UC San Diego

Marine sediments cover ~70% of the earth and host rich and diverse microbial communities. These microbial communities play an integral role in global nutrient cycling and the food web. They can be both a source of disease and/or an agent of mitigation through the natural products they produce, which can have cascading impacts on community structure and ecosystem function. Despite their importance, marine sediment microbes remain woefully understudied. The goal of this dissertation was to use next generation sequencing technology and newly developed bioinformatic pipelines to gain insight into these complex communities. First, I sought to reevaluate the 1% culturability paradigm by comparing sediment microbial communities using culture-dependent and culture-independent techniques. This comparative approach not only highlighted that >1% of sediment bacteria could be cultured, but also revealed the biases associated with culture-independent methods. Thirty-nine genera were identified in culture that were not detected with culture-independent methods, including some taxa that were fairly divergent from known cultured representatives. Next, I wanted to assess connections between sediment microbial communities, the sediment metabolome and sediment characteristics across varying spatial scales. To do this, microbial communities were sampled at three spatial scales, 1 m2 quadrats, 10 m transects, and sites across a 12 km2 area. Additionally, a small molecule in situ resin capture (SMIRC) method was employed to capture the metabolome present in sediments. The results from this study indicate that microbial diversity significantly increases with spatial scale and that sediment characteristics, such as grain size and nitrate concentrations, are significantly correlated with microbial communities. The SMIRC method was able to capture natural products and revealed the vast chemical landscape of marine sediments, much of which remains unexplored. Finally, I sought to evaluate how microbial communities in marine sediments vary in relation to the surrounding benthic environment by comparing fringing and back reefs of Mo’orea, French Polynesia. Even within a small area, ~1 km2, fringing and back reef sediment communities were distinct from each other. Back reefs exhibited greater richness and diversity in the microbial communities while fringing reefs had greater metabolomic richness. Supervised correlative analyses identified connections between microbes, metabolites and environmental characteristics such as nutrient concentration. Many of the taxa identified in the network analyses belong to relatively unknown lineages, providing important insight into the role these lineages may be playing in their communities. In conclusion, the results of this dissertation provide fundamental baseline information about the microbial communities and metabolites associated with marine sediments.