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The present study reports the first incidence of intersex in Cobia, Rachycentron canadum maintained at sea cages in the Gulf of Mannar, India. During the 10 year study period (2010–2019), at total of 815 broodstock (386 wild captured and 429 captive raised) were maintained under captivity in sea cages in the Gulf of Mannar, India for the purpose of seed production. Of which, 318 male and 252 female broods’ gonads were examined post-mortem following a natural death. Only one male fish was found with a visible gonadal anomaly. Microscopic analysis of gonad revealed the presence of both the characteristic female and male tissues in testes of a single specimen (testis-ova). Only the abnormal nodular portion contained primary oocytes, whereas the central testicular tissue contained spermatocytes and spermatids in the seminiferous lobules. This is the first reported intersex of cobia from the Gulf of Mannar, India. It could be interpreted as low-level rare incidence of natural aberration.

In mariculture, often the locations of fish hatcheries and farming are distantly situated, and hence, there is a need to transport the seeds/seedlings to a longer distance with maximum survival rate. In the present study, length and weight of fingerlings, duration of starvation, packing density, water volume, water temperature and oxygen level in the packing bags were standardized to ensure maximum survival during transportation. The cobia fingerlings with mean length and weight of 48±12 mm and 3.0±1.0 g, respectively were transported for a duration 48 h at 25 °C with 100 % survival at a packing density of 2.5 fingerlings per litre (L) (7.5±2.5 g/L). Similarly, silver pompano fingerlings with mean length and weight of 24±0.48 mm and 0.6±0.08 g, respectively were transported for a duration of 48 h at 25 °C with 100 % survival at a packing density of 18.75 fingerlings/L (11.25±1.9 g/L). Experiments on bulk transportation of pompano fingerlings in 1000 litres capacity HDPE tanks containing 600 litres of seawater with continuous aeration using oxygen cylinders fitted in a transportation vessel revealed that the silver pompano fingerlings can be transported for a duration of 48 h at 25 °C and 5 - 6 ppm dissolved oxygen concentration with 100 % survival at a packing density of 8.3 fingerlings/L (4.98±0.8 g/L). [ABSTRACT FROM AUTHOR]

Cobia (Rachycentron canadum, Rachycentridae) is one of the prospective species for mariculture. The transcriptome-based study on cobia was hampered by an inadequate reference genome and a lack of full-length cDNAs. We used a long-read based sequencing technology (PacBio Sequel II Iso-Seq3 SMRT) to obtain complete transcriptome sequences from larvae, juveniles, and various tissues of adult cobia, and a single SMRTcell generated 99 gigabytes of data and 51,205,946,694 bases. A total of 8609435, 7441673 and 9140164 subreads were generated from the larval, juvenile, and adult sample pools, with mean sub-read lengths of 2109.9, 1988.2 and 1996.2 bp, respectively. All samples were combined to increase transcript recovery and clustered into 35661 high-quality reads. This is the first report on a full-length transcriptome from R. canadum. Our results illustrate a significant increase in the identified amount of cobia LncRNAs and alternatively spliced transcripts, which will help improve genome annotation. Furthermore, this information will be beneficial for nutrigenomics and functional studies on cobia and other commercially important mariculture species. Measurement(s) Full length transcriptome of Cobia (Rachycentron canadum) Technology Type(s) PacBio Sequel 2 Sample Characteristic - Organism Rachycentron canadum Sample Characteristic - Environment Marine environment Sample Characteristic - Location India [ABSTRACT FROM AUTHOR]

Keywords: compensatory growth; Snubnose pompano; stunting; Trachinotus blochii EN compensatory growth Snubnose pompano stunting Trachinotus blochii 403 409 7 12/23/20 20210101 NES 210101 Compensatory growth has been reported in stunted fish by several researchers, and the same has been applied at field level for enhancing the fish production. During stunting phase, the size variation was more prominent in stunted fish than normal fish, whereas it registered a reverse trend during post-stunting phase wherein the size variation was lesser in stunted fish than normal fish. The 90 days stunting study reveals that the growth retarded fish could fully regain the growth when adequately fed, since the final weight and SGR/day % at the end of the poststunting rearing were higher in stunted fish than the normal fish. The FCR at the end of the experiment was slightly higher in the case of 30 days stunted fish, whereas in 60 days stunted fish, it was slightly lower and in 90 days stunted fish it was only half of normal fish (Tables 2-4). [Extracted from the article]

