Full-length transcriptome from different life stages of cobia (Rachycentron canadum, Rachycentridae).

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.

Monitoring of Harmful Algal Bloom (HAB) of Noctiluca scintillans (Macartney) along the Gulf of Mannar, India using in-situ and satellite observations and its impact on wild and maricultured finfishes.

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.

Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.

Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.

Isolation and characterization of pathogenic Vibrio alginolyticus from sea cage cultured cobia (Rachycentron canadum (Linnaeus 1766)) in India.

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.