Communities vary across space and time. In addition, they may vary differently at different spatial and temporal scales. It is well established that marine bacterial communities are temporally structured by seasons. However, there are other environmental changes that occur at different temporal scales. Here, we quantified the community variation at three temporal scales across three time series. We found that communities varied at the three time scales with the majority of community variation occurred within seasons. Additionally, we found that community variation correlated with different environmental variables at different temporal scales.

Next I wanted to identify the effect phylogenetic scale has on biodiversity patterns. Most of bacterial ecology defines a taxon as a group that shares more than 97% similarity of the 16S rRNA. However, these groups are not independent of each other. They share evolutionary history charted by divergences into different niches. In order to identify the role of phylogentic resolution on population dynamics, I undertook a 4.5-year sampling project and analysed the variation in relative abundance at different taxonomic levels (genus level, clade level, and subgroup level). I found that the frequency of variation increased as I moved to finer phylogentic resolutions. In addition, the correlation with temperature also changed by changing phylogentic resolution.

Finally, I wanted to identify antibiotic resistance genes in marine environments. Natural environments are quickly being discovered to harbor a number of antibiotic resistance genes. However, marine environments have been mostly overlooked even though they cover more than 70% of Earth's surface, and hold on the order of 1029 bacterial cells. As part of my dissertation, I wished to fill this knowledge gap. By using the culture independent method of functional metagenomics, I discovered genes that conferred antibiotic resistance. Of these genes, 28% were identified as previously known antibiotic resistance genes. The majority were unknown to confer resistance, but had activities similar to antibiotic resistance genes (e.g. transport pumps, enzymatic degradation, etc.). I also identified that the majority of these genes were found in marine bacteria, such as Pelagibacter, Roseobacter, and Prochlorococcus. Therefore, I have uncovered a potential global reservoir of antibiotic resistance genes.

Factors controlling the spatial distribution of bacterial diversity have been intensely studied, whereas less is known about temporal changes. To address this, we tested whether the mechanisms that underlie bacterial temporal β-diversity vary across different scales in three marine microbial communities. While seasonal turnover was detected, at least 73% of the community variation occurred at intra-seasonal temporal scales, suggesting that episodic events are important in structuring marine microbial communities. In addition, turnover at different temporal scales appeared to be driven by different factors. Intra-seasonal turnover was significantly correlated to environmental variables such as phosphate and silicate concentrations, while seasonal and interannual turnover were related to nitrate concentration and temporal distance. We observed a strong link between the magnitude of environmental variation and bacterial β-diversity in different communities. Analogous to spatial biogeography, we found different rates of community changes across temporal scales.

Extracellular enzymes are functional components of marine microbial communities that contribute to nutrient remineralization by catalyzing the degradation of organic substrates. Particularly in coastal environments, the magnitude of variation in enzyme activities across timescales is not well characterized. Therefore, we established the MICRO time series at Newport Pier, California, to assess enzyme activities and other ocean parameters at high temporal resolution in a coastal environment. We hypothesized that enzyme activities would vary most on daily to weekly timescales, but would also show repeatable seasonal patterns. In addition, we expected that activities would correlate with nutrient and chlorophyll concentrations, and that most enzyme activity would be bound to particles. We found that 34–48% of the variation in enzyme activity occurred at timescales <30 days. About 28–56% of the variance in seawater nutrient concentrations, chlorophyll concentrations, and ocean currents also occurred on this timescale. Only the enzyme β-glucosidase showed evidence of a repeatable seasonal pattern, with elevated activities in the spring months that correlated with spring phytoplankton blooms in the Southern California Bight. Most enzyme activities were weakly but positively correlated with nutrient concentrations (r = 0.24–0.31) and upwelling (r= 0.29–0.35). For the enzymes β-glucosidase and leucine aminopeptidase, most activity was bound to particles. However, 81.2% of alkaline phosphatase and 42.8% of N-acetyl-glucosaminidase activity was freely dissolved. These results suggest that enzyme-producing bacterial communities and nutrient dynamics in coastal environments vary substantially on short timescales (<30 days). Furthermore, the enzymes that degrade carbohydrates and proteins likely depend on microbial communities attached to particles, whereas phosphorus release may occur throughout the water column.