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The aim of this study was to characterize the transcriptional response of representative genes from the four crustin types (Type I, LvCrustin Ia-6 and LvCrustin Ia-8; Type II, Crustin Lv and Crustin-like Lv; Type III, LvSWD; and Type IV, LvSLPI) in circulating hemocytes and intestine of Litopenaeus vannamei shrimp using an immersion-based challenge with the Gram-negative pathogen Vibrio harveyi. Tissue distribution pattern analysis showed that transcripts of both Type I crustins and Crustin-like Lv were only quantifiable in the intestine and hemocytes, respectively. Comparatively, the basal mRNA levels of Crustin Lv, LvSWD, and LvSLPI were higher in circulating hemocytes than in the intestine. While the expression of Crustin Lv increased 2.4-fold change in the intestine at 12 h after the bacterial immersion challenge, the transcriptional levels of the other crustin genes remained unaltered in the analyzed immune-related tissues. In conclusion, crustins from L. vannamei exhibit a distinct pattern of basal gene expression in hemocytes and intestine and are differentially modulated in response to a Vibrio immersion challenge. [ABSTRACT FROM AUTHOR]

Simple Summary: Identification of differentially expressed genes (DEGs) between disease-resistant and -susceptible animals is a method to screen genes contributing to anti-disease. Previously, we found that there were few genes differentially expressed in hemocytes between V. parahaemolyticus-resistant and -susceptible shrimp. The present study hypothesized that these shrimp had different immune responses against pathogen infection and tested it using comparative transcriptome analysis. Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before infection. We considered that there should be different immune responses between them after a pathogen infection. Here, the transcriptome data of hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before and after a pathogen infection were compared. The results showed that there were 157 DEGs responsive to infection in V. parahaemolyticus-resistant shrimp, while 33 DEGs in V. parahaemolyticus-susceptible shrimp. DEGs in V. parahaemolyticus-resistant shrimp were mainly related to immune and glycolytic processes, while those in V. parahaemolyticus-susceptible shrimp were mainly related to metabolism, with only two DEGs in common. A further analysis of genes involved in glucose metabolism revealed that GLUT2, HK, FBP, and PCK1 were lowly expressed while PC were highly expressed in hemocytes of the V. parahaemolyticus-resistant shrimp, indicating that glucose metabolism in shrimp hemocytes was related to a V. parahaemolyticus infection. After the knockdown of PC, the expression of genes in Toll and IMD signaling pathways were down-regulated, indicating that glucose metabolism might function through regulating host immunity during V. parahaemolyticus infection. The results suggest that the immune responses between V. parahaemolyticus-resistant and -susceptible shrimp were apparently different, which probably contribute to their different V. parahaemolyticus resistance abilities. [ABSTRACT FROM AUTHOR]

Designation of essential fish habitat requires a detailed understanding of how species-specific vital rates vary across habitats and biogeographical regions. This is especially true for species like the economically important brown shrimp (Farfantepenaeus aztecus) which occurs in multiple habitat types across a wide geographic range (southeastern US Atlantic and Gulf of Mexico (GoM) coasts) and exhibits variation in vital rates to small-scale variability in habitat conditions. As juveniles, brown shrimp occupy a suite of interconnected habitats within the estuarine mosaic before migrating offshore as adults. In the southeastern US, intertidal creeks make up a substantial proportion of available habitat within the estuarine mosaic, yet habitat-specific vital rates, including growth, are currently unavailable. We therefore sought to (1) estimate growth rates of juvenile brown shrimp in intertidal creek habitat within a high salinity, southeastern US estuary, the North Inlet estuary in South Carolina, and (2) compare our estimated rates with those from salt marsh habitats in northern GoM estuaries, the only other estuaries where field-derived estimates for juvenile brown shrimp are available. Juvenile brown shrimp collected over a 10-week period (May–July 2021) ranged from 25 to 95 mm TL and appeared to emigrate from the intertidal creek to deeper waters beginning at ~ 65 mm TL. Daily growth rates ranged from 0.45 to 2.30 mm day−1, with the highest rates estimated early in the study period. Despite differences in estimation method, salt marsh habitat type, and region, estimated growth rates from the North Inlet estuary were nearly identical to those from northern GoM estuaries. Collectively, our results suggest that despite differences in habitat geomorphology, spatial extent, and temporal availability, intertidal creeks may provide juvenile brown shrimp with similar nursery function to other habitats within the estuarine seascape. [ABSTRACT FROM AUTHOR]

Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach. [ABSTRACT FROM AUTHOR]

Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before infection. We considered that there should be different immune responses between them after a pathogen infection. Here, the transcriptome data of hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before and after a pathogen infection were compared. The results showed that there were 157 DEGs responsive to infection in V. parahaemolyticus-resistant shrimp, while 33 DEGs in V. parahaemolyticus-susceptible shrimp. DEGs in V. parahaemolyticus-resistant shrimp were mainly related to immune and glycolytic processes, while those in V. parahaemolyticus-susceptible shrimp were mainly related to metabolism, with only two DEGs in common. A further analysis of genes involved in glucose metabolism revealed that GLUT2, HK, FBP, and PCK1 were lowly expressed while PC were highly expressed in hemocytes of the V. parahaemolyticus-resistant shrimp, indicating that glucose metabolism in shrimp hemocytes was related to a V. parahaemolyticus infection. After the knockdown of PC, the expression of genes in Toll and IMD signaling pathways were down-regulated, indicating that glucose metabolism might function through regulating host immunity during V. parahaemolyticus infection. The results suggest that the immune responses between V. parahaemolyticus-resistant and -susceptible shrimp were apparently different, which probably contribute to their different V. parahaemolyticus resistance abilities.

Simple Summary: Identification of disease-resistant genes and their application for disease-resistance breeding is an important way to solve disease problems in shrimp aquaculture. Although some transcriptomics studies have been performed to identify genes related to pathogen infection and host defense, there is still a lack of deep understanding of the host-resistant characteristics against V. parahaemolyticus infection. The present study established a method to obtain hemocytes from shrimp with clear resistant abilities against V. parahaemolyticus infection. We also proposed a strategy to identify key biological processes and genes related to disease resistance based on the analysis of the present transcriptome data. Vibrio parahaemolyticus carrying plasmid encoding toxins PirA and PirB is one of the causative agents leading to the severe disease of AHPND in shrimp aquaculture. However, there is a lack of deep understanding of the host-resistant characteristics against V. parahaemolyticus infection. Here, we established a method to obtain hemocytes from shrimp with different V. parahaemolyticus-resistant abilities and performed comparative transcriptome analysis on the expression profiles at the background level of hemocytes from shrimp in two independent populations. Principal component analysis and sample clustering results showed that samples from the same population had a closer relationship than that from shrimp with similar disease-resistant abilities. DEGs analysis revealed that the number of DEGs between two populations was much more than that between V. parahaemolyticus-resistant and susceptible shrimp. A total of 31 DEGs and 5 DEGs were identified from the comparison between V. parahaemolyticus-resistant and susceptible shrimp from populations 1 and 2, respectively. DEGs from population 1 were mainly cytoskeleton-related genes, metabolic related genes, and immune related genes. Although there was no DEGs overlap between two comparisons, DEGs from population 2 also included genes related to cytoskeleton and metabolism. The data suggest that these biological processes play important roles in disease resistance, and they could be focused by comprehensive analysis of multiple omics data. A new strategy for screening key biological processes and genes related to disease resistance was proposed based on the present study. [ABSTRACT FROM AUTHOR]

