title: Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.
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.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA.
authors.forename: Cindy J
authors.initials: CJ
authors.lastname: Castelle
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA.
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Hug
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA; School of Earth Sciences, The Ohio State University, Columbus, OH 43210 USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964 USA.
authors.forename: Kyle R
authors.initials: KR
authors.lastname: Frischkorn
authors.affiliation: Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA 94598 USA.
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Singh
authors.affiliation: Environmental Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA.
authors.forename: Lye Meng
authors.initials: LM
authors.lastname: Markillie
authors.affiliation: Environmental Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Taylor
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720 USA. Electronic address: jbanfield@berkeley.edu.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000693:Anaerobiosis / Q000235:genetics; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D044822:Biodiversity; D057486:Carbon Cycle / Q000235:genetics*; D020745:Genome, Archaeal; D056186:Metagenomics; D008954:Models, Biological; D008957:Models, Genetic; D010802:Phylogeny