Abstract

The deep terrestrial biosphere harbours a substantial fraction of Earth’s biomass and remains understudied compared with other ecosystems. Deep biosphere life primarily consists of bacteria and archaea, yet knowledge of their co-occurring viruses is poor. Here, we temporally catalogued viral diversity from five deep terrestrial subsurface locations (hydraulically fractured wells), examined virus–host interaction dynamics and experimentally assessed metabolites from cell lysis to better understand viral roles in this ecosystem. We uncovered high viral diversity, rivalling that of peatland soil ecosystems, despite low host diversity. Many viral operational taxonomic units were predicted to infect Halanaerobium, the dominant microorganism in these ecosystems. Examination of clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins (CRISPR–Cas) spacers elucidated lineage-specific virus–host dynamics suggesting active in situ viral predation of Halanaerobium. These dynamics indicate repeated viral encounters and changing viral host range across temporally and geographically distinct shale formations. Laboratory experiments showed that prophage-induced Halanaerobium lysis releases intracellular metabolites that can sustain key fermentative metabolisms, supporting the persistence of microorganisms in this ecosystem. Together, these findings suggest that diverse and active viral populations play critical roles in driving strain-level microbial community development and resource turnover within this deep terrestrial subsurface ecosystem.

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Data availability

Halanaerobium isolate genome and MAGs are publicly available in the JGI Genome Portal database (http://img.jgi.doe.gov/) or in NCBI; see Supplementary Table 1 for accession numbers. All of the metagenomic nucleotide files used in this study are publicly available through JGI or NCBI; accession numbers are listed in Supplementary Data 1.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Acknowledgements

R.A.D., M.A.B, D.M.M, A.E.B, A.J.H, P.J.M., K.C.W. and M.J.W. are partially supported by funding from the National Sciences Foundation Dimensions of Biodiversity (award no. 1342701). R.A.D., M.A.B., D.M.M., A.E.B., K.C.W. and M.J.W. also received support from Dow Microbial Control for this work. Samples from wells M-4 and M-5 were provided by the Marcellus Shale Energy and Environment Laboratory funded by the Department of Energy’s National Energy Technology Laboratory, grant no. DE-FE0024297. Metagenomic sequencing for this research was performed by the Department of Energy’s Joint Genome Institute (JGI) via a large-scale sequencing award to K.C.W (award no. 1931). Metabolite support was provided by Environmental Molecular Sciences Laboratory (EMSL) support via a JGI–EMSL Collaborative Science Initiative awarded to K.C.W (award no. 48483) and an EMSL instrument time award to M.J.W. (award no. 49615). Both JGI and EMSL facilities are sponsored by the Office of Biological and Environmental Research and operated under contract nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). M.B.S. was partially supported by a Gordon and Betty Moore Foundation grant (no. 3790).

Author information

Affiliations

  1. Department of Microbiology, Ohio State University, Columbus, OH, USA

    • Rebecca A. Daly
    • , Anne E. Booker
    • , Richard A. Wolfe
    • , Matthew B. Sullivan
    • , Kelly C. Wrighton
    •  & Michael J. Wilkins
  2. Joint Genome Institute, Walnut Creek, CA, USA

    • Simon Roux
  3. Environmental Sciences Graduate Program, Ohio State University, Columbus, OH, USA

    • Mikayla A. Borton
  4. School of Earth Sciences, Ohio State University, Columbus, OH, USA

    • David M. Morgan
    • , Michael D. Johnston
    •  & Michael J. Wilkins
  5. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA

    • David W. Hoyt
  6. Molecular and Cellular Imaging Center, Ohio State University, Wooster, OH, USA

    • Tea Meulia
  7. Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA

    • Andrea J. Hanson
    • , Paula J. Mouser
    •  & Matthew B. Sullivan
  8. Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, USA

    • Andrea J. Hanson
    •  & Paula J. Mouser
  9. Dow Microbial Control, Collegeville, PA, USA

    • Joseph D. Moore
  10. Dow Microbial Control, Houston, TX, USA

    • Kenneth Wunch

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Contributions

R.A.D., K.C.W. and M.J.W. designed the study. A.J.H. and P.J.M. collected the samples. R.A.D., R.A.W. and M.A.B. performed bioinformatic analyses. D.M.M., A.E.B. and M.D.J. conducted laboratory induction analyses, while D.W.H. performed quantitative metabolite NMR measurements. T.M. conducted electron microscopy on Halanaerobium cultures. J.D.M. and K.W. participated in constructive manuscript discussions that resulted in an improved manuscript. M.J.W., K.C.W., M.B.S., S.R. and R.A.D. integrated the data and drafted the manuscript. All authors reviewed the results and approved the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Michael J. Wilkins.

Supplementary information

  1. Supplementary Information

    Supplementary Tables 1–4, Supplementary Figures 1–5.

  2. Reporting Summary

  3. Supplementary Data 1

    Sequencing information for metagenomes.

  4. Supplementary Data 2

    Viral OTU table.

  5. Supplementary Data 3

    Halanaerobium relative abundance in the Utica-2 well.

  6. Supplementary Data 4

    Prophage induction metabolites.

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DOI

https://doi.org/10.1038/s41564-018-0312-6