UC Irvine

Marine bacterial metabolism of oxygen (O), carbon (C), nitrogen (N), phosphorus (P), iron (Fe), and silica (Si) are essential for elemental cycling on our planet. Because of this, understanding the spatial distribution of marine bacteria, how these bacteria are functioning and interacting with physical processes, and what environmental conditions impact them is essential for understanding current biogeochemical dynamics and for predicting how these dynamics might change in the future. My dissertation research is divided into three projects that aimed to connect large microbial genomic datasets with geochemical and physical processes in open ocean and coastal ecosystems. These studies consisted of a biogeographic survey of the Indian Ocean, an in-depth analysis of mesoscale eddies, and a coastal study at Newport Beach, California.In the first chapter, I linked broad-scale spatial patterns of marine bacteria with geochemical and physical dynamics across the eastern and western Indian Ocean. To achieve this, I incorporated 16S rRNA gene sequences from 465 samples with in-situ CTD data, nutrient concentrations, particulate organic matter (POM) concentrations, stoichiometric ratios, and remote sensing data of sea surface height and geostrophic currents. This extensive analysis revealed 23 unique community structures within the Indian Ocean. It highlighted the southeastern gyre as the area with the largest gradient in bacterial alpha-diversity, identified that the Indian Ocean microbiome was dominated by a core set of taxa, and linked changes in community structure with transitions in physical and geochemical conditions. Importantly, the study identified distinct community structures within mesoscale studies, which served as the foundation for my next chapter. In the second chapter, I investigated the role of mesoscale eddies in shaping bacterial community composition and function across various Indian Ocean regions. This project integrated genomics (16S rRNA and short-read metagenomes), nutrient concentrations, and remote sensing data of 26 eddies of varying age, intensity, and size. Within this study, mesoscale eddies were viewed as physical disturbances that altered communities through dispersal and/or environmental selection. It was found that the origin of the eddy (i.e., coastal waters versus open ocean waters) played a pivotal role in determining how dispersal and environmental selection affected microbial community outcomes. In the third chapter, I examined the interactions between pollutants, marine bacterial diversity and function, and ecosystem recovery within the coastal waters of Newport Beach, California, following the Orange County oil spill. This investigation incorporated short-read metagenomic data, flow cytometry data, polycyclic aromatic hydrocarbon (PAH) concentrations, nutrient concentrations, and POM concentrations. The acute bacterial response to the oil spill was assessed by comparing metagenomically derived taxonomic and functional trends to a 10-year time-series. Notably, there was a rapid and anomalous decline in the abundance of the dominant picophytoplankton, Synechococcus. This decline was coupled with an increase in sulfur-oxidizing and potential hydrocarbon-degrading heterotrophic lineages. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and one week after the taxonomy shifts were observed, unique functional changes were seen. This pattern of response was observed two times during our sampling period and corresponded with the potential resuspension of PAHs. Thus, the impact of the oil spill was temporally extended and demonstrates the need for continued monitoring long after initial exposure.