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

Abstract

Background Microbial 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. Results We 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. Conclusions These 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.

New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

“…S7B). These findings are consistent with the dynamics in the lower-salinity STACK formation, where Thermotogae species were detected in high abundance [66]. Based on the findings of our 16S rRNA sequencing meta-study, lineages implicated with sulfide production are common regardless of salinity range, suggesting the sulfidogenic niche appears to be occupied throughout the formations considered here.…”

“…As noted above, the influence of salinity on community composition is strong, inducing physiological and thermodynamic constraints on the fractured shale microbiome [ 66 ]. We hypothesize that varying salinity levels lead to different organisms occupying similar niches in the shale microbiome, such as the potential to generate sulfide from thiosulfate or sulfur.…”

Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales

“…Spacers within CRISPR arrays therefore provide a record of past interactions between a host and viral population, and host-viral linkages can be made by matching the hosts' CRISPR spacers to protospacers in viral genomes (11,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). However, the presence of CRISPR systems within the microbial community is often a limiting step to making strong host-virus connections; CRISPR defense is most likely advantageous in ecosystems where host and viral populations repeatedly interact, such as environments dominated by biofilms or those hosting lower microbial and viral diversity (28)(29)(30).…”

“…To address this knowledge gap, we used a temporally-resolved dataset from six subsurface fractured shale wells to interrogate host-virus dynamics and CRISPR arrays in a natural ecosystem. Subsurface fractured shales, which are relatively closed ecosystems with limited immigration, elevated temperatures, lower microbial diversity and likely dominated by biofilms, present an opportunity to address these questions through strong CRISPR-based host-viral linkages (21,23,46–49). We hypothesized and found that CRISPR viral defense systems were widely encoded across hosts within shale microbial communities.…”

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

“…Following the publication of the original article [ 1 ], the author reported that Figs. 2 and 5 contains extra images at the topmost right that should have not been a part of these figures.…”