The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (Oncorhynchus mykiss) is one such species in which the strain ARS-Sel has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth and plasma and digesta metabolomes between ARS-Sel and two commercial strains (CS-1 and CS-2), when fed plant-protein (PM) and fishmeal-based (FM) diets, and to correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-Sel fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma and digesta metabolite profiles of ARS-Sel and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of enteritis development, which was confirmed by intestinal histology. As reported in previous studies, the ARS-Sel strain performed better than the commercial strains when fed the PM diet. Our findings also suggest that metabolomic profiles of plasma and digesta, samples of which can be obtained through non-lethal methods, offer valuable insight in monitoring the occurrence of enteritis in carnivorous aquaculture species due to plant-based diets.

Replacement of fishmeal (FM) with alternative plant proteins, especially soybean meal (SBM), can cause a diarrhea-like symptom in rainbow trout (RBT), characterized by very fine fecal particles. These fines do not settle out in raceway effluent for collection and can contribute to pollution of receiving waters. In this study, two experiments were conducted. Experiment 1 examined effects of nine protein sources (sardine meal, menhaden meal, soy protein concentrates (SPC) (three types), SBM (regular and high protein), corn protein concentrate (CPC), and poultry by-product meal (PBM)) on fecal particle size distribution. Results showed that all five soy-based diets produced feces in RBT having 75.7–89.3% fines and only about 1.0% large particles, while the remaining four diets yielded feces having a balanced particle size distribution. Oligosaccharides present naturally in soy products, thought to contribute fecal fines, were not correlated to fecal particle size classes. Instead, high crude fiber content in soy-based diets was found to be responsible for unbalanced fecal particle distribution in RBT. Experiment 2 examined if improvements in formulation could reduce the negative effect of soy-based ingredients. Eight practical diets (FM, SPC, SPC + 0.3% guar gum, PBM + CPC, PBM + CPC + 20 or 30% SPC, and PBM + CPC + 20 or 30% SPC + 0.3% guar gum) were formulated to contain 40% protein and 20% lipid. Results showed that diets containing mixtures of PBM, CPC, and 20% or 30% SPC plus guar gum produced trout feces with the highest percentage of large particles and lowest of fines, while the diet containing SPC alone (56%) plus guar gum resulted in trout feces having the highest content of mid-size particles. It was concluded that crude fiber in soy protein products (SBM and SPC) caused undesirable fecal particle profiles in RBT, and the addition of guar gum could significantly alleviate this negative effect.

This study aims to construct a novel and sustainable approach for remediating aquaculture-generated water contamination using various engineered biochars. Particularly, this study focuses on capturing nitrogen and phosphorus from downstream water of commercial fish farms in Magic Valley, Idaho, containing approximately 2.26 mg/L of nitrogen and 0.15 mg/L of phosphorous. The results indicate that the proposed approach can improve downstream waters by adsorbing micronutrients (e.g., nitrogen-ammonia, nitrate-n + nitrite-n, and total phosphorus). Water treatment time and biochar pH are two key parameters strongly associated with adsorbed compounds. Molecular-level characterization of solvent-extracted organics from biochar materials (before and after water treatment) suggests increased levels of highly oxygenated molecules as a function of increasing water treatment time. Also, the results show the enrichment in organic species with higher molecular weight and increased double bond equivalents, with a compositional range similar to that of dissolved organic matter. Upon water treatment, extracted organics revealed higher abundances of compounds with higher H/C and O/C ratios. The engineered biochars, after water treatment, can be reused as nutrient-rich fertilizers. This study concluded that the engineered biochars could sequester more nitrogen and phosphorous over time. Also, the proposed approach can simultaneously increase fish production capacity and support the aquaculture industry in different regions by improving water quality and enabling aquaculture expansion.

