ABSTRACTBIOTIC AND ABIOTIC FACTORS INFLUENCE FORMATION AND ONTOGENIC DYNAMICS OF MOLECULARLY DEFINED GASTRO-INTESTINAL MICROBIAL COMMUNITIES IN LAKE STURGEON (Acipenser fulvescens) AND CHANNEL CATFISH (Ictalurus punctatus).ByShairah Abdul RazakGastrointestinal (GI, gut) microbial communities (microbiota/ microbiomes) play essential roles in host development and physiology. During early life stages, fish gut microbiome composition is shaped by complex interactions of factors including dispersal of bacteria from the surrounding water, age-dependent changes in the gut ecosystem, and changes in dietary regimes. To investigate ecological processes that generate and maintain compositional patterns of gut microbiome diversity, I integrated molecular methods with experimental gut microbiome research and community ecology theory in two important fish species, lake sturgeon (Acipenser fulvescens) and channel catfish (Ictalurus punctatus) during early larval stages. Sequence reads of 16S rRNA gene were analyzed using multivariate ordination methods based on Bray-Curtis distance matrices followed by hypothesis testing using permutational multivariate analysis of variance (PERMANOVA). In the first chapter, sturgeon larvae were raised in four rearing hatchery treatments representing a combination of two factors: water source (stream vs ground water) and diet (Artemia vs Artemia supplemented with detritus). As fish grew, microbiota shifted from dominance by phyla Proteobacteria to Firmicutes. Water possibly served as the primary bacterial inoculant during early (pre-feeding) stages of development. Neutrality tests indicated that neutral processes were not strongly structuring community composition. Sturgeon gut microenvironment appears to have selected for microbial taxa, regardless of differences in treatments. The second chapter focused on alteration of gut microbiota modulated by diet and nutrient availability. Sturgeon gut microbiota differed among fish raised on different dietary regimes (control vs transition). Gut microbiota of fish exposed to a dietary transition from Artemia to frozen Chironomids were dominated by the genus Aeromonas (phylum Proteobacteria) while fish from the control group were dominated by genus Clostridium_sensu_stricto (phylum Firmicutes) at the end of experiment. Screening for cultured bacteria with extracellular protease activity revealed that fish fed with Chironomids harbored protease-positive taxa from phylogenetically distinct and more diverse clades. Next, I documented the impact of prophylactic treatments (Chloromine-T, NaCl followed by hydrogen peroxide; and hydrogen peroxide) on lake sturgeon larvae gut microbiota compared to ambient environmental conditions (control) using hatchery-produced and wild-origin fish. Gut microbiome responses to prophylactic treatments were found to be inconsistent across fish genotypes. The last chapter documented variability in channel catfish larval gut microbiome composition among families and nursery ponds characterized by different rearing water in a pond aquaculture setting. I documented a strong influence of rearing environment (pond water) on gut microbiome colonization. Gut microbiome composition was dominated by different phyla before (Proteobacteria) vs after pond stocking (Firmicutes). Different predominant genera were also detected over time. Results from my research inform community ecology theory concerning effects of stochastic and deterministic forces affecting microbial community establishment and stability. This research is also relevant for downstream applications incorporating microbial-based management strategies in commercial and conservation aquaculture.
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