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Groundwater $$Elusimicrobia$$ are metabolically diverse compared to gut microbiome $$Elusimicrobia$$ and some have a novel nitrogenase paralog

M$'e$heust, R.*; Castelle, C. J.*; Matheus Carnevali, P. B.*; Farag, I. F.*; He, C.*; Chen, L.-X.*; Amano, Yuki  ; Hug, L. A.*; Banfield, J. F.*

We reconstructed 94 draft-quality, non-redundant genomes from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated $$Elusimicrobia$$ are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration of fatty acids, or a variety of organic compounds and Rnf-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated $$Elusimicrobia$$ often encode a new homologous group of nitrogenase-like proteins that co-occur with an extensive suite of radical SAM-based proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria and Myxococcus phyla and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated $$Elusimicrobia$$ clades nest phylogenetically within two groundwater-associated clades. Thus, we propose an evolutionary trajectory in which some $$Elusimicrobia$$ adapted to animal-associated lifestyles from groundwater-associated species via genome reduction.

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