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

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 higherature 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:
 [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [9] ;  [1] ;  [1] ;  [1] ;  [4] ;  [10] ;  [1] ;  [1] ;  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of Calgary, Calgary, AB (Canada)
  3. Univ. of Nevada, Las Vegas, NV (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Geological Survey of Canada, Calgary, AB (Canada)
  6. McMaster Univ., Hamilton, ON (Canada)
  7. Miami Univ. Oxford, OH (United States)
  8. Univ. of Alaska-Anchorage, Anchorage, AK (United States)
  9. Sun Yat-Sen Univ., Guangzhou (China)
  10. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Report Number(s):
LLNL-JRNL-737993
Journal ID: ISSN 2041-1723; ark:/13030/qt0pw5c72r
Grant/Contract Number:
AC02-05CH11231; AC52-07NA27344
Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE National Nuclear Security Administration (NNSA)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; Biodiversity; Metagenomics; 59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1467799
Alternate Identifier(s):
OSTI ID: 1379050

Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen -Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N.. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States: N. p., Web. doi:10.1038/ncomms10476.
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen -Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., & Ivanova, Natalia N.. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States. doi:10.1038/ncomms10476.
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen -Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N.. 2016. "Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs". United States. doi:10.1038/ncomms10476. https://www.osti.gov/servlets/purl/1467799.
@article{osti_1467799,
title = {Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs},
author = {Eloe-Fadrosh, Emiley A. and Paez-Espino, David and Jarett, Jessica and Dunfield, Peter F. and Hedlund, Brian P. and Dekas, Anne E. and Grasby, Stephen E. and Brady, Allyson L. and Dong, Hailiang and Briggs, Brandon R. and Li, Wen -Jun and Goudeau, Danielle and Malmstrom, Rex and Pati, Amrita and Pett-Ridge, Jennifer and Rubin, Edward M. and Woyke, Tanja and Kyrpides, Nikos C. and Ivanova, Natalia N.},
abstractNote = {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 higherature 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.},
doi = {10.1038/ncomms10476},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {1}
}