PNNL

Abstract

Currently about 60% of natural gas production in the United States comes from the hydraulic fracturing of shale. This process inoculates and enriches for halotolerant microorganisms in shales overtime, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of these methanogens across shales, and report that members of the genus Methanohalophilus are recovered from every fractured shale play sampled by metagenomics. We provide the first genomic sequencing of 3 isolate genomes, as well as 2 metagenome assembled genomes. Utilizing 6 other previously sequenced genomes, we perform a comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with the constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same shale well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in the CRSIPR-Cas systems of Methanohalophilus, with genomes from geographically distinct hydraulically fractured shales sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic 47 methane production 48 in hydraulically fractured shales.