Monitoring and managing microbes in aquaculture - Towards a sustainable industry

Abstract

Microorganisms are of great importance to aquaculture where they occur naturally, and can be added artificially, fulfilling different roles. They recycle nutrients, degrade organic matter and, occasionally, they infect and kill the fish, their larvae or the live feed. Also, some microorganisms may protect fish and larvae against disease. Hence, monitoring and manipulating the microbial communities in aquaculture environments hold great potential; both in terms of assessing and improving water quality, but also in terms of controlling the development of microbial infections. Using microbial communities to monitor water quality and to efficiently carry out ecosystem services within the aquaculture systems may only be a few years away. Initially, however, we need to thoroughly understand the microbiomes of both healthy and diseased aquaculture systems, and we need to determine how to successfully manipulate and engineer these microbiomes. Similarly, we can reduce the need to apply antibiotics in aquaculture through manipulation of the microbiome, i.e. by the use of probiotic bacteria. Recent studies have demonstrated that fish pathogenic bacteria in live feed can be controlled by probiotics and that mortality of infected fish larvae can be reduced significantly by probiotic bacteria. However, the successful management of the aquaculture microbiota is currently hampered by our lack of knowledge of relevant microbial interactions and the overall ecology of these systems.

Figure 1

The relative contribution from aquaculture and wild catches to the total increase in seafood production from 1950 to 2014. Data were obtained from the Fisheries Global Information System (FIGIS) at the Fisheries & Aquaculture Department, The Food and Agricultural Organization of the United Nations (FAO).

Figure 2

Suggested processes and organisms to incorporate in the design of a synthetic biofilm community in a biological aerated filter (BAF) for use in microbial reconditioning of rearing water. Denitrification is carried out in the anoxic, bottom layer by heterotrophs or autotrophs, whereas nitrification takes place in the upper oxic part of the biofilm. Other processes and organisms could be included, e.g. annamox bacteria or archaea, in the bottom layer, and, potentially, probiotic bacteria could be embedded in the upper layer seeding the rearing water upon release from the biofilm.