Abstract:[Background] Anoxygenic phototrophic bacteria (APB) have been widely investigated and applied in the bioremediation of nitrogen-polluted aquaculture. Various organic compounds are predominated in the contaminated aquaculture water, among them, organic nitrides significantly hamper the nitrogen removal efficiency. [Objective] In order to investigate the effects of organic compounds and salinity on inorganic nitrogen removal (ammonia, nitrate and nitrite) and elucidate the mechanism of inorganic nitrogen removal by Rhodobacter azotoformans YLK20, moreover, further to develop well-adapted microbial agents with high nitrogen removal efficiency. [Methods] RAST and KEGG analyses were used to elucidate carbon and nitrogen metabolic pathways and salt-tolerant mechanism(s) of YLK20. The removals of ammonia, nitrate and nitrite were measured by sodium hypobromite oxidation, UV spectrophotometry and N-(1-naphtyl)-ethylenediamine dihydrochloride spectrophoto-metric method, respectively. [Results] Genomic analysis revealed that YLK20 possesses EMP, HMP, TCA, nitrogen fixation, ammonium assimilation and ammonification and denitrification pathways. It contains several salt-tolerant genes such as sohB, nhaC, betB and gbsA. Pyruvate, acetate, citrate, ethanol and mannitol stimulated the cell growth and the nitrogen removal of YLK20, while glucose and fructose decreased the nitrogen removal level. Nitrate and nitrite were removed efficiently in the presence of sucrose while it is difficult to remove ammonia. In the presence of high concentration of peptone (3.21 g/L) and urea (1.43 g/L), inorganic nitrogen concentrations were significantly decreased. YLK20 was able to tolerate to at least 3% of NaCl, efficiently remove the inorganic nitrogen under low salinity conditions while nitrite removal was significantly inhibited in the presence of the high salinity. The inorganic nitrogen both from freshwater and marine rearing water could be efficiently removed by YLK20. [Conclusion] YLK20 could efficiently remove the inorganic nitrogen by ammonium assimilation and denitrification pathways, especially in the presence of high concentration of organics nitrogen. YLK20 was tolerant of high salinity, which is suitable for both freshwater aquaculture and marine aquaculture. YLK20 as a specific microecological modulator, was capable of removing efficiently nitrogen, showing the great potentials in the application in aquaculture remediation.