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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.

The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).

Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.

Studies on Sisorinae systematics have been largely restricted to morphological data with few studies on examination of phylogenetic relations. However, no study has been done to evaluate genetic distance of the genera under Sisorinae sub-family and detailed phylogenetic relations within it. We used nuclear recombination activating 2 (rag2) gene and mitochondrial cytochrome c oxidase I (COI) gene from 64 species to examine genetic differentiation and phylogenetic relationships within 11 Asian Sisorinae genera. The range of interspecies K2P distance for rag2 was 0-0.061 and COI was 0-0.204. Phylogenetic analysis based on maximum likelihood (ML) and Bayesian (BI) approaches for each locus individually and for the concatenated rag2 and COI sequences revealed three major subclades viz. Bagariini, Sisorini and Erethistini under subfamily Sisorinae. The analysis based on COI gene showed ((Sisorini, Bagariini), Erethistini) relationship. Rag2 and combined rag2 and COI showed ((Sisorini, Erethistini), Bagariini) relationship. Combined rag2 and COI analyses resulted into better resolved trees with a good bootstrap support. In this study, new record of Pseudolaguvia foveolata (Erethistini) has been documented based on 13 specimens collected from Torsa River, Jaldapara, Alipurduar district, West Bengal, India (26°43'44.66″ N and 89°19'32.34″ E), extending its distribution range in Brahmaputra drainage, India. The genetic distance between the P. foveolata new record and the reported P. foveolata (holotype: UMMZ 244867) was 0.00 at both rag2 and COI locus and it was further grouped with P. foveolata Type specimen (holotype: UMMZ 244867) with 100% bootstrap support. This report gives additional information on occurrence of the species P. foveolata, along with discussion on morphometric, meristic and molecular (COI and rag2 gene) data.

The rapid degradation, overexploitation and encroachment of floodplain wetlands have led to considerable decline in fish diversity and production from these invaluable aquatic resources threatening livelihood of the dependent fishers. The climate change evident in the fast few decades have further aggravated the problem of eutrophication causing water stress, sedimentation leading to rampant macrophyte proliferation affecting ecological and economic functioning of these ecosystems. Macrophyte control and management needs serious attention for sustaining ecosystem services provided by these resources. In this direction pen culture of grass carp, Ctenopharyngodon idella as a biocontrol for macrophytes along with Indian major carps was implemented in a co-management mode in Beledanga, a typical floodplain wetland, a gradually shrinking, macrophyte dominated floodplain wetland in lower Ganga basin. Indian major carps Labeo catla (6.28±0.23g), Labeo rohita (5.1±0.12g), Cirrhinus mrigala (3.5±0.08g) were stocked in the ratio 4:3:3 at the rate of 20 no./m2 in pens (0.1ha each) in triplicate. Grass carp (7.1±0.42g) was stocked in pen at the rate of 20 no./m2. The fishes were fed with pelleted feed twice a day at the rate of 2-3% of body weight per day. The seed was overwintered in pens for a period of 90 days from November 2019-January 2020. Average weight recorded at the end of culture period was 25.13±1.70g, 18.11±0.63g, 14.53±0.87g and 39.20±1.90g in L. catla, L. rohita, C. mrigala and C. idella respectively. The survival of fish ranged from 70 to 81%. Growth performance and feed utilization efficiency of grass carp was significantly higher (p

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization has profoundly affected river microflora and their function thus its health. In this study, potential of whole genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like, Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing), and Syntrophobacter fumaroxidans (sulfate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages were also noticed along the downstream of river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e., Nakaseomyces, Aspergillus, Schizosaccharomyces, and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most abundant pollution degrading enzymes in polluted sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

East Kolkata Wetland (EKW) is one of the largest sewage-fed wetlands in the world, which support the livelihood of thousands of peoples. However, at present, EKW system has become ecologically vulnerable due to the discharge of toxic waste through the sewage canal from the Kolkata metropolitan city. Hence, it becomes very important to understand the inflow and load of potentially toxic elements (PTE) in the sediment, water, and fish of sewage-fed wetland used for aquaculture activities. In this study, one of the polluted wetland from EKW, Sardar bherry, was selected as the study area. Sediment samples (45) were collected from 15 sites to characterize the PTEs concentrations levels utilizing inductively coupled plasma mass spectrometry, and their spatial distribution pattern and pollution quality indices were estimated. Water (45) and fish (7) samples were also analyzed to understand the distribution pattern of PTEs from sediment to water and water to fish. The geostatistical prediction map showed that the concentration range of Cr, Fe, Cu, Co, Zn, Cd, Ni, Pb, and Mn in sampling stations were 27.3-84.1 μg g

