Deep Underground, Viruses Destroy and Build Microbial Communities

Scientists looked at interactions between bacteria and viruses in fractured shale to understand their roles and impacts.

The Science

Bacteria and the viruses that infect them play central roles in all ecosystems that have been studied to date. But what about deep underground? That biosphere remains one of the least studied areas on Earth. Using samples from hydraulic fracturing wells, scientists studied viruses and their host bacteria to better understand how they interact below ground. The results of the work suggest diverse and active viruses drive the dynamics of microbial community development and turnover within this deep terrestrial ecosystem.

The Impact

When water and chemicals are injected into the ground to free up natural gas and oil deposits during the hydraulic fracturing of shale, surface bacteria and viruses come along too, and they subsequently colonize the fractured shale. By better understanding community dynamics underground, scientists can determine how these microbes may affect oil and gas recovery. They can also better predict how interactions among these microbes influence community development and the chemistry of other ecosystems.


Scientists from The Ohio State University (OSU) and the University of New Hampshire teamed with the Joint Genome Institute (JGI) and EMSL, the Environmental Molecular Sciences Laboratory, for this innovative study of Halanaerobium genomes from isolates and metagenomes from five different hydraulically fractured wells in Pennsylvania, Ohio, and West Virginia. The scientific team conducted the most complete census of viral populations in the deep terrestrial ecosystem to date, revealing a wide-variety of viral-host interactions. Working with OSU scientists, JGI staff employed a set of virus-specific analysis tools, including an extensive database of viral genomes (the largest of its kind), to analyze the novel viral genomes recovered from deep underground samples. Using an advanced 600-MHz nuclear magnetic resonance instrument, EMSL staff studied metabolites from the same samples. The data revealed extremely diverse viral populations in the fractured shales, despite low diversity within the microbial populations. The team also discovered that these viruses infect the bacteria during the hydraulic fracturing process, causing cells to break open and spill metabolites into the fluid. These metabolites in turn feed the remaining bacteria, making viruses both a destroyer and a builder of the microbial community. The results of this pioneering study will allow scientists to establish more standardized tools to examine viruses and their impacts in any ecosystem.

Principal Investigator(s)

Michael Wilkins
Colorado State University


This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL) and Joint Genome Institute (JGI), both DOE Office of Science user facilities, as well as the National Science Foundation. The capabilities at JGI and EMSL were jointly accessed through the Facilities Integrating Collaborations for User Science (FICUS) solicitation process.


Daly, R.A., S. Roux, M.A. Borton, D.M. Morgan, M.D. Johnston, A.E. Booker, D.W. Hoyt, T. Meulia, R.A. Wolfe, A.J. Hanson, P.J. Mouser, M.B. Sullivan, K.C. Wrighton, and M.J. Wilkins. “Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.” Nature Microbiology 4, 352-361 (2018). DOI:10.1038/s41564-018-0312-6