Search

Over the last decade shale gas obtained from hydraulic fracturing of deep shale formations has become a sizeable component of the US energy portfolio. There is a growing body of evidence indicating that methanogenic archaea are both present and active in hydraulically fractured shales. However, little is known about the genomic architecture of shale derived methanogens. Here we leveraged natural gas extraction activities in the Appalachian region to gain access to fluid samples from two geographically and geologically distinct shale formations. Samples were collected over a time series from both shales for a period of greater than eleven months. Using assembly based metagenomics, two methanogen genomes from the genus Methanohalophilus were recovered and estimated to be near complete (97.1 and 100%) by 104 archaeal single copy genes. Additionally, a Methanohalophilus isolate was obtained which yielded a genome estimated to be 100% complete by the same metric. Based on metabolic reconstruction, it is inferred that these organisms utilize C-1 methyl substrates for methanogenesis. The ability to utilize monomethylamine, dimethylamine and methanol was experimentally confirmed with the Methanohalophilus isolate. In situ concentrations of C-1 methyl substrates, osmoprotectants, and Cl- were measured in parallel with estimates of community membership. The appearance of the methanogenic genus Methanohalophilus followed different geochemical trends in the two shale environments. To adapt to the high osmolarities measured in the two shale systems, all recovered genomes encoded three distinct strategies for osmoprotection. This includes the synthesis of the compatible organic solute glycine betaine from glycine, which has been shown to be a capability in some methanogenic archaea. The overall scheme of carbon cycling for the three analyzed Methanohalophilus genomes is described. Collectively, this investigation constitutes the first in depth genomic and complementary physiological analysis of methanogens obtained from the economically important shale environment.