Abstract Background Numerous microorganisms are found in aquaculture ponds, including several pathogenic bacteria. Infection of cultured animals by these pathogens results in diseases and metabolic dysregulation. However, changes in the metabolic profiles that occur at different infection stages in the same ponds and how these metabolic changes can be modulated by exogenous metabolites in Penaeus vannamei remain unknown. Results Here, we collected gastrointestinal tract (GIT) samples from healthy, diseased, and moribund P. vannamei in the same aquaculture pond for histological, metabolic, and transcriptome profiling. We found that diseased and moribund shrimp with empty GITs and atrophied hepatopancreas were mainly infected with Vibrio parahaemolyticus and Vibrio harveyi. Although significant dysregulation of crucial metabolites and their enzymes were observed in diseased and moribund shrimps, diseased shrimp expressed high levels of taurine and taurine metabolism-related enzymes, while moribund shrimp expressed high levels of hypoxanthine and related metabolism enzymes. Moreover, a strong negative correlation was observed between taurine levels and the relative abundance of V. parahaemolyticus and V. harveyi. Besides, exogenous taurine enhanced shrimp survival against V. parahaemolyticus challenge by increasing the expression of key taurine metabolism enzymes, mainly, cysteine dioxygenase (CDO) and cysteine sulfinic acid decarboxylase (CSD). Conclusions Our study revealed that taurine metabolism could be modulated by exogenous supplementation to improve crustacean immune response against pathogenic microbes. Video Abstract

Many environmental and pathogenic insults induce endoplasmic reticulum (ER) stress in animals, especially in aquatic ecosystems, where these factors are crucial for life. In penaeid shrimp, pathogens and environmental stressors induce hemocyanin expression, but the involvement of hemocyanin in ER stress response is unknown. We demonstrate that in response to pathogenic bacteria (Vibrio parahaemolyticus and Streptococcus iniae), hemocyanin, ER stress proteins (Bip, Xbp1s, and Chop), and sterol regulatory element binding protein (SREBP) are induced to alter fatty acid levels in Penaeus vannamei. Interestingly, hemocyanin interacts with ER stress proteins to modulate SREBP expression, while ER stress inhibition with 4-Phenylbutyric acid or hemocyanin knockdown attenuates the expression of ER stress proteins, SREBP, and fatty acid levels. Contrarily, hemocyanin knockdown followed by tunicamycin treatment (ER stress activator) increased their expression. Thus, hemocyanin mediates ER stress during pathogen challenge, which consequently modulates SREBP to regulate the expression of downstream lipogenic genes and fatty acid levels. Our findings reveal a novel mechanism employed by penaeid shrimp to counteract pathogen-induced ER stress. [ABSTRACT FROM AUTHOR]

Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach.

Background: Numerous microorganisms are found in aquaculture ponds, including several pathogenic bacteria. Infection of cultured animals by these pathogens results in diseases and metabolic dysregulation. However, changes in the metabolic profiles that occur at different infection stages in the same ponds and how these metabolic changes can be modulated by exogenous metabolites in Penaeus vannamei remain unknown. Results: Here, we collected gastrointestinal tract (GIT) samples from healthy, diseased, and moribund P. vannamei in the same aquaculture pond for histological, metabolic, and transcriptome profiling. We found that diseased and moribund shrimp with empty GITs and atrophied hepatopancreas were mainly infected with Vibrio parahaemolyticus and Vibrio harveyi. Although significant dysregulation of crucial metabolites and their enzymes were observed in diseased and moribund shrimps, diseased shrimp expressed high levels of taurine and taurine metabolism-related enzymes, while moribund shrimp expressed high levels of hypoxanthine and related metabolism enzymes. Moreover, a strong negative correlation was observed between taurine levels and the relative abundance of V. parahaemolyticus and V. harveyi. Besides, exogenous taurine enhanced shrimp survival against V. parahaemolyticus challenge by increasing the expression of key taurine metabolism enzymes, mainly, cysteine dioxygenase (CDO) and cysteine sulfinic acid decarboxylase (CSD). Conclusions: Our study revealed that taurine metabolism could be modulated by exogenous supplementation to improve crustacean immune response against pathogenic microbes. 5E3vY5nuGW9ktCAisXY2Ak Video Abstract [ABSTRACT FROM AUTHOR]

Acute Hepatopancreatic Necrosis Disease (AHPND), caused by bacterial isolates expressing PirAB binary toxins, represents the severest and most economically destructive disease affecting penaeid shrimp. Its rapid disease progression and associated massive mortalities call for vigilant monitoring and early diagnosis, but molecular detection methods that simultaneously satisfy the requirements of sensitivity, specificity, and portability are still scarce. In this work, the CRISPR‐Cas12a technology was harnessed for the development of two fluorescent assays compatible with naked‐eye visualization. The first assay, AP4‐Cas12a, was based on the OIE‐recommended AP4 two‐tubed nested PCR method and was designed to bypass the time‐consuming and potentially hazardous agarose gel electrophoresis step. Using AP4‐Cas12a, the detection limit of 10 copies per reaction could be achieved within less than 30 minutes post‐PCR. The second assay, RPA‐Cas12a, utilized recombinase polymerase amplification (RPA) to rapidly and isothermally amplify the target DNA, followed by amplicon detection by Cas12a, resulting in a protocol that can be completed in less than an hour at a constant temperature of 37°C. The detection limit of RPA‐Cas12a is 100 copies of plasmid DNA or 100 fg of bacterial genomic DNA per reaction. Importantly, we validated that both assays are compatible with a previously reported smartphone‐based device for facile visualization of fluorescence, thereby providing an affordable option that requires less consumables than lateral flow detection. Using this portable device for readouts, the AP4‐Cas12a and RPA‐Cas12a methods showed excellent concordance with the AP4‐agarose gel electrophoresis approach in the evaluation of clinical samples. Therefore, the developed Cas12a assays have the potential to streamline both in‐laboratory and onsite diagnosis of AHPND. [ABSTRACT FROM AUTHOR]

