Introduction: The biofilter of a RAS is a key element for the water treatment since it removes byproducts originated during the fish production. A proper balance of the microbial community maintains safe levels of these residual compounds. An imbalance in the biofilter's microbiome reduces the water quality, which causes stress to the fish physiological system. This situation could result in a disease outbreak and great economic losses.

Aim: The aim of the present work is the selection of microorganisms to enhance the biofiltration system in a RAS, and investigate its capacity to reduce the abundance of pathogens in the system.

Methods: Samples were obtained from the biofilter of a freshwater RAS with reared Clarias gariepinus. Different bacterial colonies growing on Tryptic Soy Agar (TSA) plates were isolated and biochemically characterized. The phytase, lipase, amylase, caseinase, gelatinase, cellulase, nitrate reduction and nitrite reduction activities were determined with differential mediums. Isolates with interesting metabolic profiles were selected and tested for biofilm formation ability, quorum sensing activity and antagonistic effect against seven potentially pathogenic bacteria.

Results: Two strains identified as Bacillus sp. and Lysinibacillus sp. were selected according to their overall metabolic profile. Bacillus sp. showed a strong inhibition of the growth from Staphylococcus aureus and Pseudomonas veronii. It was able to catalyze phosphate, glucose, casein, gelatin, cellulose and reduce nitrate. Lysinibacillus sp. had an antagonistic effect on the growth of Vibrio anguilarum and P. veronii, and could reduce nitrite and catalyze gelatin. The two Gram-positive spore-forming bacterial strains have the capacity to recover after a lyophilization treatment and were able to cohabit together on the same medium.

Conclusions: The two candidates had essential functional traits with the potential to improve the water biofiltration processes and control the overgrowth of pathogenic bacteria. They also had advantageous biotechnological and functional characteristics for the future development of probiotics which could be used at the production sector.