Biofloc culture system shapes the structure and function of environmental and intestinal bacterial communities in the river prawn Cryphiops caementarius

Biofloc technology (BFT) has emerged as a sustainable method for prawn cultivation, particularly for regions with limited freshwater resources. The freshwater prawn Cryphiops caementarius exhibit improved survival and growth rates when cultivated using BFT compared to traditional clear water (CW) systems. Despite the importance of bacterial microbiota in organismal health and performance, our study represents the first comprehensive investigation into the impact of BFT and CW culture systems on the composition, dynamics, stability, and functional potential of bacterial communities in both the rearing environment and intestines of C. caementarius . Utilizing deep amplicon 16S rRNA sequencing, we assessed the diversity and relative abundances of bacterial microbiota in CW and BFT water systems and in the intestines of prawns cultured in these systems over an extended period. Results revealed higher host-environment interaction in BFT, and higher bacterial diversity in BFT water systems and prawn intestines. The environment and prawn intestines from BFT were enriched with beneficial bacteria, while CW counterparts harbored potentially pathogenic bacteria. Planctomycetota was the dominant phylum in BFT, while Proteobacteria predominated in CW. Functional profiling indicated efficient support for chemoheterotrophic bacteria in both systems, with greater nitrogen processing in CW but greater nitrite detoxification in BFT system. Cellulolysis was higher in the intestines of prawns from BFT, potentially enhancing nutrient availability. Prawn intestine microbiota exhibited high plasticity post-immune challenge, with notable colonization by potentially pathogenic bacteria ( Aeromonas and Pseudomonas ) at the expense of a decrease in beneficial bacteria, in both systems. However, prawn intestines from BFT also showed high colonization by beneficial bacteria such as Shewanella , with potential for improving immune response. Overall, our study sheds light on the complex interplay between water and intestinal microbiota in BFT and CW systems during C. caementarius cultivation, offering insights into the potential for harnessing beneficial microbiota to improve prawn health and performance, particularly through the BFT system. • Biofloc technology (BFT) enriches prawn intestines with beneficial bacteria. • Enhanced host-environment interaction in BFT fosters microbiota diversity. • BFT supports efficient cellulolysis, potentially boosting nutrient availability. • Post-immune challenge: Pathogenic bacteria rise as beneficial bacteria decline. • Post-challenge Shewanella intestine´s colonization suggests BFT's potential for fostering beneficial bacteria, improving shrimp immunity.