Aquaporin's (AQPs) are the major superfamily of small integral membrane proteins that facilitates transportation of water, urea, ammonia, glycerol and ions across biological cell membranes. Despite of recent advancements made in understanding the biology of Aquaporin's, only few isoforms of aquaporin 1 (AQP1) some of the teleost fish species have been characterized at molecular scale. In this study, we made an attempt to elucidate the molecular mechanism of water transportation in AQP1 from walking catfish (Clarias batrachus), a model species capable of breathing in air and inhabits in challenging environments. Using state-of-the-art computational modelling and all-atoms molecular dynamics simulation, we explored the structural dynamics of full-length aquaporin 1 from walking catfish (CbAQP1) in lipid mimetic bilayers. Unlike AQP1 of human and bovine, structural ensembles of CbAQP1 from MD revealed discrete positioning of pore lining residues at the intracellular end. Snapshots from MD simulation displayed differential dynamics of aromatic/arginine (ar/R) filter and extracellular loop C bridging TM helix H3 and H4. Distinct conformation of large extracellular loops, loop bridging TM2 domain and HB helix along with positioning of selectivity filter lining residues controls the permeability of water across the bilayer. Moreover, the identified unique and conserved lipid binding sites with 100% lipid occupancy signifies lipid mediated structural dynamics of CbAQP1. All-together, this is the first ever report on structural-dynamics of aquaporin 1 in walking catfish which will be useful to understand the molecular basis of transportation of water and other small molecules under varying degree of hyperosmotic environment.

Chemical and biological contaminants are of primary concern in ensuring seafood safety. Rapid detection of such contaminants is needed to keep us safe from being affected. For over three decades, immunoassay (IA) technology has been used for the detection of contaminants in seafood products. However, limitations inherent to antibody generation against small molecular targets that cannot elicit an immune response, along with the instability of antibodies under ambient conditions greatly limit their wider application for developing robust detection and monitoring tools, particularly for non-biomedical applications. As an alternative, aptamer-based biosensors (aptasensors) have emerged as a powerful yet robust analytical tool for the detection of a wide range of analytes. Due to the high specificity of aptamers in recognising targets ranging from small molecules to large proteins and even whole cells, these have been suggested to be viable molecular recognition elements (MREs) in the development of new diagnostic and biosensing tools for detecting a wide range of contaminants including heavy metals, antibiotics, pesticides, pathogens and biotoxins. In this review, we discuss the recent progress made in the field of aptasensors for detection of contaminants in seafood products with a view of effectively managing their potential human health hazards. A critical outlook is also provided to facilitate translation of aptasensors from academic laboratories to the mainstream seafood industry and consumer applications.

The biofloc system has recently attracted great attention as a cost-effective, sustainable, and environmentally friendly technology and expected to contribute toward human food security (Zero Hunger SDG 2). It is also expected that this endeavor can be adopted widely because of its characteristics of zero water exchange and reduced artificial feeding features. In the biofloc system, the flocs which are generally formed by aggregation of heterotrophic microorganisms, serve as natural bioremediation candidates. These microbes effectively maintain water quality by utilizing the nutrient wastes, mostly originated from digested, unconsumed, and metabolic processes of feed. Additionally, the flocs are important sources of nutrients, mainly a protein source, and when these are consumed by aquaculture animals they improve the growth performance, immunity, and disease tolerance of host against pathogenic microbial infection. Here in this review, we focus on recent advances that could provide a mechanistic insight on how the microbial community developed in the biofloc system helps in the bioremediation process and enhances the overall health of the host. We have also tried to address the possible role of these microbial communities against growth and virulence of pathogenic microbes.

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

The geographic information systems (GIS) play an important role in all geospatial aspects of assessment, monitoring and management of inland open water resources for strategic development in fisheries sector. In India, reservoir fisheries development is one of the flagship programme and several initiatives have been taken up towards enhancement and sustainable development. The present study investigates spatio-temporal changes in ecology and fisheries in Hirakud reservoir, Odisha build across river Mahanadi which features one of the largest dam in South Asia. The reservoir is mainly utilized for electricity generation, irrigation and offers tremendous scope to support fisheries and livelihood. As per the seasonal variation analysis, water spread area was at the minimum during premonsoon period. Most of the water quality parameters including nitrate, phosphate, BOD and alkalinity were higher in the premonsoon period and overall the parameters were under favourable range for fisheries. The present investigation from the fish landing sites of the reservoir, recorded merely 40 fish species, indicating loss of fish diversity as compared to the historical reports. The IUCN conservation status showed that among the 40 species only one species, Wallago attu is under VU category and 4 species Chitala chitala, Ompok bimaculatus, Ailia colia and Bagarius bagarius are under NT category. The analysis of time series annual fish catch data using ARIMA model forecasted the increasing trend of fish production. The water quality parameters were presented in GIS platform for better understanding of the spatial variations over time. Habitat protection of fish breeding grounds, closed seasons, mesh size regulations, scientific management and community participation are recommended as the measures for conservation of fish diversity and sustainable enhancement of fish production in the reservoir.

