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The ability of bacteria to adapt to the external environment is fundamental for their survival. A halotolerant microorganism Enterococcus faecalis able to grow under high salt stress conditions was isolated in the present study. The SDS-PAGE analysis of the secretome showed a protein band with a molecular weight of 28 kDa, gradually increased with an increase in salt concentration, and the highest intensity was observed at 15% salt stress condition. LC-MS/MS analysis of this particular band identified fourteen different proteins, out of which nine proteins were uncharacterized. Further, the function of uncharacterized proteins was predicted based on structure-function relationship using a reverse template search approach deciphering uncharacterized protein into type III polyketide synthases, stress-induced protein-1, Eed-h3k79me3, ba42 protein, 3-methyladenine DNA glycosylase, Atxa protein, membrane-bound respiratory hydrogenase, type-i restriction-modification system methylation subunit and ManxA. STRING network analysis further a showed strong association among the proteins. The processes predicted involvement of these proteins in signal transduction, ions transport, synthesis of the protective layer, cellular homeostasis and regulation of gene expression and different metabolic pathways. Thus, the fourteen proteins identified in the secretome play an essential role in maintaining cellular homeostasis in E. faecalis under high-salinity stress. This may represent a novel and previously unreported strategy by E. faecalis to maintain their normal growth and physiology under high salinity conditions.

An experiment was conducted to study the influence of environmental parameters and stocking density on growth, survival, feed utilization, and economic feasibility of a high value butter catfish, Ompok bimaculatus in floating cages in a large tropical reservoir of India for 180 days. The fingerlings (11.44 ± 1.33 cm; 8.05 ± 3.27 g) were stocked at three stocking densities, viz., 15, 25 and 35 fingerlings m-3 in GI cages (32m3) in triplicates. Commercial floating pellets were fed to fish at 5–3% of fish biomass. The results indicated that the fishes at the lowest stocking density of 15 fingerlings m-3 had significantly higher (p 0.05) between stocking densities of 15 fingerlings m-3 and 25 fingerlings m-3. The condition factor was insignificantly higher at lower densities and its values close to 1 indicated congeniality of reservoir ecosystem for cage culture of the species. The coefficient of variation of weight was significantly higher (24.19 ± 1.20) at 35 fingerlings m-3. The highest economic gains in terms of benefit cost ratio (1.77) were achieved at the lowest stocking density. The present study indicated better growth and economic returns at lower stocking densities of 15–25 fingerlings m-3. The nutrient load and plankton abundance were higher at culture site, however, did not vary significantly from reference sites throughout the culture period. Although most of the environmental parameters showed significant seasonal variations, dissolved oxygen showed significant positive relation (r = 0.86) with the growth of the fish. This is the first study reporting feasibility of cage culture of this highly renumerative species in open waters. The cage culture of this species will not only ensure better economic returns to the marginal cage farmers but will aid in the conservation of this species in natural ecosystem. Being a low volume high value species, the impact on environment will be less compared with high volume low value species. This study will serve as baseline for standardization of its grow-out protocol in cages and will be a step towards much needed species diversification for sustainable small scale cage farming in tropical reservoirs of Asia.