Fishing of the brown shrimp Penaeus aztecus is an important socioeconomic activity, generating income and different jobs for the fishing sector; however, this species is exposed to contaminants such as toxic metals. The objective of this research was to determine the concentrations of Cd, Pb, Cr, and Ni in brown shrimp P. aztecus from the northwestern Gulf of Mexico, and to analyse morphometric measurements in this species. The determination of toxic metals in shrimp was carried out according to the method proposed by the USEPA. Sexual identification was carried out by examining the first pleopods of P. aztecus specimens; the stages of maturity and proportion of sexes were also determined, finding specimens at maturity stages I and II. Specimens collected in the Veracruz area presented higher morphometric values, with an average TL of 136.15 mm. It was identified in the same area that the batches were formed by a higher proportion of males at 72.2%. Ni was the metal with the highest concentration in the Veracruz area at 15.5 µg g−1, while Pb had a maximum concentration of 8.3 µg g−1. The concentrations obtained for the toxic metals in the shrimp exceeded the values of the international permissible limits established for Pb and Cd. [ABSTRACT FROM AUTHOR]

Simple Summary: Mannooligosaccharides (MOS) can promote growth and immunity in aquatic animals. Although most commercial MOS are derived from yeast, the use of MOS from copra meal, a waste product of the coconut industry, is of interest. MOS from copra meal, when given as a dietary supplement to shrimp, could help improve resistance to pathogenic Vibrio and could also act as an immunostimulant. Our objective was to identify bacterial isolates that could be used as probiotics for shrimp and together with MOS as synbiotics to synergistically improve shrimp performance and feed utilization. In this study, two bacterial candidates, Man26 and Man122, were isolated from shrimp intestines and screened for mannanase, the enzyme for mannan digestion. The crude enzymes were evaluated for their biological properties and potential application in the digestion of feedstuffs in vitro. Both strains were able to produce and secrete mannanase to digest MOS and other mannan-rich materials and could tolerate a wide pH range. The addition of crude enzymes significantly increased the reducing sugars of copra meal, palm kernel cake, and soybean meal (p < 0.05) as well as protein release. The synergistic effect of our bacteria and MOS on shrimp growth performance will be further explored in the field. Prebiotics such as mannan-oligosaccharides (MOS) are a promising approach to improve performance and disease resistance in shrimp. To improve prebiotic utilization, we investigated the potential probiotics and their feasibility of synbiotic use in vitro. Two bacterial isolates, Man26 and Man122, were isolated from shrimp intestines and screened for mannanase, the enzyme for mannan digestion. The crude mannanase from both isolates showed optimal activities at pH 8 with optimum temperatures at 60 °C and 50 °C, respectively. The enzymes remained stable at pH 8–10 for 3 h (>70% relative activity). The thermostability range of Man26 was 20–40 °C for 20 min (>50%), while that of Man122 was 20–60 °C for 30 min (>50%). The Vmax of Man122 against locust bean gum substrate was 41.15 ± 12.33 U·mg−1, six times higher than that of Man26. The Km of Man26 and Man122 were 18.92 ± 4.36 mg·mL−1 and 34.53 ± 14.46 mg·mL−1, respectively. With the addition of crude enzymes, reducing sugars of copra meal, palm kernel cake, and soybean meal were significantly increased (p < 0.05), as well as protein release. The results suggest that Man26 and Man122 could potentially be used in animal feeds and synbiotically with copra meal to improve absorption and utilization of feedstuffs. [ABSTRACT FROM AUTHOR]

Vibrio parahaemolyticus carrying plasmid encoding toxins PirA and PirB is one of the causative agents leading to the severe disease of AHPND in shrimp aquaculture. However, there is a lack of deep understanding of the host-resistant characteristics against V. parahaemolyticus infection. Here, we established a method to obtain hemocytes from shrimp with different V. parahaemolyticus-resistant abilities and performed comparative transcriptome analysis on the expression profiles at the background level of hemocytes from shrimp in two independent populations. Principal component analysis and sample clustering results showed that samples from the same population had a closer relationship than that from shrimp with similar disease-resistant abilities. DEGs analysis revealed that the number of DEGs between two populations was much more than that between V. parahaemolyticus-resistant and susceptible shrimp. A total of 31 DEGs and 5 DEGs were identified from the comparison between V. parahaemolyticus-resistant and susceptible shrimp from populations 1 and 2, respectively. DEGs from population 1 were mainly cytoskeleton-related genes, metabolic related genes, and immune related genes. Although there was no DEGs overlap between two comparisons, DEGs from population 2 also included genes related to cytoskeleton and metabolism. The data suggest that these biological processes play important roles in disease resistance, and they could be focused by comprehensive analysis of multiple omics data. A new strategy for screening key biological processes and genes related to disease resistance was proposed based on the present study.

Anthropogenic factors and climate change have serious effects on the aquatic ecosystem and aquaculture. Among water pollutants, ammonia has the greatest impact on aquaculture organisms such as penaeid shrimp because it makes them more susceptible to infections. In this study, we explored the effects of ammonia stress (0, 50, 100, and 150 mg/L) on the molecular structure and functions of the multifunctional respiratory protein hemocyanin (HMC) in Penaeus vannamei. While the mRNA expression of Penaeus vannamei hemocyanin (PvHMC) was up-regulated after ammonia stress, both plasma hemocyanin protein and oxyhemocyanin (OxyHMC) levels decreased. Moreover, ammonia stress changed the molecular structure of hemocyanin, modulated the expression of protein phosphatase 2 A (PP2A) and casein kinase 2α (CK2α) to regulate the phosphorylation modification of hemocyanin, and enhanced its degradation into fragments by trypsin. Under moderate ammonia stress conditions, hemocyanin also undergoes glycosylation to improve its in vitro antibacterial activity and binding with Gram-negative (Vibrio parahaemolyticus) and Gram-positive (Staphylococcus aureus) bacteria, albeit differently. The current findings indicate that P. vannamei hemocyanin undergoes adaptive molecular modifications under ammonia stress enabling the shrimp to survive and counteract the consequences of the stress.

