Geological activity shapes the microbiome in deep-subsurface aquifers by advection

Proc Natl Acad Sci U S A. 2022 Jun 21;119(25):e2113985119. doi: 10.1073/pnas.2113985119. Epub 2022 Jun 13.

Abstract

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

Keywords: deep subsurface; fractured aquifers; microbial biogeography; microbial community; microbial transport.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anthropogenic Effects*
  • Bacteria* / classification
  • Bacteria* / genetics
  • Bacteria* / isolation & purification
  • Geology
  • Groundwater* / microbiology
  • Hydrology
  • Microbiota*