Aquaculture Species Research Articles

Assessment of dietary yeast-based additives for cultured catfish and tilapia health.

Channel catfish (Ictalurus punctatus) and Nile tilapia (Oreochromis niloticus) are two aquaculture species of great importance. Intensive production is often hindered by poor growth performance and disease mortality. The aim of this study was to evaluate the potential of a commercial fermented yeast product, DVAQUA, on channel catfish and Nile tilapia growth performance metrics and disease resistance. Channel catfish and Nile tilapia were fed practical diets supplemented with 0%, 0.1% or 0.4% of DVAQUA over approximately 2-month feeding periods in recirculation aquaculture systems. To assess the potential of the postbiotic against common aquaculture pathogens, juvenile catfish were subsequently challenged by immersion with Edwardsiella ictaluri S97-773 or virulent Aeromonas hydrophila ML09-119. Nile tilapia juveniles were challenged by injection with Streptococcus iniae ARS-98-60. Serum lysozyme activity, blood chemistry and growth metrics were measured at the end of the feeding period, but no differences were observed across the different metrics, except for survival. For the pathogen challenges, there were no differences in endpoint mortality for channel catfish with either pathogen (p > .05). In contrast, Nile tilapia survivability to S. iniae infection increased proportionally to the inclusion of DVAQUA (p = .005). Changes to sera lysozyme activity were also noted in the tilapia trial, with a reduction of activity in the fish fed the 0.4% DVAQUA diet compared to the control diet (p = .031). Expression profiles of proinflammatory genes and antibodies were also found to be modulated in channel catfish fed the postbiotic, indicating some degree of protective response. These results suggest that this postbiotic may be beneficial in protecting Nile tilapia against S. iniae infection by influencing immune parameters and additional research is needed to evaluate the potential of this DVAQUA for improving catfish health and disease control.

Genome sequencing and assembly of Indian major carp, Cirrhinus mrigala (Hamilton, 1822)

The freshwater aquaculture species, Cirrhinus mrigala, commonly known as mrigal, holds significance in the carp-dominated aquaculture system, globally. Despite constituting 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. However, its genome and associated information is not available. This study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, revealed 39,091 genes with functional annotations. The orthology analysis based on direct orthologs and single copy ortholgs places C. mrigala in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.

Salinity tolerance assessment of different families of the razor clam Sinonovacula constricta using physiological traits

Salinity tolerance is a complex multigenic trait influenced by genetic factors, environmental factors, and their interactions. However, there are few reports of salinity tolerance assessments using multiple indexes in aquaculture animals. Membership function (MF) analysis is a comprehensive, reliable and valid approach to evaluating resistance by considering multiple indexes. This study primarily aimed to evaluate the salt tolerance of the razor clam Sinonovacula constricta based on physiological traits. In this study, six families of S. constricta (1–1, 1–2, 19–1, 19–2, 17–1, and 14–2) were subjected to high salt stress (30 and 35 ppt). Eight physiological traits (enzyme activity) were employed to assess the high salt tolerance using MF analysis. The razor clams in family 19–2 were all dead at the end of the experiment. The mortality rate (MR) of family 17–1 was significantly lower than that of the other families (P < 0.05). The eight physiological traits showed a remarkable positive or negative correlation among them and did not exhibit specificity with salinity. The MF analysis indicated that family 17–1 displayed the highest resistance and family 19–2 showed weak resistance. The high-resistance families showed lower MR and higher enzyme activity compared with the low-resistance families. The degree of dispersion of enzyme activity at different time points was also a good indicator of the resistance based on the boxplots. Grey relational analysis (GRA) showed that most physiological traits reflected salinity tolerance, with a significant correlation observed with malondialdehyde content. Different families of razor clam showed different sensitivities to high salt levels, which is an important prerequisite for family selection. Additionally, we demonstrated the feasibility of using MF and GRA for evaluating high salt tolerance based on physiological traits. Thus, this study serves as a foundation for stress resistance assessment using physiological traits in aquaculture species.

Automated phenotyping empowered by deep learning for genomic prediction of body size in the tiger pufferfish, Takifugu rubripes

Although genomic selection (GS) is accelerating the genetic improvement of economically important traits in aquaculture species, the accurate phenotyping of thousands of individuals remains a bottleneck in GS programs. Computer vision (CV) technologies with the assistance of deep learning may provide a cost-efficient solution for automated phenotyping of fish body size. In this study, we designed a CV-based automated phenotyping system based on the deep learning model Mask R-CNN (region-based convolutional neural networks) and tested its ability to predict standard length (SL) of tiger pufferfish (Takifugu rubripes) fed low fishmeal (LFM) diet. Simultaneously, we investigated the impact of the automated phenotyping on genetic parameter estimation and genomic prediction for growth-related traits. We raised a test population (n = 1001) that was fed the LFM diet from three months old until harvest at 22 months. Manual phenotyping of the fish was performed at 10-, 14-, 17-, and 22-months-old. At the last two measurement times, images of each fish were collected to train Mask R-CNN for fish detection and pixel-level segmentation of the fish body excluding the tail fin. An automated phenotyping pipeline combining the trained Mask R-CNN and standard CV algorithms were designed to estimate SL. We found a high correlation (0.965–0.971) and low relative difference (0.015–0.027) between the CV-derived and manually measured SL, indicating high precision of our CV system. A high correlation (0.912–0.956) was also observed between CV-derived body area and manual body weight. The heritability estimations and genomic predictions on manual SLs were conducted using a Genomic Best Linear Unbiased Prediction (GBLUP) model using a total of 16,471 single nucleotide polymorphism (SNP). Estimated heritability at the four sampling points ranged from 0.573 to 0.622, and the predictive ability of genomic prediction for harvest size was 0.627. These values are comparable to those reported in previous studies collected from the population fed a normal fishmeal diet. Our heritability estimation and genomic prediction derived from automated SL measurements differed negligibly to those based on manual measurements. This finding indicates the utility of our CV-based automated phenotyping system for GS breeding programs.

Threonine supplementation stimulates immune, antioxidant and liver functions of largemouth bass, Micropterus salmoides

Threonine is an essential amino acid required in the diets for regular growth of fishes, but information is inadequate regarding the effects of threonine on immunity and health status of many aquaculture species. In the present study, a total of 360 juvenile largemouth bass, Micropterus salmoides (19.0 ± 0.1 g) were divided into six experimental groups, and fed diets supplemented with varying levels of crystalline L-threonine at 0 g kg−1 (control), 2.5 g kg−1 (Thr-2.5), 5.0 g kg−1 (Thr-5.0), 7.5 g kg−1 (Thr-7.5), 10.0 g kg−1 (Thr-10.0) and 12.5 g kg−1 (Thr-12.5) for eight weeks. The results revealed that white blood cell count (P = 0.024) and albumin content (P = 0.006) in fish were significantly modulated by the dietary threonine, with the highest levels recorded in fish fed diets Thr-5.0 and Thr-12.5, respectively. White blood cell increased with dietary threonine levels up to Thr-5.0, then decreased thereafter. The other hematological variables such as red blood cell (P = 0.571), hemoglobin (P = 0.259), hematocrit (P = 0.985), mean corpuscular volume (P = 0.631), mean corpuscular hemoglobin (P = 0.280) and mean corpuscular hemoglobin concentration (P = 0.691) remained unchanged as compared to the control group. Serum lysozyme increased (P = 0.000) with increasing levels of threonine up to 5.0 g kg−1. Fish receiving diet Thr-2.5 had relatively higher (P = 0.000) immunoglobulin M and the level decreased when fed with increasing levels of threonine. The activities of superoxide dismutase (P = 0.008) and malondialdehyde (P = 0.005) were elevated at 10.0 g kg−1 and 12.5 g kg−1 supplementation levels, respectively. Moreover, diets Thr-5.0 and Thr-10.0 induced lower serum alanine aminotransferase (P = 0.011) and aspartate aminotransferase activities (P = 0.000) in fish. These results suggest that threonine supplementation led to a positive effect on the hematology, humoral immunity, antioxidant capacity and liver function enzyme activities of economically important largemouth bass. Therefore, threonine has a clear role in fish nutrition and is important in formulating nutritionally balanced feeds.

