Prokaryotic and eukaryotic microbial community dynamics in biofloc systems supplemented with non-starch polysaccharides

Biofloc technology has been developed as a sustainable system in aquaculture, which uses microbial processes to remove nutrients from the water and convert them into microbial biomass. For optimal performance, the addition of carbohydrates is essential, while their type can regulate microbial activity and composition. Specifically, we hypothesize that dietary supplementation of wheat bran, containing indigestible carbohydrates such as non-starch polysaccharides, can provide complex substrates supporting diverse microbial communities within the biofloc. In this study, we investigated how higher dietary wheat bran input affected the biofloc prokaryotic and eukaryotic microbial communities in Pacific white shrimp (Litopenaeus vannamei) culture. Two pelleted diets were made: a control diet (CONdiet) with a composition similar to a commercial shrimp diet, and a diet rich in non-starch polysaccharides (WBdiet), which was created by adding wheat bran to the control diet ingredient mix, before pelleting. These two diets were fed isonitrogenous to the shrimp for 42 days, and sampling of the biofloc was performed every three weeks. The results showed shifts in both the alpha and beta diversity in biofloc during the experiment. Diet had a significant effect on the prokaryotic community composition in the biofloc at the end of the culture period, with several genera being enriched in biofloc tanks fed the WBdiet such as Muricauda, Pirellula, and Cyanobacteriaceae. Regarding the eukaryotic communities, overall, only a few taxa were significantly affected within the WBdiet, belonging to the Trebouxiophyceae and Suillus groups. Interestingly, when feeding the WBdiet, the biofloc microbial communities exhibited predicted functionalities that were more abundant in carbohydrate metabolism, and specifically related to pentose, fructose, mannose and galactose metabolism. These results provide a basis for the control of biofloc microbial communities by using ingredients rich in plant-derived non-starch polysaccharides which shrimp cannot digest but are good energy source for the microbiota in the biofloc.