Natural gas energy extraction using horizontal drilling and hydraulic fracturing technologies in deep hydrocarbon-bearing shale significantly alters biogeochemical conditions and microbial ecological function at depth. We tracked changes in microbial community dynamics and functional potential via genome reconstruction over an 11-month period in fluids produced from three wells drilled and fractured in the Marcellus shale. A marked shift in 16S rRNA sequences occurred over time; communities shifted from those closely associated to low-salt tolerance, mesophilic aerobic bacteria to dominance by halophilic, thermotolerant anaerobic associated bacteria and archaea. Genomes from halotolerant microorganisms, including Halolactibacillus, Vibrio, Marinobacter, Halanaerobium and Halomonas encoded the potential for fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, while Arcobacter contained potential for chemoautotrophic sulfide oxidation metabolism. Relative to earlier samples, the 11-month samples were enriched in genes for the acquisition and degradation of aromatic compounds, sulfur, iron, and nitrogen, supporting the importance of these processes in later produced fluids when anaerobic conditions prevail. Later time points also show the enrichment of microorganisms closely related to Methanohalophilus and Methanolobus. These methanogens are known to disproportionate methylamines, and the recovery of genes associated with the fermentation of trimethylamine to dimethylamine suggests a pathway for methane production exists within detected genomes. These data provide insight into the microbial changes that occur from hydraulic fracturing in deep shale ecosystems.
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