HCNSO Student Theses and Dissertations

Defense Date


Document Type


Degree Name

M.S. Marine Biology

First Advisor

Jose Lopez

Second Advisor

Robert Smith

Third Advisor

Nicholas Aumen


South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, and the surrounding farm lands. I hypothesized that there would be noticeable shifts in the microbial communities (also known as “microbiomes”) at the agriculture and urban sites due to anthropogenic influences such as agricultural and sewage runoff. It is also hypothesized that the diversity and stability of these sites will differ from the natural environment Grassy Waters Preserve (GWP), which we studied as a control. The northern section of GWP is a rain-fed Everglades ecosystem with little influence from manmade canal systems, so GWP can represent wetlands before human influences. High-throughput 16s rRNA sequencing was conducted on 112 GWP, canal, and agricultural water samples taken over a one-year period from September 2016 to November 2017. Data were processed in Qiime2 using DADA2 and resulted in 67732 unique taxa. Nineteen metadata factors were measured for 87 of the sampling points to investigate environmental effects. These factors explained 25% (r2=0.25, p=0.002) of the variation between sample locations. Conductivity was found to have the highest effect on microbial diversity (r2=0.078, p=0.002) while latitude and month also significantly influenced the microbial makeup. Urban and agricultural sites were found to have higher stability with lower variation in microbiomes over the course of study. The GWP site was found to have a high seasonality, probably due to its dependence on rain. The most abundant taxa for all sites (urban, agriculture, and control) were; family Spirochaetaceae, phylum Actinobacteria, and family Burkholderiaceae, respectively. Contamination of GWP and canal sites was also investigated using SourceTracker code. Intracoastal waters that receive canal water were found to be heavily influenced in the peak wet season when there is high flow through from the canals. GWP had little influence from farm lands compared to a high influence of agriculture on the urban sites.