Recirculated aquaculture systems (RAS) represent a promising approach to improving sustainable aquatic food production for human consumption through reuse of water resources and management of nutrient discharge. However, several challenges remain, including management of disease outbreaks, maintaining high water quality, and controlling microbial off-flavor compounds, calling for effective methods of early monitoring of microbial pathogen density and dynamics. The rapidly advancing field of environmental nucleic acid (eNA)-based monitoring offers opportunities for cost-effective and non-invasive tools for the identification and quantification of novel and known microorganisms. It is a promising method for the development of early monitoring and warning systems and for integrating high-throughput molecular technology in RAS facilities. eNA offers fresh perspectives on aquatic animal health condition monitoring and for advancement of aquacultural biosecurity.
This study focuses on a comprehensive, early eNA-based monitoring of pathogens and off-flavor producers, including method development and downstream application on RAS farms. Optimized procedures for eDNA collection and extraction methods were established to mitigate environmental inhibitors and to ensure adequate eNA yields. Subsequently, a novel eNA-based qPCR chip was developed by using a high-throughput Fluidigm platform. The chip is capable of rapid detection of multiple targets/indicators in parallel in large sample sets (e.g., 48 assay with 48 samples, generating 2304 datapoints), providing a powerful tool for comprehensive pathogen quantification and hence for monitoring health risks to improve management before uncontrollable disease breakouts and economic loss. Currently, a repertoire of 60 primer pairs has been devised to target an array of variables, including pathogenic (bacterial/viral/parasitic) agents, off-flavor producers, and associated factors (e.g., stress indicators). These assays are adaptable for customized combinations according to different host organisms and interests and can be seamlessly integrated into the chip platform for efficient implementation. Preliminary application has been carried out on RAS farms in Denmark, the Faroe Islands and Hungary, comprising rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and European catfish (Silurus glanis) aquaculture.