What an animal consumes and what an animal digests and assimilates for energetic demands are not always synonymous. Sharks, uniformly accepted as carnivores, have guts that are presumed to be well suited for a high protein diet. However, the bonnethead shark (Sphyrna tiburo), which is abundant in critical seagrass habitats, has been previously shown to consume copious amounts of seagrass (up to 62.1% of gut content mass), although it is unknown if they can digest and assimilate seagrass nutrients. To determine if bonnetheads digest seagrass nutrients, captive sharks were fed a 13C-labeled seagrass diet. Digestibility analyses, digestive enzyme assays and stable isotope analyses were used to determine the bonnethead shark’s capacity for digesting and assimilating seagrass material. Compound-specific stable isotope analysis showed that sharks assimilated seagrass carbon. Additionally, cellulose-component-degrading enzyme activities were detected in shark hindguts. I show that a coastal shark is digesting seagrass with at least moderate efficiency, which has ecological implications due to the stabilizing role of omnivory and nutrient transport within fragile seagrass ecosystems. Furthermore, the intestinal microbiome of vertebrates has been shown to play a crucial role in their digestive capabilities. This is particularly true for omnivores and herbivores that rely on enteric microbes to digest components of plant material that are indigestible endogenously. The bonnethead shark represents an interesting opportunity to explore how intestinal microbes provide a mechanism for omnivory in a marine vertebrate. I use digestive enzyme assays, histological imaging, measurements of microbial fermentation, and 16S rDNA sequencing to identify processes by which the bonnethead shark can digest and assimilate plant material. Finally, I delve into the functional morphology of the spiral intestine in sharks since this unique structure appears to be important in terms of housing enteric microbes and slowing the transit rate of digesta. I use CT scanning technology to provide a new way of investigating the spiral intestine. In addition to being one of the most conclusive investigations of shark nutritional physiology to date, my results highlight the importance combining studies of structure and function in order to better understand the nutritional physiology of organisms.

Marine invertebrates are a critical component to understanding how global change is affecting coastal marine environments. This dissertation encompasses two chapters investigating the relationships between marine invertebrates and their microbiomes in the context of pollution. Chapter one focuses on the emerging field of marine invertebrate larval microbiomes. Organisms heavily rely on consortial symbioses with microbes, yet little is known about marine invertebrate microbiomes, especially during early development. Using 16S short-read sequencing, bacterial composition and relative abundances of S. purpuratus gametes, larvae, habitat, and diet was tracked. The results show that the S. purpuratus larval microbiome changes in composition and relative abundance throughout development, with specific bacterial taxa associated with these variations. Notably, the S. purpuratus larval microbiome is unique compared to the microbiota associated with its habitat and diet. Furthermore, vertical transmission of bacterial genus Psychromonas via eggs is likely critical to S. purpuratus embryonic development, and horizontal transmission via sea water habitat is crucial to seeding the feeding S. purpuratus larval microbiome. These results help elucidate what bacterial taxa are important to developing marine invertebrates and how the microbiome is initially seeded. Chapter two investigates marine invertebrate Holobionts in the context of persistent pollutants used by the shipping industry. Organotins (OTCs), specifically TBT, continue to threaten coastal marine environments despite global bans. A literature review and meta-analysis was conducted to investigate the status of OTC pollution and to highlight the ongoing threat posed by TBT and other OTCs to marine invertebrates. The Holobiont is absent from OTC ecotoxicological studies on marine invertebrates, so an experiment investigating how TBT affects the microbiome of early stage S. purpuratus and the microbiota of its diet and habitat was also conducted. Results reveal that OTCs are still freshly input into the marine environment, impact a wide range of marine invertebrate phyla at low concentrations, and are not all regulated or well-studied. Re-prioritization of OTC research is required with a Holobiont-scale approach to address OTC contamination, especially because there are bacterial genera that are capable of OTC resistance and degradation. The experimental results reveal that TBT impacts the microbiota associated with S. purpuratus eggs and sea water, potentially compromising the vertical and horizontal transmission of bacteria important for marine invertebrate development. For effective and ongoing monitoring and management of OTC contamination in marine environments, understanding the effects of OTCs on marine invertebrate Holobionts is critical.

The physiological underpinnings of many marine host-pathogen systems are poorly understood, and even less is known about how climate change will affect the physiology of these systems. In the abalone and Rickettsiales-like organism (RLO) system, the RLO infects abalone digestive tissues and leads to extreme starvation and a characteristic “withering” of the gastropod foot. The withering syndrome-causing RLO (WS-RLO) has led to large declines in most abalone species on the northeastern Pacific coast, but disease resistance levels are species-specific and dependent on environmental temperature.

In order to clarify differential susceptibility in species whose geographic ranges overlap substantially (such as the highly susceptible Black Abalone and relatively resistant Green Abalone), I estimated the phylogenetic relationships of northeastern Pacific Haliotis species using concatenated data from two mitochondrial and two nuclear regions. The most susceptible species form a monophyletic grouping apart from the other northeastern Pacific taxa, implying that WS susceptibility could be a derived trait that traces back to the last common ancestor of this hypothesized clade, and that patterns of WS resistance and susceptibility have a quite deep evolutionary basis.

