Cited by 541Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesMethane Hydrates and Related Phenomena

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

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Castelle, Cindy J., Wrighton, Kelly C., Thomas, Brian C., Hug, Laura A., Brown, Christopher T., Wilkins, Michael J., Frischkorn, Kyle R., Tringe, Susannah G., Singh, Andrea, Markillie, Lye Meng, Taylor, Ronald C., Williams, Kenneth H., Banfield, Jillian F.·2015·Current Biology

DOI 10.1016/j.cub.2015.01.014

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Abstract

Background Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown. Results We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles. Conclusions The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.

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Authors: Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C., Williams, K. H., & Banfield, J. F.
Affiliations: University of California, Berkeley (US)
The Ohio State University (US)
Lamont-Doherty Earth Observatory (US)
Joint Genome Institute (US)
Pacific Northwest National Laboratory (US)
Lawrence Berkeley National Laboratory (US)
Corresponding author: Banfield, Jillian F.
ORCID: Castelle, Cindy J.
Wrighton, Kelly C.
Thomas, Brian C.
Hug, Laura A.
Brown, Christopher T.
Wilkins, Michael J.
Frischkorn, Kyle R.
Tringe, Susannah G.
Markillie, Lye Meng
Taylor, Ronald C.
Williams, Kenneth H.
Banfield, Jillian F.
Venue: Current Biology
Publisher: Elsevier BV
Published: 2015-03
Volume: 25
Issue: 6
Pages: 690-701
ISSN: 0960-9822 (ISSN-L)
DOI: 10.1016/j.cub.2015.01.014
OpenAlex: W2117349822
Cited by: 536
References: 72
Citations by year: 2026: 19 · 2025: 22 · 2024: 29 · 2023: 38 · 2022: 52 · 2021: 59 · 2020: 64 · 2019: 54 · 2018: 65 · 2017: 60 · 2016: 57 · 2015: 14
FWCI: 59.19
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 381 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Current Biology (publishedVersion)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders: US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (DE-AC02-05CH11231, DE-SC0004918)
US DOE Joint Genome Institute, a DOE Office of Science User Facility (DE-AC02-05CH11231)
DOE Office of Biological and Environmental Research
US DOE (DE-AC06-76RLO 1830)
Natural Sciences and Engineering Research Council of Canada postdoctoral fellowship
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Environmental Chemistry › Methane Hydrates and Related Phenomena
Keywords: genome-resolved metagenomics, fermentation, aquifer sediments, archaeal diversity
MeSH terms: Anaerobiosis, Archaea, Models, Biological, Models, Genetic, Phylogeny, Genome, Archaeal, Biodiversity, Metagenomics, Carbon Cycle

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

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