With growing environmental and health concerns over persistent organic compounds such as organophosphates, regulatory bodies have imposed strict regulations for their use and monitoring in water bodies. Although conventional analytical tools exist for the detection of organophosphorus pesticides, new strategies need to be developed to fulfil the ASSURED (affordable, sensitive, specific, user-friendly, rapid, equipment-free and deliverable to end users) criteria of the World Health Organisation. One such strategy is to employ the ability of certain nanoparticles to mimic the enzymatic activity of natural enzymes to develop optical sensors. We show that the intrinsic peroxidase-mimic NanoZyme activity of tyrosine-capped silver nanoparticles (Ag-NanoZyme) can be exploited for highly specific and rapid detection of chlorpyrifos, an organophosphorus pesticide. The underlying working principle of the proposed aptasensor is based on the dynamic non-covalent interaction of the chlorpyrifos specific aptamer (Chl) with the NanoZyme (sensor probe) vs. the pesticide target (analyte). The incorporation of the Chl aptamer ensures high specificity leading to a colorimetric response specifically in the presence of chlorpyrifos, while the sensor remains unresponsive to other pesticides from organophosphate and non-organophosphate groups. The robustness of the sensor to work directly in environmental samples was established by evaluating its ability to detect chlorpyrifos in river water samples. The excellent recovery rates demonstrate the sensor robustness, while the simplicity, and rapid sensor response (2 min) to detect the presence of chlorpyrifos highlights the capabilities of the proposed colorimetric sensing system.

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.

Vibrio parahaemolyticus is known to cause disease and infection in humans. This study was conducted to understand the prevalence of V. parahaemolyticus and the presence of virulence factors in environmental isolates of V. parahaemolyticus, collected from three major shrimp producing states viz, West Bengal, Andhra Pradesh and Gujarat of India during February 2014 to June 2017. Total 183 V. parahaemolyticus were isolated from moribund shrimp and identified using toxR and 16S rRNA gene. Polymerase Chain Reaction (PCR) was performed to detect virulence genes under T3SS1 and T3SS2 along with AHPND. All the isolates showed presence of vcrD1, vp1680 and vopD1 gene under T3SS1 but negative for AHPND. Only 3% of isolates showed presence of all the virulence genes (vcrD2, vopD2, vopB2 and vopC) used in the present study under T3SS2. The isolates were also tested for the presence of tdh, trh or both the genes; 8% of the isolates had trh gene and 3% of the isolates had tdh gene. The genetic diversity within and between V. parahaemolyticus isolated from three different geographical locations, was analyzed by using 16S rRNA gene. Though the biotype diversity (h) was high for all three populations, phylogenetic study of V. phaemolyticus revealed an admixture of biotypes. Tajima's D (−2.59470; p

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.

Human norovirus (NoV) remains the most common cause of viral gastroenteritis and the leading cause of viral foodborne outbreaks globally. NoV is highly pathogenic with an estimated median viral infective dose (ID50) ranging from 18 to 1015 genome copies. For NoV detection, the only reliable and sensitive method available for detection and quantification is reverse transcription quantitative polymerase chain reaction (RTqPCR). NoV detection in food is particularly challenging, requiring matrix specific concentration of the virus and removal of inhibitory compounds to detection assays. Hence, the RTqPCR method poses some challenges for rapid in-field or point-of-care diagnostic applications. We propose a new colorimetric NanoZyme aptasensor strategy for rapid (10 min) and ultrasensitive (calculated Limit of Detection (LoD) of 3 viruses per assay equivalent to 30 viruses/mL of sample and experimentally demonstrated LoD of 20 viruses per assay equivalent to 200 viruses/mL) detection of the infective murine norovirus (MNV), a readily cultivable surrogate for NoV. Our approach combines the enzyme-mimic catalytic activity of gold nanoparticles with high target specificity of an MNV aptamer to create sensor probes that produce a blue color in the presence of this norovirus, such that the color intensity provides the virus concentrations. Overall, our strategy offers the most sensitive detection of norovirus or a norovirus surrogate achieved to date using a biosensor approach, enabling for the first time, the detection of MNV virion corresponding to the lower end of the ID50 for NoV. We further demonstrate the robustness of the norovirus NanoZyme aptasensor by testing its performance in the presence of other nontarget microorganisms, human serum and shellfish homogenate, supporting the potential of detecting norovirus in complex matrices. This new assay format can, therefore, be of significant importance as it allows ultrasensitive norovirus detection rapidly within minutes, while also offering the simplicity of use and need for nonspecialized laboratory infrastructure.