Shrimp aquaculture is the biggest source of export income in Vietnam. However, the development of the shrimp poses a serious threat to coastal mangroves by converting coastal mangroves into shrimp farms. Much effort has been made to replant mangroves and reduce the impacts of shrimp farming on the environment, and maintaining mangrove coverage at 30–50% of total farm area has provided the highest benefits in the integrated mangrove shrimp model. In this study, we re-examine the benefits of forest cover on the survival and yield of tiger shrimp (Penaeus monodon) in the integrated mangrove shrimp farming systems in Ca Mau province, Vietnam. The study found positive linear correlations of log transformed survival and yield of tiger shrimp with forest cover of the forms: Ln (survival) = − 1.39 + 0.038 × forest coverage (r2 = 0.22; p value = 0.0007); Ln (yield) = 3.55 + 0.026 × forest coverage (r2 = 0.16; p value = 0.004). The households with high forest cover (i.e., > 45%) also had 1.07 ± 0.29 and 1.39 ± 0.36 (CI 95%, p value = 0.000) kg ha−1 higher yield per night harvest than those with medium and low forest cover, respectively. As a result, households with high forest cover have higher benefits than those with lower forest cover. Our findings together with previous published studies lead to the recommendation that farmers maintain mangroves in farming systems for better economic and environmental benefits. [ABSTRACT FROM AUTHOR]

Shrimp research has been focused on the development of feeds with minimal levels of fishmeal, as well as using alternative, lower cost protein sources. The study objective was to evaluate the performance of the Pacific white shrimp Penaeus vannamei fed with four different protein‐based extruded diets [plant‐based (AP), 8% poultry by‐product meal (PM8), 8% fishmeal (FM8) and 12% fishmeal (FM12)] while cultured in two independent trials with clear water and biofloc type systems. Additionally, the pellet durability index (PDI) and hardness of these diets were determined. Results from the clear water experiment showed that the shrimp fed with PM diet had the lowest final individual weight, biomass (g) and weight gain (g), and the poorest feed conversion ratio (FCR). It was observed that the shrimp fed with AP, FM8 and FM12 diets had significantly higher weight gain than shrimp offered the PM8 diet. Results from the biofloc experiment showed that shrimp fed with AP diet had the lowest biomass (g), weight gain (g) and thermal growth coefficient and the poorest FCR. No significant differences in survival rate were observed among the four diets in both experiments. The extruded diets showed high PDI when measured using the tumbling box and the Holmen tester. Additionally, the pellet hardness showed no significant differences among the four diets. The low inclusion of fishmeal, as well as the use of alternative protein sources in these diets, did not adversely affect the final weight, weight gain and percent weight gain of P. vannamei. [ABSTRACT FROM AUTHOR]

Immunostimulants represent the most innovative approach for combating shrimp diseases. They are molecules that effectively enhance the host's nonspecific defenses against invading microorganisms. However, methodological differences exist among immunostimulants based on the same source. Therefore, conducting a meta-analysis is essential to derive valid conclusions. The effect size value utilized in this study was Hedges' d. Heterogeneity among studies was assessed using the DerSimonian and Laird tests (Q-statistic). Meta-regression analysis was conducted to explore the sources of heterogeneity in treatment effects. In this study, dose served as a covariate because it was the only continuous variable that significantly contributed to the observed heterogeneity. Funnel plots and the fail-safe number were employed to assess publication bias within the datasets. The article collection process followed the PRISMA methodology. Based on the results of the meta-analysis and meta-regression conducted with 83 articles, it can be concluded that immunostimulants have a significant effect, characterized by high category standard mean difference (SMD) values, on the survival, growth, and immune response of Penaeid family shrimp. Among potential immunostimulants options, algae ingredients exhibited the most favorable effects on the survival, growth, and immune response of Penaeid family shrimp. Subgroup analysis outcomes revealed that various extraction methods significantly impacted the efficacy of immunostimulants, with the ethanol solvent method proving to be the most effective. Among different administration methods, no significant effect was observed on immunostimulant efficacy across all parameters, with positive SMD values for all administration methods. Regarding challenged test pathogens, immunostimulants were observed to enhance immune response, survival, and weight gain against various pathogens. Meta-regression results indicated that algal treatments had a lower optimal dose point, leading to decreased efficacy as the dose increased. In contrast, fungi exhibited a higher optimum dose point, resulting in increased efficacy at higher doses. • A meta-analysis of 83 immunostimulant studies showed that immunostimulant affect immune response, survival, and weight gain. • The method of administering immunostimulants did not influence immune response, survival, and growth. • Elevated dosages immunostimulant of algae and terrestrial plants result in a reduction of the immune response. • Increased dosages immunostimulant of fungi lead to heightened immune responses. • Efficacy of immunostimulants is higher in shrimp infected with viral pathogens than bacteria. [ABSTRACT FROM AUTHOR]

Heat shock proteins (HSPs) serve as an evolutionarily conserved superfamily in response to various environmental stressors in almost all organisms. The Pacific white shrimp, Litopenaeus vannamei , is a worldwide aquaculture species, which have to face various environmental stressors during the whole aquaculture process. Landscapes of HSPs at genomic level will be helpful for understanding the mechanism of this species in environment adaptation. In this study, a comprehensive analysis on the composition and expression profile of HSPs have been performed in L. vannamei. A total of 76 HSP encoding genes (one LvHSP10 s, four LvsHSP s, 38 LvHSP40 s, ten LvHSP60 s, 14 LvHSP70 s, five LvHSP90 s and four LvHSP100 s) have been identified. Most of these genes are dispersedly distributed in the genome, except for seven pairs of tandemly duplicated genes. Multi-transcriptome analyses indicated that LvHSP s are sensitive to various stressors, including pathogen infection, salinity, ammonia or temperature stress. The Lv HSP family exhibited obvious tissue specificity in response to various stressors. Additionally, we found that both tandem duplication and alternative splicing of LvHSP s contributed to the adaptation to various stresses. These findings will provide clues for stress adaptation and development of aquaculture management strategies in penaeid shrimp. • Seventy-six LvHSP s were identified in the Pacific white shrimp Litopenaeus vannamei. • LvHSP s involved in the response to various stressors and showed diverse expressions. • Tandem duplication and alternative splicing of LvHSP s contributed to the adaptation to various stresses. [ABSTRACT FROM AUTHOR]

Many environmental and pathogenic insults induce endoplasmic reticulum (ER) stress in animals, especially in aquatic ecosystems, where these factors are crucial for life. In penaeid shrimp, pathogens and environmental stressors induce hemocyanin expression, but the involvement of hemocyanin in ER stress response is unknown. We demonstrate that in response to pathogenic bacteria (Vibrio parahaemolyticus and Streptococcus iniae), hemocyanin, ER stress proteins (Bip, Xbp1s, and Chop), and sterol regulatory element binding protein (SREBP) are induced to alter fatty acid levels in Penaeus vannamei. Interestingly, hemocyanin interacts with ER stress proteins to modulate SREBP expression, while ER stress inhibition with 4-Phenylbutyric acid or hemocyanin knockdown attenuates the expression of ER stress proteins, SREBP, and fatty acid levels. Contrarily, hemocyanin knockdown followed by tunicamycin treatment (ER stress activator) increased their expression. Thus, hemocyanin mediates ER stress during pathogen challenge, which consequently modulates SREBP to regulate the expression of downstream lipogenic genes and fatty acid levels. Our findings reveal a novel mechanism employed by penaeid shrimp to counteract pathogen-induced ER stress.

