Microbe to microbe: Monthly microbial community dynamics and interactions at the San Pedro Ocean Time-series

Our ability to define and quantify individual microbe-microbe interactions with traditional community ecology principles is still in development yet these relationships are key to understanding microbial roles in the ocean. Application of molecular methods, such as community fingerprinting and metagenomics have added significant insight into marine viral and microbial ecology in general over the last decade. Great progress has been made in identifying what organisms or taxonomic groups are present, their abundances and their genomic context. Metagenomic and genomic studies have highlighted the phylogenetic and functional diversity of viruses in the ocean. However, aside from work on the limited number of cultured organisms, our understanding of microbe-microbe relationships is often broad and does not typically lead to systematic identification of multiple relationships from the environment at the same time. The ease and feasibility of these molecular tools are increasingly an essential part of the microbial ecologists' toolbox. Continuing research with microbial association networks can lead to a better understanding of how individual members of a diverse microbial community relate to one another and will ultimately facilitate predictions on how resilient or susceptible the microbial community may be to their future ocean climate.;The microbial community at the San Pedro Ocean Time-series was characterized in great detail --- with a specific focus on viral and bacterial communities and inter-microbe relationships as part of the USC Microbial Observatory program. First, ten-years of observations of bacterial communities in the euphotic zone revealed seasonal and annual trends in the surface ocean (Chapter 2). There were only a few dissimilarities between the surface and deep chlorophyll maximum (DCM) depths in terms of the microbial constituents; thus, a core euphotic zone microbiome at this location was described based on taxonomic identity and persistence of organisms. Differences between depths were not in the taxonomic composition of the bacterial communities, but rather were observed in depth-specific association networks. More specifically, it was the relative abundances and correlations between the OTUs that differed, suggesting that microbial interactions differ between depths. Second, a new molecular fingerprinting assay was developed to characterize the T4-like myovirus family --- an abundant and diverse group of viruses in the ocean (Chapter 3). Seasonal trends were also observed for this virus family over a three-year period. A persistent subset of all OTUs was also identified, some of which demonstrated seasonality while others were moderately abundant and steady year-round. Third, interrogation of individual relationships between members of viral, bacterial and protistan communities in the surface ocean by statistical and network-based analyses led to identification of individual virus-bacteria and protist-bacteria correlations (Chapter 4). In general, T4-like viruses and bacteria were more tightly coupled than protists to bacteria based on network analysis and shifts in community composition. Lastly, differences in the water column were observed by viral metagenomics and found that mesopelagic viruses differed from the upper water column (Chapter 5). Photosynthesis genes, from cyanophage most likely, were primarily seen in the euphotic zone. Siphoviruses were a larger proportion of the community below the euphotic zone. Collectively, this dissertation detailed temporal variability in microbial communities by identifying several hundred viral and bacterial OTUs over time and the underlying connections. These results will provide new insights into the individual links that sustain community-level relationships within the microbial loop and our understanding of microbial roles in the ocean.