad algal symbionts (Pedimonas noctilucae), appearing as clumps of green particles, scattered throughout the cytoplasm. Scale bar: 200 µm.
Supplementary data files for Manzano-Marín et. al. 2022 "Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages"
<p>The data set consists of four parts:</p> <p>1) "FISH_data":TIF-formatted files or unmerged and merged fluorescent channels of FISH microscopies of <em>Anoecia corni</em> and <em>Sipha maydis</em> embryos.</p> <p>2) "genome_data": GenBank- and FASTA-formatted files of genome assemblies and annotations for <em>Buchnera</em> and co-obligate symbionts.</p> <p>3) "pathway_data": Presence/absence tables of genes/pseudogenes coding for enzymes involved in the biosynthesis of essential amino acids and B vitamins in ODS spreadsheets and tab-separated value formats. Also, list of genes and pseudogenes of <em>Buchnera</em> genomes.</p> <p>4) "phylogeny_data": FASTA-formatted nucleotide alignment files, NEXUS-formatted files used for Bayesian phylogenetic reconstruction, and resulting trees. For <em>Buchnera</em>, manually-curated orthologous groups of proteins are also included as flat text files. In addition, the files to infer gene losses by maximum parsimony in Count are included in the "Buchnera_count" folder.</p>
Appendices B to E for the Thesis: Investigating the Evolution and Ecology of Obscure Bacterial Symbioses found in Invertebrates, Ciliates and Algae
<p><strong>Appendix B1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find supporting data for Chapter 2.</strong></p> <p><strong>Yellow tabs contain:</strong></p> <ul> <li>accessions and species information for all whole genomes used</li> <li>brief details on hosts and environment for new genomes described in this study</li> <li>metadata such as N50s and genome lengths for all new genomes</li> <li>completeness scores and assembly levels for all genomes</li> <li>information on where all the published genomes were used in this study</li> <li>taxonomy calculations from GTDBtk</li> </ul> <p><strong>Red tabs contain:</strong></p> <ul> <li>Phi scores from reticulate analysis for all core genome clusters extracted from the pangenome aswell as their associated COG and KEGG functions</li> <li>Functional enrichment tables exploring the association of different metabolic functions with different groups of bacteria</li> </ul> <p>----------------------------------------------------------------------------------------------------</p> <p><strong>Appendix C1 contains all metadata for genomes assembled and genomes used, including accession numbers and CheckM scores. You will also find raw data used to produce the figures in Chapter 3.</strong></p> <p><strong>Yellow tabs contain: </strong></p> <p>S1 - Meta data tables for draft genomes examined in this study </p> <p>S2 - Accessions for additional genomes used</p> <p><strong>Red tabs contain: </strong></p> <p>S3 - AAI % similarity across Ca. Megaira used in figure 3a</p> <p>S4 - ANIb % Similarity across Ca. Megaira used in figure 3b</p> <p>S5 - KEGG ko hits </p> <p>S6 - KEGG module completeness used in figure 5 and 6 </p> <p>S7 - 16S rRNA accessions used in phylogeny Figure 2</p> <p>S8 - Gene cluster presence absence matrix used in figure 3.4 and Appendix figure 1 </p> <p>S9 - GTDBtk results for SRA and GenBank Environmental MAGs </p> <p>S10 - top 10 blastp results for RiPP, NRPS and CDPS regions identified by antiSMASH</p> <p>----------------------------------------------------------------------------------------------------</p> <p><strong>Appendix D1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find raw data used to produce the figures in Chapter 4.</strong></p> <p><strong>Yellow tabs contain:</strong></p> <p>S1 - Metadata for genomes assembled in this study</p> <p>S2 - Metadata for environmental MAGs recovered from NCBI non redundant sequence database</p> <p>S3 - Metadata for additional Chlamydiota genomes used</p> <p><strong>Red tabs contain:</strong></p> <p>S4 - AAI percentage similarity scores used to produce genera similarity networks</p> <p>S5 - ANIb percentage similarity scores used to produce species similarity networks</p> <p>S6 - CRISPRcas finder results</p> <p>S7 - KEGG pathway hits</p> <p>S8 - KEGG pathway completeness</p> <p>S9 - Gene cluster presence absence matrix used in figure 4.3a for Rhabdochlamydiaceae</p> <p>S10 - Gene cluster presence absence matrix used in figure 4.3b for Simkaniaceae</p> <p>----------------------------------------------------------------------------------------------------</p> <p><strong>Appendix E1 contains screening results, environmental data extracted from climate databases and additional genome information.</strong></p> <p><strong>Yellow tabs contain:</strong></p> <p>S1 - 'Ca. Tisiphia' in Anopheles plumbeus across Germany. PCR screening and geographic data</p> <p>S2 - additional genome accessions and metadata</p> <p><strong>Red tabs contain:</strong></p> <p>S3 - KEGG completeness</p> <p>S4 - KEGG ko_hits presence</p> <p> </p>
