Integrative analysis of the microRNA and mRNA response of barramundi (Lates calcarifer) under acute cold stress and Vibrio harveyi challenge

Abstract

Barramundi (Lates calcarifer) are emerging as a key species in warm-water aquaculture worldwide; however, disease outbreaks caused by Vibrio spp. are impeding industry expansion. Climate change is expected to exacerbate this issue by intensifying extreme weather events, including unusually cold temperatures, thereby increasing the risk of disease. In this study, we investigated the combined effect of cold stress and V. harveyi infection on the early transcriptome (mRNA) and microRNA responses of juvenile barramundi to enhance our understanding of host-pathogen interactions. High levels of differential gene expression were observed in fish subjected to cold stress (22 °C) post-infection with V. harveyi, with 3231 differentially expressed genes and an extensive pro-inflammatory immune response. In contrast, most differentially expressed microRNAs were associated with fish infected with V. harveyi housed under optimal temperature conditions (30 °C). MicroRNAs play a crucial role in regulating gene expression, typically through downregulation of target mRNAs. The significant upregulation of miRNAs in barramundi kept at 30 °C, and the lack of miRNA upregulation in cold stressed fish, suggests that cold stress impaired the immune-regulatory capacity of affected fish, resulting in a hyper-inflammatory response that may account for the increased mortality observed. This study is the first dual study of the transcriptome and microRNA response of barramundi to V. harveyi infection and expands understanding of the innate immune response in barramundi and the regulatory role of microRNAs in teleost fish.