Exploration of the Synergistic Regulation Mechanism in Cerebral Ganglion and Heart of Eriocheir sinensis on Energy Metabolism and Antioxidant Homeostasis Maintenance under Alkalinity Stress.

(1) The development and utilization of the vast saline-alkali land worldwide is an important way to solve the worsening food crisis. Eriocheir sinensis, due to its strong osmotic regulation capability and its characteristics of being suitable for culturing in alkaline water, has become a potential aquaculture species in saline-alkali water. The brain and heart are the key tissues for signal transduction and energy supply under environmental stress. (2) This study is the first to explore the synergistic regulatory molecular mechanism by integrated analysis on cerebral ganglion proteomics and heart metabolomics of Eriocheir sinensis under alkalinity stress. (3) The results indicate that the cerebral ganglion and heart of E. sinensis were closely related in response to acute alkalinity stress. The differential regulatory pathways mainly involved regulation of energy metabolism, amino acid metabolism, and homeostasis maintenance. Importantly, alkalinity stress induced the regulation of antioxidants and further adjusted longevity and rhythm in the cerebral ganglion and heart, reflecting that the cerebral ganglion and heart may be the key tissues for the survival of Eriocheir sinensis under an alkalinity environment. (4) This study provides a theoretical reference for research on the regulation mechanism of E. sinensis under alkalinity condition and contributes to the development of aquaculture in saline-alkali water.

Quantitative genetic analysis indicate non-heritability of major fatty acid in the muscle of Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species, and crab meat generally has the high percentage of long-chain polyunsaturated fatty acids (LC-PUFAs) in the total fatty acids, which contributes the unique flavor and high nutrition value for adult crab. Muscle is the largest edible tissue in crustaceans, containing a variety of fatty acids, and understanding the genetic parameters of fatty acids in the meat of E. sinensis would be useful for the aquaculture of this species. This study investigated the heritability, genetic and phenotypic correlations of major fatty acids in the muscle of E. sinensis. Progeny from 25 full-sib families were reared under a common environment until they reached market size, and 429 mature crabs were selected for analysis. The results showed that the heritabilities of most fatty acids were low ranged from 0.01 (n-3PUFA) to 0.21 (MUFA), but the high heritabilities were recorded for C20:3n3 and C20:3n6 with values of 0.99 and 0.32, respectively. Furthermore, the strongest positive genetic correlations were found between C20:5n3 and C22:6n3(0.99), n-3PUFA(0.99), and PUFA and LC- PUFAs (0.99), n-3PUFA(0.99), whereas the strongest phenotype correlation was found between C20:5n3 and n-3 PUFA (0.96); C20:3n6 showed a significant negative genetic correlation with C20:3n3(−0.86) and C18:0 (−0.98), whereas C20:3n6 showed significant negative phenotypic correlation with C20:3n3(−0.14), C20:5n3(−0.15) and C22:6n3(−0.18). In conclusion, the percentages of major fatty acids, particularly C20:5n3, C22: 5n3 and C20:4n6, in E. sinensis muscle have very low heritabilities, suggesting that these fatty acids contents/composition in the muscle are ineffective targets for the selective breeding programs of E. sinensis.

Dietary salt concentrations influence growth, nutrient utilization, and fatty acid profiles of turbot (Scophthalmus maximus) reared in brackish water.