We evaluated the relationship between southern brown shrimp Penaeus subtilis (Pérez Farfante, 1967) yield and environmental parameters on the Amazon continental shelf. We analysed monthly fishing effort data (number of days spent at sea) and yield (kg of tails) collected between 1978 and 2009. A causal relationship had been expected between Amazon River discharge during the main period of shrimp occurrence in estuarine waters (considering post larval settlement and juvenile recruitment in second semester of each year) and adult abundance (represented by fishery yield in the first semester of the following year). We detected significant correlations between monthly river discharge and yield with a negative lag of four months, and between river discharge during the dry season (June to November) and yield in the following year. In general, low and high discharges during a given year were associated with high and low fishery yields, respectively, during the following year. [ABSTRACT FROM AUTHOR]

The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50¼234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus. [ABSTRACT FROM AUTHOR]

Gene edition using the CRISPR/Cas9 system has been achieved in few crustaceans, but in penaeid shrimps, several hurdles exist, restraining the potential of CRISPR‐Cas9 technology in shrimp Aquaculture. A key step for gene editing is the efficient introduction of the CRISPR‐Cas9 system into the cells. Although microinjection is an effective method for CRISPR‐Cas9 system delivery into zygotes, the successful gene edition in this commercially important taxon is hindered due to the challenges posed by this technique. Therefore, experimental approaches based on microinjection‐free protocols are of scientific interest for Aquaculture researchers. In this work, we performed physical (electroporation) and chemical (polyethylenimine and cationic lipids) transfection methods in P. vannamei zygotes. For Cas9 delivery, we used three different cargoes: DNA plasmid, mRNA and a recombinant protein. Different ratios of sgRNA designed to recognize the PvCatL gene were used to prepare the CRISPR‐Cas9 complexes. Treated shrimp zygotes were genotyped by HRM analysis and Sanger sequencing. Although high hatching rates were observed for most treatments, no irrefutable evidence of typical CRISPR‐Cas9‐induced gene edition was found; instead, an enrichment of gene variants was observed in treated organisms, which was detectable by HRM. Our effort is of interest to Aquaculture researchers working on this challenging topic, helping to improve their experimental design or as a reference to evaluate additional conditions to achieve the gene editing in penaeid shrimps. [ABSTRACT FROM AUTHOR]

Los camarones penaeidos están expuestos constantemente a infecciones por agentes patógenos. Como respuesta a éstos y a pesar de la aparente simplicidad de su sistema inmune, se han descrito diferentes mecanismos defensivos contra patógenos virales, bacterianos y micóticos, que incluyen complejos procesos de inmunidad celular y humoral. Como parte de esta respuesta, en múltiples ocasiones, se ha reportado la presencia de hiperplasias nodulares del órgano linfoide, denominadas “esferoides del órgano linfoide” (LOS por sus siglas en inglés). Este trabajo presenta una revisión sobre estas estructuras, su descripción histopatológica y la relación que guardan con patologías infecciosas reportadas hasta la fecha. Asimismo, se presentan ejemplos de los principales agentes reportados en su formación. Finalmente, se discute sobre la importancia y limitantes de estas estructuras y su valor diagnóstico mediante técnicas histopatológicas, realizadas en el órgano linfoide y a otras ubicaciones en distintos órganos y tejidos de los camarones (“esferoides ectópicos”).

Abstract Most mercury exposure to humans comes from consumption of fish and shellfish; however, mercury concentrations are not known for all available seafood, particularly shrimp. Our objective was to estimate the concentration of mercury in a variety of store‐bought shrimp and then to compare total mercury concentrations to other information such as brand, harvest type, and total fat. We sampled a total of n = 159 shrimp from 10 different brands. Across 10 brands of shrimp, there was a significant effect of brand, with mean mercury concentrations among brands varying by up to an order of magnitude. We found no significant differences comparing shrimp between two capture types (wild‐caught and farm‐raised), which was perfectly collinear to whether shrimp were domestic or foreign. We did detect significant differences in mercury levels among different amounts of total fat in shrimp, with the lowest fat shrimp (1 g) having significantly more mercury than the highest fat shrimp (2 g). Although our results confirm that shrimp contains relatively low levels of mercury and is generally considered a good choice for consumers, this study is the first to report significant differences in mercury among both brands of shrimp and total fat content in shrimp.

Fishing of the brown shrimp Penaeus aztecus is an important socioeconomic activity, generating income and different jobs for the fishing sector; however, this species is exposed to contaminants such as toxic metals. The objective of this research was to determine the concentrations of Cd, Pb, Cr, and Ni in brown shrimp P. aztecus from the northwestern Gulf of Mexico, and to analyse morphometric measurements in this species. The determination of toxic metals in shrimp was carried out according to the method proposed by the USEPA. Sexual identification was carried out by examining the first pleopods of P. aztecus specimens; the stages of maturity and proportion of sexes were also determined, finding specimens at maturity stages I and II. Specimens collected in the Veracruz area presented higher morphometric values, with an average TL of 136.15 mm. It was identified in the same area that the batches were formed by a higher proportion of males at 72.2%. Ni was the metal with the highest concentration in the Veracruz area at 15.5 µg g−1, while Pb had a maximum concentration of 8.3 µg g−1. The concentrations obtained for the toxic metals in the shrimp exceeded the values of the international permissible limits established for Pb and Cd.

The ingestion of microplastics by diverse marine organisms induces behavioral disorders, physiological changes, and immune and stress responses. The negative effects of microplastic exposure in penaeid shrimps are still unclear despite the annual increase in the consumption of these food sources by humans and in marine aquaculture. Therefore, this study aimed to investigate the potential negative effects of microplastic exposure and gain a deeper understanding of its impacts on culturing penaeid shrimp. We generated RNA sequencing data from the whiteleg shrimp (Penaeus vannamei) artificially exposed to microplastics and analyzed the differentially expressed genes. Based on transcriptional comparisons, exposure to microplastics induces cardiac muscle dysfunction and promotes stress and immune responses in whiteleg shrimp. Thus, we confirmed the negative impact of microplastic exposure in whiteleg shrimp. These results provide a foundation for studies on the biological effects of microplastic ingestion on aquaculture species and their potential impact on humans through their consumption of these important marine resources.

