title: Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.
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.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Emiley A
authors.initials: EA
authors.lastname: Eloe-Fadrosh
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: David
authors.initials: D
authors.lastname: Paez-Espino
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Jarett
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Dunfield
authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada 89154, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hedlund
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Dekas
authors.affiliation: Geological Survey of Canada, Calgary, Alberta T2L 2A7, Canada.
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Grasby
authors.affiliation: School of Geography &Earth Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada.
authors.forename: Allyson L
authors.initials: AL
authors.lastname: Brady
authors.affiliation: Department of Geology and Environmental Earth Sciences, Miami University, Oxford, Ohio 45056, USA.
authors.forename: Hailiang
authors.initials: H
authors.lastname: Dong
authors.affiliation: Department of Biological Sciences, University of Alaska-Anchorage, Anchorage, Alaska 99508, USA.
authors.forename: Brandon R
authors.initials: BR
authors.lastname: Briggs
authors.affiliation: School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
authors.forename: Wen-Jun
authors.initials: WJ
authors.lastname: Li
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Goudeau
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Rex
authors.initials: R
authors.lastname: Malmstrom
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Pett-Ridge
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.|Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D045482:Hot Springs / Q000737:chemistry / Q000382:microbiology*; D006358:Hot Temperature; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
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