Groundwater Elusimicrobia Diverse Metabolisms Community

Community ID CommunityMech:000242

Ecological State STABLE

Environment groundwater Elusimicrobia habitat
ENVO:01001004

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	NCBITaxon:641853	PRIMARY_DEGRADER PRIMARY_PRODUCER CROSS_FEEDER	N/A
PMID:32681159 - SUPPORT (IN_VIVO) "Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles"
animal-associated Elusimicrobia	NCBITaxon:641853	CROSS_FEEDER	N/A
PMID:32681159 - SUPPORT (IN_VIVO) "The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Versatile Heterotrophic/Autotrophic Respiration

CROSS_FEEDING

Metabolites: nitrate (CHEBI:17632), nitrite (CHEBI:16301), dioxygen (CHEBI:15379)

Biological Processes:

oxidation-reduction process (GO:0055114)

Evidence

PMID:32681159 - SUPPORT (IN_VIVO)

"reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds"

Rnf-Dependent Acetogenesis from H2 and CO2

CROSS_FEEDING

Metabolites: dihydrogen (CHEBI:18276), carbon dioxide (CHEBI:16526), acetate (CHEBI:30089)

Biological Processes:

carbon fixation (GO:0015977)

Evidence

PMID:32681159 - SUPPORT (IN_VIVO)

"Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates"

Novel Nitrogenase Paralog and Radical SAM Cluster

COMMENSALISM

Evidence

PMID:32681159 - SUPPORT (IN_VIVO)

"a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins"
PMID:32681159 - SUPPORT (IN_VIVO)

"predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor"

External Resources

Name	Repository	Resource ID
Primary publication for the groundwater Elusimicrobia community PubMed record for the Meheust et al. 2020 ISME J paper.	OTHER	PMID:32681159
PMID:32681159 - SUPPORT (IN_VIVO) "Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia"
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
PMID:32681159 - SUPPORT (IN_VIVO) "94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments"