Effects of Shifts in Bacterial Community on Improving Water Quality and Growth Performance of Pacific Whiteleg Shrimp (Litopenaeus vannamei) in Biofloc Systems

This study aimed to induce a shift in a bacterial community by adding substrate into a biofloc system to characterize this shift and estimate its benefits in improving water quality and aquatic animal growth. We compared the bacterial communities between two biofloc systems, either with (sB treatment) or without (nB treatment) the addition of substrate (elastic solid packing filler), and we also analyzed the effects of the shift on the water quality and growth performance of shrimp (Litopenaeus vannamei). Beta diversity analysis indicated that the bacterial communities in the two treatments were significantly different (Jaccard index 0.94 ± 0.01, pseudo-F = 3.96, p = 0.001). The addition of substrate showed significant positive effects on bacterial alpha diversity indices (Shannon, Heip, Pielou, and Simpson; p < 0.05) and the abundances of beneficial genera (e.g., Arenimonas, Arthrobacter, Exiguobacterium, Leadbetterella, Luteolibacter, Marinobacter, Nitratireductor, Novosphingobium, Thermomonas, Plesiocystis, and Rubrivivax; p < 0.05). In addition, the substrate also showed significant positive effects on water quality parameters (TAN, TSS, turbidity, biofloc volume, pH, and carbonate alkalinity; p < 0.05), and it also significantly improved shrimp zootechnical performance indices (survival rate, feed conversion ratio, and productivity; p < 0.05). Redundancy analysis revealed that 94.25–98.58% of the variation in the water quality and the shrimp growth performance between the two treatments could be attributed to the shift in bacterial composition and diversity induced by the addition of substrate. These findings characterize the shift in the microbial community in the biofloc system induced by the substrate, and demonstrate how this shift could be beneficial to the water quality and the growth performance of shrimp.