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

The DOI matches its Crossref record; 72 of the 72 references it cites were found in a registry or an index.

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

Open access
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
Open this paper in CoChat — free accountOpen PDF

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.

Overview

Integrity signals

Registry

Crossref · 10.1016/j.cub.2015.01.014

Cites

72 of 72 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Flagged first, then by citations

Show all 72 references

Cited by

Sorted by citations

Items 501–541 of 541

Related

See all

Metadata

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
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
Licence
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review