|In this dissertation, I aimed to characterize the microbiota of finfish including identification of the bacteria present as well as the factors that influence their composition. I examined the microbiota of the skin, gill, gut, and/or blood of 7 marine and 3 freshwater fish species. I looked at the impact of fish species, geographic location, season, DNA extraction protocol, and oil exposure on bacterial community structure. Methods used included ribosomal intergenic spacer analysis (RISA) for identification of patterns in bacterial community structure followed by sequencing techniques to determine the bacteria responsible for observed differences. My research indicated that fish species exerts a stronger influence on fish microbiota structure than environmental parameters. Studies included on the skin and gut indicated a species-specific portion of the microbiota that remained stable across various locations and seasons as well as exposure to varying levels of oil. These results challenge the current paradigm that the microbiota of fishes simply reflects that of the surrounding water. My results also indicate that choice of DNA extraction protocol can greatly influence the observed diversity in the fish gut microbiota. Finally, analysis of the microbiota from the blood of apparently healthy fish revealed high bacterial diversity that was similar in structure to that of the gill. Thus isolation of bacteria from the blood or internal organs of a diseased fish may not be sufficient to identify the causative agent of disease.
Overall my work identified Proteobacteria as the dominant bacterial phyla in marine fish samples whereas Fusobacteria dominated the gut microbiota of freshwater fish species included in these studies. My results indicate that fish harbor microbial communities that are distinct from that of the surrounding water and that this community is primarily influenced by fish species. Species-specific microbiota were seen in both fish skin and gut, with influence from the surrounding environment on bacterial community structure indicating the presence of both core and transient members of these bacterial communities.