Abstract The genealogical information of a small captive population of the cobia fish was evaluated to assess the genetic variability and the status of inbreeding through pedigree analyses. Pedigree data (n = 238) for 6 years (2010–2016) were analyzed and offspring born from 2015 to 2016 were considered as reference population to compute the population genetic parameters based on the gene origin probabilities using the program ENDOG (version 4.8). Molecular marker based FAP (Family Assignment Program, version 3.6) was used for parentage assignment. The pedigree completeness was 68% for the parent, 29% for the grandparents and 7% for the great-grandparents generations with a mean equivalent to complete generations of 2.66. Mean generation interval, computed from four pathways, was 2.38 years. Considering the reference population into account the coefficients of average inbreeding and average relatedness were computed as 9.6% and 9.9%, respectively. The mean values of individual increase in inbreeding (rate of inbreeding) were 6.5% and 2.5% for the reference population and for the whole pedigree, respectively. Realized effective population size was computed from the individual increase in inbreeding and from the individual increase in coancestry as 7.7 and 10.6, respectively. The effective numbers of founders (f e), ancestors (f a), founder genomes (f g) and non-founder genomes (n fe) for the reference population were computed as 6, 6, 3.8 and 11.1, respectively. About 85% of total genetic variation was explained by 7 most influential ancestors, with a maximum individual contribution of 33.5%. Though the genetic bottleneck, as expressed by the f e /f a ratio as 1.0, was not evident, the loss of genetic variability caused by genetic drift was evident by f g /f e ratio which was 0.64 for the reference population. The analysis revealed the evidences on loss of genetic diversity with a very critical effective population size. Recommendations were made to improve the genetic variability in the herd. The present study signifies the importance of maintaining the pedigree and can help in carrying out similar studies on captive-bred fish species where small populations are inevitable. Highlights • This work is the first of its kind to carry out pedigree analysis of captive-bred population in the field of marine fisheries. • The present study in the marine fishes will encourage the researchers to carry out pedigree based genetic analysis. • The results of this study emphasize the importance of monitoring the genetic variability in any genetic improvement programs. • It signifies the importance of pedigree and helps in carrying out similar studies where small populations are inevitable. [ABSTRACT FROM AUTHOR]

Mass mortalities of cobia, Rachycentron canadum, sub-adults occurred during August 2013 in cage culture in the Gulf of Mannar, Mandapam Tamil Nadu, India. The epizootic of disease was started with typical classical clinical signs followed by acute mortality. Grossly, severe haemorrhage and congestion were observed in the gastric mucosa. The abdomen was distended with peritoneal fluid. The heart revealed haemopericardium and fibrinous pericardium. Histologically, the gastric mucosa showed severe erosion and necrosis. Haemorrhagic pericarditis and an increased size of the melano macrophage centre ( MMC) in the tail kidney were other histopathological changes. Vibrio sp. was isolated from the gastric lesions and heart blood swab of moribund fishes and it was found to be virulent to the cobia fingerlings. After the challenge, the same bacterium could be re-isolated from moribund fingerlings. The 16S ribosomal RNA of the isolate was amplified and blast analysis of the sequence confirmed that the pathogen was Vibrio alginolyticus. The confirmation was also correlated with its cultural, biochemical and pathomorphological changes. This is the second report and the first incidence of epizootics with severe pathological lesions in cultured cobia in India. The study throws light on the pathology of vibriosis. By practising cage farm management measures, occurrences of infection may be prevented. Significance and Impact of the Study The epizootics of vibriosis caused serious economic losses to farmers. Natural blooms of the pathogen can be prevented by sea cage management measures such as, changing the inner net of the cages, changing the location of the cages to relatively clean water (about 50 m apart) from the affected site and providing shade over the cages while the water temperature rises. Supplementation of the feed with immunostimulants and mineral mixture may be practised to improve the immune response against infection. Early diagnosis and sea cage management measures may prevent occurrences of the infection. [ABSTRACT FROM AUTHOR]

