Methane (CH4) is a greenhouse gas with implications in global climate change. Methanotrophs, organisms capable of consuming CH4, play a key role in regulating atmospheric CH4 emissions. Current estimates and understanding of factors regulating microbial CH4 fluxes are limited. This work contributes to current understanding of methanotroph impacts on CH4 fluxes and biotechnological applications to mitigate CH4 emissions from wastewater. First, empirical relationships between biomarker gene and transcript amounts and activity in model methanotroph M. trichosporium OB3b grown in membrane bioreactors (MBRs) were explored. A strong correlation between per cell CH4 oxidation biomarker pmoA transcript and per cell CH4 oxidation rate was observed across three orders of magnitude. These correlations and effects of short-term substrate (CH4 and O2) limitation on gene expression were further explored in methanotrophs, Methylocystis parvus OBBP and Methylomicrobium album BG8. Results showed correlations between per cell pmoA transcript and per cell activity were maintained across the three methanotroph species studied. A potential, universal trend between cell activity and biomarker levels could allow for better estimates of in situ methanotrophic activity. Substrate limitation induced changes in central carbon metabolism gene expression and elicited a strong stress response in M. album BG8. Lastly, the feasibility of aerobic, single-stage MBRs for treatment of CH4- and NH4+-rich anaerobic wastewaters was investigated. Substrates (CH4 and O2) were delivered via membrane permeation. Effects of O2 membrane pressure, inoculation, retention time, and NO2- additions were explored. Simultaneous nitrification and denitrification occurred in single-stage reactors and removal rates were comparable to those available in the literature. O2 membrane pressure was the main driver for reactor performance and reactor microbial community composition. This work relied on MBRs in the context of microbial CH4 cycling, to explore fundamental relationships between gene expression and microbial activity, and to harness ability of extant microbes in wastewater treatment. These results serve as a foundation for CH4 oxidation biomarkers as predictors of CH4 oxidation rates. The MBR treatment method performance was comparable to available alternative technologies. The results found herein further our knowledge of CH4 cycling organisms and wastewater treatment options, with implications on the global CH4 cycle.