Using Molecular Tools to Elucidate Controls on Microbes Driving the Nitrogen Cycle in Marine Sediments

Abstract

Marine sediments harbor metabolically versatile bacteria whose activities can influence the cycle of nutrients on global scales. Microbial communities driving nitrogen (N) cycling are extremely diverse, thus making it difficult to identify the functional groups and elucidate controls on their activity. Denitrifiers in sediments remove significant amounts of N from the coastal ocean, while diazotrophs are typically considered inconsequential. Recently, N fixation has been shown to be a potentially important source of N in coastal sediments, however, the environmental drivers controlling this process are poorly understood. The goal of this dissertation was to identify and target the likely active denitrifiers and N fixers in coastal marine sediments through the analysis of genes expressed for proteins essential for denitrification, a nitrite reductase (nirS) and nitrogen fixation, a nitrogenase subunit (nifH). Subsequently, quantitative PCR and RT-PCR were used to follow the changes in abundance, distribution and nifH expression of the dominant diazotrophic groups in response to environmental conditions. Two groups of diazotrophs related to anaerobic sulfur/iron reducers and sulfate reducers dominated nifH expression in Narragansett Bay (RI, USA) sediments. Increased seawater temperature and severe hypoxia appear to be influencing the proliferation and activity of these two bacterial groups. Oxygen depletion also affects sediment porewater nutrients, indicating a shift in benthic microbial processes. In offshore sediments, nifH expression was related to UCYN-A, a unicellular cyanobacterium. These findings suggest that UCYN-A, a known tropical and subtropical open ocean symbiont, has a broader thermal tolerance than previously assumed and can survive in the benthos after the lifespan of its eukaryotic host. Diazotrophic activity by these microbial communities in marine sediments is an unanticipated contribution of fixed N to coastal systems. Climate change may exacerbate the environmental conditions in which these microbes become active, consequently altering the global marine nitrogen cycle in unprecedented ways.