The rapid expansion in shrimp farming comes with problems such as inadequate culture technology, disease outbreak, water pollution and other environmental degradation‐related problems. Prominent among these is the level of ammonia, which has been rising steadily in the last couple of years, mainly due to farming practices and other anthropogenic activities, and therefore has had consequent effects on marine life, especially shrimp. While optimal ammonia levels are a good source of nitrogen for marine phytoplankton that increases the level of dissolved oxygen in water as well serves as food for shrimp, high levels of ammonia are harmful to shrimp. When shrimp pond ammonia levels go beyond the tolerance limits, it inhibits chitinase expression, moulting, growth, phenoloxidase and haemolymph antimicrobial activity, thereby attenuating shrimp innate immune response. In this review, we bring together recent information on the effects of ammonia stress on the growth, physiology, biochemistry, ammonia‐metabolizing enzymes and immunity of shrimp. We also propose areas of research that can be explored in the breeding of new ammonia‐tolerant and disease‐resistant shrimp with robust immune and/or physiological systems that could withstand environmental stress and pathogens.

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BackgroundAcute hepatopancreatic necrosis disease (AHPND) has emerged as a major debilitating disease that causes massive shrimp death resulting in substantial economic losses in shrimp aquaculture. Given that several diseases and infections have been associated with microRNAs (miRNAs), we conducted a comparative transcriptomic analysis using the AHPND (VA) and non-AHPND (VN) strains of Vibrio parahemolyticus to identify miRNAs potentially involved in AHPND pathogenesis in Litopenaeus vannamei.ResultsA total of 83 miRNAs (47 upregulated and 36 downregulated) were significantly differentially expressed between the VA and VN challenged groups, while 222 target genes of these miRNAs were predicted. Functional enrichment analysis revealed that the miRNAs target genes were involved in multiple biological processes including metabolic pathways, amoebiasis, Vibrio cholerae infection etc. Finally, interaction network and qPCR (Real-time Quantitative PCR) analysis of 12 potential key AHPND-related miRNAs and their predicted target genes, revealed their possible involvement in modulating several immune-related processes in the pathogenesis of AHPND.ConclusionsWe have shown using comparative transcriptomic analysis, miRNAs and their target genes that are responsive to AHPND V. parahemolyticus infection in shrimp, therefore suggesting their possible role in defense response to AHPND V. parahemolyticus infection.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4728-4) contains supplementary material, which is available to authorized users.