Shrimp, as a high-protein animal food commodity, are one of the fastest growing food producing sectors in the world. It has emerged as a highly traded seafood product, currently exceeding 8 MT of high value. However, disease outbreaks, which are considered as the primary cause of production loss in shrimp farming, have moved to the forefront in recent years and brought socio-economic and environmental unsustainability to the shrimp aquaculture industry. Acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio spp., is a relatively new farmed penaeid shrimp bacterial disease. The shrimp production in AHPND affected regions has dropped to ~60%, and the disease has caused a global loss of USD 43 billion to the shrimp farming industry. The conventional approaches, such as antibiotics and disinfectants, often applied for the mitigation or cure of AHPND, have had limited success. Additionally, their usage has been associated with alteration of host gut microbiota and immunity and development of antibiotic resistance in bacterial pathogens. For example, the Mexico AHPND-causing V. parahaemolyticus strain (13-306D/4 and 13-511/A1) were reported to carry tetB gene coding for tetracycline resistance gene, and V. campbellii from China was found to carry multiple antibiotic resistance genes. As a consequence, there is an urgent need to thoroughly understand the virulence mechanism of AHPND-causing Vibrio spp. and develop novel management strategies to control AHPND in shrimp aquaculture, that will be crucially important to ensure food security in the future and offer economic stability to farmers. In this review, the most important findings of AHPND are highlighted, discussed and put in perspective, and some directions for future research are presented.

Vibrio parahaemolyticus is a gram-negative halophilic bacterium responsible for gastrointestinal infection in human and vibriosis in aquatic animals. The thermostable direct hemolysin (tdh), tdh-related hemolysin (trh) and thermolabile hemolysin (tlh) positive strains of V. parahaemolyticus were identified from brackishwater aquaculture farms of West Bengal and Andhra Pradesh, India. Moreover, the presence of other virulent genes like vcrD1, vopD, vp1680 under type three secretion system 1 (T3SS1) and vcrD2 vopD2, vopB2, vopC2 under type three secretion system 2 (T3SS2) were detected in tdh positive strain of V. parahaemolyticus. Furthermore, the study revealed that the tdh and trh positive isolates were resistant to β-lactam antibiotics and were able to lyse more than 95% of human Red Blood Cells (RBCs). In addition, both the isolates showed high cytotoxicity in Human Embryonic Kidney (HEK) cell line compared to tlh positive strain. Additionally, intraperitoneal and oral administration of tdh and trh positive strain of V. parahaemolyticus in Indian Major Carp, Labeo rohita caused 100% mortality at the level of 2.0 × 108 CFU ml−1 and 1.6 × 108 CFU ml−1, respectively. In contrast, only 10% mortality was observed in the case of tlh positive strain at the level of 2.5× 108 CFU ml−1. The histopathological changes like infiltration of blood cells and degenerated hepatic tissue in the liver of L. rohita were observed after the experimental challenge. The changes like degeneration of glomeruli, necrosis of renal tubules and Bowman's capsule were observed in the kidney section. Ragged, irregular shaped villi and necrosis of the villus were observed in the intestinal lumen. Overall, the study demonstrates that isolated V. parahaemolyticus is a potent aquatic microbial pathogen. Additionally, as V. parahaemolyticus is also a human pathogen and might pose a threat to the human population, proper management strategies are required to prevent the possible occurrence of disease.

Vibrio parahaemolyticus is a zoonotic bacterium that causes infections in shellfish, fish and higher vertebrates as well as in humans. The Tdh and Trh positive strains of V. parahaemolyticus are generally considered as major virulent strains. The pathogenic mechanisms of Trh positive strain of V. parahaemolyticus are poorly understood. Therefore, in the present study Indian Major Carp, Labeo rohita was intraperitoneally challenged with a Trh positive strain of V. parahaemolyticus below lethal dose 50 (LD

The complete mitogenome of Heteropneustes fossilis is described using Ion Torrent (PGM sequencer), which showed it was 16,489 bp in size comprising 13 mRNAs, 22 tRNAs, 2 rRNA genes, and 858 bp as D-Loop control region, along with gene order and organization, being similar to most of the other related Siluriformes fish mitogenome of NCBI databases. The 20 RNAs were packed into a typical cloverleaf structure. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of H. fossilis mitogenome reported earlier and also would be helpful in understanding the population genetics, phylogenetics, and evolution of catfishes.

