Unveiling associations between ciliate parasites and bacterial microbiomes under warm‐water fish farm conditions – a review

Abstract Intensive fish production has arguably resulted in a consequential increase in the incidence of disease within the aquaculture industry. The frequency and the severity of disease events are in part affected by changing global climatic conditions. More importantly, these changes directly influence changes in water quality parameters and the dynamics of a microbiome, pathogenic or not, in aquatic farming. Changes in temperature, for example, have both direct and indirect effects on the health status of fish, potentially increasing their predisposition to infections. In general terms, fish infections are rarely caused by a single agent or factor – frequently, multiple pathogens, changes in water quality parameters, production factors (e.g. feed quality, stocking density) and host immunity are concomitantly responsible for the establishment of infections in fish farms. Ciliate protozoans represent an important microfauna in aquatic environments. Ciliated protozoans can proliferate quickly, debilitating the host, and, in the absence of an intervention, can lead to a significant loss of stock. Ciliate infections frequently facilitate the establishment of secondary microbial species, both of which are linked to environmental and culture conditions. In this review, economically important ciliated protozoans of warm‐water cultured fish and their potential interactions with their associated bacterial microbiomes (both on/in their hosts and their surrounding environment) are discussed. Also, potential environmental triggers behind ciliate outbreaks within warm‐water aquaculture are reviewed. With better knowledge about such interactions, it will be possible to highlight innovative strategies to control ciliate parasites and bacterial infections in aquaculture.