UC San Diego

To address the major role microorganisms play in the biogeochemical cycling of carbon and nutrients in the marine environment, the work presented in this dissertation uses a combination of geochemical and molecular biological techniques to investigate carbon and nitrogen metabolism in the planktonic microbial community of the deep ocean. A method was developed to isolate microbial DNA from the marine water column suitable for radiocarbon analysis, which was then applied to determine the sources of carbon fueling microbial production in the mesopelagic. Fresh organic matter delivered from sinking particles was confirmed as an important carbon source for free-living microbes, but the extent of autotrophic carbon fixation was also significant and variable with depth, highlighting the requirement for particle-delivered reduced nitrogen by the total microbial community in the deep ocean. Both findings stressed the importance of constraining particle-derived carbon and nitrogen flux to the deep ocean. The importance of methane as a carbon source in unique environments above cold methane seeps was examined using both stable carbon isotope measurements of microbial DNA and quantitative PCR of the gene encoding for particulate methane monooxygenase. The carbon isotope measurements showed that methane-carbon played an insignificant role in fueling planktonic microbial production in the deep water column just above methane seeps. The PCR measurements substantiated this result by showing that the methane oxidizing community represented only a small percentage of the microbial community in this environment. And finally, bacterial heterotrophic nitrate assimilation was studied and determined to increase with depth and/or nitrate concentration, but appeared to only be a possible nitrogen acquisition method for a small (> 1%) fraction of the bacterial community. Sequencing of the heterotrophic nitrate assimilation gene isolated from the marine environment further demonstrated that these genes were depth stratified. In addition both isotopic analyses and molecular biological techniques such as quantitative PCR indicated distinct differences between free-living and particle-attached microbial communities. Overall, future research efforts should be focused on expanding the current data set, constraining particle flux, and gaining a better understanding of microbial physiology, including in situ growth rates, in the subsurface marine environment