Effects of the dietary therapeutic dose of oxytetracycline (OTC) at 80 mg/kg biomass/day for consecutive 10 days on the behaviour, feed intake, mortality, residue accumulation and depletion, antioxidant capacity and immune-related genes expression in juvenile Nile tilapia Oreochromis niloticus were evaluated. OTC-dosing caused mortalities, reduced feed intake, and biomass reduction at 24.5–28.5 °C. OTC residues recorded on day 10 (161.40 ± 11.10 ng/g) were within the maximum residue limits of the Codex Alimentarius. The withdrawal period was 7 days as per the European Commission's regulation. Traces of residues were present even on day 42 post-OTC-dosing. Dietary OTC reduced the antioxidant capacity of the liver and muscle tissues and down-regulated the expression of tumour necrosis factor-α, interleukin-1β, and heat shock protein-70 genes in the liver significantly during the dosing period. The data generated on the biosafety of OTC-dosing may offer inputs for the development of management strategies in maintaining fish health and food safety.

The toll-like receptor 5 (TLR5) is the most conserved important pattern recognition receptors (PRRs) often stimulated by bacterial flagellins and plays a major role in the first-line defense against invading pathogenic bacteria and in immune homeostasis. Experimental crystallographic studies have shown that the extracellular domain (ECD) of TLR5 recognizes flagellin of bacteria and functions as a homodimer in model organism zebrafish. However, no structural information is available on TLR5 functionality in the major carp Cirrhinus mrigala (mrigala) and its interaction with bacterial flagellins. Therefore, the present study was undertaken to unravel the structural basis of TLR5-flagellin recognition in mrigala using structural homodimeric TLR5-flagellin complex of zebrafish as reference. Integrative structural modeling and molecular dynamics simulations were employed to explore the structural and mechanistic details of TLR5 recognition. Results from structural snapshots of MD simulation revealed that TLR5 consistently formed close interactions with the three helices of the D1 domain in flagellin on its lateral side mediated by several conserved amino acids. Results from the intermolecular contact analysis perfectly substantiate with the findings of per residue-free energy decomposition analysis. The differential recognition mediated by flagellin to TLR5 in mrigala involves charged residues at the interface of binding as compared to the zebrafish complex. Overall our results shows TLR5 of mrigala involved in innate immunity specifically recognized a conserved site on flagellin which advocates the scientific community to explore host-specific differences in receptor activation.

The complete mitogenome of Osteobrama belangeri is described using Ion Torrent (PGM sequencer), which was 16,609 bp in size comprising 13 mRNAs, teo rRNA genes, 22 tRNAs, and 926 bp as D-Loop control region, in addition to gene order and organization, being similar to most of the other related Cypriniformes fish mitogenome of NCBI databases. The all 22 tRNAs were packed into a typical clover-leaf structure. In the present study, the mitogenome has 99% similarity to the complete mitogenome sequence of O. belangeri mitogenome details previously and also would be helpful in understanding the phylogenetics, population genetics, and evolution of family Cyprinidae fishes.

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus–Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

The present study aims to develop a linseed oil coated quartz crystal microbalance sensor to detect trimethylamine (TMA), an important freshness indicating agent of fish. The strong odor of TMA is often termed as “Fish odor”. It is likely to be generated when bacteria starts growing on dead fish. Therefore to detect TMA, a simple approach of vegetable oil film as a receptor element in the quartz crystal transduction platform has been elucidated herein. The developed sensor exhibits a significant sensitivity towards TMA with a sensitivity of 0.1841 kHz/ppm (R2=0.92). Alongside, satisfactory repeatability, reproducibility, and selectivity of the prepared sensor have been studied successfully.

The feasibility of near- infrared (NIR) spectroscopy to discriminate the freshness of an Indian Major Carp, Rohu (Labeo rohita) was investigated in this paper. The spectroscopic readings of Rohu samples were recorded for the wavelength range between 900 and 1700 nm in absorbance mode. The Principal Component Analysis (PCA) was applied to analyze the spectral data and distinguishable clusters were obtained. Study revealed that, the freshness of the Rohu could be distinguished by NIR Spectroscopy. The Separability Index (SI) of the raw data was also measured as 873.7008. Preliminary results showed that, this technique could be applied for discrimination of Rohu fish freshness.

