Graduate Thesis Or Dissertation


The Influence of Microbial Communities on Spatiotemporal Elemental Cycling in Coastal Margins Revealed by Community- and Population-level Genomics and Proteomics Public Deposited

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  • Biotic and abiotic processes at continent-ocean interfaces cycle a disproportionate mass of carbon and nutrients relative to their global surface area, and microbial activity is a principal determinant of organic and inorganic matter flux in these transition zones. Most studies using modern high-throughput ‘omics techniques to link microorganisms with costal biogeochemical cycles have focused on large riverine-estuarine continuums, yet there is emerging evidence that smaller, more numerous rivers and estuaries are also key contributors to regional element fluxes, especially in temperate ecosystems. In this work, I characterized microbe-mediated carbon and nutrient flux through an estuary in the highly-productive Oregon coastal margin. To achieve this aim, I used multiple ‘omics techniques to characterize the functional and taxonomic composition, diversity, and activity of estuarine and coastal microorganisms at the community and population levels and across ecologically- relevant spatial scales. Chapter 2 presents the first spatially-resolved effort to measure microbial metabolic capacity for altering carbon and nitrogen flowing from the Yaquina River to the coastal ocean. Overall, we concluded that the microbial activity in Yaquina Bay is (1) a net source of carbon dioxide to the atmosphere via a biased capacity for respiratory processes and (spatially-constrained) carbon monoxide oxidation, and (2) a net sink of inorganic nitrogen via imbalanced assimilation and mineralization potentials. Population-level life strategies of microbial groups were also important for carbon and nitrogen cycling, with high and low molecular weight organic matter specialization divided between two dominant lineages within this system. These results represent a significant step toward constraining the flow of carbon and nitrogen through estuaries and provide future avenues of research for linking microbial populations with the specific pools of bioavailable resources. Chapter 3 describes the first investigation of microbial community composition across a winter freshwater plume on the Oregon coast. Using population distributions across space from the coastline to the continental shelf, we identified many coastal populations that may be directly involved in the turnover of plume-derived particulate organic carbon and inorganic nutrients. When these data were considered with the observations that (1) community respiration rate peaked at the plume particle maximum and (2) high concentrations of resources were ejected to the coastal ocean in plume water, we concluded that winter river plumes supplement food webs during the cold and wet season of low primary productivity on the central Oregon coast. Chapter 4 characterizes the metabolic roles of microorganisms in transforming organic matter in the Oregon coastal margin. In this project, we performed proteomic stable isotope probing (SIP) on native Yaquina Bay microbial communities using 13Carbon-labeled substrates that simulate naturally-occurring organic matter inputs from active phytoplankton into the heterotrophic food web. SIP patterns and estimated growth rates showed that these resources were partitioned among distinct bacterial taxa and assimilated by populations in taxon-specific patterns. Highly enriched community metaproteomes indicated that substrate addition primarily elicited the de novo synthesis of growth, transcription, and translation functions. Altogether, results from these experiments suggested that rapid (< 18 hours) assimilation into the biomass of many estuarine populations is a major fate of complex dissolved organic matter in Yaquina Bay, thereby making this resource available to different components of the food web in this system. A major outcome of my dissertation is the generation and interpretation of multiple datasets that help advance our understanding of microbe-mediated carbon and nutrient cycling within the Oregon coastal margin. This work is a significant contribution to the scientific community, particularly to biological oceanographers, ecosystem modelers, and microbial ecologists, by providing a prototype investigation of a small estuarine ecosystem and adjacent coastal ocean through microbiological, biogeochemical, and spatial ecology lenses, which can be extended to similar systems to constrain the role of microbes in altering carbon and nutrient flow from the land to the seas.
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  • The Gordon and Betty Moore foundation funded a large part of my PhD, along with the National Science Foundation (EAPSI), the OSU Graduate School (Travel Award, Provost’s Award), and the Department of Microbiology (Margaret and Charles Black Scholarship).
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