Spring 2023

Document Type

Master's Thesis (Open Access)

Degree Name

Master of Science (M.S.)


Applied Environmental Science


Coastal environments are some of the most productive and valuable ecosystems in the world while also having some of the highest levels of non-point source pollution. Genetic analyses of bacteria have provided scientists with a better understanding of how pollution affects functional potential within the environment. This is done by evaluating the presence/absence of particular taxonomic classifications as well as genes and gene functional groups. This study aimed to use genetic information isolated from bacteria found in two coastal watersheds, as well as a field bioremediation system, to learn how bacterial diversity and taxonomic groups differ between locations, the potential of sampled environments to remediate pollutants, and which functional groups are significantly represented within different locations. Amplicon sequencing of the 16S rRNA gene as well as whole metagenome shotgun sequencing were performed using isolated DNA from sediment samples collected from sites in two coastal watersheds, the Salinas River Watershed and the Tijuana River Watershed. Amplicon sequencing showed significant differences in alpha and beta diversity within different location sites. Beta diversity was also observed to be significantly affected by various environmental variables within location sites. Whole metagenome shotgun sequencing produced 60 high-quality dereplicated metagenomically assembled genomes (MAGs). MAGs from two location sites were found to have all genes necessary to complete two functional KEGG pathways related to agricultural runoff reduction. Hierarchical clustering of sequences within the high-quality dereplicated MAGs was also observed revealing over and under representation of 7 and 19 Level-3 GO categories, respectively. The genetic properties of bacteria found within this study’s sampling locations provides local policymakers with information related to an ongoing bioremediation project as well as the function of the ecosystems that are vital for the regional and national economy.