Studies on

In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and treated, respectively, were obtained. The coverage per base (CPB) statistics were analyzed for both the samples. Gene ontology (GO) analysis has been categorized at varied graph levels based on three primary ontology studies viz. cellular components, biological processes, and molecular functions. The KEGG analysis of the assembled transcripts using KAAS showed presumed components of metabolic pathways which perhaps implicated in diverse metabolic pathways responsible for salt tolerance viz. glycolysis/gluconeogenesis, oxidative phosphorylation, glutathione metabolism, etc. further involving in salt tolerance. Overall, 90 salt stress tolerant genes were identified as of 186 salt-related transcripts. Several genes have been found executing normally in the TCA cycle pathway, integral membrane proteins, generation of the osmoprotectants, enzymatic pathway associated with salt tolerance. Recognized genes fit diverse groups of salt stress genes viz. abc transporter, betaine, sodium antiporter, sodium symporter, trehalose, ectoine, and choline, that belong to different families of genes involved in the pathway of salt stress. The control sample of the bacterium showed elevated high proportion of transcript contigs (29%) while upto 20% salt stress treated sample of the bacterium showed a higher percentage of transcript contigs (31.28%). A total of 1,288 and 1,133 transcript contigs were measured entirely as novel transcript contigs in both control and treated samples, respectively. The structure and function of 10 significant salt stress tolerant genes of Staphylococcus sp. have been analyzed in this study. The information acquired in the present study possibly used to recognize and clone the salt stress tolerant genes and support in developing the salt stress-tolerant plant varieties to expand the agricultural productivity in the saline system.

Surging demand of fish production for nutritional and livelihood security manifested with irrational use of synthetic growth enhancer and immunostimulants which are fostering the awful health concerned to human being and negatively affecting the beneficial micro-biota in aquatic ecosystem. The need of hour is to use environment friendly herbal therapy, as an alternate to those chemicals and compounds. The Terminalia arjuna is known for its excellent array of ethnomedicinal properties including antimicrobial, antioxidant and was reported to have positive effects on metabolomics of the animals. A 90-day experiment was conducted to ensure effective valorization of Terminalia arjuna bark powder (TABP) based feed in Labeo rohita. Four iso-nitrogenous {305.74 g crude protein (CP)/ kg diet} and iso-caloric {18.15 MJ gross energy (GE)/kg diet} experimental diets were formulated incorporating 0.0, 5.00, 10.00 and 15.0 g TABP /kg feed and designated as TABP0, TABP5, TABP10 and TABP15, respectively. 540 juveniles (average weight, 20.7 g, 45 fish per tank) were randomly stocked in 12 fibre reinforced plastic (FRP) tank (500 L water capacity). Fish were fed twice at 9.30 h and 5.00 h to satiation level. Results of this study revealed the highest growth rates {weight gain percentage (WGP) and specific growth rate (SGR)}, nutrient utilization {protein efficiency ratio (PER), apparent net protein utilization (ANPU), fat retention (FR) and energy retention (ER)} and survival percentage (SRP) in L. rohita at 10 g TABP/ kg feed. While feed conversion ratio (FCR) followed an inverse trend (P 0.05). Viscerosomatic index (VSI) and craniosomatic index (CSI) were significantly affected (P 0.05). Whole body composition was influenced (P 0.05). RNA content and RNA: DNA ratio were positively correlated to growth rates and nutrient retentions (P

The present research study was carried out to investigate the causative agent responsible for infection and mortality of farmed Labeo rohita. Samples of infected fishes were collected from aquaculture farms of West Bengal, India. Biochemical and molecular identification revealed that isolated strain EM4 was Citrobacter freundii. Furthermore, a challenge study was carried out to determine the number of bacterial colonies required for 50% mortality (LD50) of the experimental fish population. LD50 of the pathogenic bacterial isolates (C. freundii) was found to be 1.2 × 103 CFU per fish. Histopathological studies revealed damaged glomerulus in kidney and necrosis of hepatocytes in liver of diseased L. rohita. Additionally, non-specific and specific immune responses of L. rohita were also studied after C. freundii challenge. At early stages of infection, elevated expression level of few non-specific responses viz. respiratory burst activity, myeloperoxidase activity and alpha 2 macroglobulin were observed. However, the antiprotease activity was found to be lowered at the early stages of infections. Sequential changes in the immune-related genes viz. complement component 3 (C3) and interleukin 6 (IL- 6) were also studied in the liver, kidney and muscle tissues of the artificially infected fishes. In the liver and muscle tissues, the C3 gene was significantly up-regulated at the early stages of infections, whereas the IL-6 expression in liver was found to be down-regulated throughout the infection process. Expression of C3 and IL-6 genes in kidney were found to be down-regulated at the early stages of infections, but later, it was up-regulated with the progression of the infection. The result of the present study suggests that C. freundii is a concerning threat towards developing aquaculture sector. The pathology and pathogenesis study will help to understand the infection process as well as in the development of therapies to control the infection.