Expansion of economically viable turbot (Scophthalmus maximus) aquaculture depends on access to brackish-cold ground water sources in various parts of the world. Since brackish water sources can adversely affect the physiology and zoo technical performance of fish due to the burden of osmoregulation, dietary salt inclusion can alleviate the negative impacts of low-saline waters in several aquaculture species. This study investigated the effects of increasing dietary salt levels on the growth, feed utilization, body composition, and tissue fatty acid composition of juvenile turbot (initial live weight 120.3 ± 0.03g/fish). Fish were fed five experimental diets supplemented with varying levels of sodium chloride (1.8-6.4%) or a control diet without salt. Each diet was tested in triplicate tanks for 9weeks. Results showed that increasing dietary salt intake negatively impacted turbot performance, with significant reductions in weight gain, specific growth rate, and feed conversion ratio. Dry matter and ash content in the whole body and filet increased quadratically with increasing salt levels, whereas gill moisture and protein content decreased linearly. Furthermore, the nitrogen, lipid, and energy utilization efficiencies decreased with their respective intake and gain levels. Dietary salt significantly influenced the fatty acid profiles of gill, liver, and filet tissues. In the gill, monounsaturated fatty acids (16:1n-7, ΣMUFA) and n-6 PUFA (20:2n-6) increased, whereas EPA and DHA decreased. Liver ΣSFA (16:0, 18:0) increased, and n-3 PUFA (18:3n-3, 20:5n-3) decreased with increasing dietary salt. Filet saturated fatty acids (14:0, 15:0, 17:0) and n-6 PUFA (20:2n-6, 20:4n-6) increased, while n-3 PUFA (18:3n-3, EPA) decreased with dietary salt. DHA levels in filets showed a quadratic increase. Overall, this study shows that increasing dietary salt negatively impacts turbot growth, feed utilization, and tissue fatty acid composition in brackish water, highlighting the need for further studies on salinity management strategies for turbot aquaculture.

Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) intended for river stocking

Microbiomes play an essential role in promoting host health and fitness in fishes, but the factors driving variation in gut microbiomes among individuals are not fully recognized. Understanding the biological and environmental factors influencing variation in the gut microbiome in fishes is needed to link microbiome composition to host physiology and potentially design manipulations to improve rearing success in fisheries and aquaculture. In this study, we characterized the gut microbiomes of Atlantic salmon (Salmo salar), a globally important species in commercial aquaculture and recreational fishing, considering life stage, vaccination status, and hatchery origin. Microbiomes diverged between hatchery sub-adults (age-0 parrs) and wild adults, with sub-adults exhibiting higher diversity and more similar microbiome communities when compared to adults. The diversity and composition of gut microbiomes did not differ between groups of adults that were reared in two different hatcheries and sampled from the wild. We also found that oral vaccines against bacterial kidney disease (BKD) reduced gut microbial diversity within individual sub-adult salmon, driving increased differentiation of gut microbial communities among individuals. Unvaccinated sub-adults displayed a stable core gut microbiome that was greatly reduced upon vaccination for BKD. Our results suggest that life stage is an essential factor shaping the gut microbiome of Atlantic salmon, likely driven by differences in habitat and diet, and that BKD vaccination can lead to a rapid disruption of the gut microbiome. Conditions experienced in the hatchery environment appear to have a strong influence on host gut microbiomes, but differences at early life stages may be lost due to environmental factors experienced in the wild. The plasticity of the gut microbiome throughout the life of individuals may have important implications for understanding host health, with potential applications for improving the rearing and reintroduction success of the ecologically and economically important Atlantic salmon.

Physiological and Transcriptomic Analyses Provide Insights into Nitrite Stress Responses of the Swimming Crab Portunus trituberculatus.

