Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.; Thomas, Brian C.; Williams, Kenneth H.; Wu, Dongying; Tringe, Susannah G.; Singer, Steven W.; Eisen, Jonathan A.; Banfield, Jillian F.

doi:10.1038/ncomms3120

Title: Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Journal Article · Tue Aug 27 04:00:00 UTC 2013 · Nature Communications

DOI: https://doi.org/10.1038/ncomms3120 · OSTI ID:1407195

Castelle, Cindy J. ^[1]; Hug, Laura A. ^[1]; Wrighton, Kelly C. ^[1]; Thomas, Brian C. ^[1]; Williams, Kenneth H. ^[2]; Wu, Dongying ^[3]; Tringe, Susannah G. ^[4]; Singer, Steven W. ^[2]; Eisen, Jonathan A. ^[5]; Banfield, Jillian F. ^[6]

Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Univ. of California, Davis, CA (United States). UC Davis Genome Center
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Univ. of California, Davis, CA (United States). UC Davis Genome Center. Dept. of Evolution and Ecology. Dept. of Medical Microbiology and Immunology
Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division

Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth’s biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a ‘dark matter’ of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member of a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; SC0004733

OSTI ID:: 1407195

Journal Information:: Nature Communications, Journal Name: Nature Communications Vol. 4; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Viral dark matter and virus–host interactions resolved from publicly available microbial genomes Roux, Simon; Hallam, Steven J.; Woyke, Tanja eLife, Vol. 4 https://doi.org/10.7554/elife.08490	journal	July 2015
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2777	journal	January 2016
Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep Cui, Guojie; Li, Jun; Gao, Zhaoming PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6961	journal	January 2019
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking Sekiguchi, Yuji; Ohashi, Akiko; Parks, Donovan H. PeerJ, Vol. 3 https://doi.org/10.7717/peerj.740	journal	January 2015

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