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We investigated changes in the metabolome in juvenile red drum (Sciaenops ocellatus) induced by increasing amounts of soybean meal (0% to 60%) in extruded, fishmeal-free diets using a nuclear magnetic resonance spectroscopy (NMR)-based metabolomics approach in a 12-week feeding trial. All of the diets were composed of ≈40% total crude protein, ≈11% total crude lipid and were energetically balanced. A fishmeal-containing, commercial extruded diet was used as a control diet throughout the trial. Each week, liver, muscle, intestine and plasma samples were collected and analyzed by NMR to provide a "snapshot" of the metabolome at different time points. Results indicate significant time-dependence of the metabolic profiles in various tissues with stable metabolomic profiles forming after about 9-weeks on the experimental diets. We identify a previously unexploited biomarker of potential dietary stress (N‑formimino‑l‑glutamate (FIGLU)) in the fish that may prove to be useful for optimization of alternative diet formulations.

Commercial aquaculture feeds rely heavily on fishmeal and fish oil, which can be expensive and ecologically unsustainable. To evaluate the efficacy of reduced fishmeal diets for outgrowth, a dietary study was conducted on the finfish cobia, Rachycentron canadum . NMR-based metabolomic techniques were used to assess the effect of decreasing dietary fishmeal on the health of the cobia. Filtered serum 1 H NMR spectra analysed by principal components analysis (PCA) showed cobia fed reduced fishmeal diets were metabolically different than cobia on control diets. In particular, tyrosine and betaine increased in cobia fed reduced fishmeal diets while glucose decreased, suggesting that these cobia were not receiving the necessary nutritional components required for energy and growth. The formulated control diet contributed to enriched growth and significantly elevated lactate levels suggesting enhanced gut microflora metabolism in response to dietary components. The results show that NMR-based metabolomic analysis is a useful tool in aquaculture studies.

Microalgae hold a key role in the diet of the world's highest-valued seafood species, Pacific white shrimp Litopenaeus vannamei, but ingestion, digestion, and feeding mechanisms employed for consuming suspended microbes are not well studied. The goal of this work was to determine whether juvenile L. vannamei could consume and digest several microbes of varying sizes and structures in suspended monocultures. Diatoms Thalassiosira weissflogii and Amphiprora sp., eustigmatophyte Nannochloropsis salina, and cyanobacterium Synechococcus bacillarus were chosen based upon their common occurrence in intensive shrimp aquaculture systems. Juvenile 2 g L. vannamei, previously starved for 24 h, were individually stocked in aerated flasks containing axenic monocultures of T. weissflogii, Amphiprora sp., N. salina or S. bacillarus for 15, 30, 60, and 90 min. After designated immersion times, shrimp were dissected for collection of stomach and intestine content samples. Fluorometry was used to measure chlorophyll a (μg/g) within the stomach and intestine contents at each time increment. Counts of intact cells (cells/g) within the stomach and intestine contents were completed for shrimp that had been immersed for 60 min. Shrimp demonstrated a sweeping behavior of the third maxillipeds during submersion in some algal cultures, which led to examination through scanning electron microscope photography. Counts of intact cells and chlorophyll a levels in the stomach and intestine indicated that juvenile shrimp actively ingested and digested T. weissflogii and Amphiprora sp. from suspended monocultures. Diatom consumption and digestion were evident across all immersion times, with increasing levels of chlorophyll a in stomach samples up to but not significantly beyond 60 min, indicating that the experimental time period represented a continuous feeding period and spanned the gut passage time. Shrimp were able to ingest S. bacillarus and N. salina to a very limited degree, but there was no evidence of digestion of these cells. Examination under the scanning electron microscope revealed that the third maxillipeds have net-like setae which could potentially select for microorganism > 10 μm in size. Since this cell size reflected the difference between those cells consumed or not consumed in this study, we hypothesize that these appendages may be used by juvenile L. vannamei to filter food particles. These observations provide valuable insight regarding this shrimp's ability to capture and digest microalgae both within its natural environment and in aquaculture systems.