The population structure of Barbodes carnaticus species was studied using conventional (based on body morphometrics and meristic) and image-based analysis (truss network system) methods. The study was carried out with four stocks, namely Karnataka (KA) and Tamil Nadu (TN) stocks from the River Cauvery, Kerala (KE) stock from the River Chalakudy and farm-reared stock (CI) from Central Institute of Freshwater Aquaculture, Bangalore. A total of 27 morphometric, 9 meristic and 30 truss measurements were used in the study for the stock structure. Fifteen landmarks were used to generate 30 truss distance measurements. The principal component analysis (PCA), factor analysis (FA), discriminant function analysis (DFA) and cluster analysis (CA) were deployed to determine the variation using both the conventional and truss variables. Variations (86.9%) among the morphometric characters were explained by five principal components, while four principal components explain 96.01% of the variation among the truss distances. DFA using conventional method correctly classified 100% of the original grouped classes of the KA, KE and CI and 93.8% of TN stocks. The DFA employed with truss distance was classified into the stocks CI, KA, KE and TN, and the values are 100, 89.1, 8.6 and 6.1%, respectively. Factor analysis based on truss morphometry showed that factor one is related to body shape and factor two is related to head shape. Two clusters were identified in both the conventional and the truss distance analysis. Truss distance-based cluster showed that the KE and CI stocks are similar compared to the TN stock. In contrary, morphometry-based cluster showed the KE and TN stocks are similar compared to CI stock. The multivariate analysis showed that the farm-reared stock (CI) is different from the wild stocks (KA, KE and TN). This study explained that the combination of the conventional and image-based truss network analysis helps to discriminate various stocks of B. carnaticus. Based on the PCA, bilinear data models were generated using R 3.5.3 software for predicting the stock of each individual. Stock discrimination of this species was mainly due to the geographic isolation, river ecology and temperature variations. The stocks of B. carnaticus are highly exploited from the studied rivers, and the species is an important candidate for species diversification to enhance aquaculture production. Within stock variations are found to be minimum in the present morphometric study, hence the gene pool identification and marker study are required for better understanding of the stocks. This stock structure study may help to develop conservation programmes for this endemic species through a more scientific approach.

In recent years, large-scale mortalities are observed in tilapia due to infection with a novel orthomyxo-like virus named, tilapia lake virus (TiLV) which is marked to be a severe threat to universal tilapia industry. Currently, there are knowledge gaps relating to the antiviral peptide as well as there are no affordable vaccines or drugs available against TiLV yet. To understand the spreading of infection of TiLV in different organs of Oreochromis niloticus, RT-PCR analysis has been carried out. The gene segments of TiLV were retrieved from the NCBI database for computational biology analysis. The 14 functional genes were predicted from the 10 gene segments of TiLV. Phylogenetic analysis was employed to find out a better understanding for the evolution of tilapia lake virus genes. Out of 14 proteins, only six proteins show transmembrane helix region. Moreover, molecular modeling and molecular dynamics simulations of the predicted proteins revealed structural stability of the protein stabilized after 10-ns simulation. Overall, our study provided a basic bioinformatics on functional proteome of TiLV. Further, this study could be useful for development of novel peptide-based therapeutics to control TiLV infection.

Hilsa, Tenualosa ilisha, is a popular fish in northern Bay of Bengal and Hooghly-Bhagirathi river system in India. Despite the high commercial and cultural importance of the species in the region, data on its catch status and fishing effort are highly fragmentary and, sometimes, not reliable as these have not been systematically gathered. By adopting ‘Stratified Multistage Random Sampling’ method, mostly followed for marine fish catch estimation, with modifications to suit the nature of inland fish landings and migratory habit of the species, the annual catch of hilsa in Hooghly-Bhagirathi river system and associated coastal waters in northern Bay of Bengal was estimated for four consecutive years, from 2013 to 2016, as 16,318 t, 45,615 t 12,192 t and 48,922 t, respectively. The catch thus estimated was validated by comparing it with the daily catch data collected by enumerators for three months each during fishing seasons in the first two years from two locations. The catch, seasonality, CPUE and the fishing gear and crafts used were recorded. Comparison of the estimated catch of hilsa with the earlier reported catches indicated that the commercial fisheries of the fish in the Hooghly-Bhagirathi river system have seriously declined, highlighting the compelling need for conservation of the species and managing its fishery.

Enterocytozoon hepatopenaei (EHP) is an emerging microsporidian pathogen in shrimp aquaculture. In the present study, prevalence rate of EHP in cultured Litopenaeus vennamei from West Bengal, east coast of India, was investigated. Histology of hepatopancreas of the infected animals showed eosinophilic to basophilic inclusions in the epithelial cells with moderate necrotic tubular detachment from the basal membrane. Extracted DNA from the hepatopancreatic tissues were subjected to PCR by using two different sets of primers targeting the ssu rRNA genes. An expected PCR product of 951 and 510 bp were yielded for the EHP-positive shrimp samples. Based on the BLASTP, the sequence of ssu rRNA gene (KU179095) of the collected samples showed 100% homology with EHP ssu rRNA gene sequences submitted in NCBI from different countries viz. Vietnam, Thailand, China and India. Further, all the field samples were found to be EHP+ by using a new second-generation primer targeting the spore wall protein gene (SWP) of EHP. For detection of EHP, 119 samples from East Midnapur district, 50 samples from North 24 Parganas district and 50 Samples from South 24 Parganas district were being screened. Overall prevalence rate of EHP in the cultured L. vennamei farm in West Bengal was estimated to be 84.9%, which was highest in comparison to earlier reports in India. Our finding showed that EHP could be detected from slow growing shrimps as well as in some cases from White Faeces Syndrome-affected animals. This is the first report on the occurrence of Enterocytozoon hepatopenaei in cultured L. vannamei in West Bengal, east coast of India.

