Biofloc culture systems potentially reduce the nutrient losses in aquaculture. However, knowledge of the nutrient flows in the system is not yet well-developed. This study deployed experimental data to develop a semi-physical model to understand the dynamics and flows of carbon (C), nitrogen (N), and phosphorus (P) in a biofloc-Nile tilapia-rearing system. The model involved eight process variables, which are pelleted feed A, C, N, P, fish, biofloc, periphyton, and water volume. Model calibration and validation were done under a Control-diet and High-NSP-diet, respectively. The diets differed by the type of starch in which the latter contains three times higher fibrous starch, called non-starch polysaccharides, than the former. Except for biofloc, the behaviour of the process variables fit the observations with a root mean square error (RMSE) of less than 30% of the corresponding average observations. The biofloc biomass was predicted using exponential growth model and results in a RMSE of 49% and 56% for the Control and High-NSP-diet, respectively. Scenario analyses, using the validated model, showed that the biofloc system generates less waste when the stocking density is doubled, which means double fish production and less nutrient losses. In terms of different diets, the high-NSP-diet resulted in more organic waste than the Control-diet. However, the amount of loss and unutilised C and P were similar which was mainly caused by the ability of biofloc and periphyton to assimilate more waste, especially C, in the High-NSP-diet.
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