I then determined differences in gene expression in the digestive gland, the site of infection, in infected and uninfected Pinto Abalone over seven months. Pinto Abalone showed changes in gene expression at seven months post-infection, compared to naïve conspecifics. Differentially expressed gene groups were identified that likely correspond to advanced disease state and to general stress response of being held in captivity.

The third chapter examined the effects of heat stress on metabolic rate, digestibility, and digestive enzyme activities in Red Abalone and Pāua. Metabolic rates were significantly elevated in heat treatment animals. Digestibility did not significantly change, but this may be balanced by changes in transit time and total intake. Digestive enzyme activities changed independently, with amylase remaining the same, maltase increasing, and trypsin decreasing.

In summary, WS susceptibility follows a phylogenetic pattern. Genes associated with immune and hunger are upregulated, but protein transport and reproduction are downregulated in infected Pinto Abalone guts. Heat stress leads to metabolic rate increases, digestibility decreases, and digestive enzyme changes in abalone.

A population of Italian Wall Lizards (Podarcis sicula) on a small island in Croatia has become primarily herbivorous and morphologically distinct from its source population on a nearby island in ~30 generations, making it a compelling example of rapid evolution. What changes in digestive physiology and morphology have facilitated this switch to a novel diet? How does this dietary shift affect digestive performance? Do these accommodations for plant eating vary through time or with aspects of the lizards’ life history? I compared gut size and histology, eight digestive enzyme activities, and products of microbial fermentation across the two island populations, with selected comparisons to a mainland outgroup of P. sicula. The newly omnivorous population had several targeted biochemical differences in their hindguts compared to their source population, but no large-scale changes in physiology or gut morphology to match the scale and direction of divergence in their diets. In fact, island-mainland effects were far more prominent, even between insectivorous populations.

To test digestive performance, in the lab I fed lizards insect, mixed, or plant diets daily (high frequency, island males only) or on alternating days (low frequency, island and mainland males and females). When fed with high frequency, the newly omnivorous population was better at digesting plant proteins than their source population counterparts. However, when feed a low frequency, the males did not differ by population on any diet type. The females from the insectivorous source population, however, digested insect diets less efficiently than the other two populations.

To better elucidate dietary differences between the new and source populations lizards, I used stable isotope analyses to track 13C and 15N enrichment in their livers in concert with measurements of body and gut size over time and in males and females. Isotopic enrichment and gut length vary considerably by both year and season and suggest that the diet these lizards actually digest is not as different between the populations as stomach contents have suggested. Measurements of six digestive enzymes show differing patterns between populations depending on season and sex. The lizards’ responses to this dietary shift are dependent on multiple contexts.

What an animal eats and how it digests its food determines that animal’s contribution to its ecosystem. However, the nutritional physiology (including digestion) of animals is commonly overlooked, even though such data are needed for conservation of many ecosystems. This is particularly true for wild fishes in comparison to terrestrial vertebrates or even fishes farmed for aquaculture. The goal of my dissertation is to understand how prickleback fishes specialize to use specific resources, and how their nutritional physiology impacts their roles in their environment. I aimed to address the research gap in our understanding of dietary specialization and fish nutritional physiology, which are topics that I briefly review in the first chapter of my dissertation.In the second chapter, I integrated nutritional physiology and transcriptomics to further our understanding of digestive system plasticity in response to dietary perturbations. This study showed that prickleback fishes with different diets can respond to dietary perturbations in different ways. Our dataset elegantly shows how gut length of fishes change with dietary perturbations, even within a single species over a four-week feeding experiment. Although there were hundreds of genes differentially expressed among the three diet groups in the intestine (pyloric ceca and mid-intestine), three of the four species didn’t appreciably alter gene expression in the liver in response to different diets in the laboratory. Thus, we find a species-specific pattern in liver gene expression and metabolic pathways within prickleback fishes. In the third chapter of my dissertation, I aimed to advance our understanding of the factors that can influence gut physiology and function to provide insight into ecological adaptations and potential impacts on ecosystem dynamics. I investigated the effects of different diets that vary in protein content, on the physiology, host gene expression, and gut microbiome of Cebidichthys violaceus, a marine herbivorous fish. This integrative study highlighted the complex interactions between diet, gut physiology, gene expression and the hindgut microbiome in a marine herbivorous fish. Interactions between gut microbes and animal hosts impact the physiology and health of animals, yet we lack a thorough understanding of the determinants of gut microbial community structure. In chapter four of my dissertation, I examined the factors that shape the gut microbial communities of prickleback fishes within the context of their environment, diet, and genetics. We discovered that changes in the gut microbiome were linked more to individual differences and species identity within closely-related fishes living in the same area, rather than being primarily influenced by diet or location. In summary, dietary perturbations can alter the gut physiology, transcriptome, and microbiome of prickleback fishes. My dissertation work advances our understanding of dietary specialization in vertebrates and fish nutritional physiology.