One of the major issues confronting aquaculture is the outbreaks of diseases and related crop loses resulting reduced farm productivity. Active disease surveillance carried out in about 400 shrimp farms on the east coast of India during 2015-2018 by ICAR-CIBA has revealed predominance of Enterocytozoon hepatopenaei (EHP), White spot disease (WSD) and aquaculture management related syndromes such as white faeces syndrome (WFS) and running mortality syndrome (RMS). EHP was prevalent in as many as 27% of the farms and white spot syndrome virus (WSSV) was the primary viral disease in 16% of the farms investigated. Lately, the emergence of infectious myonecrosis virus (IMNV) was detected with a prevalence of about 2% in certain areas of Tamil Nadu and Andhra Pradesh. Besides these infectious diseases, substantial damage caused to the Indian shrimp farms is due to the management related syndromes such as WFS, RMS, stunted growth etc., which have been recorded in as high as one third of the 400 shrimp farms investigated, affecting farm productivity. Epidemiological investigations by CIBA stongly suggest association of WFS affected ponds with EHP infection leading to stunted growth of shrimp.
Microbes constitute at least 50% of biomass in the ocean and possibly in aquaculture waters and hence would play a very important role on the outcome of shrimp crops in brackishwater aquaculture ponds. Considering increasing incidences of WFS in shrimp farming in India, where the aetiology could not be fixed, a metagenomics study was undertaken to understand the microbial diversity and the role of microbes in WFS of shrimp. The microbial diversity in healthy and WFS affected shrimp ponds was analysed using next generation sequencing (NGS) of 16S V3-V4 regions using Illumina Miseq platform. Results threw light on the diversity of bacteria associated with WFS and their possible role in the disease. While bacteria of the family Pseudoaltermonadaceae were found to be dominant in both the healthy and WFS affected ponds, it was notable that the bacteria of the family viz. Deinococcaceae, Sphaerochaetaceae, Halanaerobiaceae, Victivallaceae, etc., were found only in WFS affected ponds. Fungal diversity based on the ribosomal internal transcribed spacer (ITS) region indicated significant variation in the fungal diversity in the WFS affected ponds compared to healthy pond. Among the fungal genera, while the Candida species were predominant in WFS affected ponds, genera such as Malassezia, Ganoderma were present only in WFS affected ponds.
Results of this metagenomic study has indicated significant differences in the bacterial and fungal signature of the healthy and WFS affected aquaculture ponds, and suggest that management of pond and animal microbiomes could be important means of mitigating aquaculture management related disease losses. How we manipulate microbial diversity in the pond ecosystems to promote the proliferation of certain groups of desired microbes usually present in healthy ponds, for ameliorating aquatic health management related disease syndromes is a challenge, while these science based solutions are realistic possibility.