Microbial infections can be lethal if not treated promptly, as well as creating significant economic losses for the aquaculture business; thus, aquaculture biosecurity issues addressing pathogens and illnesses should be prioritised. As a result, the current study was carried out to investigate the prevalence of bacterial and fungal pathogens in the water as well as in the intestinal tracts of the usually occurring fishes in this system. The samples for this study were taken from the River Cauvery at Lower Anicut, Thanjavur District, Tamil Nadu. This river features a diverse fish population that includes murrels, catfish, carps, and eels. The size and weight of the numerous fishes studied in this study, as well as the bacterial load in the water and the fishes studied. Water had the highest bacterial count burden. Channa punctatus had the highest bacterial load (38 x 103cfu/ml), followed by Puntius conchonius (36 x 103Cfu/ml) and Mystus vittatus (34 X 103Cfu/ml). Catla catla had the least level of bacterial burden (1.2 x 103Cfu/ml). A total of 13 fungus species were discovered in the system’s water samples. C. catla was found to have 8 fungus species in its intestinal system among the fishes. C. punctatus, on the other hand, reported the presence of 9 fungal species, C. batrachus, the presence of 10 fungal species, and M. vittatus and P. conchonius, the presence of 11 fungal species apiece. Overall, water has the highest number of fungal species, followed by M. vittatus and P. conchonius. Rhizopus nigricans and Achlya hypogyna were not found in M. vittatus, while Alternaria alternata and Achlya prolifera were not found in P. conchonius. C. catla and L. rohita found the fewest fungus (8 each). C. catla, A. fumigatus, Penicillium citrinum, R. nigricans, A. prolifera, and A. hypogyna were not reported, however L. rohita, A. fumigatus, A. alternata, Curvularia lunata, A. prolifera, and Mycelia sterilia were. As a result, it appears that each fish had a unique fungus. This is most likely due to the bodily composition of each fish, as well as its resilience to certain fungus. A closer examination indicates, however, that four fungi (Aspergillus niger, Aspergillus flavus, Fusarium oxysporium, and Cladosporium herbarum) were found in all fish species. The degree of infection, on the other hand, varied from species to species and appeared to be a reflection of the species makeup of the water.

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