Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
Abstract
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.
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1407195
- Grant/Contract Number:
- AC02-05CH11231; SC0004733
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 4; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; microbial communities; phylogenomics
Citation Formats
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., and Banfield, Jillian F. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. United States: N. p., 2013.
Web. doi:10.1038/ncomms3120.
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. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. United States. https://doi.org/10.1038/ncomms3120
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., and Banfield, Jillian F. Tue .
"Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment". United States. https://doi.org/10.1038/ncomms3120. https://www.osti.gov/servlets/purl/1407195.
@article{osti_1407195,
title = {Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment},
author = {Castelle, Cindy J. and Hug, Laura A. and Wrighton, Kelly C. and Thomas, Brian C. and Williams, Kenneth H. and Wu, Dongying and Tringe, Susannah G. and Singer, Steven W. and Eisen, Jonathan A. and Banfield, Jillian F.},
abstractNote = {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.},
doi = {10.1038/ncomms3120},
journal = {Nature Communications},
number = ,
volume = 4,
place = {United States},
year = {Tue Aug 27 00:00:00 EDT 2013},
month = {Tue Aug 27 00:00:00 EDT 2013}
}
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