Background: Mucosal surfaces of fish provide cardinal defense against environmental pathogens and toxins, yet these external mucosae are also responsible for maintaining and regulating beneficial microbiota. To better our understanding of interactions between host, diet, and microbiota in finfish and how those interactions may vary across mucosal tissue, we used an integrative approach to characterize and compare immune biomarkers and microbiota across three mucosal tissues (skin, gill, and gut) in Atlantic salmon receiving a control diet or diets supplemented with mannan-oligosaccharides, coconut oil, or both. Dietary impacts on mucosal immunity were further evaluated by experimental ectoparasitic sea lice (Lepeophtheirus salmonis) challenge. Results: Fish grew to a final size of 646.5 g ± 35.8 during the 12-week trial, with no dietary effects on growth or sea lice resistance. Bacterial richness differed among the three tissues with the highest richness detected in the gill, followed by skin, then gut, although dietary effects on richness were only detected within skin and gill. Shannon diversity was reduced in the gut compared to skin and gill but was not influenced by diet. Microbiota communities clustered separately by tissue, with dietary impacts on phylogenetic composition only detected in the skin, although skin and gill communities showed greater overlap compared to the gut according to overall composition, differential abundance, and covariance networks. Inferred metagenomic functions revealed preliminary evidence for tissue-specific host–microbiota coadaptation, as putative microbiota functions showed ties to the physiology of each tissue. Immune gene expression profiles displayed tissue-specific signatures, yet dietary effects were also detected within each tissue and peripheral blood leukocytes. Procrustes analysis comparing sample-matched multivariate variation in microbiota composition to that of immune expression profiles indicated a highly significant correlation between datasets. Conclusions: Diets supplemented with functional ingredients, namely mannan-oligosaccharide, coconut oil, or a both, resulted in no difference in Atlantic salmon growth or resistance to sea lice infection. However, at the molecular level, functional ingredients caused physiologically relevant changes to mucosal microbiota and host immune expression. Putative tissue-specific metagenomic functions and the high correlation between expression profiles and microbiota composition suggest host and microbiota are interdependent and coadapted in a tissue-specific manner.

We tested the hypothesis that the growth of fish exposed to high temperatures can be limited by available food energy whereas that of fish exposed to low temperatures can be limited by their metabolic capacity to exploit the available food energy. Under laboratory conditions we evaluated growth (%/d) and marginal metabolic scope (MMS; L·g⁻¹·h⁻¹) of juvenile red drum Sciaenops ocellatus exposed to two levels of dietary energy, low (LE; ∼4.1 kJ/g) and high (HE; ∼15.9 kJ/g), and to three temperatures, approximately 19, 25, and 29°C, for a period of 6 weeks. Growth rate and MMS increased with temperature, but only growth rate increased with dietary energy and then only at the higher two temperatures. The simulation model Ecophys. Fish was employed to elucidate experimental results potentially confounded by interactions between fish weight and the controlling effects of temperature on metabolism. The simulated and observed results both showed that performance is enhanced at higher temperatures, especially for fish consuming the HE diet. A subsequent 6‐week‐long experiment confirmed results for fish fed the two diets at ambient temperature (∼26°C) and sought to further resolve responses by examining body condition indices and proximate composition. Additionally, these fish were assayed for differential cortisol response to 15 min of confinement stress. The feed efficiency, hepatosomatic index, intraperitoneal fat ratio, and whole‐body fat of fish fed the LE diet were significantly lower than those of fish fed the HE diet, indicating relative energy malnutrition in the LE group. As with MMS, no apparent differential effect of feed energy on the pre‐ or poststress values of plasma cortisol was observed. These findings support the ideas that red drum obtain greater metabolic capacity when they are exposed to a near‐optimal temperature and that their ability to transform that capacity into growth is maximized only when they are provided a nutritious, high‐energy diet.

Atlantic salmon (Salmo salar) producers harvest over 2.4 million metric tons each year. Salmon feed producers are now including higher levels of alternative proteins due to fish meal production limits and consumer demand for more efficient and sustainable ingredients. We examined the effects of histidine in smolt (~355 g/fish) and juvenile (~600 g/fish) North American St. John River strain Atlantic salmon. Salmon were fed graded levels of histidine (0.5, 0.7, 0.9, 1.1, 1.3, and 1.5%) to determine optimum levels necessary to support growth. In the first trial, only percent gain was ranged between 157 to 225%, while thermal growth coefficient (TGC) 1.6–2.0, and FCR ~1 were similar. In the smolt first trial, the final percent gain ranged between 157 and 225%, thermal growth coefficient (TGC) was 1.6–2.0, and feed conversion ratio (FCR) was approximately 1.0. Regression analysis indicated that maximum growth occurred at a dietary histidine level of 0.9% (p = .0012). In the juvenile trial, percent weight gain ranged 35–45%, TGC ranged from 1.4 to 1.9, and FCR ranged from 1.1 to 1.3; these responses were not different between diets. Cataracts were observed in only 3 fish between both studies (3% of the total population). Using regression analysis, both studies suggest histidine levels of at least 0.9% of the diet adequately support Atlantic salmon growth.

Geosmin and 2-methylisoborneol are volatile organic compounds of microbial origin that frequently occur in recirculating aquaculture systems and confer unpleasant odors and flavors to fish therein, even at extremely low concentrations. Existing analytical methods for these compounds in fish struggle to achieve enough sample throughput and are oftentimes not automated, requiring extensive hands-on preparation. We have developed methods for analyzing geosmin and 2-methylisoborneol from water and fish tissues, respectively, using a metal probe bearing a high-capacity sorptive extraction phase. A robust and quantitative detection was achieved from both water and fish tissues, with minimum detection limits of 1.2 ng/L for geosmin and 1.1 ng/L for 2-methylisoborneol from water and 18.1 ng/kg and 13.6 ng/kg, respectively, from fish tissue. These concentrations were well below human detection thresholds. Hence, we concluded that these methods could detect geosmin and 2-methylisoborneol before they became perceptible to humans. In contrast to other high-capacity sorptive extraction techniques, such as stir-bar sorptive extraction, this technique is fully automatable, dramatically improving throughput and precluding manual handling errors, while the durable design of the probe precludes breakage, such as is common with solid phase microextraction (SPME) fiber. This method is suitable for odorant monitoring in all water quality settings, as well as for the detection of off-flavor compounds in solid and semi-solid matrices.