UC Irvine

Fish biodiversity has been in decline in recent decades due to several compounding anthropogenic factors on the landscape such as habitat fragmentation, urbanization, pollution, and invasive species introductions. The complexity of these challenges has necessitated multifaceted approaches to provide solutions to fisheries conservation issues. Microbiome research with application to conservation questions is a burgeoning field and, in combination with physiological metrics, has the potential to elucidate underlying mechanisms driving organismal responses to environmental changes. The goal of my dissertation was to understand how microbiome and physiology vary among populations of fish resident to different habitats and whether nonlethally collected samples (skin mucus, cloacal swabs, and feces) could provide a valid, repeatable way to collect and estimate information about the fish gut microbiome. In the first chapter, I utilized physiological and microbiome approaches to understand how wild mosquitofish (Gambusia affinis) resident to ponds with varying conditions differed from one another and their source population from which they had been removed for over 20 years. This study showed that mosquitofish show high levels of variation in their physiology and gut microbiomes with respect to their source populations. In the second chapter, I explored the effects of a common garden experiment on individuals collected from the same source populations as Chapter 1 and their offspring. This study further emphasized the plasticity of this species in response to changes in their environment as all morphological and microbial metrics converged in the common garden experiment. In the third chapter, I explored the feasibility of using nonlethal samples to estimate gut microbial diversity among California grunion (Leuresthes tenuis), topsmelt (Atherinops affinis), and jacksmelt (Atherinopsis californiensis). This study showed that there are significant differences between the gut microbiome and fecal, cloacal, and skin mucus samples within species and they were distinguishable among species, thus meaning that no nonlethal samples accurately estimate the gut microbiome of these fish but mucosal samples may provide valuable information regarding fish health. In summary, the gut microbiome is highly influenced by the environment and while nonlethal samples do not estimate gut microbial diversity, skin mucus samples may be a promising approach for fisheries conservation.