Resting time before slaughter restores homeostasis, increases rigor mortis time and fillet quality of surubim Pseudoplatystoma spp.

This study assesses the respiratory dynamics related to stress parameters and resting time before slaughter, in the quality of surubim (Pseudopatystoma spp.) fillets. A completely randomized design was conducted using five treatments: resting time before slaughter of 0, 2, 4, 8 and 24 hours, with 15 fish sampled per treatment. Time 0 corresponded to the treatment without resting time, where the fish were slaughtered immediately after arriving at the processing plant. The resting time did not affect the electrolyte balance, hemoglobin, plasma, hepatic glycogen, myofibrillar fragmentation index (MFI) and water holding capacity (WHC) of surubins. However, with increased resting time, there was a significant decrease in muscle glycogen and an increase in blood pH and blood bicarbonate levels. Additionally, respiratory parameters showed an increase in pO2 and, consequently, in O2 saturation and a decrease in pCO2.The hematocrit and MCV values of the surubins after 24 hours of resting decreased significantly. In the first hours of resting, the highest values of erythrocytes and CHCM were observed. The lowest level of stress was observed for fish having 24 hours of resting. Fish having longer resting periods (8 and 24 hours) presented fillets with a higher pH (P <0.05) and the rigor mortis establishment time was shorter for the first 2 hours and 24 hours of resting time. There was a linear decrease in fillet lightness and an increase in the intensity of red (CIE a*) color up to 24 hours when resting was increased. In CIE b*, a linear decrease (P <0.05) of the yellow intensity of the fillets was observed as the surubim resting time increased. A resting time of 4 to 8 hours before slaughter is effective in reestablishing homeostasis after transporting surubim, providing fillets with higher quality and a greater length of the pre-rigor mortis period.

Biofilm and Sediment are Major Reservoirs of Virulent Aeromonas hydrophila (vAh) in Catfish Production Ponds.

The genus Aeromonas comprises more than 60 recognized species that include many important fish pathogens such as the causative agents of furunculosis and motile Aeromonas septicemia (MAS). Although MAS is typically considered a secondary infection, a new virulent A. hydrophila (vAh) strain has been causing devastating losses to the catfish industry in Alabama since 2009. The objective of this study was to characterize the spatiotemporal distribution of Aeromonas sp. and, specifically, vAh in a commercial catfish farm in western Alabama. We sampled biofilm, sediment, and water from three ponds during four consecutive months during the growing season. Total aerobic counts were between 8.8 × 105 and 1.5 × 106  CFU/mL but were significantly higher in biofilm and sediment than in water throughout the sampling period. Total Aeromonas counts in water samples significantly increased in all three ponds after the month of August and ranged from 7.8 × 103 to 4.9 × 104  CFU/mL. A similar trend was observed in biofilm and sediment samples for which total Aeromonas counts increased in samples taken in late summer to early fall. Over time, the concentration of Aeromonas in water samples decreased by one order of magnitude, while there was a significant increase in sediments as temperature dropped. The virulent vAh was detected in 35.4% of biofilm samples and 22.9% of sediment samples, suggesting that both environments serve as the major reservoir for this pathogen. Future monitoring efforts should focus on targeting sediment and biofilms since samples of these appear to naturally enrich for the presence of vAh and other Aeromonas species.

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Farm size, seining practices, and salt use: risk factors for Aeromonas hydrophila outbreaks in farm-raised catfish, Alabama, USA.

In freshwater aquaculture systems, Aeromonas hydrophila is usually considered to be an opportunistic pathogen most often associated with secondary bacterial infections. Since 2009, the U.S. catfish industry, especially in West Alabama, has been affected by mortality from a strain of A. hydrophila that has been acting as a primary pathogen. Tens of millions of pounds of catfish production have been lost as a consequence of this disease. This study used data from two whole-population farmer surveys to examine farm-level risk factors for two A. hydrophila outbreaks in foodsize Alabama catfish, one in 2009 (surveyed in 2010), and one in 2011 (surveyed in 2012). The response to the 2010 survey was 85% and the response to the 2012 survey was 82%. Univariate analyses were used to examine biologically plausible variables (farm size, pond stocking density, seine exposure, use of salt (NaCl) in ponds), and used categorical disease outcome and dependent variables. Farm size was included in bivariate analyses with the other variables, because it was a potential confounding variable. For both study years, the odds of an A. hydrophila outbreak were significantly greater for farms larger than the mean size (2009: mean=132 acres (53.4 hectares), odds ratio (OR)=8.2; 95% confidence interval (CI)=3.3-20.6, p<0.001; 2011: mean=116 acres (46.9 hectares), OR=5.3, CI=1.7-17.0, p=0.009). Compared with 42% of control farms, every case farm was seined by a commercial or processing plant seining crew in 2009. The bivariate analysis of the 2011 variable "average number of times each pond was seined per year" indicated that regardless of farm size, farms with ponds that were seined more than twice per year had a significantly greater odds of an A. hydrophila outbreak (OR=4.1, CI=1.2-14.4, p=0.02). For 2009, the results of the bivariate analyses of chloride concentrations indicated that farms that had chloride concentrations >135 ppm had a significantly lower odds of experiencing A. hydrophila outbreaks (OR=0.2, CI=0.05-0.6, p-value=0.004). To achieve economies of scale, catfish farmers raise fish on large farms at higher stocking densities, but this practice may result in increased susceptibility to disease outbreaks. Producers should prioritize implementing biosecurity measures such as improved seining practices and other management practices to protect fish grown at high population densities. Further work will determine what the detailed seining protocols should include, and whether the use of salt, and at what concentrations, reduces the risk of A. hydrophila outbreaks.