Terrestrial freshwater wetlands are carbon rich environments that play a significant role in the global release of methane to the atmosphere. Our research provides an understanding of how methane emissions in freshwater wetlands are controlled by biogeochemistry and microbial metabolism. Here the contributions of these interconnected components are quantified across horizontal (microsite), vertical, and seasonal scales. To understand microbial changes along these gradients, high-throughput biomarker analyses for archaea and bacteria will map site-wide organismal abundance and distribution patterns. Community genomics and transcriptomics of natural samples will identify the organisms, expressed genes, and pathways responsible for carbon degradation and methane metabolism. Coordinated high-resolution analyses of carbon from these same pore-waters via FT ICR MS and NMR will greatly add to our tracking of carbon transformation and the linkages to active microbial enzymes identified in transcriptomics data. Given the high organismal complexity of wetland systems, we complement field approaches with laboratory physiological investigations. Here again we use a combination of genomics, proteomics, and geochemistry to more cleanly interrogate the individual roles specific taxa play in carbon degradation, methanotrophs, and methanogens. It is our intention that these laboratory studies will inform field level interactions and enable assignment of physiological processes to organism strains. This proposal will identify the ecological, geochemical, and microbial variables driving methane emissions, generating an intellectual framework to improve methane emission predictions.