Microbial Ecology and Biogeochemistry of the Engineered Deep Biosphere Exposed to Carbon Storage and Hydraulic Fracturing Environments

This dissertation investigates the microbial deep biosphere in important energy systems relevant to long-term carbon storage and unconventional natural gas reservoirs in the Michigan and Delaware Basins. Microorganisms inhabiting the deep geologic subsurface will drive important biogeochemical reactions with significant implications for carbon storage and shale gas recovery. The three main objectives of this work were to (1) characterize the microbiology and geochemistry of CO₂ enhanced oil recovery (CO₂-EOR) reservoirs exposed to super critical CO₂ conditions that would be expected during geologic carbon storage (GCS), (2) evaluate the biogeochemistry of produced water from the Antrim Shale natural gas reservoir including microbial abundance and taxa relevant to hydraulic fracturing operations and key geochemical drivers of the microbial community, (3) perform a metagenomic analysis of produced water collected from a hydraulic fracturing well in the prolific Wolfcamp formation to investigate the metabolic potential of the predominate microorganisms during the initial stages of hydrocarbon production.

For my first objective I characterized produced water collected from CO₂-EOR well separators in the oil-producing Niagaran Pinnacle Reef, a proposed target for future GCS. I found wells were characterized by high salinity and total dissolved solids (TDS) contributing to the overall low microbial abundance observed. There was little well-to-well communication, suggesting low permeability reservoirs with reduced flow and fluid migration that allowed the subsurface microbiomes to evolve independently of one another and suggests the need for site-specific examination of potential carbon storage units. Our microbial community analysis revealed important microbial taxa with putative functions including sulfide and acid production, and biofilm formation that could affect reservoir quality and the long-term storage of CO₂ in this system.

For the second objective I analyzed produced water collected from well heads of the shallow, vertical drilled, hydraulically fractured Antrim Shale for biogeochemical characterization. Statistical analysis showed that TDS and salts were significantly correlated with the observed community and potential drivers of the subsurface microbiome in this region. I observed a trend of rising salinity concentrations of produced water with increasing proximity of the well to the basin center. 16S rRNA sequencing revealed that wells were characterized by relatively low abundance with high variability in microbial taxa amongst geospatially close well. Putative functional capabilities of the identified taxa included sulfur reduction and fermentation that could have important implications for hydraulic fracturing operations. Overall, these results suggest that differing geochemical conditions between Antrim wells fosters unique environmental niches that drive the heterogeneous microbial community composition observed from well to well and that there is an important relationship between well location and geochemistry and the microbial community that persists in these gas reservoirs.

For my third objective I analyzed production fluid samples collected during the early phase of production of the Hydraulic Fracturing Test Site 2 (HFTS 2) in the prolific, shale gas-bearing Wolfcamp formation, in the Permian Delaware Basin. Prior analysis of 16S rRNA data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. I performed a metagenomic analysis of produced water sampled on Day 33 of production to further investigate the functional capacity of the produced fluid and generated three high-quality metagenome-assembled-genomes (MAGs). Draft genome annotation revealed the presence of genes encoding for metabolic processes including thiosulfate reduction, mixed acid fermentation, and biofilm formation suggesting the potential of this community to contribute to well souring, biocorrosion, and biofouling in the reservoir.

This dissertation work sheds light on microbial community composition in a potential carbon storage reservoir to understand how CO₂-impacted microbial communities may influence the fate and permeance of stored CO₂. This research also expands the current knowledge of shale microbiology of produced water in a shallow shale reservoir and during early phase production in two natural gas recovery regions. Ultimately, this study aims to characterize the deep microbial biosphere of three hydrocarbon recovery systems in the Michigan and Delaware Basins with important implications for energy extraction and climate change mitigation.