Microbially-driven methane and sulfur cycling in a Gulf of Mexico methane seep and the White Oak River estuary

Methane is a globally relevant greenhouse gas, but many key questions remain about the microbes that produce it, and the microorganisms responsible for oxidizing it anaerobically to CO2 via sulfate reduction. I used DNA- and RNA-based techniques coupled to geochemistry to study the spatial relationship and functions of microbes at a Gulf of Mexico deep-sea hydrocarbon seep, and methane-cycling archaea in the shallow White Oak River estuary, North Carolina. In particular, I concentrated on ribosomal RNA for the small 16S subunit and messenger RNA encoding Dissimilatory Sulfite Reductase or Methyl Coenzyme M Reductase, which are key enzymes in sulfate reduction or anaerobic methane production/oxidation. First, I examined different nucleic acid extraction techniques and found that avoiding silica column purification procedures appears to be necessary to avoid yield loss in humic acid-rich samples like the White Oak. In the Gulf of Mexico, Mississippi Canyon 118 (MC118), subseafloor hydrocarbon seeps fuel large Beggiatoa spp. mats at the sediment-water interface. In a transect of cores across a Beggiatoa spp. mat, I found that the mat accurately circumscribes near-surface hydrocarbon seepage and surface microbial communities, but deeper in the sediments, seep-related communities appear uncoupled from the immediate presence of either seeping fluids or sulfate as an electron acceptor. In the White Oak River estuary, I found that the organisms thought to mediate the anaerobic oxidation of methane transcribe genes and maintain stable population sizes well into the methane production zone, agreeing with previous indications from the literature that they are also capable of methane production. After making primers specific for the uncultured Miscellaneous Crenarchaeotal Group (MCG), I found that they dominate the archaeal DNA and RNA content of White Oak River estuary sediments, although their RNA content may decrease after sulfate is depleted. Altogether this work has shown that microbial distribution patterns are relevant at deep-sea hydrocarbon seeps, anaerobic methane oxidizing archaea are most likely capable of methane production as well, and that the MCG group may be quite important to biogeochemistry