Taxonomic and Functional Composition of Microbial Communities Across Marine Ecosystems

The majority of the world's diversity is composed of microbial communities, and while out of site, these communities regulate ecosystem processes. Microbes cycle nutrients at a global level, within ecosystems microbes influence community interactions, and at the organism level microbes are part of healthy, diseased and even dead and decaying host microbiome. The advancement of high throughput DNA sequencing has revealed the diversity of these communities and how they interact with each other and the ecosystem at large. Annotation of vast amounts of randomly sequenced microbial DNA and the functional proteins they encode, act as community surveys not limited to a few marker genes. The surveys include both taxa and functional composition of whole communities across location, environment, and time. I have used shotgun metagenomic sequencing of marine microbial communities, predominantly bacterial, to assess taxonomic and functional composition at a global scale across environments and locations, with changes in benthic coral reef organisms, and throughout the decomposition process of a single alga species. By performing these studies, I have applied foundational concepts of macroecology to microbes, manipulated the fraction of the microbial community that mediate coral reef microbialization and described the pattern of microbial succession during the degradation of a carbon source that is the primary food source of coastal ecosystems.;I tested foundational hypotheses of macroecological theories to determine whether microbial communities have biogeography. Microbes may be everywhere, because they are small and numerous enough to be passively transported by wind and currents and thus homogenous distributed across biogeographic environments. Alternatively, microbes may be globally distributed but their composition selected for by the environment, or shaped by evolution over distance as communities in a location evolve and become distinct. Finally, microbes may show a pattern of community composition like macro-organisms, in which communities will be differentiated by both environment and distance. These questions were applied to both the taxonomic and functional characterization of the marine microbial community. Taxa and functional characterization of the community was correlated and I found the dominant microbial families clustered into four trophic groups -- phototrophic, oligotrophic, eutrophic and copiotrophic. The strength of this correlation cannot be assumed to indicate consistent biogeographic patterns because some genes required for microbial survival are transferred laterally (thus used as marker genes to assign taxonomic classification), while other functional pathways are auxiliary and may be transferred horizontally via phage or plasmids to microbes of different taxa. Differences in lateral versus horizontal gene transfer resulted in taxonomic and functional composition having different biogeographic patterns. The macro-ecological drivers of distance and environment were further demonstrated to be influenced by the complexity of the microbial community and the trophic groups surveyed. Taxonomic composition of complex, multi-trophic level communities reflected environmental differences, but not geographical distance; whereas functional gene composition in phototrophic and oligotrophic dominated communities were independent of environmental dissimilarity and reflected distance. Changes in community composition were best modeled by longitude for free-living communities and dissolved oxygen for mixed communities of free-living and particle-associated bacteria.;While I was able to identify changes in pattern of abundance between taxa and function in Chapter 1, I used deeper sequencing of communities of lower diversity to assemble sequence fragments into population genomes and inform the process of coral reef microbialization in Chapter 2. Coral reefs are undergoing microbialization as labile carbon shifts from higher trophic levels (fish and sharks) into the microbial food web fueling the growth of super-heterotrophic bacteria and causing higher rates of coral disease. Changes in super-heterotroph abundance are correlated to the dominant benthic organisms shifting from coral to algae dominated. While the scarcity of super-heterotrophs in the microbial community hinders deep sequencing, I enriched for super-heterotrophs after pre-exposure of water column microbiomes to benthic organisms. Enriched communities were less diverse than native water and healthy and diseased coral, Mussismilia braziliensis, and I assembled subpopulations of super-heterotrophs, Vibrio, Pseudoalteromonas and the sulfur oxidizing Arcobacter. The subpopulations had greater number of genes compared with cultured isolates from NCBI and therefore I defined the coral reef ecotype of these species. The coral reef Vibrio ecotype had more genes for the metabolism of carbon and nitrogen sources that are typically found in mucus and stored by corals. The coral reef Pseudoalteromonas ecotype had more genes associated with anaerobic metabolism which occurs on coral reefs at night when algae and coral respire. The coral reef Arcobacter ecotype was composed of sequences predominantly from coral and crustose coralline algae exposed communities and had more secretion genes and genes for the degradation of complex carbons and phosphates than cultured Arcobacter. Coral reef Arcobacter may be under greater competition for resources with super-heterotrophs and by taking advantage of coral derived sulfur can utilize these less labile resources, thus Arcobacter are more competitive than can be predicted from cultured representatives. I identified genes in the microbial community that could not be predicted form known organisms and may become enriched upon microbialization and cause coral degradation affecting the functioning of coral reef ecosystems.;The microbial communities of Chapter 2 were influenced by the different nutrient resources from each benthic organism. In Chapter 3, the nutrient (kelp) resource was kept consistent and monitored through time while manipulating temperature and sterilization to explore how the external environment affects microbial succession. Decomposing alga, giant kelp, Macrocystis pyrifera, is the primary food source of many marine and terrestrial organisms in temperature environment. However, microbes may play a role in regulating nutritional quality of this primary producer. Fresh kelp blades were divided into four treatments of sterilized/non-sterilized and 12 and 22 °C. Subsampled at day 0, 3 and 12 showed that while kelp tissue and bacterial abundance did not change significantly with time or treatment the changes in microbial community taxa and function showed strong successional changes. A successional change in dominated genera occurred from Pseudomonas to Pseudoalteromonas to Sulfitobacter. Taxonomic composition became increasingly similar and less diverse over time. Functional composition, also distinct through time, was most consistent at day three with no change in diversity. Microbial communities followed a succession in which both taxa and function indicated a transition from a biofilm adapted to the carbon and antifouling properties of live kelp, to a biofilm dominated by competitive copiotrophs utilizing transport systems, to a biolfilm of sulfur oxidizing oligotophs decomposing fatty acids and derivatives. Genome assembly reveal these changes in functional strategy were only partially attributed to the dominant genera, suggesting that rare organism contribute to microbial processes.;While each Chapter represented microbial ecology at different scales, there is a consistent pattern of disparity between taxonomic and functional composition, and a consistent pattern in the transition of trophic strategies in marine ecosystems. Functional changes across environments was greatest in communities dominated by competitive heterotrophic bacteria. The macroecological patterns of taxa and function showed the functional composition of communities, including copiotrophs and eutrophs, were selected for by both environment and distance. The heterotrophic fractions of coral reefs proved to be similarly driven by environmental selection, via nutrient availability, as I was able to identify functional characteristics that defined the coral reef ecotype of the dominant super heterotrophs that could not be predicted from cultured isolates. In kelp decomposition, despite the least diversity and most consistent taxonomic classification at late stages of decomposition, functional similarity was greatest in early stages of kelp decomposition. These studies demonstrate that the functional potential of a community cannot be fully assumed from the taxonomic characterization. Despite this discontinuity, there was a consistent pattern in which communities of nutrient rich resources, particle associated, nutrient rich media or algal tissue take on two dominant trophic strategies, 1) a highly competitive heterotrophic fraction in which Vibrio and Pseudoalteromonas were consistently represented and known competitive biofilm producers and 2) an alternate dominant metabolic strategy that utilize sulfur oxidation as a source of energy, thus allowing the sulfur oxidizing bacteria to scavenge for complex carbons and organophosphates. Arcobacter was the dominant sulfur oxidizing bacteria identified on coral reefs and were able to compete with Vibrio and Pseudoalteromonas when exposed to organisms rich in sulfur. As kelp decomposed, Sulfitobacter dominated later stages of alga ti.