Prebiotics such as mannan-oligosaccharides (MOS) are a promising approach to improve performance and disease resistance in shrimp. To improve prebiotic utilization, we investigated the potential probiotics and their feasibility of synbiotic use in vitro. Two bacterial isolates, Man26 and Man122, were isolated from shrimp intestines and screened for mannanase, the enzyme for mannan digestion. The crude mannanase from both isolates showed optimal activities at pH 8 with optimum temperatures at 60 °C and 50 °C, respectively. The enzymes remained stable at pH 8–10 for 3 h (>70% relative activity). The thermostability range of Man26 was 20–40 °C for 20 min (>50%), while that of Man122 was 20–60 °C for 30 min (>50%). The Vmax of Man122 against locust bean gum substrate was 41.15 ± 12.33 U·mg−1, six times higher than that of Man26. The Km of Man26 and Man122 were 18.92 ± 4.36 mg·mL−1 and 34.53 ± 14.46 mg·mL−1, respectively. With the addition of crude enzymes, reducing sugars of copra meal, palm kernel cake, and soybean meal were significantly increased (p < 0.05), as well as protein release. The results suggest that Man26 and Man122 could potentially be used in animal feeds and synbiotically with copra meal to improve absorption and utilization of feedstuffs.

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.

Shrimp aquaculture is an essential economic venture globally, but the industry faces numerous challenges, especially pathogenic infections. As invertebrates, shrimp rely mainly on their innate immune system for protection. An increasing number of studies have shown that ubiquitination plays a vital role in the innate immune response to microbial pathogens. As an important form of posttranslational modification (PTM), both hosts and pathogens have exploited ubiquitination and the ubiquitin system as an immune response strategy to outwit the other. This short review brings together recent findings on ubiquitination and how this PTM plays a critical role in immune modulation in penaeid shrimps. Key findings inferred from other species would help guide further studies on ubiquitination as an immune response strategy in shrimp-pathogen interactions.

Shrimp aquaculture is an essential economic venture globally, but the industry faces numerous challenges, especially pathogenic infections. As invertebrates, shrimp rely mainly on their innate immune system for protection. An increasing number of studies have shown that ubiquitination plays a vital role in the innate immune response to microbial pathogens. As an important form of posttranslational modification (PTM), both hosts and pathogens have exploited ubiquitination and the ubiquitin system as an immune response strategy to outwit the other. This short review brings together recent findings on ubiquitination and how this PTM plays a critical role in immune modulation in penaeid shrimps. Key findings inferred from other species would help guide further studies on ubiquitination as an immune response strategy in shrimp-pathogen interactions. [ABSTRACT FROM AUTHOR]

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies. [ABSTRACT FROM AUTHOR]

The bunyavirus Mourilyan virus (MoV) occurs commonly in Black tiger (Penaeus monodon) and kuruma shrimp (Penaeus japonicus) farmed in eastern Australia. There is circumstantial evidence of MoV causing mortalities among P. japonicus moved from farm ponds to tanks for rearing as broodstock. To directly assess its pathogenic potential, independent cohorts of pond‐ (n = 24) or tank‐reared juvenile (n = 21) P. japonicus were challenged intramuscularly with a cephalothorax tissue homogenate of P. monodon containing high loads of MoV (1.48 ± 0.28 × 108 MoV RNA copies/µg total RNA). In each trial, mortalities accumulated gradually among the saline‐injected controls. Mortality onset occurred 12–14 days earlier in the pond‐reared shrimp, possibly due to them possessing low‐level pre‐existing MoV infections. Despite the time to onset of mortality differing, Kaplan–Meier survival analyses confirmed mortality rates to be significantly higher in both the pond‐ (p =.017) and tank‐reared shrimp (p =.031) challenged with MoV. RT‐qPCR data on shrimp sampled progressively over each trial showed high loads of MoV to establish following challenge and discounted GAV and other endemic viruses from contributing to mortality. Together, the data show that acute MoV infection can adversely compromise the survival of juvenile P. japonicus. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the structural changes in the microbiota of Penaeus monodon during its ontogenetic development and evaluate functional shifts in metabolic pathways. To address these questions, shrimp were maintained under isolated conditions to avoid cross-contamination with other environmental bacteria and reared in twelve 50 L plastic tanks connected to a recirculation system. The replicates of pooled intestine specimens from 15 shrimp were analyzed at postlarvae, juvenile, and adult phases for nucleic acid extraction. We tested the V3 region of the 16S rRNA gene from the postlarvae, juvenile, and adult stages. Resulting amplicon sequence variants (ASVs) were used to evaluate both structural and functional shifts during tiger shrimp development. Although the richness and diversity of microbiota were only slightly affected, the phylum Proteobacteria (genus Vibrio) was significantly predominant in the earliest stages of life, while Actinobacteria (genus Actinotalea) significantly increased in adult shrimp. Moreover, functional predictions by PICRUSt suggested that microbiota is primarily involved in metabolic activities during each developmental stage. Overall, these results suggest that each ontogenetic stage may provide specific conditions for the proliferation of certain bacterial taxa. Nerveless, alternative microbiota maintains similar ecological activities; thus, we posit that "stage-specific" changes in microbiota may be regulated to guarantee pivotal host functions. [ABSTRACT FROM AUTHOR]

The Pacific white shrimp Litopenaeus vannamei is one of the major economic aquaculture species. The growth trait is considered as the most important trait in L. vannamei aquaculture. Identification of the genetic components underlying growth-related traits in L. vannamei could be useful for the selective breeding of growth trait. Our previous work identified several growth-related SNPs by genome-wide association study (GWAS). Based on the assembled genome, we identified a new candidate gene (LvMMD2) beside the associated marker. This gene encodes the progestin and AdipoQ receptor 10 (PAQR10) protein. We further investigate the polymorphisms of LvMMD2 and their association with body weight of L. vannamei. By resequencing the coding region of LvMMD2, a total of 8 SNPs were identified, including 6 synonymous mutations and 2 nonsynonymous mutations. Association analyses based on a population of 322 individuals revealed that several SNPs located in the coding region of LvMMD2 were significantly associated with the body weight, especially the nonsynonymous mutation named as MMD_5 contributed the most association to the trait and it could explain 10.5% of phenotypic variance. In addition, several genes involved in growth and development have been identified as LvMMD2-interacting genes. These findings strongly suggested that LvMMD2 might be an important gene regulating the shrimp growth. More importantly, the MMD_5 could be a promising candidate locus for marker-assisted selection (MAS) of the body weight in L. vannamei. [ABSTRACT FROM AUTHOR]

