Ecological and Geochemical Factors Underlying the Distribution of the Aerobic Methane-Oxidizing Microbial Community in Aquatic Systems

Methane gas plays an important role in both modulating global temperatures and in providing carbon to deep-sea ecosystems. Aerobic methanotrophs, microbes that oxidize methane into more labile compounds, mitigate its global warming potential and make methane-derived carbon accessible to entire ecosystems. While capable of oxidizing methane without assistance from other microbes, a growing body of evidence suggests that nonmethanotrophic methylotrophs—bacteria that cannot oxidize methane but can oxidize other single-carbon compounds like methanol—may aid in this process, leading to higher rates of methane oxidation. While much research has been conducted investigating how aerobic methanotrophs alone respond to changing environmental conditions, how co-occurring nonmethanotrophic methylotrophs also respond to those conditions is often overlooked. It is also unclear what factors influence the taxonomic and functional distribution of the aerobic methane-oxidizing community on a fine-scale in natural ecosystems.

My dissertation utilizes two culture-independent techniques—16S rRNA gene amplicon sequencing and shotgun metagenomics—to investigate how biotic and geochemical factors combine to influence the structure and capabilities of naturally occurring aerobic methane-oxidizing communities. First, I review current knowledge regarding aerobic methanotrophs and their proposed syntrophic partner species that aid in the process of methane oxidation, the nonmethanotrophic methylotrophs. Then, novel in situ incubation technology is used to study how aerobic methanotrophs and nonmethanotrophic methylotrophs in a methane-rich lake each respond to natural variations in geochemistry and in turn affect the methane oxidation rate constant. Next, the community structure, response to geochemical and physical environmental factors, and spatiotemporal stability of the overall prokaryotic community and specifically of the aerobic methane-oxidizing community is investigated throughout two North Atlantic seep fields over two years. Finally, the functional potential of the microbial community within those two seep fields is assessed within the recovered metagenome-assembled genomes and functional roles that Methylophilaceae, Thioglobaceae, and Nitrosopumilaceae may play in the aerobic methane-oxidizing community is determined.