Utilizing RNA-seq, this study compared the transcriptomic responses of three improved strains (VSel, PSel, and CSel) of rainbow trout fry during acute stages of challenge with infectious hematopoietic necrosis virus (IHNV). The VSel strain has been selected for resistance against the specific strain of IHNV used in our challenge, PSel has undergone selection for utilization of plant-protein based feeds and previously has shown elevated non-specific disease resistance despite no disease related selection pressures, and the final strain, CSel, is a commercial strain that has been domesticated for several years but has not been selected for specific viral disease resistance. Following a 21-day IHNV challenge, Kaplan-Meier survival estimator curves and cumulative percent mortality (CPM) showed significant differences in IHNV resistance across strains: VSel - 19.3 ± 5.0%, PSel - 67. ± 3.03%, CSel - 94.6 ± 4.1% CPM. To evaluate acute responses to IHNV infection, whole blood, as well as samples from the kidney, liver, and intestine, were collected at 0, 4, 12, 24, and 48 h post infection (hpi). Serum lysozyme activity, a marker of non-specific innate immunity, showed strain and temporal effects during the acute infection phase with PSel showing the highest activity at 0 and 48 hpi. Differential gene expression responses were detected, with varying degrees, in all tissues, both between strains, as well as across acute timepoints within strains. The VSel strain showed upregulation for a particular subset of viral recognition genes during early infection timepoints and rather limited upregulation of immune genes later, while maintaining and reactivating metabolic pathways. The CSel strain showed a downregulation of metabolic related genes and a limited upregulation of immune genes, while the PSel strain showed similar downregulation of metabolic genes during acute infection, yet when compared to the CSel strain, showed a more robust innate immune response. Evaluation of upregulated immune response genes, as well as interferon-related genes showed the PSel strain to have the greatest number of uniquely upregulated immune genes in both the kidney and intestine, with CSel and PSel showing a similar number of such genes upregulated in liver. A moderate number of immune response genes were shared between PSel and CSel in all tissues, though both PSel and VSel showed a high number of uniquely overexpressed immune response genes in the kidney, and PSel showed the highest number of uniquely upregulated interferon related genes in the intestine. Overall, the VSel response was unique from the CSel with very little overlap in activated immune responses. Findings from this study highlight the disparity in IHNV resistance among genetic strains of rainbow trout, while identifying molecular mechanisms underlying differences in disease phenotypes. Furthermore, our results on trout strains with distinct selection backgrounds yields comparative insights into the adaptive gains brought about by selection programs for pathogen-specific disease resistance, as well as the non-specific immune enhancement associated with selection for utilization of plant-based diets.

Juvenile rainbow trout (125 ± 0.8 g) were fed a fishmeal control diet (C), a high soy protein concentrate diet (SP), a high soybean meal diet (HiS), or a diet with high levels of fermented soy protein concentrate (fSP) for 12 weeks in a tank system capable of receiving 1st and 3rd use water from a serial-reuse production hatchery. Water quality was generally lower in 3rd use compared to 1st use water and after passing through tanks (inflow vs. outflow). Total dissolved solids were significantly higher (p = 0.003) for 3rd use compared to 1st use water, and values were also higher (p < 0.001) for the fSP diet. Turbidity and ammonia were highest in tanks for trout fed the HiS and fSP and SP and fSP diets, respectively, but were characterized by high variation, which likely prevented the detection of significant differences. Weight gain (p < 0.001) and survival (p = 0.008) were significantly lower for trout in 3rd use compared to 1st use water. Trout fed the HiS diet were generally in poorer physiological condition with lower body fat stores (p = 0.05) and lower growth rate (p < 0.001) and survival (p = 0.05) compared to the other diets, which were similar. The expression of several stress-associated genes (FK506, DIO2, REGPS, Cyp1a, G6PH, GADD45a, and IRF-1) in the liver and gill showed that diet and water source affected their regulation. Replacement of FM by SP providing 50% of dietary protein promotes acceptable growth performance compared to an FM diet and was superior to HiS. The impacts of soy protein concentrate on water quality under commercial production conditions, however, require further study.

The United States (U.S.) has a nearly USD 17 billion seafood trade deficit annually. However, the U.S. aquaculture industry faces strict micronutrient (e.g., phosphorus and nitrogen) level mandates that negatively impact fish production, especially for the state of Idaho, which produces 70–75% of the nation’s rainbow trout. This study investigates the sustainability benefits of producing engineered biomaterials from lignocellulosic-based feedstocks near collection sites via portable biorefineries for use by fish farms to reduce eutrophication (oversupply of micronutrients) impacts. In this study, sustainability assessments are performed on a case study in southern Idaho, the largest U.S. commercial producer of rainbow trout. The results show that 20 and 60 min of water treatment, using small particle size biomaterial from lodgepole pine, has the highest total phosphorus removal rate, at 150–180 g of phosphorus per 1 metric ton of engineered biomaterials. The results of techno-economic and environmental impacts studies indicate that pinewood-based biomaterials production cost ranges from USD 213 USD 242 per ton and reduces the eutrophication potential by 5–17 kg PO₄eq/ton. Additionally, the environmental impact results show that the total greenhouse gas emission for biomaterial production is 47–54 kg CO₂eq/ton; however, the used biomaterials after water treatment can be sold for around USD 850 per ton as nutrient-rich soil conditioners. This study concluded that engineered biomaterials from lignocellulosic-based feedstocks could be a sustainable solution to the challenge that aquaculture faces, particularly capturing micronutrients from eutrophic water and reusing them as fertilizers.