Physiology and phylogeny of the candidate phylum “Atribacteria” (formerly OP9/JS1) inferred from single-cell genomics and metagenomics

Tuesday, 16 December 2014: 1:55 PM
Jeremy A Dodsworth1,2, Senthil Murugapiran1, Paul C Blainey3, Masaru Nobu4, Christian Rinke5, Patrick Schwientek5, Esther Gies6, Gordon Webster7, Peter Kille7, Andrew Weightman7, Wen-Tso Liu4, Steven Hallam6, George Tsiamis8, Wesley Swingley9, Christian Ross1, Susannah G Tringe5, Patrick SG Chain5,10, Matthew B Scholz5,10, Chien-Chi Lo5,10, Jason Raymond11, Stephen R Quake12, Tanja Woyke5 and Brian P Hedlund1, (1)University of Nevada Las Vegas, Las Vegas, NV, United States, (2)California State University San Bernardino, Department of BIology, San Bernardino, CA, United States, (3)Broad Institute, Cambridge, MA, United States, (4)University of Illinois at Urbana Champaign, Urbana, IL, United States, (5)DOE Joint Genome Institute, Walnut Creek, CA, United States, (6)University of British Columbia, Department of Microbiology and Immunology, Vancouver, BC, Canada, (7)Cardiff University, Cardiff, United Kingdom, (8)University of Patras, Patras, Greece, (9)Northern Illinois University, DeKalb, IL, United States, (10)Los Alamos National Laboratory, Genomic Science Group, Los Alamos, NM, United States, (11)Arizona State University, School of Earth and Space Exploration, Tempe, AZ, United States, (12)Stanford University, Department of Bioengineering, Stanford, CA, United States
Single-cell sequencing and metagenomics have extended the genomics revolution to yet-uncultivated microorganisms and provided insights into the coding potential of this so-called "microbial dark matter", including microbes belonging candidate phyla with no cultivated representatives. As more datasets emerge, comparison of individual genomes from different lineages and habitats can provide insight into the phylogeny, conserved features, and potential metabolic diversity of candidate phyla. The candidate bacterial phylum OP9 was originally found in Obsidian Pool, Yellowstone National Park, and it has since been detected in geothermal springs, petroleum reservoirs, and engineered thermal environments worldwide. JS1, another uncultivated bacterial lineage affiliated with OP9, is often abundant in marine sediments associated with methane hydrates, hydrocarbon seeps, and on continental margins and shelves, and is found in other non-thermal marine and subsurface environments. The phylogenetic relationship between OP9, JS1, and other Bacteria has not been fully resolved, and to date no axenic cultures from these lineages have been reported. Recently, 31 single amplified genomes (SAGs) from six distinct OP9 and JS1 lineages have been obtained using flow cytometric and microfluidic techniques. These SAGs were used to inform metagenome binning techniques that identified OP9/JS1 sequences in several metagenomes, extending genomic coverage in three of the OP9 and JS1 lineages. Phylogenomic analyses of these SAG and metagenome bin datasets suggest that OP9 and JS1 constitute a single, deeply branching phylum, for which the name "Atribacteria" has recently been proposed. Overall, members of the "Atribacteria" are predicted to be heterotrophic anaerobes without the capacity for respiration, with some lineages potentially specializing in secondary fermentation of organic acids. A set of signature "Atribacteria" genes was tentatively identified, including components of a bacterial microcompartments gene cluster that may be involved in carbohydrate catabolism. The "Atribacteria" may play important roles in biomass processing in anaerobic geothermal and subsurface environments.