Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Kaela K Amundson,Rebecca A Daly,Michael J Wilkins,Joseph Moore,Elizabeth Eder,Kenneth Wunch,Kelly C Wrighton,David W Hoyt,Allison Wong,Mikayla A Borton

doi:10.1186/s40168-021-01194-8

Abstract

BackgroundMicrobial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.ResultsWe collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.ConclusionsThese findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.FLC2hWdvCQdk4dv7tGhc3oVideo

Highlights

Deep terrestrial shale formations underly much of North America, and due to extremely low permeability and very small, disconnected pore spaces (~10 nm) [1] are generally thought to lack suitable habitat for microbial life [2]
Deep subsurface physicochemical conditions enrich for a conserved microbial community over time Chemical and microbial dynamics were interrogated across three wells within the STACK shale play, OK, USA
Despite initial differences in microbial community composition and chemical inputs, microbial communities in produced fluids collected 100 days after hydraulic fracturing (HF) could no longer be statistically distinguished between the wells, suggesting deep subsurface shale conditions enriched for similar microbial taxa

Summary

Introduction

Deep terrestrial shale formations underly much of North America, and due to extremely low permeability and very small, disconnected pore spaces (~10 nm) [1] are generally thought to lack suitable habitat for microbial life [2]. Microorganisms present in injected materials (e.g., drill muds) colonize these new fracture networks and encounter nutrient rich HF additives that act as substrates for microbial growth [4,5,6] Under these conditions, established microbial communities can persist for extended periods of time (>300 days) [5, 7]. These fractured shales differ from pristine subsurface ecosystems, they are confined by the surrounding hard rock matrix and are isolated from any other sources of microbial immigration [2, 8]. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation

Methods

Results

Conclusion