The myxovirus resistance (Mx) proteins belong to interferon-induced dynamin GTPase and play pivotal role in the inhibition of replication of numerous viruses. These antiviral proteins are released in usual or diseased condition to prevent the viral attack and to carry regular cellular activities like endocytosis and trafficking of nucleoproteins into the nucleus. The invasion of virus up-regulates the expression of Mx transcripts and double-stranded RNA mimic like polyinosinic polycytidyilic acid (Poly I:C). To understand the tissue-specific expression profiling and mechanism of GTP recognition of Mx protein from Labeo rohita (rohu), the full-length gene was cloned, sequenced and characterized through various Bioinformatics tools for the first time. The Mx cDNA was comprised of 2297 bp, and the open reading frame of 1938 bp encodes polypeptide of 631 amino acids. The coding sequence of Mx protein possess the signature motif of dynamin superfamily, LPRG(S/K)GIVTR, the tripartite guanosine-5/triphosphate (GTP)-binding motif (GXXXSGKS/T, DXXG and T/NKXD) and the leucine zipper motifs at the C-terminal end, well conserved in all interferon-induced Mx protein in vertebrates. Western blotting confirmed the molecular weight of Mx protein to be 72 kDa. After the intraperitoneal challenge of L. rohita with a Poly I:C, up-regulation of Mx protein was observed in brain, spleen, liver, kidney, intestine, heart, muscle, and gill. Ontogeny study displayed pronounced expression of Mx protein in all stages of the developmental of Rohu after Poly I:C induction. However a persistent expression of Mx transcript was also observed in Rohu egg as well as milt without induction with Poly I:C. Higher expression of Mx gene was observed on 96 h where it was 6.4 folds higher than the control. The computational modelling of Mx protein portrayed the tripartite N-terminal G-domain that binds to GTP, the bundle-signaling element (BSE) which interconnects the G-domain to the elongated stalk domain and C-terminal helical stalk domain. In agreement with the experimental studies, a series of conserved residues viz., Gln52, Ser53, Ser54, Leu68, Pro69, Gly71, Gly73, Thr76, Asp151, Gly154, Thr220, Lys221, Val251, Cys253, Arg254, and Gly255 were computed to be indispensable for tight anchoring of GTP within binding cavity of G-domain. The binding free energy calculation study depicted that the van der Waals and electrostatic terms contributs significantly to molecular recognition of GTP. Collectively, our study provides mechanistic insights into the tissue-specific expression profiling and GTP binding mechanism of Mx protein from Labeo rohita, which is expected to drive further research on several cellular events including viral resistance and endocytosis in the near future.

A total of 206 bacterial isolates were obtained from soil, water and sediment samples using three different culture media with a pH of 7.3 ± 0.2 and an incubation temperature of 37 °C. Of these isolates, 48 bacteria were selected for functional screening and molecular characterization. The functional screening for salt stress tolerance revealed that, 17 bacteria were identified as moderately halotolerant and 31 were halophilic, capable of growing at 5–15 % (w/v) and ≥15 % (w/v) of NaCl concentration respectively. The 16S rRNA gene sequence analysis and taxonomic identification of isolates were performed using Ribosomal Database Project Release-10 and SILVA SSU database. Based on the sequence length >1,300 bp, 40 bacteria were identified out of 48 isolates. Study showed that, Staphylococcus spp. was highly resistant to salt stress followed by Enterococcus faecalis, Vagococcus fluvialis and Vibrio parahaemolyticus. The phylogenetic analysis revealed that, 24 bacterial isolates belong to Firmicutes and 16 isolates come under Proteobacteria. These bacterial strains would be of great use for prospecting novel and candidate salt stress tolerant genes.