Data from: Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera
How species interactions shape global biodiversity and influence diversification is a central – but also data-hungry – question in evolutionary ecology. Microbially-based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen. These symbioses are ecologically-important interactions, influencing community assembly, diversity, and succession, contributing ~100-290 million tons of N annually to natural ecosystems, and enhancing growth of agronomically-important forage and crop plants worldwide. In recent work attempting to determine whether mutualism with N-fixing bacteria led to increased diversification across legumes, we were unable to definitively resolve the relationship between diversification and nodulation. We did, however, succeed in compiling a very large searchable, analysis-ready database of nodulation data for 749 legume genera (98% of Leguminosae genera; LPWG 2017), which, along with associated phylogenetic information, will provide a valuable resource for future work addressing this question and others. For each legume genus, we provide information about the species richness, frequency of nodulation, subfamily association, and topological correspondence with an additional data set of 100 phylogenetic trees curated for database compatibility. We found 386 legume genera were confirmed nodulators (i.e., all species examined for nodulation nodulated), 116 were non-nodulating, 4 were variable (i.e., containing both confirmed nodulators and confirmed non-nodulators), and 243 had not been examined for nodulation in published studies. Interestingly, data exploration revealed that nodulating legume genera are ~3× more species-rich than non-nodulating genera, but we did not find evidence that this difference in diversity was due to differences in net diversification rate. Our metadata file describes in more detail the structure of these data that provide a foundational resource for future work as more nodulation data become available, and as greater phylogenetic resolution of this ca. 19,500-species family comes into focus.
Data from: Mycorrhizal symbioses influence the trophic structure of the Serengeti
It is known that tropical grasslands such as Serengeti host large populations of arbuscular mycorrhizal (AM) fungi and that they respond to abiotic and biotic factors. It is also known that AM symbioses are important for the uptake of essential plant nutrients, which, in turn, influences the biomass and nutritional quality of herbivores and their predators. The purpose of this study was to investigate the influence of AM symbioses on the biomass of different trophic levels of an ecosystem. To do this, we first measured the neutral lipid fatty acid biomarker 16:1ω5 to estimate the biomass of AM fungi in a long-term grazing exclusion experiment. Then, we used model selection of Bayesian linear regressions to infer the primary factors that influence AM fungal biomass. Using model selection of different combinations of soil characteristics, we selected the best model using the leave-one-out cross-validation information criterion. Finally, we used the Madingley model to simulate the influence of AM fungi on higher trophic levels. We combined spatially explicit information about soil phosphorus and AM fungal biomass to explore the emergent patterns of the Serengeti resulting from AM symbioses. Our Bayesian analysis indicated that total soil phosphorus was the strongest predictor of AM fungal biomass, and there were significant interactions with grazing. Arbuscular mycorrhizal fungal biomass is lowest in soil where phosphorus is limited and increases with increasing phosphorus concentration. Biomass was also significantly higher in plots that were not grazed. The Madingley model indicated that nutritional benefits of AM symbioses maintain a substantial proportion of the biomass across all trophic levels. Synthesis. Our analysis shows that inputs of phosphorus through arbuscular mycorrhizal symbioses substantially increase the ability of plants to grow and maintain nutritional quality, cascading through the biomass of consumers and predators in the ecosystem. Although they account for less than 1% of the total modelled biomass, the predicted nutritional benefit provided by arbuscular mycorrhizal fungi increased the biomass of macro-organisms in the Serengeti by 48%. When considering the management of biodiversity, future ecosystem models should account for the influence of arbuscular mycorrhizal fungi on all trophic levels.
Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years
<p><span>Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus <em>Cephalotes</em>. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that <em>Cephalotes</em> cospeciate with their most abundant adult symbionts. We find, also, that winged queens harbor worker-like microbiomes prior to colony founding, suggesting that vertical inheritance promotes ancient partner fidelity. While some adult-abundant symbionts colonize guts of larvae, microbiomes from this stage are by environmental bacteria from the Enterobacteriales, Lactobacillales, and Actinobacteria. Re-acquisition of such bacteria, each generation, for >40 million years suggests conserved environmental filtering and, hence, a second mechanism behind distinct symbioses divided by metamorphosis.</span></p>
Data for: Tree symbioses sustain nitrogen fixation despite excess nitrogen supply
<p>Symbiotic nitrogen fixation (SNF) is a key ecological process whose impact depends on the strategy of SNF regulation – the degree to which rates of SNF change in response to limitation by N vs. other resources. SNF that is obligate or exhibits incomplete down-regulation can result in excess N fixation, whereas a facultative SNF strategy does not. We hypothesized that tree-based SNF strategies differed by latitude (tropical vs temperate) and symbiotic type (actinorhizal vs rhizobial). Specifically, we expected tropical rhizobial symbioses to display strongly facultative SNF as an explanation for their success in low-latitude forests. In this study, we used <sup>15</sup>N isotope dilution field experiments in New York, Oregon, and Hawaii to determine SNF strategies in six N-fixing tree symbioses. Nitrogen fertilization with +10 and +15 g N m<sup>-2</sup> y<sup>-1</sup> for 4-5 years alleviated N limitation in all taxa, paving the way to determine SNF strategies. Contrary to our hypothesis, all six of the symbioses we studied sustained SNF even at high N. <em>Robinia</em> <em>pseudoacacia</em> (temperate rhizobial) fixed 91% of its N (%N<sub>dfa</sub>) in controls, compared to 64% and 59% in the +10 and +15 g N m<sup>-2</sup> y<sup>-1</sup> treatments. For <em>Alnus</em> <em>rubra</em> (temperate actinorhizal), %N<sub>dfa</sub> was 95%, 70%, and 60%. For the tropical species, %N<sub>dfa</sub> was 86%, 80%, and 82% for <em>Gliricidia</em> <em>sepium</em> (rhizobial); 79%, 69%, and 67% for <em>Casuarina</em> <em>equisetifolia</em> (actinorhizal); 91%, 42%, and 67% for <em>Acacia</em> <em>koa</em> (rhizobial), and 60%, 51%, and 19% for <em>Morella</em> <em>faya</em> (actinorhizal). Fertilization with phosphorus did not stimulate tree growth or SNF. These results suggest that the latitudinal abundance distribution of N-fixing trees is not caused by a shift in SNF strategy. They also help explain the excess N in many forests where N-fixers are common. In addition to influencing community dynamics and rates of nutrient cycling, excess N accumulation and export from sustained SNF may exacerbate water pollution and greenhouse gas fluxes.</p>
Data from: Antibiotics disrupt bacteria-phytoplankton symbioses: Unveiling ecological risks in aquatic ecosystems
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Data from: Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera
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Data from: Mycorrhizal symbioses influence the trophic structure of the Serengeti
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Data from: Discordance Down Under: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids
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Data for: Tree symbioses sustain nitrogen fixation despite excess nitrogen supply
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Even obligate symbioses show signs of ecological contingency: impacts of symbiosis for an invasive stinkbug are mediated by host plant context
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Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years
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Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics.
Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
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Data from: Genetic structure of coral-Symbiodinium symbioses on the world’s warmest reefs
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Data from: Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics
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Tripartite symbioses regulate plant-soil feedback in alder
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