Vibrio cholerae is a gram-negative bacteria known for causing epidemics and pandemics conditions, comprised of both non-pathogenic and pathogenic strains. The present study identified a non O1, non-O139 V. cholerae (EMM1) serotype isolated from diseased Labeo rohita cultured in a wetland system at Purba Medinipur district, West Bengal, India. Identification of the isolate was done by biochemical test, 16S rRNA gene sequencing and phylogenetic analysis. The in vivo challenge experiment revealed that intraperitoneal injection of EMM1 serotype at a dose of 1.04× 107 CFU/ml resulted in 100% mortality of L. rohita. Furthermore, the presence of hlyA and rtxA virulent genes, confirmed by sequencing, in V. cholerae (EMM1) serotype might be, atleast partially involved in the mortality of L. rohita. In histological analysis, we found that EMM1 serotype challenge had a significant effect in L. rohita like degenerated hepatocytes in the liver, shrunken glomeruli in the kidney, necrosis of the intestinal villi epithelium and degeneration of muscle bundle were observed. Overall, the study demonstrated that, V. cholerae (EMM1) serotype is a potent aquatic microbial pathogen and draws the attention for proper management to prevent the possible occurrence of disease in aquaculture.

Plesiomonas shigelloides was isolated from diseased silver carp in Kolkata Wetland, West Bengal, India. It was associated with mortality of Silver Carp, Hypophthalmichthys molitrix, which is the most widely cultivable fish species in fresh water aquaculture. The P. shigelloides was identified based on the biochemical and molecular characterization and the pathogenicity was studied on H. molitrix. The 16S rRNA gene sequence of the present isolate (NCBI GenBank Accession Number- KX986915) revealed that, the isolate was 100% identical with P. shigelloides (NCBI GenBank Accession Number- MF100995). P. shigelloides killed 10–100% fish in experimental infection and the LD50 value was calculated as 1.3× 105CFU per fish with intraperitoneal injection. The challenged fish had subcutaneous haemorrhagic ulcers and reddening at injection sites, however there was no clinical sign observed in the gill. The histology of experimentally challenged H. molitrix showed the kidney alterations and exhibited shrinkage of epithelial cells in renal tubule and enlargement of glomerular cells.Liver showed focal accumulation of edematous fluid, necrosis and infiltration of heterophils indicative of bacterial infection. The pathology and pathogenesis studies of this pathogen in inland open waters like wetlands and lakes would help in management of the outbreak of disease in these aquatic ecosystems.

Aquaporins (AQPs) constitute a super family of major intrinsic proteins (MIPs) and aquaporin 4 (AQP4) is one of the most popular protein, participating in different types of bio-physiological pathways in animal, plant and even in bacteria. Zebrafish, considered as a novel model organism, possess an Aquaporine 4 protein (zAQP4) that shares a high degree of homology with mammalian orthologs which was mostly found to be express in brain, ovary, testis, and low levels in other tissues. To focus more light on AQP4 medical related therapeutic applications, the structure of zAQP4 as a drug target protein is extremely essential and there is no such structural information available in protein data bank (PDB). Herein, for the first time we generate the 3D structure of zAQP4 was modeled through a Homology modeling approach. The root-mean-square deviation (RMSD) of atomic positions between the generated model structure and human AQP4, revealed 69.2% sequence identity over align region with RMSD value 2.723 A. Structural integrity of the model was assessed using molecular dynamics simulation studies to achieve a better understanding of the progress, structure, and function of AQP4. Finally residual involvements for druggable pocket identification were made and some important residues such as VAL-237, PRO-272, GLN-274, PRO-277, TYR-278, VAL-118, LEU-122 and LEU-126 which shows highest druggability probability (1.0) that can emphasize the importance of aquaporin-4 as a target protein in the field of drug research in near feature.

In eukaryotes, the serine/threonine kinases (STKs) belonging to cyclin-dependent protein kinases (CDKs) play significant role in control of cell division and curb transcription in response to several extra and intra-cellular signals indispensable for enzymatic activity. The zebrafish cyclin-dependent protein kinase-like 1 protein (zCDKL1) shares a high degree of sequence and structural similarity with mammalian orthologs and express in brain, ovary, testis, and low levels in other tissues. Regardless of its importance in the developmental process, the structure, function and mode of ATP recognition have not been investigated yet due to lack of experimental data. Henceforth, to gain atomistic insights in to the structural dynamics and mode of ATP binding, a series of computational techniques involving theoretical modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energies were employed. The modeled bi-lobed zCDKL1 shares a high degree of secondary structure topology with human orthologs where ATP prefers to lie in the central cavity of the bi-lobed catalytic domain enclosed by strong hydrogen bonding, electrostatic and hydrophobic contacts. Long range MD simulation portrayed that catalytic domain of zCDKL1 to be highly rigid in nature as compared to the complex (zCDKL1-ATP) form. Comparative analysis with its orthologs revealed that conserved amino acids i.e., Ile10, Gly11, Glu12, Val18, Arg31, Phe80, Glu 130, Cys143 and Asp144 were crucial for ATP binding mechanism, which needs further investigation for legitimacy. MM/PBSA method revealed that van der Waals, electrostatic and polar solvation energy mostly contributes towards negative free energy. The implications of ATP binding mechanism inferred through these structural bioinformatics approaches will help in understanding the catalytic mechanisms of important STKs in eukaryotic system.

