UC Irvine

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.