Characterization of the Bacterial Communities Associated with Biofilters in Two Full-Scale Recirculating Aquaculture Systems

Bacteria play a major role in metabolizing ammonia and other metabolites in recirculating aquaculture systems (RASs). To characterize and compare the bacterial communities in the biofilters of two full-scale RASs for the culture of puffer fish, Takifugu rubripes , at different ages and densities were studied. In overall, 47 807 optimized reads of the 16S rRNA gene with V4–V5 region were obtained from four biofilm samples collected after biofilm maturation. At 97% cut-off level, these sequences were clustered into 500 operational taxonomic units, and were classified into 19 bacterial phyla and 138 genera. At the phylum level, Proteobacteria and Bacteroidetes were the most abundant, followed by Nitrospirae and Planctomycetes. At the genus level, Colwellia , Marinifilum , Oceanospirillum , Lutibacter , Winogradskyella , Pseudoalteromonas , Arcobacter , and Phaeobacter were the top members. Nitrosomonas and Nitrospira were main ammonia- and nitrite-oxidizing bacteria. Differences in bacterial communities at different sampling dates and similarities of both biofilters were revealed in the Venn diagram and cluster analysis. Maintaining a good water quality and health of farmed fish in RASs depended on the correct management of the bacterial communities. This study provides more accurate information on the bacterial communities associated with the bifilters of both RASs.