Nitrite is a common environmental pollutant in intensive aquaculture systems. In this study, physiological and transcriptomic analyses were performed to investigate nitrite stress responses in the swimming crab Portunus trituberculatus, an important aquaculture species in China. The results revealed that nitrite can affect neurotransmitter signaling via the expression of neurotransmitter receptors such as octopamine receptor (OAR) and 5-hydroxytryptamine receptor (5-HTR), and depress ecdysteroid signaling by downregulating ecdysteroid receptor (EcR) as well as its downstream transcription factors in hepatopancreas. In addition, nitrite suppressed the expression of hemocyanins, the oxygen-transporting protein, which at least partly contributed to tissue hypoxia, resulting in a switchover of energy metabolism from aerobic to anaerobic pathway. To meet the energy demand, glycogens and lipids were mobilized and transported to the hemolymph, and the catabolism of amino acids and fatty acids was enhanced to provide energy for hepatopancreas. β-oxidation of fatty acids, the major process by which fatty acids are oxidized to generate energy, seems to occur mainly not in mitochondria but in peroxisomes. Although the cellular protective mechanisms, including antioxidant defense, heat shock response (HSR), unfolded protein response (UPR), and autophagy, were activated, nitrite-induced cellular stress overwhelmed the repairing capacity and caused significant increase in the levels of apoptosis. These results indicated that nitrite stress influences neurotransmitter and endocrine signaling, disturbs energy metabolism, damages cellular components, and induces apoptosis in P. trituberculatus. The findings of this study provide new insights into nitrite stress response in the swimming crab and provide valuable information for aquaculture management of this species.

Development and characterization of primary cell culture from the spinal cord of Asian seabass, Lates calcarifer.

Asian seabass, Lates calcarifer, is one of the most important fish species in aquaculture. An attempt was made to develop a primary cell culture from the spinal cord of Lates calcarifer by the enzymatic and mechanical dissociation method. The primary cell culture was sub-cultured for 20 times in Leibovitz's L-15 medium with 20% fetal bovine serum (FBS) and 0.5nM of human neurotrophin-3 at 28°C. The primary cell culture was cryopreserved at different passage levels and recovery of cells after long-term storage was estimated about 75-85%. The authenticity of origin of primary cell culture from L. calcarifer was confirmed by polymerase chain reaction assay using species-specific mitochondrial 12S rRNA primer. The primary cell culture was designated as seabass spinal cord cells (SBSC). The cells morphologically resembled the neurons due to their neural-like prolongations and star-like structure. Immunophenotypic analysis of the SBSC revealed that they are of neuronal origin. The SBSC were found to be highly susceptible to striped jack nervous necrosis virus (SJNNV) and infection in the cells was confirmed by RT-PCR. In conclusion, this is the first innovative euryhaline fish neuronal primary cell culture of L. calcarifer now available for neurophysiological and neurotoxicological studies.

Nonintrusive and Effective Volume Reconstruction Model of Swimming Sturgeon Based on RGB-D Sensor.

The sturgeon is an important commercial aquaculture species in China. The measurement of sturgeon mass plays a remarkable role in aquaculture management. Furthermore, the measurement of sturgeon mass serves as a key phenotype, offering crucial information for enhancing growth traits through genetic improvement. Until now, the measurement of sturgeon mass is usually conducted by manual sampling, which is work intensive and time consuming for farmers and invasive and stressful for the fish. Therefore, a noninvasive volume reconstruction model for estimating the mass of swimming sturgeon based on RGB-D sensor was proposed in this paper. The volume of individual sturgeon was reconstructed by integrating the thickness of the upper surface of the sturgeon, where the difference in depth between the surface and the bottom was used as the thickness measurement. To verify feasibility, three experimental groups were conducted, achieving prediction accuracies of 0.897, 0.861, and 0.883, which indicated that the method can obtain the reliable, accurate mass of the sturgeon. The strategy requires no special hardware or intensive calculation, and it provides a key to uncovering noncontact, high-throughput, and highly sensitive mass evaluation of sturgeon while holding potential for evaluating the mass of other cultured fishes.