Tilapiines are one of the most widely farmed fish species and currently being cultured in > 100 countries in the World. Over the last few years, large-scale mortalities have been reported in tilapia due to infection with orthomyxo-like virus i.e. Tilapia Lake Virus (TiLV) which is considered as a threat to global tilapia industry. In the present study, we report outbreaks of TiLV disease in farmed tilapia in two states, West Bengal and Kerala from India. Diseased fish exhibited lethargy, inappetance and skin erosions with > 85% mortality. TiLV infection was confirmed on the basis of PCR amplification and sequencing of segment 3 of TiLV, histopathology, infection of fish cell line and bioassay. CLUSTALW alignment of the partial sequences of segment 3 of the TiLV revealed that North 24 Parganas (MF502419) and South 24 Parganas (MF582636) of West Bengal, India showed 97.2% and Ernakulam, Kerala, India (MF574205) showed 96.4% similarity with TiLV from Israel (KJ605629.1). In histopathology, typical syncytial giant cells in liver and congestion of the blood vessels along with haemorrhages in sections of brain tissue were observed. The filtered tissue homogenate prepared from liver and brain of affected tilapia produced cytopathic effects in CFF cell line derived from Pristolepis fasciatus. The disease was successfully reproduced in naive tilapia following injection of culture supernatant from infected cell line and TiLV was successfully reisolated from experimentally infected tilapia. This is the first report of TiLV from India and adds to the reports of TiLV outbreaks in five countries across three continents.

The present study was conducted to identify and characterize the etiological agent causing mortality in Indian Major Carp, Rohu ( Labeo rohita ) in West Bengal, India. Diseased fish samples having hemorrhages near the tail and intraperitonial region was collected from culture ponds of Burdwan, West Bengal for the isolation of the pathogenic bacteria. Primarily the bacterium was characterized using biochemical and antibiogram studies. The 16S rRNA gene sequence of the isolated bacteria revealed that the isolate was having 100% homology with Klebsiella pneumoniae (NCBI Accession Number- KY003130). Intraperitoneal injection with 1.05 × 10 6 CFU per fish causes 50% mortality. The challenged fish showed hemorrhages in the intraperitonial region. The histopathology of the challenged fish liver showed vacuolation, necrosis and disruption of hepatocytes. However, focal necrosis and vacuolation was observed in kidney tissue. This study highlights the first time involvement of Klebsiella pneumoniae in the disease outbreak of cultured Labeo rohita . Understanding the pathology and pathogenesis studies of this emerging pathogen in cultured carps would help in control of this disease in aquaculture.

Due to continuous anthropogenic activities and other natural changes, aquatic ecosystems are under increasing stress. Metagenomics aided by next-generation sequencing techniques provides in-depth insights into microbiome dynamics from multitude of aquatic resources thus contributes in understanding the physiological, metabolic, and ecological roles of microbial assemblies. Monitoring of diverse aquatic resources using metagenomics has the potential to efficiently characterize diverse range of microbiomes with relevant functional pathways. Contributions made by high-throughput second and third generation sequencing platforms are noteworthy in monitoring aquatic microbial biodiversity through characterization of genetic variations which is indicative of changing environmental adaptations. Analysis of sequence and function driven metagenomics enable elucidation of enzymatic pathways leading to the discovery of novel gene sequences with desired functions having ecological, industrial and pharmaceutical importance. This review seeks to define the role of metagenomics in exploring aquatic microbiota in terms of toxicological exposure, genome heterogeneity, assessment, and the management of aquatic ecosystem by utilizing microbial bio-indicators. We have also enlisted various high-throughput computational biology packages and tools exclusively used to handle metagenomic data along with the challenges and future perspectives. Owing to global climate change and massive human-induced alterations in aquatic ecosystems, we expect that the on-going whole-genome metagenomics studies in combination with "meta-OMICS" approaches would transform our comprehension of microbiome community structure, function and ecology at high resolution.