Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii).

Introduction: Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii. Methods: The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed. Results: A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, ≤10 DPH (days post-hatching) and > 10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations. Conclusion: The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.

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.

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.

Enzymological, histological, and serum biomarker responses of snubnose pompano on complete replacement of fishmeal using cottonseed meal supplemented with lysine and methionine in the diet.

In a feeding experiment, cottonseed meal (CSM) was used to replace fishmeal (FM) in the diet of snubnose pompano, Trachinotus blochii, supplemented with lysine and methionine to assess the growth, nutritive profile, hematological, histological, and stress biomarker response. Experimental fishes were randomly stocked in five treatments each with triplicates. Five isonitrogenous and isolipidic diets with graded level of CSM (0, 8.7, 17.4, 26.0, and 34.7%) as replacement for FM protein (0, 25, 50, 75, and 100%) were formulated and fed to respective treatments. Comparison between various parameters among the treatments was made using orthogonal polynomial contrasts to indicate the statistical significance. Higher alkaline phosphatase, acid phosphatase, lactate dehydrogenase, malate dehydrogenase, aspartate, and alanine aminotransferase activities were observed in 0CSM group and followed by 100CSM group as higher inclusion level of CSM with higher free gossypol content did not affect the metabolic enzyme activities. The maximum muscular free gossypol accretion of 1.28 mg kg-1 (on wet basis) was recorded in 100CSM group which was very well below the critical limit set by FDA. As a conclusion, fishmeal can be completely replaced using cottonseed meal in the diet of pompano without adverse effect on growth, metabolism, and general health.

Antioxidant defence system based oxidative stress mitigation through dietary jamun tree leaf in experimentally infected snubnose pompano, Trachinotus blochii.

A 45-day feeding trial was conducted to evaluate the effect of dietary jamun tree leaf (JL) on the antioxidant defence system-based disease resistance in juveniles of Trachinotus blochii. The juveniles of snubnose pompano were distributed into four treatment groups in triplicates. Each treatment was fed with a diet containing either 0 (0JL), 0.5 (0.5JL), 1 (1JL) and 1.5% JL (1.5JL) in the feed. After feeding trial, the fishes were experimentally infected with Vibrio parahaemolyticus. The activities of oxidative stress enzymes such as superoxide dismutase and catalase were found to be increasing with increasing level of dietary JL incorporation, and the lower value was witnessed in control group in pre- and post-challenge. After challenge, the alanine and aspartate aminotransferase activities in all the treatments were significantly increased (P < 0.05) than the pre-challenge condition and exhibited reverse trend with the antioxidant enzymes. The alkaline and acid phosphatase activities were found higher in 1.5JL group and showed significant difference (P < 0.05) among the treatments. The respiratory burst activity and liver glycogen content showed an increasing trend as the level of inclusion of JL increased in the diet. The acetylcholinesterase activity was significantly plunged (P < 0.05) after experimental infection, and JL diet fed groups showed better activity. After experimental infection with V. parahaemolyticus, the highest relative percentage of survival was observed in 1JL and 1.5JL groups. Hence, dietary supplementation of jamun tree leaf at the level of 1% is adequate to reduce the oxidative stress and improved the innate immune status through antioxidant defence system.