Methane-cycling microbial communities across changing environments

Abstract

Methane is a potent greenhouse gas that is responsible for ~0.5 °C of global warming since pre-industrial times. The majority of methane emissions to the atmosphere come from microbes, and the impacts of changing climate on ecosystems also affect their methane-cycling microbial communities. This relationship between biology and climate forms a feedback loop, the nature of which is crucial to characterizing and contextualizing climate change impacts. This dissertation discovers novel pathways of methane production and examines methane cycling microbial communities from anthropogenically-impacted environments. We developed and performed various microbial ecology and microbiology techniques to characterize these microbial communities and the physiology of their members. These analyses were done in conjunction with the collection of environmental data and methane flux from methane-relevant environments, including thawing permafrosts, rivers, and saline lakes. Through this research, we demonstrate that methane cycling does not always conform to historic assumptions. We identified a novel pathway for aerobic methane synthesis that can be conferred to E. coli by the heterologous expression of a single gene. In melting permafrosts, the highest methane fluxes emanated from sites with small relative abundances of methanogens near the surface, suggesting that the highest methane emissions from the arctic are coming from deep permafrost thaw and encouraging caution when modeling methane flux from near-surface characteristics. In the Yellowstone River, dissolved methane concentrations imprecisely predict flux, a result that also has major implications for methane-emission modeling. Additionally, our results indicate that microbial community dynamics can impact methanogen physiology and prevalence more than environmental factors. A novel halophilic methanogen was discovered in high-methane fluxing soils and brought into culture. The methane yield and proteome from cultures of this methanogen were relatively unaffected by changes in salinity; however, co-culturing with a particular bacterium significantly altered protein expression patterns. In permafrosts, methanogen relative abundance was better predicted by the presence of syntrophic bacteria than by environmental conditions. Comprehensively, this dissertation highlights the impact of community dynamics on methanogen physiology and methane flux in changing environments.