UC Santa Cruz

Patterns of marine microbial community composition are observable across ocean depths, with distinct ecological niches based on the environmental conditions at each depth. A fundamental biogeochemical role of microbes in the marine carbon cycle is the degradation of particulate organic matter. Identifying the microbes that are actively degrading organic matter in the deep sea is challenging. The main objective of this dissertation is to understand variations in vertical distributions of microbial communities and to develop methods that could allow us to understand which community members contribute actively to degradation of organic matter. Vertical gradients of marine bacterial diversity and overall abundances were characterized from the surface to the seafloor (Chapter 2), and the variability of deep sea sediment bacterial communities was identified through replicated sampling of sediments (Chapter 3). Flow cytometric cell enumeration showed that bacterial abundance decreased with increasing water depth regardless of the region studied or distance from shore. V1-V2 16S rRNA gene amplicon analyses at 100% nucleotide identity as amplicon sequence variants (ASVs) identified distinct bacterial communities in four defined zones: photic (0 – 200 m), mesopelagic (200 – 1000 m), bathypelagic (> 1000 m) and surface sediments (0 to 20 cmbsf). Bacterial communities of surface sediments >10 km apart were distinct from each other, while those sampled from within 1 m were similar. Phylogenetic approaches focusing on the ubiquitous pelagic bacteria, Alphaproteobacteria Pelagibacterales (SAR11 clade) and Deltaproteobacteria SAR324, expanded our evolutionary understanding about the diversity of these groups while also distinguishing potential ecological niches based on vertical depth distributions. Building on characterization of bacterial diversity, deep water in situ incubation experiments were performed to identify bacterial groups activity involved in phytodetrital organic matter degradation (Chapter 4). The addition of phytodetritus led to an increase in relative abundance of taxa known to degrade polysaccharides. The results provided in this thesis provide high-resolution analyses of marine bacterial community composition throughout the water column and into the upper 20 cm of deep sea sediments in the eastern North Pacific Ocean. Collectively, these studies provide a baseline for assessment of future changes, as the influences of global climate change reshape ocean communities.