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

Author

Listed:
  • 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
    Lawrence Berkeley National Laboratory)

  • 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)

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.

Suggested Citation

  • 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 , 2016. "Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs," Nature Communications, Nature, vol. 7(1), pages 1-10, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10476
    DOI: 10.1038/ncomms10476
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    Cited by:

    1. Xi Peng & Shang Wang & Miaoxiao Wang & Kai Feng & Qing He & Xingsheng Yang & Weiguo Hou & Fangru Li & Yuxiang Zhao & Baolan Hu & Xiao Zou & Ye Deng, 2024. "Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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