Transcriptome and pathophysiological analysis during Bacillus cereus group infection in Pelodiscus sinensis uncovered the importance of iron and toll like receptor pathway

The Chinese softshell turtle (CST; Pelodiscus sinensis) is an important freshwater aquaculture species with high economic value. CST is farmed throughout Asia, especially in China and Taiwan. However, the presence of diseases, particularly those caused by the Bacillus cereus group, poses significant threats to commercial CST farming. A recent study has unveiled new genospecies within the B. cereus group, Bacillus shihchuchen. Within this group, strain QF108–045 stands out for its high virulence, notably leading to severe septicemia in CST. This study aimed to explore the transcriptome and pathophysiological changes in CSTs infected with QF108–045. Upon infection with QF108–045, turtles exhibited upregulation of Toll-like receptor (TLR) 2, 4, and 5, among which, TLR5 was significantly upregulated. Activation of TLR signaling leading to elevated levels of IL-1β, TNFα, and Th17 cytokines, which subsequently activate nuclear factor kappa B (NF-κB). CSTs challenged with QF108–045 exhibited a substantial decrease packed cell volume, indicating severe hemolysis. The notable upregulation of transferrin, ZIP8/14, and HO-1 indicates an active transfer of iron or heme into cells, and melanomacrophages in the spleen showed a positive signal in Perl's Prussian blue staining, implying their importance as essential iron storage cells. However, despite the hemolysis, ferroptosis was inhibited by the upregulation of system Xc− related genes. Additionally, our study revealed a notable increase in TLR5 expression following immunization with recombinant flagellin from QF108–045, coupled with analysis of protein tertiary docking modules. These findings advance our understanding of defense mechanisms in CSTs during QF108–045 infection, providing valuable insights for future vaccine development efforts.

Effects of Gene Alternative Splicing Events on Resistance to Cryptocaryonosis of Large Yellow Croaker (Larimichthys crocea).

Large yellow croaker (L. crocea) is a productive species in marine aquaculture with great economic value in China. However, the sustainable development of large yellow croaker is hampered by various diseases including cryptocaryonosis caused by Cryptocaryon irritans. The genetic regulation processes for cryptocaryonosis in large yellow croaker are still unclear. In this present study, we analyzed differential alternative splicing events between a C. irritans resistance strain (RS) and a commercial strain (CS). We identified 678 differential alternative splicing (DAS) events from 453 genes in RS and 719 DAS events from 500 genes in CS. A set of genes that are specifically alternatively spliced in RS was identified including mfap5, emp1, and trim33. Further pathway analysis revealed that the specifically alternative spliced genes in RS were involved in innate immune responses through the PRR pathway and the Toll and Imd pathway, suggesting their important roles in the genetic regulation processes for cryptocaryonosis in large yellow croaker. This study would be helpful for the studies of the pathogenesis of cryptocaryonosis and dissection of C. irritans resistance for L. crocea.

QTL mapping and candidate gene identification for lower temperature tolerance and growth traits using whole genome re-sequencing in Argopecten scallops

Lower temperature tolerance (LTT) and growth traits are vital to the success of overwintering scallop farming in the North China Sea. Bohai Red, a novel selected scallop strain is the main aquaculture species in this region. However, its poor LTT hinders its growth. To improve these traits, the larger Bohai Red scallop was crossed with the smaller bay scallop (A. irradians irradians) which tolerates low temperatures. The full-sib F1 hybrids and the whole-genome resequencing (WGR) method were used to construct a high-density genetic linkage map comprising 5925 single nucleotide polymorphisms (SNPs). The consensus linkage map consisted of 16 linkage groups spanning 1343.46 cM with an average distance of 0.23 cM. Based on this genetic linkage map, 42 potentially significant quantitative trait loci (QTLs) for LTT and growth were detected in eight different linkage groups (LGs) explaining 9.2–18.6% of the phenotypic variation. LG11 may regulate both LTT and growth as 20 QTLs were localized there. Eighteen candidate genes were identified, including 2 (SCARF1, SLC28A3) for LTT and 16 for the growth-related traits. To the best of our knowledge, the present work is one of the first to fine-map the LTT and growth-related QTLs in a genetic linkage map for hybrid Argopecten spp. scallops.

Barramundi (Lates calcarifer) rare coloration patterns: a multiomics approach to understand the "panda" phenotype.

