Microbiology of biological filters in recirculating aquaculture systems

Abstract

As aquaculture production continues to increase, new technologies have been developed to minimize nutrient emissions or even recover them into other applications. Recirculating aquaculture systems (RAS) may increase aquaculture production in areas where water source is limited, and the amount of nutrient discharges affects the granting of environmental licenses. The cost–effectiveness of RAS limits the future expansion of the technology, and in particular, the management of the microbial environment has become one of the main challenges affecting the operation of RAS farms. In this dissertation, I examined the microbiology of RAS. The work focused on the nitrification process and microbial community composition in bioreactors and their connections to changes in water quality. Nitrification may be rapidly started by adding ammonia and nitrite salts to the system. I found that bioreactors had diverse microbial communities that affected several water quality parameters. The main function of microbial communities found in freshwater RAS compartments was the degradation of carbohydrates, amino acids, and lipids. When RAS was changed to use brackish water, microbial communities were seen to slowly adapt. However, the degradation of carbohydrates decreased, which was also reflected in elevated concentrations of total organic carbon and the dissolved organic matter in the water. Desinfectant (peracetic acid) addition improved water quality and did not disturb biofilter microbial communities. The fixed bed bioreactors (FBBR) trap solids and organic matter inside the reactor, but potentially also host bacterial communities specialised in the degradation of organic matter. Nitrification performance was decreased in the FBBR, but this may have been caused by the incorrect design of the reactor. The moving bed bioreactors (MBBR) may release the excess bacterial biomass into the water, but the technique kept the biofilm thin and allowed for a functionally diverse bacterial community. Keywords: 16S rRNA gene; bacterial communities; microbiome; next-generation sequencing; nitrification; rainbow trout; quantitative PCR.