In the Gulf of Mannar, Noctiluca scintillans blooms have been observed three times in September 2019, September and October 2020, and October 2021. It was determined and measured how the bloom period affects ichthyo-diversity. Noctiluca cell density varied slightly from year to year, ranging from1.8433 × 103 cells/L to 1.3824 x 106cells/L. In surface and sea bottom waters, high ammonia levels and low dissolved oxygen levels were noted. During the bloom period a significant increase in chlorophyll concentration was found. The amount of chlorophyll in GOM was extremely high, according to remote sensing photos made using MODIS-Aqua 4 km data. Acute hypoxia caused the death of wild fish near coral reefs and also in fish reared in sea cages. The decay of the bloom resulted in significant ammonia production, a dramatic drop in the amount of dissolved oxygen in the water, and ultimately stress, shock, and mass mortality of fishes. • Harmful Algal Bloom incidents were recorded frequently over the past three years • After ten years, a Noctiluca scintillans bloom has been seen in the GoM. • Fish raised in cages and wild fishes on coral reefs were both found dead from severe hypoxia. • By using near real-time ocean colour determined chlorophyll concentration model derived current patterns it will be possible to alert cage culture farmers [ABSTRACT FROM AUTHOR]

Microbial dynamics across multiple ontogenetic stages represent one confounding feature in teleost microbiome research. The present study recorded the dynamics in the whole microbiome of early life stages and the juvenile gut microbiome of a high-value mariculture species, cobia (Rachycentron canadum), during standard culturing practices. This is the first report on using the PacBio system targeting full-length 16S rRNA sequences, for deciphering fish microbiomes. The results highlighted a temporal shift in the whole microbiome compositions along the host's ontogenetic development. There was a significant decrease in Cyanobacteria and Firmicutes to Bacteroidetes ratio with a corresponding increase in Plactomycetacea and Bacteriodata in the whole microbiome profiles of the post-metamorphosis samples. The gut microbiome data suggested an adaptive mechanism toward establishing beneficial strains (Bacilli and Actinobacteria) alongside the ontogenetic progression. Nevertheless, a small, abundant core bacterial community occupied ∼50% and ∼ 64% of total abundance in the whole microbiome and gut microbiome, respectively. The results revealed high-dimensional microbial biomarkers for various ontogenetic stages of cobia during standard culturing practices. The composite dataset generated offers several possible sustainable means of microbiome manipulations to improve the low survival encountered in the early life stages of cobia. • First report on using the PacBio system for deciphering fish microbiome. • Defines the core microbiome in the early life stages of cobia. • Revealed high-dimensional biomarkers for various ontogenetic stages. • Presents microbiome manipulation strategies to improve survival of early stages. [ABSTRACT FROM AUTHOR]

Cobia (Rachycentron canadum) is a high-value marine aquaculture species. Knowledge of the microbial dynamics in various aquaculture operations is crucial for developing suitable management practices. The present study revealed the critical dysbiotic events in the whole larval and juvenile-gut microbiome of cobia, through an inevitable aquaculture operation, viz. live transportation. The results through both culture-dependent and independent techniques demonstrated the sensitivity of the cobia microbiome during early life, where live transport is inevitable. In detail, there was a significant change in the microbial composition and reduction in the cultivable load of all the life stages. Further, a significant reduction in functional metagenomics along with an increase in taxonomic metagenomics was recorded in the L21 stage. Significant reductions of the putative healthy microbiota, viz. , Proteobacteria and Actinobacteria were remarkable in the whole larval microbiome. The analysis through linear discriminant analysis effect size revealed that the opportunistic fish pathogens, viz., Vibrio spp., Arcobacter spp., and Acinetobacter spp. were increased whereas, Pseudomonas spp. was decreased in larvae following transportation. The significant reduction in the taxonomic diversity measures was noteworthy in the juvenile-gut microbiome. Transportation promoted Serratia spp., Enterobacter spp., an unidentified genus in Flavobacteriaceae, Pseudoalteromonas spp., Alteromonas spp., and Enterovibrio spp., and inhibited Empedobacter spp. in the juvenile gut. Collectively, the results provide the prospective metagenomic signatures of health and stress in the early life stages of cobia and novel possible explanations for increased disease susceptibility post-transportation. The study warrants future research on the microbes which were found to be decreased following transportation, as potential probiotics to mitigate the stress in the marine aquaculture practices. The metagenomic signatures revealed through the study can be further applied for evaluating different husbandry practices to mitigate stress during live transportation. • First data on gut microbial dynamics following transportation in marine fish • Displays probiotic microbes to design fish health improvisation strategies • Decodes novel reasons for increased disease susceptibility post-transportation • Provides metagenomic signatures of health and stress in early life stages of cobia • Generates insights on the whole larval and juvenile gut microbiome of cobia [ABSTRACT FROM AUTHOR]