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

Daly, Rebecca A.; Roux, Simon; Borton, Mikayla A.; Morgan, David M.; Johnston, Michael D.; Booker, Anne E.; Hoyt, David W.; Meulia, Tea; Wolfe, Richard A.; Hanson, Andrea J.; Mouser, Paula J.; Moore, Joseph D.; Wunch, Kenneth; Sullivan, Matthew B.; Wrighton, Kelly C.; Wilkins, Michael J.

doi:10.1038/s41564-018-0312-6

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

Journal Article · 03 December 2018 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-018-0312-6· OSTI ID:1501526

Daly, Rebecca A.; Roux, Simon; Borton, Mikayla A.; Morgan, David M.; Johnston, Michael D.; Booker, Anne E.; ; Meulia, Tea; Wolfe, Richard A.; Hanson, Andrea J.; Mouser, Paula J.; Moore, Joseph D.; Wunch, Kenneth; ; ;

The deep terrestrial biosphere harbors a significant fraction of earth’s biomass and remains understudied compared to 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, rivaling that of peatland soil ecosystems, despite low host diversity. Many viral OTUs were predicted to infect Halanaerobium, the dominant microbe in these ecosystems. Examination of CRISPR-Cas spacers elucidated lineage-specific virus-host dynamics suggesting active in situ viral predation of Halanaerobium. These dynamics indicate an ongoing arms-race with 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.

Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1501526

Report Number(s):: PNNL-SA-134613

Journal Information:: Nature Microbiology, Vol. 4, Issue 2; ISSN 2058-5276

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

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