Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

Emiley A. Eloe-Fadrosh, David Paez-Espino, Jessica Jarett, Peter F. Dunfield, Brian P. Hedlund, Anne E. Dekas, Stephen E. Grasby, Allyson L. Brady, Hailiang Dong, Brandon R. Briggs, Wen-Jun Li, Danielle Goudeau, Rex Malmstrom, Amrita Pati, Jennifer Pett-Ridge, Edward M. Rubin, Tanja Woyke, Nikos C. Kyrpides and Natalia N. Ivanova ()
Additional contact information
Emiley A. Eloe-Fadrosh: Department of Energy Joint Genome Institute
David Paez-Espino: Department of Energy Joint Genome Institute
Jessica Jarett: Department of Energy Joint Genome Institute
Peter F. Dunfield: University of Calgary
Brian P. Hedlund: School of Life Sciences, University of Nevada, Las Vegas
Anne E. Dekas: Lawrence Livermore National Laboratory
Stephen E. Grasby: Geological Survey of Canada
Allyson L. Brady: School of Geography & Earth Sciences, McMaster University
Hailiang Dong: Miami University
Brandon R. Briggs: University of Alaska-Anchorage
Wen-Jun Li: School of Life Sciences, Sun Yat-Sen University
Danielle Goudeau: Department of Energy Joint Genome Institute
Rex Malmstrom: Department of Energy Joint Genome Institute
Amrita Pati: Department of Energy Joint Genome Institute
Jennifer Pett-Ridge: Lawrence Livermore National Laboratory
Edward M. Rubin: Department of Energy Joint Genome Institute
Tanja Woyke: Department of Energy Joint Genome Institute
Nikos C. Kyrpides: Department of Energy Joint Genome Institute
Natalia N. Ivanova: Department of Energy Joint Genome Institute

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: Abstract Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

Date: 2016
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DOI: 10.1038/ncomms10476

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