The barramundi (Lates calcarifer), a significant aquaculture species, typically displays silver to bronze coloration. However, attention is now drawn to rare variants like the "panda" phenotype, characterized by blotch-like patterns of black (PB) and golden (PG) patches. This phenotype presents an opportunity to explore the molecular mechanisms underlying color variations in teleosts. Unlike stable color patterns in many fish, the "panda" variant demonstrates phenotypic plasticity, responding dynamically to unknown cues. We propose a complex interplay of genetic factors and epigenetic modifications, focusing on DNA methylation. Through a multiomics approach, we analyze transcriptomic and methylation patterns between PB and PG patches. Our study reveals differential gene expression related to melanosome trafficking and chromatophore differentiation. Although the specific gene responsible for the PB-PG difference remains elusive, candidate genes like asip1, asip2, mlph, and mreg have been identified. Methylation emerges as a potential contributor to the "panda" phenotype, with changes in gene promoters like hand2 and dynamin possibly influencing coloration. This research lays the groundwork for further exploration into rare barramundi color patterns, enhancing our understanding of color diversity in teleosts. Additionally, it underscores the "panda" phenotype's potential as a model for studying adult skin coloration.

Use of tuf gene sequencing for Identification of Lactococci isolated from diseased rainbow trout (Oncorhynchus mykiss)

Lactococcosis is a bacterial infection that is characterized by the appearance of septicemia in fish. Traditionally, the identification of causes of disease outbreaks in aquaculture poses a major challenge due to their comparable characteristics. In this study, simple PCR and sequencing based on the tuf gene were developed to identify isolates belonging to the Streptococcaceae family. The outbreaks of lactococcosis in rainbow trout have been mainly associated with Lactococcus garvieae, but the emergence of closely related species, Lactococcus petauri and Lactococcus formosensis pose a challenge in accurate identification. The study aimed to identify Gram-positive catalase-negative cocci and differentiate between Lactococcosis-causing bacteria (LCB) in rainbow trout isolates associated with lactococcosis outbreaks in Iran. Seventy-five Gram-positive cocci strains from diseased rainbow trout were tested using a PCR and sequencing method targeting the tuf gene. Sequence and phylogenetic analyses were conducted to distinguish between closely related Lactococcus species. The PCR results revealed a successful amplification with tuf gene primers for all strains, allowing species identification. The sequence analysis showed that all 29 isolates initially identified as L.garvieae were 100% identical to L.petauri, indicating a previous misclassification. This work is the first report by L.petauri of Iran. Analysis of tuf gene sequences revealed different patterns of single nucleotide polymorphism (SNP) for accurate species differentiation and phylogenetic analysis confirmed different clusters for LCB. The study highlights the misidentification of L.petauri as L.garvieae in lactococcosis outbreaks and the importance of accurate species differentiation in disease management. The tuf gene sequencing method shows promise for practical, cost-effective, and accurate differentiation of closely related streptococcal species in aquaculture. These findings strongly indicate the need to re-evaluate the initial identification of isolates from fish with lactococcisis. The findings of this study also suggest that the tuf gene sequencing, established in this research for its practicality and cost-efficiency, could potentially be integrated into routine diagnostic procedures for Gram-positive, catalase-negative cocci associated with outbreaks of infections in aquatic animals; however, further experimental works are warranted.

Genome assembly of redclaw crayfish (Cherax quadricarinatus) provides insights into its immune adaptation and hypoxia tolerance

