Integrative chemical and omics analysis of the ammonia nitrogen removal characteristics and mechanism of a novel oligotrophic heterotrophic nitrification-aerobic denitrification bacterium

A novel oligotrophic heterotrophic nitrification-aerobic denitrification bacterium designated as Pseudomonas sp. N31942, was isolated from a eutrophic lake. Strain N31942 exhibits high ammonia nitrogen removal ability in oligotrophic environment as ammonia nitrogen can be efficiently (86.97 %) removed within 10 h with no accumulation of nitrite. In the nitrification process, strain N31942 can convert ammonia into nitrate in the absence of hydroxylamine oxidase and nitrite oxidoreductase. As for the denitrification process, nitrate or nitrite were reduced to ammonia and further converted into glutamate by dissimilatory nitrate reduction pathway. Transcriptomic analysis detected 2080 differentially expressed genes. Among them, the expression of the related genes in dissimilatory nitrate reduction process was all up-regulated at low ammonia concentrations, which indicates that the strain has excellent nitrogen removal efficiency for further nitrogen removal. Integrative omics analyses revealed that strain N31942 may have two possible pathways for the NH4+-N removal as direct GDH/GS-GOGAT pathway (NH4+-N → Glutamate) and indirect GDH/GS-GOGAT pathway (NH4+-N → NH2OH → NO2−-N → NO3−-N → NO2−-N → NH4+-N → Glutamate). Moreover, strain N31942 also has excellent nitrogen removal ability for real sewage and 77.21 % total nitrogen could be removed within 48 h. The results presented here provide new insights into ammonia nitrogen removal characteristics and mechanism of heterotrophic nitrification-aerobic denitrification bacterium under oligotrophic conditions.