HCNSO Student Theses and Dissertations

Defense Date


Document Type


Degree Name

M.S. Marine Biology


Oceanographic Center

First Advisor

Jose V. Lopez

Second Advisor

Christopher Sinigalliano

Third Advisor

Donald McCorquodale


We applied culture-independent, next-generation sequencing (NGS) high throughput pyrosequencing, to characterize the microbial communities associated with near shore seawater in Broward County, FL. These waters flow over coral reef communities, which are part of the Florida reef tract, and are close to shore where bathers frequent. Through a close partnership with the NOAA FACE program, 38 total seawater samples were taken from 6 distinct locales -the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and the associated reef waters-over the course of one year. Tagged 16S rRNA amplicons were used to generate longitudinal taxonomic profiles of marine bacteria and archaea for one year. 236,322 rRNA quality checked sequences with an average length of 250 base pairs were generated. Sequences were found to vary significantly due to seasonal effects, but depth showed no significant correlation. The most abundant taxa among these samples included Synechococcus, Pelagibacteraceae (SAR11), Bacteroidetes, various Proteobacteria, and Archaea, such as Thermoplasmata. Other taxa found, albeit in low numbers, were the Thiotrichales, and some members of which can indicate pollution, the Alteromonadales, a biofilm forming order. Inlet sequences were found to be significantly different from the outfall and reef communities by various analyses. Unifrac analysis of microbial beta diversity showed a significant clustering pattern for the inlet samples. Precipitation during the three days before and after sampling was low meaning there was little to no high terrestrial runoff during the sampling days. Higher levels of turbidity were seen at the inlet sites and significantly affected the growth of surface colonizing and biofilm forming bacterial families such at the Rhodobacteraceae and Flavobacteriaceae. This study represents one of the first to apply NGS analyses for a deep analysis of microbial community dynamics in these S. Florida waters.

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