A genomic survey of 94 draft-quality, non-redundant Elusimicrobia genomes (30 newly reconstructed) from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 previously lacking reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, oxygen- or nitrate/nitrite-dependent respiration, degradation of a variety of organic compounds, and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis using hydrogen and carbon dioxide. Two groundwater-associated clades often encode a new nitrogenase paralog co-occurring with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. Similar genomic loci occur in Gracilibacteria and Myxococcales genomes and are predicted to reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated clades nest within free-living clades, supporting an evolutionary trajectory from free-living to animal-associated lifestyles via genome reduction.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| groundwater-associated Elusimicrobia — ontology label: Elusimicrobia | NCBITaxon:641853 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
PRIMARY_PRODUCER
CROSS_FEEDER
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N/A |
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| animal-associated Elusimicrobia — ontology label: Elusimicrobia | NCBITaxon:641853 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Comparative Elusimicrobia Genomic Metabolic Repertoires
The 94-genome survey compares habitat-associated groups with different inferred metabolic repertoires. These genomes represent multiple sites and lineages, not a demonstrated coexisting community. Both canonical habitat labels are retained despite sharing a taxon CURIE; the comparison does not establish niche partitioning or a causal sequence among the component findings.
Participating Taxa: groundwater-associated Elusimicrobia, animal-associated Elusimicrobia
Evidence
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PMID:32681159 - SUPPORT (COMPUTATIONAL)"Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia"
Predicted Lineage-Specific Respiratory Capacities
Selected groundwater-associated lineages encode respiratory machinery consistent with oxygen or nitrogen-oxide use. Capacities differ by lineage; they are not a universal complete respiratory or denitrification route and are not demonstrated cross-feeding. These are source-only genomic predictions, not measured growth or electron flux.
Source Taxon: groundwater-associated Elusimicrobia
Metabolites: nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech), nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech), dioxygen (CHEBI:15379 · MediaIngredientMech · CMMMech)
Evidence
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PMID:32681159 - PARTIAL (COMPUTATIONAL)"reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds"
Predicted Rnf-Associated Acetogenesis from H2 and CO2
Genomic features in lineages VII, VIII and IX support predicted hydrogen/carbon-dioxide acetogenesis involving Wood-Ljungdahl and Rnf components. The study does not demonstrate acetogenic flux, obligatory Rnf dependence or transfer of acetate to a partner. The Rnf name is not evidence of nitrogen fixation.
Source Taxon: groundwater-associated Elusimicrobia
Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), acetate (CHEBI:30089 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
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PMID:32681159 - PARTIAL (COMPUTATIONAL)"Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates"
Nitrogenase-Paralog Loci with Predicted Tetrapyrrole Function
Genomic neighborhoods contain divergent nitrogenase-paralog genes, often near radical-SAM genes. Their proposed tetrapyrrole-related function remains unresolved. These loci do not demonstrate nitrogen fixation, a chemically identified cofactor, metabolite donation or commensalism.
Source Taxon: groundwater-associated Elusimicrobia
Biological Processes:
- tetrapyrrole metabolic process (GO:0033013 · PathwayMech)
Evidence
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PMID:32681159 - SUPPORT (COMPUTATIONAL)"a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins"
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PMID:32681159 - PARTIAL (COMPUTATIONAL)"predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which predicted capacities operate in these organisms and their actual communities?
Genome annotation and pathway-completeness thresholds are not cultivation, catalytic activity or exchange measurements. Determine strain-level pathway activity, partner identities and co-occurrence before assigning ecological interaction mechanisms. Establish the paralog product experimentally before equating it with nitrogen fixation or a specific cofactor. Preserve the two distinct habitat labels sharing one CURIE; groundwater predictions must not silently propagate to animal-associated organisms. The three former arrows were overview inclusion links, not causal evidence. Non-graph functional roles and evidence classifications are preserved outside this graph review, not certified.
Attaches to: ecological_interactions#Comparative Elusimicrobia Genomic Metabolic Repertoires, ecological_interactions#Predicted Lineage-Specific Respiratory Capacities, ecological_interactions#Predicted Rnf-Associated Acetogenesis from H2 and CO2, ecological_interactions#Nitrogenase-Paralog Loci with Predicted Tetrapyrrole Function
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the groundwater Elusimicrobia community
PubMed record for the Meheust et al. 2020 ISME J paper. |
OTHER | PMID:32681159 |
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DOI landing page
DOI link to the ISME J paper. |
OTHER | doi:10.1038/s41396-020-0716-1 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Habitat diversity | animal-associated, sediments, soils, groundwater | N/A |
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Cross-Mech Suite Links
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