Isolation and characterization of a methanogenic archaea from Boom Clay borehole water

Methanogens are an ancient life form present in a wide variety of anoxic habitats and are the only known organisms capable of producing methane, thereby playing a key role in the global carbon cycle. Methane production was also observed in borehole water samples from the HADES URF located in Mol at -225 m depth. Here, the presence of an active methanogenic microbial community hampered the validation of the geochemical models used for predicting the geochemistry of the Boom Clay pore water.
The emergence of sequencing technologies identified a large number of uncultured archaeal lineages and their possible impact in the biogeochemical cycles. Although these culture-independent techniques have provided a large amount of data and new knowledge, pure cultures are essential for understanding the precise role of a specific organism in complex environments. Moreover, they can be useful in the search for new bioactive compounds.
We isolated a novel methanogenic archaea from a Boom Clay borehole water sample from the HADES URF. We determined its growth potential in the presence of different substrates and temperatures. In addition, the full genome was sequenced to confirm the observed phenotypical results.
Analysis of the genomic data indicate that the isolate probably belongs to the species Methanosarcina. The coccoid isolate (in aggregates or single cells) produced methane at temperatures from 20°C to 42°C. The highest methane production was observed at 37°C with a rate of 0.5 mg/mL CH4 per day, during 1 week. Genomic analysis indicate that the isolate harbours all three methanogenic pathways, i.e. hydrogenothrophic, methylothrophic and aceticlastic, similar as what has been described in literature. However, first experimental data indicate that the isolate can be considered as a methylotrophic methanogen as methane was only produced from methanol and H2. Also some methane was produced with methanol in the absence of H2. No methane was detected when acetate or H2 were provided as electron donor. More experiments should be performed to further confirm this.
Altogether, this is the first time a pure methanogenic archaea was isolated from Boom Clay borehole water. Further detailed analysis of methane production rates in different conditions can be used to improve and validate the geochemical models used to predict the evolution of the Boom Clay pore water geochemistry.