BackgroundThe introduction of non-native species is a primary driver of biodiversity loss in freshwater ecosystems. The redclaw crayfish (Cherax quadricarinatus) is a freshwater species that exhibits tolerance to hypoxic stresses, fluctuating temperatures, high ammonia concentration. These hardy physiological characteristics make C. quadricarinatus a popular aquaculture species and a potential invasive species that can negatively impact tropical and subtropical ecosystems. Investigating the genomic basis of environmental tolerances and immune adaptation in C. quadricarinatus will facilitate the development of management strategies of this potential invasive species.ResultsWe constructed a chromosome-level genome of C. quadricarinatus by integrating Nanopore and PacBio techniques. Comparative genomic analysis suggested that transposable elements and tandem repeats drove genome size evolution in decapod crustaceans. The expansion of nine immune-related gene families contributed to the disease resistance of C. quadricarinatus. Three hypoxia-related genes (KDM3A, KDM5A, HMOX2) were identified as being subjected to positive selection in C. quadricarinatus. Additionally, in vivo analysis revealed that upregulating KDM5A was crucial for hypoxic response in C. quadricarinatus. Knockdown of KDM5A impaired hypoxia tolerance in this species.ConclusionsOur results provide the genomic basis for hypoxic tolerance and immune adaptation in C. quadricarinatus, facilitating the management of this potential invasive species. Additionally, in vivo analysis in C. quadricarinatus suggests that the role of KDM5A in the hypoxic response of animals is complex.

Fermentability assessment of selected oligosaccharides by Lactiplantibacillus plantarum BIOTECH 1074 towards short-chain organic acid production with anti-vibrio efficacy

Vibriosis, caused by Vibrio harveyi and Vibrio parahaemolyticus, poses a significant threat to aquaculture, resulting in substantial economic losses. Oligosaccharides are known for their ability to improve gut health and prevent vibriosis in aquaculture species. This study explored the fermentative utilization of galacto-oligosaccharides (GOS), manno-oligosaccharides (MOS), and inulin by Lactiplantibacillus plantarum BIOTECH 1074. GOS and glucose were the preferred substrates for L. plantarum growth, producing high levels of lactic acid, propanoic acid, and acetic acid. These compounds showed substantial anti-Vibrio activities, having inhibitory concentration values of 0.252 ± 0.005 and 0.656 ± 0.015 mg total organic acid/mL against V. harveyi, V. cholerae, and V. parahaemolyticus from GOS fermented supernatant. The fermentative capabilities of L. plantarum BIOTECH 1074, in utilizing specific oligosaccharide substrates to produce organic acids with anti-Vibrio potential, offers a promising strategy for enhancing disease management and overall efficiency in aquaculture systems.

Effects of replacing fishmeal with Spirulina platensis powder on the Zig-zag eel (Mastacembelus armatus): Growth performance, flesh quality, digestibility, and gut microbial composition

Protein demand from aquaculture exacerbates environmental pressures. Zig-zag eel (Mastacembelus armatus, MA) is a new aquaculture species in southern China and has great potential for future promotion. In this study, we used Spirulina platensis powder (SPP) to replace 0–20 % of fishmeal in the feed, respectively. A 10-week aquaculture experiment was conducted on 600 MAs with five groups of F0 (0 %), F1 (5 %), F2 (10 %), F3 (15 %), and F4 (20 %) set up with equal nitrogen (approximately 50.00 % crude protein) and equal fat (about 5.50 % crude fat) feeds. The experimental results showed that replacing fishmeal with different proportions of SPP significantly reduced FCR (p < 0.05), increased WGR and SGR (p < 0.05), and reduced the feeding cost, with the best performance in F2. Polynomial analysis combining WGR and SGR showed that the optimum percentage of substitution was 10.93 % and 11.09 % in MA diets, respectively. The addition of SPP significantly reduced the levels of EPA and DHA content (p < 0.05), significantly increased the proportion of C14:0, C16:1, C20:5n3, and C22:6n3 (p < 0.05), and a high proportion of SPP addition significantly decreased saturated fatty acid content (p < 0.05). The length of intestinal villi and the secretion levels of Chymotrypsin and Pepsin were significantly increased (p < 0.05), and the secretion level of Lipase was significantly decreased (p < 0.05) in the experimental group. A low percentage of SPP increased microbial diversity in MA’s gut. Functional pathways related to metabolic functions were the most obvious broad groups with the most significant changes in relative abundance in the experimental group, and Plesiomonas and Aeromonas may be the key microorganisms involved in regulating the digestion and metabolism of SPP in the gut of MA.