The present work investigates the effect of biofloc supplementation, as an environmentally clean aqua-feed technique, on water quality, growth performance, feed utilization, and histological status of Nile tilapia (Oreochromis niloticus). Moreover, indicators of zooplankton diversity, community structure, abundance, similarities, and cluster analysis were studied during the experiment. A 60-day growth experiment based on biofloc supplementation was performed to evaluate, in addition to the control group (BF0), the effects of five groups of biofloc supplementation (BF1 = 14.20, BF2 = 28.40, BF3 = 42.60, BF4 = 56.80, and BF5 = 71.0 g L−1, respectively) on Nile tilapia juveniles (initial body weight: 13.30 ± 0.01 g fish−1). During the 15 days of acclimation, the juveniles in all groups were fed twice daily on the same control diet (a commercial diet containing 28% protein). Then, the juveniles were randomly distributed to 18 tanks (each 0.5 m3 with a stocking of 40 fish/tank). The feed rate was 3% of the total fish biomass, adjusted weekly. The water quality indicators were in the ideal range recommended for Nile tilapia culture. The results found that the highest weight gain, specific growth rate and survival rate, and the lowest feed conversion ratio of fish were reported in the BF5 group. Moreover, this group achieved the highest zooplankton abundance (20,706 Ind. L−1) compared to the control group (457 Ind. L−1). The results showed that sections of the muscles in the control group (BF0) revealed fibers arranged into bundles. Comparisons between the muscles in the control group (BF0) and the bioflocs groups (BF1–BF5) showed unclear differences. However, sections of the muscle group BF1 showed increased splitting of muscle fibers and the separation of individual muscle fibers into smaller units. The liver showed multiple pathological lesions in all experimental groups (BF0–BF5). Zooplankton diversity indicators and cluster analysis data also reported a significant difference between the control group (BF0) and the biofloc groups, especially the BF5 group. The present study concluded that the addition of biofloc (71 g L−1) to culture ponds significantly improves the growth, feed utilization, and survival rates of Nile tilapia while enhancing zooplankton diversity, community, and abundance.
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