Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing

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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Fig. 1: Overview of viruses detected in hydraulically fractured shale wells.
Fig. 2: Viral and Halanaerobium dynamics in hydraulically fractured wells.
Fig. 3: Alluvial plots showing dynamics of Halanaerobium genomes (isolates and MAGs) and viruses within the Utica-2 well.
Fig. 4: Network of genomic links between viral genera and Halanaerobium hosts.
Fig. 5: Halanaerobium strain WG8 prophage induction.

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.

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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).

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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.

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Correspondence to Michael J. Wilkins.

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Supplementary information

Supplementary Information

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

Reporting Summary

Supplementary Data 1

Sequencing information for metagenomes.

Supplementary Data 2

Viral OTU table.

Supplementary Data 3

Halanaerobium relative abundance in the Utica-2 well.

Supplementary Data 4

Prophage induction metabolites.

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Daly, R.A., Roux, S., Borton, M.A. et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol 4, 352–361 (2019). https://doi.org/10.1038/s41564-018-0312-6

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