Estuarine microbial communities, including plankton, algae, and cyanobacteria, play important roles in nutrient cycling and food web structure. They are sensitive to changes in abiotic conditions and shifts in community composition can provide insight into estuarine ecosystem functioning. Therefore, monitoring these communities is essential for understanding and maintaining estuarine health. DNA metabarcoding is an emerging technique for enhancing biological monitoring, allowing for the detection of multiple species within a single sample. This dissertation first focuses on how methodological decisions impact DNA metabarcoding results and then implements these optimized methods to perform an assessment of community composition across the Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR). In Chapter 2, I compared seven different DNA extraction kits in regard to DNA yield, PCR inhibitor removal, and taxonomic resolution using 18S V9 and 16S V3-V4 amplicon sequencing. I found that extraction method choice significantly influenced DNA yield and PCR inhibition. Differences in richness were statistically significant but small, with all methods sharing 84-90% of resolved taxa. In Chapter 3, I employed these methods to characterize microbial eukaryotic and prokaryotic communities in the GTMNERR. Using univariate and multivariate statistical analyses, I evaluated relationships between richness, relative abundance, and β-diversity across ten sampling sites and 22 environmental variables, including dam management in the impounded Guana Lake. Results show that salinity, productivity, and nutrient ratios were strong drivers of microbial community structure and that dam status corresponded with shifts in nutrients, pigments, and diversity. Together, this research contributes both to methodological decision-making and a baseline understanding of how abiotic and anthropogenic conditions shape estuarine microbial communities.
Ashley Reaume
Dr. Michelle R. Gaither, Advisor
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