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Formerly the domain of small-scale producers, technological advances are increasingly moving aquaponics into larger-scale commercial production by focusing on improved macro- and micronutrient recovery whilst providing technical innovations to reduce water and energy requirements. However, scaling up of aquaponics to an industrial scale requires a much better understanding and maintenance of microbial assemblages, and the implementation of strong biocontrol measures that favour the health and well-being of both fish and crops, whilst still meeting food safety standards for human consumption. Further research on biocontrol of microbial pathogens in aquaponics, including potential human, fish and plant pathogens are needed, in light of the sensitivity of such systems to perturbation, and the fact that the use of chemicals and antibiotics can have profound effects on microbial populations, fish and plant physiologies, as well as overall system operation. Elucidating microbial interactions can improve the productivity of aquaponics system given the crucial roles of microbes in converting organic matter into usable forms that can allow fish and plants to thrive.