The genetic diversity of five feral populations of Asian Sea bass, Lates calcarifer collected from five isolated locations in India viz., Paradeep, Chilka lake, Kakinada, Chennai and Mumbai was studied using randomly amplified polymorphic DNA. Out of 20 primers screened, 5 decamer random primers amplified a total of 373 DNA bands of which 137 bands were polymorphic. The Kakinada population showed the highest polymorphism (65.71 %) whereas the Chennai population showed the lowest (48.28 %). The inter-population genetic similarity (GS) values estimated for the five populations were checked by one-way ANOVA and found to be significantly different at P

The major hindrance in the development and sustainability of aquaculture industry is the occurrence of various diseases in the farming systems. Today, preventive and management measures are central concern to overcome such outbreak of diseases. Immunostimulants are considered as an effective tool for enhancing immune status of cultured organisms. Among different immunostimulants used in aquaculture practices, β-glucan is one of the promising immunostimulant, which is a homopolysaccharide of glucose molecule linked by the glycoside bond. It forms the major constituents of cell wall of some plants, fungi, bacteria, mushroom, yeast, and seaweeds. Major attention on β-glucan was captivated with the gain in knowledge on its receptors and the mechanism of action. The receptor present inside the animal body recognizes and binds to β-glucan, which in turn renders the animal with high resistance and enhanced immune response. This review highlights β-glucan as an immunostimulant, its effective dosages, and route of administration and furthermore provides an outline on role of β-glucan in enhancing growth, survival, and protection against infectious pathogens pertaining to fishes and shellfishes. Study also summarizes the effect of β-glucan on its receptors, recognition of proteins, immune-related enzymes, immune-related gene expression and their mechanisms of action.

Polyunsaturated fatty acids (PUFAs) consumption is known to be associated with a number of health benefits and fish oils, especially marine, are rich in PUFAs. Tenualosa ilisha, a highly preferred food fish in South-Asian countries, is rich in oils; however, information on fatty acid profiles of different size-groups of hilsa is scanty. In the present investigation, information on fatty acid profiles of different size groups of hilsa has been generated. Analysis showed that medium-sized fish contained the highest amount of unsaturated fatty acids as well as ω-3 PUFAs, EPA plus DHA and the lowest amount of saturated fatty acids (SFAs). PUFA content was highest in small-sized hilsa; however, ω-3 PUFA content was lower and SFAs content was higher than medium-sized fish. In large-sized fish, although ω-3/ω-6 ratio was highest, quantitatively they contained the lowest amount of PUFAs and highest amount of SFAs. Thus, on basis of fatty acid profiles, medium-sized hilsa is the best followed by the small-sized fish for human health and nutrition.

Aquaculture is emerging as one of the most viable and promising enterprises for keeping pace with the surging need for animal protein, providing nutritional and food security to humans, particularly those residing in regions where livestock is relatively scarce. With every step toward intensification of aquaculture practices, there is an increase in the stress level in the animal as well as the environment. Hence, disease outbreak is being increasingly recognized as one of the most important constraints to aquaculture production in many countries, including India. Conventionally, the disease control in aquaculture has relied on the use of chemical compounds and antibiotics. The development of non-antibiotic and environmentally friendly agents is one of the key factors for health management in aquaculture. Consequently, with the emerging need for environmentally friendly aquaculture, the use of alternatives to antibiotic growth promoters in fish nutrition is now widely accepted. In recent years, probiotics have taken center stage and are being used as an unconventional approach that has numerous beneficial effects in fish and shellfish culture: improved activity of gastrointestinal microbiota and enhanced immune status, disease resistance, survival, feed utilization and growth performance. As natural products, probiotics have much potential to increase the efficiency and sustainability of aquaculture production. Therefore, comprehensive research to fully characterize the intestinal microbiota of prominent fish species, mechanisms of action of probiotics and their effects on the intestinal ecosystem, immunity, fish health and performance is reasonable. This review highlights the classifications and applications of probiotics in aquaculture. The review also summarizes the advancement and research highlights of the probiotic status and mode of action, which are of great significance from an ecofriendly, sustainable, intensive aquaculture point of view.