Carbon and aeration modulate the flux of reductive pathways in nitrite metabolism by shaping the structure of the functional microbiota in agricultural upland soil

Abstract

Abstract Background Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) share the common intermediate nitrite during nitrogen anaerobic reduction metabolism. Compared with DNF, which incurs nitrogen loss through gas emission and leaching, DNRA is more economical and environmentally friendly due to the conservation of nitrogen in the form of ammonium. However, the competition mechanism between DNF and DNRA is currently unclear. Results Incubations with agricultural soil from the North China Plain (NCP) were conducted under different aeration conditions with the addition of nitrite and different doses of glucose. By measuring the activity of DNF and DNRA, we found that DNF exclusively dominated nitrate reduction when NCP soil was directly anaerobically incubated regardless of the carbon content. However, a significant increase in DNRA activity and attenuation of that of DNF was detected by 15N stable isotopic measurement when the soil samples were incubated aerobically with the addition of glucose prior to anaerobic incubation; specifically, as much as 24 ~ 56% DNF activity was attenuated, and most of that part of nitrite was reduced by DNRA activity under high carbon conditions. Quantitative assays of the nrfA gene and metagenomics data showed a significant increase in DNRA reaction-encoding genes after aerobic incubation. Furthermore, the nrfA sequence analysis showed a significant shift in the composition of DNRA members during aerobic preincubation with an increased relative abundance of specific phylotypes. Hence, environmental changes, especially oxygen and carbon availability, resulted in changes in nitrogen reduction metabolism. Conclusions Results from this study indicated that DNRA could be promoted by regulating abiotic factors, such as aeration and the carbon content, to modulate the competition of two metabolic pathways of nitrate/nitrite reduction in agricultural soil, which could be achieved by shifting the abundance of functional facultative anaerobes.