Bacterial communities and predicted nitrogen metabolism of heterotrophic‐ and probiotic‐based biofilms used for super‐intensive indoor shrimp culture

Biofilm‐based aquaculture systems constitute a promising alternative for intensive shrimp rearing. Microorganisms forming biofilms can recycle the nitrogen compounds the production units improving the water quality while using zero or limited water exchange. This study aimed to compare the taxonomic profiles and the predicted functions related to the transformation of nitrogenous compounds between a heterotrophic‐ (HtB) and a probiotic biofilm (PrB), and the effect of these on the water quality and the productive response of cultured shrimp. Libraries of the 16S‐rRNA gene (V3‐V4 region) were prepared and sequenced to be used as a taxonomic biomarker. Analysis of metagenomic datasets revelated that genera Halomonas, Planctomycetes and Rhodopirellula were the most abundant genera in HtB; meanwhile, Bacillus, Halobacillus and Flavobacterium dominated in PrB. Regarding nitrogen metabolism, the proportion of genes encoding enzymes catalyzing the six pathways shaping the nitrogen metabolism showed differences between biofilms, which could also explain the difference in water quality between treatments. Concerning the productive response of shrimp, no significant differences were detected except for survival, which was higher in PrB. Finally, the results suggest that biofilms harbour functions for nitrogen metabolism, including dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, nitrification, nitrogen fixation and anammox; however, the balance of these functional capabilities seems to be relevant to maintain water quality.