title: Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.
abstract: The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Champaign-Urbana, Illinois, IL, USA.
authors.forename: Masaru K
authors.initials: MK
authors.lastname: Nobu
authors.affiliation: School of Life Science, University of Nevada, Las Vegas, NV, USA.|Department of Biology, California State University, San Bernardino, CA, USA.
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Dodsworth
authors.affiliation: School of Life Science, University of Nevada, Las Vegas, NV, USA.
authors.forename: Senthil K
authors.identifier: http://orcid.org/0000-0002-6952-4713
authors.initials: SK
authors.lastname: Murugapiran
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.|Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: Department of Microbiology and Immunology and Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Esther A
authors.initials: EA
authors.lastname: Gies
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK.
authors.forename: Gordon
authors.initials: G
authors.lastname: Webster
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Kille
authors.affiliation: School of Earth and Ocean Sciences, Cardiff University, Cardiff, Wales, UK.
authors.forename: R John
authors.initials: RJ
authors.lastname: Parkes
authors.affiliation: School of Earth and Ocean Sciences, Cardiff University, Cardiff, Wales, UK.
authors.forename: Henrik
authors.initials: H
authors.lastname: Sass
authors.affiliation: Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.
authors.forename: Bo B
authors.initials: BB
authors.lastname: Jørgensen
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Weightman
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Champaign-Urbana, Illinois, IL, USA.
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
authors.affiliation: Department of Microbiology and Immunology and Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.affiliation: Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece.
authors.forename: George
authors.initials: G
authors.lastname: Tsiamis
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: School of Life Science, University of Nevada, Las Vegas, NV, USA.|Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hedlund
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology; D060106:Lakes / Q000382:microbiology; D008969:Molecular Sequence Data; D010802:Phylogeny