Although nitrogen (N) acts as a limiting nutrient in many marine ecosystems, from estuaries to the open ocean, N in excess can be extremely detrimental. Eutrophication is of particular concern in estuaries, with over half of the estuaries in the United States experiencing its effects. Harmful levels of N in estuaries can be diminished through tightly coupled processes in the microbial nitrogen cycle, including nitrification (chemoautotrophic oxidation of ammonia to nitrite and nitrate) and denitrification (the dissimilatory reduction of nitrate to N2 gas). In fact, coupled nitrification-denitrification can remove up to 50% of external dissolved inorganic nitrogen inputs to estuaries, thereby reducing the risk of eutrophication. Despite the biogeochemical importance of both nitrification and denitrification in estuarine systems, surprisingly little is known regarding the underlying microbial communities responsible for these processes, or how they are influenced by key physical/chemical factors.
The investigators will work in San Francisco Bay - the largest estuary on the west coast of the United States - using molecular, biogeochemical and cultivation approaches to explore how the distribution, diversity, abundance, and activities of key N-cycling communities are influenced by environmental gradients over temporal and spatial scales. Denitrifying communities will be studied using functional genes (nirK and nirS) encoding the key denitrification enzyme nitrite reductase, while genes encoding ammonia monooxygenase subunit A (amoA) will be used to study both ammonia-oxidizing bacteria (AOB) and the recently-discovered ammonia-oxidizing archaea (AOA)- members of one of the most ubiquitous and abundant prokaryotic groups on the planet, the mesophilic Crenarchaeota. Analyzing sediments from sites spanning a range of physical and chemical conditions in the Bay, seasonally over the course of several years, will represent an unprecedented opportunity to examine spatial, physical/chemical, and temporal effects on both denitrifier and ammonia-oxidizer communities in this large, urban estuary. Concurrently, an intensive cultivation effort will also be undertaken, in order to compile a novel culture collection of estuarine denitrifiers and ammonia-oxidizers, for which virtually nothing is currently known. Taken together, these complimentary approaches will help reveal how complex physical/chemical gradients influence the diversity and functioning of key estuarine N-cycling communities over time and space.
The broader impacts include obtaining a critical understanding of how underlying N-cycling microbial communities are influenced by complex and fluctuating environmental gradients over time and space in the San Francisco Bay estuary which should translate to insights into the ecology and regulation of these biogeochemically-important processes in all estuarine systems. In addition, results of the research will be communicated and investigated through several key educational and outreach activities: (1) a sophomore-level course to be developed and taught focused on San Francisco Bay as a model system for understanding the biogeochemical and societal importance of large estuaries (2) Bay Area high school biology teachers will be targeted for a 4-week intensive microbiology summer course (3) development of a 'microbial community' module to the REAL (Redwood Environmental Academy of Learning) Program, focused on the hands-on ecological teaching of 'continuation' students at nearby Redwood High School and (4) mentoring and training of graduate, undergraduate, and high school students, who will be directly involved in the research project over the next 5 years.