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Abstract
This dissertation addresses four aspects of the biology of the fish gut. 1) What bacteria constitute the fish gut microbiome, how variable is the composition within a species; how different are the gut microflora of different fish species; and how do fish gut microbiomes different from those of other organisms that have been studied? 2) How do food quality and diet-associated bacteria affect the composition of the gut microbiome? 3) Ocean temperatures are expected to rise in the future in response to increased atmospheric CO2 concentrations, we know that the incidence of marine pathogenic Vibrios is higher during warm summer months and we know that Vibrios are common, and often dominant, taxa in the gut microbiome. Does increased habitat temperature influence the composition of the gut microbiome and specifically does the abundance of potentially pathogenic Vibrios increase when fish are held at higher water temperatures? 4) Conversely, can fish serve as refuges for these Vibrios when growth conditions are less favorable and as vectors for their distribution? We used 454-pyrosequencing to survey the 16S rRNA ribotypes in the gut microbiomes of 12 finfish and 3 shark species. Fish were selected to encompass herbivorous and carnivorous lifestyles, to have varied digestive physiologies, to represent pelagic and demersal species, and as representatives of a range of habitats from estuarine to marine. Proteobacteria ribotypes were present in all fish and often dominated the gut microflora community of many fish species. Firmicutes were also prevalent within the fish gut community, but at a lower relative abundance. Each species had a core gut microflora; however, no individual ribotype was present among all species suggesting that the gut microflora community is adapted to the autecological properties and physiological conditions of each fish species. We determined the effects of both diet quality and food-associated bacteria on gut microflora using mummichogs (F. heteroclitus) and pinfish (L. rhomboides) as model organisms. We identified a core gut microflora for these species and determined that food-associated microbiota strongly influenced the composition of the gut microflora in mummichogs, but not pinfish. We also tested the effect of temperature on the composition of gut microflora and on the occurrence of Vibrio spp. 16S rRNA and V. vulnificus vvh genes in the two model fish (mummichogs and pinfish) using clone libraries and quantitative PCR (qPCR). In a related set of experiments, we asked whether fish guts might serve as a refuge for Vibrio parahaemolyticus and Vibrio vulnificus during periods of sub-optimal environmental conditions. We found that both of these Vibrio species were present in the gut microbiome and that they could be transferred to other environmental reservoirs, implicating fish in the persistence and dispersal of these potential pathogens. Lastly, we examined the microbiome of the Atlantic blue crab (Callinectes sapidus) to address how the crab-associated bacterial community may affect crab, fish, and human health. INDEX WORDS: Fish gut; Gut microbiome; 16S rRNA; Gut microflora; 454-pyrosequencing; Shark gut; Blue crab microbiome; core gut microbiome; Proteobacteria; Firmicutes; Tenericutes; Vibrio sp.; Vibrio parahaemolyticus; Vibrio vulnificus; Trinectes maculatus; Bairdiella chrysoura; Lagodon rhomboides; Paralichthys lethostigma; Fundulus heteroclitus; Centropristis striata; Sciaeops ocellatus; Caranx hippos; Scomberomorus maculatus; Scomberomorus cavalla; Coryphaena hippurus; Sphyraena barracuda; Carcharhinus brevipinna; Rhizoprionodon terraenovae; Carcharhinus plumbeus; Quantitative PCR (qPCR); 16S rRNA clone library; fish health; crab health; human health