Minimal-exchange, intensive culture systems require little, if any, water exchange and have high animal stocking densities. Intensive nutrient inputs lead to an abundant community of microorganisms. These microbes are partially contained within suspended “biofloc” particles and contribute to water quality maintenance and provision of supplemental nutrition to the culture species. Optimal function of minimal-exchange, intensive systems is likely dependent on the structure of the microbial communities within them. This document offers a short review of microbial groups important for intensive marine aquaculture and descriptions of three methods for quantifying their abundance. The document also describes an experiment during which these methods were used to monitor the effects of partial biofloc removal on microbe abundance. The first method uses light microscopy, with the option of epifluorescence, along with a ranking system to enumerate the abundance of microbial taxa. The second method exclusively uses epifluorescence to illuminate chlorophyll and cyanobacteria pigments. Images are taken of each fluorescing group of pigments and processed using image analysis software to quantify the respective abundance of the two pigment types. Using the third method, changes in bacterial abundance were determined by gas chromatographic measurement of bacteria-specific fatty acids in solvent extracted water column lipids. Using these techniques, it was determined that removing solids from the culture water significantly (P ≤ 0.01) reduced the abundance of nematodes, rotifers, cyanobacteria, and bacteria. Understanding microbial composition and the effects that management protocols have on that composition may help system managers make better informed decisions.

In minimal-exchange, superintensive culture systems, the flocculated (biofloc) particles that accumulate may provide benefits for cultured shrimp; however, excessive particle accumulation can hinder shrimp performance. Also, the shrimp aquaculture industry is reliant on marine fish-based feeds. Using these products can lead to exploitation of marine resources, the introduction of contaminants to cultured shrimp, and unstable production costs. This study examined the use of simple, side-stream settling chambers as a means of controlling the abundance of particles in the water column and demonstrated the effects on water quality and shrimp production. The study also compared water quality and shrimp production parameters between a commercial, fish-based diet and a diet formulated almost entirely from vegetarian components, with expelled soybean meal as its principle protein source. The fish-based diet and the plant-based diet each contained 35.7% and 36.4% crude protein and 11.0% and 10.8% total lipid, respectively. The experiment was conducted in 3.35 m diameter, outdoor tanks, shrimp were stocked at 460 m − 3 and grown for 12 weeks. By the end of the experiment, settling chambers had removed 59% of suspended solids, decreased turbidity by 57%, reduced nitrate–nitrogen concentration by 60%, reduced phosphate concentration by 61%, and caused a 33% increase in alkalinity, all highly significant effects. Settling chambers also contributed to significantly improved shrimp feed conversion ratio, biomass, growth rate, and final weight ( P = 0.002, 0.006, − 3 ) was 41% greater in treatments with solids management than those without. Shrimp survival was not statistically different with or without settling chambers. Water quality parameters were not statistically different between the two diet types, except phosphate concentration which, by the end of the experiment, was 34% lower in the tanks receiving the plant-based diet. Shrimp production parameters were not statistically different between the two diets. The study showed that controlling the concentration of particles in superintensive shrimp culture systems can significantly improve water quality and shrimp production. Also, an environmentally friendly and potentially economical plant-based diet can produce results comparable to a fish-based feed in superintensive shrimp culture systems.

Gross and net photosynthesis, and water column respiration of a super-intensive Litopenaeus vannamei raceway culture with zero water exchange were measured over 21 weeks using the light and dark bottle method. Spearman correlation analysis was used to explore the relationship of these parameters with other water quality parameters (O2, temperature, pH, alkalinity, TAN, NO2, NO3, dissolved orthophosphate, turbidity, TSS and VSS) and of shrimp performance based on growth rate and feed conversion rate. Net photosynthesis generally had negative values, indicating that the system was predominantly heterotrophic. Gross photosynthesis was significantly related only with VSS, and water column respiration was related only with turbidity. Shrimp growth rate increased with higher temperature and dropped with higher pH. Nitrite had a strong inverse relationship with shrimp growth rate (R2 = 0.8044, p