Most mercury exposure to humans comes from consumption of fish and shellfish; however, mercury concentrations are not known for all available seafood, particularly shrimp. Our objective was to estimate the concentration of mercury in a variety of store‐bought shrimp and then to compare total mercury concentrations to other information such as brand, harvest type, and total fat. We sampled a total of n = 159 shrimp from 10 different brands. Across 10 brands of shrimp, there was a significant effect of brand, with mean mercury concentrations among brands varying by up to an order of magnitude. We found no significant differences comparing shrimp between two capture types (wild‐caught and farm‐raised), which was perfectly collinear to whether shrimp were domestic or foreign. We did detect significant differences in mercury levels among different amounts of total fat in shrimp, with the lowest fat shrimp (1 g) having significantly more mercury than the highest fat shrimp (2 g). Although our results confirm that shrimp contains relatively low levels of mercury and is generally considered a good choice for consumers, this study is the first to report significant differences in mercury among both brands of shrimp and total fat content in shrimp. [ABSTRACT FROM AUTHOR]

Skewed family distributions are common in aquaculture species that are highly fecund, communally (mass) spawned, and/or communally reared. The magnitude of skews pose challenges for maintaining family-specific genetic diversity, as increased resources are required to detect individuals from underrepresented families, or reliably determine relative survival as a measure of family performance. There is limited understanding of family skews or changes in family proportion of communally reared shrimp under commercial rearing conditions and particularly how this may affect genotyping strategies to recover family performance data in breeding programs. In this study, three separate batches of shrimp , Penaeus monodon , were communally spawned and reared, and then sampled as larvae when ponds were stocked at 30 days of culture (DOC) and as juveniles from commercial ponds during harvest at 150 DOC. A total of 199 broodstock contributed to the 5,734 progeny that were genotyped with a custom multiplex single nucleotide polymorphism (SNP) panel, and family assignments were cross-referenced using two parentage assignment methods, CERVUS and COLONY. A total of 121 families were detected, with some families contributing up to 11% of progeny at 30 DOC and up to 18% of progeny at harvest. Significant changes were detected for 20% of families from 30 to 150 DOC, with up to a 9% change in relative contribution. Family skew data was applied in several models to determine the optimal sample size to detect families, along with the ability to detect changes in relative family contribution over time. Results showed that an order of magnitude increase in sampling was required to capture the lowest represented 25% of families, as well as significantly improve the accuracy to determine changes in family proportion from 30 to 150 DOC. Practical measures may be implemented at the hatchery to reduce family skews; a cost-effective measure may be to address the initial magnitude differences in viable progeny produced among families, by pooling equal quantities of hatched larvae from each family. This study demonstrates the relationships between skews in families under commercial conditions, the ability to accurately detect families, and the balance of sampling effort and genotyping cost in highly fecund species such as shrimp. [ABSTRACT FROM AUTHOR]

Vibrio parahaemolyticus is often related to infections and high mortality rates in shrimp farming. The use of probiotics is an alternative to the use of antibiotics in farming systems. Among the benefits, probiotics can boost the immune status of shrimp, making them more resistant to diseases. An experimental rearing was conducted for 60 days to determine the effects of Bacillus subtilis and Bacillus circulans on the growth and disease resistance in Litopenaeus vannamei juveniles. Shrimp groups were designated according to the feed offered: commercial feed + B. subtilis (BS); commercial feed + B. circulans (BC); and feed without bacteria (control). The expressions of proPO, LGBP, and HEM genes were quantified by qPCR after 60 days of rearing and after 24 h of V. parahaemolyticus challenge. The growth and expression of immune genes were significantly higher in shrimp fed with BS and BC diets. Furthermore, animals fed with BC diet had a greater survival after the injection of V. parahaemolyticus. Bacillus spp. significantly increased in shrimp guts fed with BC and BS diets. Supplementation of L. vannamei diet with B. subtilis and B. circulans contributed to an increase in shrimp weight gain and enhancement of shrimp immune status. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria are groups of bacteria that have been commonly used as probiotics with functional targets controlling pathogens. In this study, BAL were isolated from penaeid shrimp intestinum was captured in natural waters and were tested of antibacterial activity against 3 types of pathogenic vibrio bacteria in shrimp. The shrimp samples were taken from the North Coast of Java (Situbondo and Semarang) and the South coast of Java (Cilacap). BAL isolation was done by pour plate method using MRS medium enriched with CaCO3. The antibacterial activity test was performed by using paper diffusion method using V. harveyi, V. anguilarum and V. parahaemolyticus as bacteria indicator. The isolation result obtained 224 isolates of BAL intestinal of penaeid shrimp. The active BAL isolates against V. Harveyi, V. anguilarum and V. parahaemolyticus were 59, 83 and 66 isolates, respectively. Isolates are active against 3 types, 2 types and 1 type of Vibrio were 51, 25 and 11 isolates respectively. Bakteri asam laktat merupakan kelompok bakteri yang telah banyak digunakan sebagai probiotik dengan target fungsional mengendalikan pathogen. Pada penelitian ini telah dilakukan isolasi BAL dari intestinum udang penaeid yang ditangkap di perairan alam dan pengujian aktivitas antibakteri terhadap 3 jenis bakteri vibrio pathogenik pada udang. Sampel udang diambil dari Pantai Utara Jawa (Situbondo dan Semarang) dan pantai Selatan Jawa (Cilacap). Isolasi BAL dilakukan dengan metode taburan menggunakan medium MRS yang diperkaya dengan CaCO3. Uji aktivitas antibakteri dilakukan dengan paper diffusion method menggunakan bakteri uji V. harveyi, V. anguilarum dan V. parahaemolyticus. Hasil isolasi diperoleh 224 isolat BAL intestinal udang penaeid. Isolat BAL yang aktif terhadap V. Harveyi, V. anguilarum dan V. parahaemolyticus berturut-turut 59, 83 dan 66 isolat. Isolat yang aktif terhadap 3 jenis, 2 jenis dan 1 jenis Vibrio uji berurut-turut 51, 25 dan 11 isolat.

Abstract Background Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp. The aim of this study was to evaluate the factors influencing the GS accuracy for growth traits in L. vannamei. Genotype and phenotype data of 200 individuals from 13 full-sib families were used for this analysis. Results In the present study, the heritability of growth traits in L. vannamei was estimated firstly based on the full set of markers (23 K). It was 0.321 for body weight and 0.452 for body length. The estimated heritability increased rapidly with the increase of the marker density from 0.05 K to 3.2 K, and then it tended to be stable for both traits. For genomic prediction on the growth traits in L. vannamei, three statistic models (RR-BLUP, BayesA and Bayesian LASSO) showed similar performance for the prediction accuracy of genomic estimated breeding value (GEBV). The prediction accuracy was improved with the increasing of marker density. However, the marker density would bring a weak effect on the prediction accuracy after the marker number reached 3.2 K. In addition, the genetic relationship between reference and validation population could influence the GS accuracy significantly. A distant genetic relationship between reference and validation population resulted in a poor performance of genomic prediction for growth traits in L. vannamei. Conclusions For the growth traits with moderate or high heritability, such as body weight and body length, the number of about 3.2 K SNPs distributed evenly along the genome was able to satisfy the need for accurate GS prediction in the investigated L.vannamei population. The genetic relationship between the reference population and the validation population showed significant effects on the accuracy for genomic prediction. Therefore it is very important to optimize the design of the reference population when applying GS to shrimp breeding.

Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in Pacific white shrimp Litopenaeus vannamei farming, which is caused by Vibrio parahaemolyticus. AHPND has led to a significant reduction of shrimp output since its outbreak. Selective breeding of disease-resistant broodstock is regarded as a key strategy in solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection in shrimp. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei. In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune-related genes of L. vannamei. By analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (false discovery rate corrected at P < 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective in identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease-resistant shrimp.

As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp.

Improvements of growth traits are always the focus in selective breeding programs for the Pacific white shrimp Litopenaeus vannamei (L. vannamei). Identification of growth-related genes or markers can contribute to the application of modern breeding technologies, and thus accelerate the genetic improvement of growth traits. The aim of this study was to identify the genes and molecular markers associated with the growth traits of L. vannamei. A population of 200 individuals was genotyped using 2b-RAD techniques for genome-wide linkage disequilibrium (LD) analysis and genome-wide association study (GWAS). The results showed that the LD decayed fast in the studied population, which suggest that it is feasible to fine map the growth-related genes with GWAS in L. vannamei. One gene designated as LvSRC, encoding the class C scavenger receptor (SRC), was identified as a growth-related candidate gene by GWAS. Further targeted sequencing of the candidate gene in another population of 322 shrimps revealed that several non-synonymous mutations within LvSRC were significantly associated with the body weight (P < 0.01), and the most significant marker (SRC_24) located in the candidate gene could explain 13% of phenotypic variance. The current results provide not only molecular markers for genetic improvement in L. vannamei, but also new insights for understanding the growth regulation mechanism in penaeid shrimp.

As a core component of the complement system, complement component 3 (C3) plays a central role in the opsonization of pathogens, immune defense and immune regulation in the mammalian for its activation is required to trigger classical as well as alternative complement pathways. However, the molecular mechanism underlying C3 activation in invertebrates remains unknown. Several C3 genes have been characterized in invertebrates but very few in crustacean. To understand the molecular characterization and immunological functions of shrimp C3, we characterized a novel complement C3 like gene (designated Lv-C3L) with full-length cDNA sequence identified from pacific white shrimp Litopenaeus vannamei in the present study. The full length cDNA of Lv-C3L sequence was 4769 bp (GenBank accession number: MH638255) containing a 4077 bp open reading frame (ORF), which encodes 1358 amino acids contained a putative signal peptide of 17 amino acids. Six model motifs of C3 were found in Lv-C3L including typical A2M domain, a highly conserved thioester region (GCGEQ) and proteolytic cleavage site of ANATO. In addition to typical conservative domains, Lv-C3L also contains a particular GLN-rich region which might be involved in the protein interaction and transcriptional activation. The transcripts of Lv-C3L were mainly detected in hemocytes and gill which might be involved in defense response. At 36 h post V.parahaemolyticus and B.thuringensis infection, the expression level of Lv-C3L gene in hemocytes were significantly upregulated. At 48 h and 72 h post WSSV infection, the expression level of Lv-C3L gene in hemocytes and gill were significantly upregulated. These results indicated that Lv-C3L gene play a pivotal role in innate immune responses to the WSSV and G+/G− bacterial infection. The obvious immune function of Lv-C3L was described as an effective membrane rupture in bacteriolytic and hemolytic activities on V.parahaemolyticus , V.anguillarum and rabbit erythrocytes. Combining with WSSV copy number, WSSV- VP28 gene expression profile and shrimp cumulative mortality analysis, RNAi knockdown of Lv-C3L gene could obviously promote the in vivo propagation of WSSV in shrimp. This is the first report in crustaceans that Lv-C3L, as a key complement like components, is involved in shrimp antiviral immune response. It is speculated that complicated complement response cascade may exist in shrimp. These results collectively indicated that the complement pathway in shrimp might play an important protective role against pathogenic infection and activation of complement pathway including C3 could restrict the propagation of WSSV. • A novel complement C3 like gene (Lv-C3L) was cloned from hemocytes of L. vannamei in this manuscript. • The expression level of Lv-C3L gene in hemocytes and gill were significantly upregulated after bacterial and WSSV infection. • The obvious immune function of Lv-C3L was described as an effective membrane rupture in bacteriolytic and hemolytic activities. • RNAi knockdown of Lv-C3L gene could obviously promote the in vivo propagation of WSSV in shrimp. [ABSTRACT FROM AUTHOR]

Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in Pacific white shrimp Litopenaeus vannamei farming, which is caused by Vibrio parahaemolyticus. AHPND has led to a significant reduction of shrimp output since its outbreak. Selective breeding of disease-resistant broodstock is regarded as a key strategy in solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection in shrimp. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei. In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune-related genes of L. vannamei. By analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (false discovery rate corrected at P < 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective in identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease-resistant shrimp. [ABSTRACT FROM AUTHOR]

The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp Penaeus vannamei. The Pvfem-1 transcript is 3778 nt long and encodes a putative protein (PvFEM-1) of 638 amino acids that presented eight ankyrin repeats. The translated protein showed a significant (P < 0.05) structural similitude by superposition with C. elegans FEM-1 protein. Pvfem-1 expression was evaluated by qPCR and in situ hybridization (ISH) during embryogenesis, larval development, and gonads of both genders in subadult and adult life stages. Pvfem-1 was found expressed in brain, intestine, hepatopancreas, and in the gonads of both genders in subadults and adults when quantified by RT-qPCR. A significant finding was the discovery of a natural antisense transcript (NAT) of Pvfem-1 by ISH. It was present in the oocyte nucleus of subadult female shrimp gonads but was not seen within oocytes from adult females, although it was detected in follicular cells, suggesting a possible post-transcriptional regulation of Pvfem-1 in female gonad. Conversely, in males, no NAT was observed, and Pvfem-1 was found expressed in spermatogonia of both, subadult and adult shrimps indicating a function in male sexual differentiation and gametes generation. This study represents the first step for future functional analysis that is expected to contribute to clarifying the role of Pvfem-1 in sex differentiation and determination. • fem-1 , a gene known to be linked to a sex-chromosome was characterized in shrimp. • During early development fem-1 was highly expressed in zygote and blastula. • A natural antisense transcript in female gonads might negatively regulate fem-1. • fem-1 sense transcript might have a role in male shrimp gonad sex-differentiation. [ABSTRACT FROM AUTHOR]