ORCID

0000-0002-3786-4457

Keywords

Metabarcoding, Estuaries, Plankton, Microbial Communites

Abstract

Estuarine microbial communities, including plankton, algae, and bacteria, 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 in the face of various physiochemical and anthropogenic stressors. 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 a year-long assessment of community composition across a northeast Florida estuary. In Chapter 2, I compared seven 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, while differences in richness between methods were statistically significant but small, with all methods sharing 84-90% of resolved taxa. These results suggest that the Qiagen PowerSoil Kit was most effective for obtaining high yields of uninhibited DNA from productive estuarine water samples. In Chapter 3, I employed these methods to characterize microbial eukaryotic and prokaryotic communities in the Guana Tolomato Matanzas National Estuarine Research Reserve. 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 parameters representing dam management in the impounded Guana Lake. Results show that salinity, nutrients, and nutrient ratios were strong drivers of microbial community structure and that dam status corresponded with shifts in nutrients, pigments, and community composition. Together, this research contributes both to methodological decision-making and a baseline understanding of how abiotic and anthropogenic conditions shape estuarine microbial communities.

Completion Date

2026

Semester

Spring

Committee Chair

Gaither, Michelle

Degree

Doctor of Philosophy (Ph.D.)

College

College of Sciences

Department

Biology

Format

PDF

Document Type

Dissertation

Identifier

DP0053182

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