The accumulation of nitrogen (-N) is a serious problem in aquaculture as it could lead to mass mortality events of the cultivated species. Chemilitotrophic nitrification is the most recognized in nitrogen removal underestimating the role of heterotrophic nitrifiers. In the present study, the heterotrophic nitrification capacity of 8 bacterial strains isolated from mangrove soil, periphyton and biofilters was evaluated. The strains were grown in heterotrophic nitrification base medium (HNM medium) with three different nitrogen sources, ammonium, nitrite or nitrate at a final concentration of 8 mg L^-1, 5 mg L^-1 and 80 mg L^-1 respectively. The concentration of nitrogen (-N) and OD (600 nm) were determined periodically. Only in 4 strains belonging to the Bacillus genus was the capacity for heterotrophic nitrification and aerobic denitrification observed. Among these strains, SM4 strain presented a good removal profile of ammonium, nitrite and nitrate, achieving an average nitrification efficiency of 98.33 ± 2.89%, 83.67 ± 7.51% and 98.00 ± 0.01% respectively, and a nitrification rate (mg L^-1 h^-1) of 1.71 ± 0.70, 0.13 ± 0.07 and 0.21 ± 0.06 respectively. The nxrB, nirS, nirK genes in the selected strains were identified by PCR. Additionally, several proteins (enzymes) involved in the nitrogen cycle were identified by proteomic analysis, reporting for the first time the presence of the enzymes ammonia monoxygenase (AMO) and nitrite oxide reductase (NXR) in the genus Bacillus. These findings suggest that the strains studied would have a potential use in the biological removal of nitrogen in aquaculture systems.