Biofloc technology (BFT) has achieved sustainable aquaculture production, intensification, and profitable food-producing activity. The colonization process in floating substrates is elemental for BFT proliferation and biomass increase. Organic substrates are feasible nucleators for the nutrient richness required by heterotrophic bacteria. This study evaluated the effect of vegetal-derived substrates on biofloc bacterial diversity generated in a 36-day hyper-intensive white shrimp (Litopenaeus vannamei) culture. The treatments were established according to the presence of vegetal-derived substrates for biofloc production, including wheat bran, amaranth seeds, oat bran, and a control (without substrate). Shrimp cultured in treatments using floating substrates registered better productive responses. Water quality results indicated that bioflocs were at the beginning of the nitrification phase, suggesting that bioflocs were entering the mature stage. Similar taxonomic profile structures throughout treatments were also observed and at least 26 bacterial phyla were detected in each treatment but only nine represented ~ 98% of the relative abundance in each treatment: Proteobacteria (35.9–49.5%), Bacteroidetes (26.4–33.5%), Planctomycetes (9.9–14.7%), Actinobacteria (4.3–5.8%), Chloroflexi (2.8–4.7%), Verrucomicrobia (1.1–3.5%), Gemmatimonadetes (1.0–1.7%), Acidobacteria (0.7–1.2%), and Chlamydiae (0.5–1.2%). Beta diversity analyses also revealed no significant differences between treatments. Permutational multivariate analysis of variance showed no statistical differences either by estimating Bray–Curtis or Weighted Unifrac distances. In conclusion, agricultural-derived floating substrates used at the beginning of culture to boost biofloc production do not modify the bacterial taxonomic profile, which seems to be mainly driven by the prevailing environmental conditions established for biofloc formation.
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