Aerobic carbon metabolism modulates nitrite ammonifiers for inhibiting nitrogen loss as revealed by microcosm experiment of agricultural upland soil

ABSTRACT Denitrification and dissimilatory nitrate reduction to ammonium (DNRA), two divergent nitrogen metabolism pathways, share nitrite as a common intermediate during anaerobic reduction. However, these pathways influence the environment and soil nutrients differently. Unlike denitrification, which involves nitrogen loss through gaseous nitrogen emission and nitrate leaching, DNRA is beneficial for the conservation of nitrogen. Nevertheless, the key mechanism underlying the joint regulation of aerobic carbon metabolism to nitrite ammonifiers in soil is still unclear, although previous studies have reported factors such as carbon and oxygen can independently affect DNRA. Here, microcosm experiments with agricultural upland soil were conducted under different aeration conditions supplemented with labile carbon to analyze the process of anaerobic nitrogen metabolism. The results indicated that denitrification exclusively dominated nitrite reduction when the soil was directly placed in an anaerobic environment. Nonetheless, a significant increase in DNRA activity and the attenuation of denitrification were detected when the soil was incubated aerobically with the addition of glucose prior to anaerobic incubation. Specifically, up to 55.8% of nitrite reduction switched to nitrogen conservation mainly via DNRA under high-carbon conditions. Quantitative assays of the nrfA gene and metagenomic data revealed a significant increase in DNRA-related genes after aerobic carbon metabolism. Furthermore, nrfA gene sequence analysis revealed a significant shift in the composition of nitrite ammonifiers community. These results indicate that nitrate/nitrite metabolic flux in the soil could be regulated to enhance DNRA by stimulating facultative anaerobic nitrite ammonifiers such as Sedimentibacter under alternating aerobic and anaerobic environments with carbon metabolism. IMPORTANCE This study revealed that aerobic conditions with a carbon supply strongly influence the community assembly of nitrite ammonifiers. Nitrite ammonifiers such as Sedimentibacter enriched under sufficient carbon and aeration conditions promoted the subsequent DNRA process under anaerobic conditions. Therefore, regulating the competition between DNRA and denitrification by altering functional microbiota would be a promising approach for improving the efficiency of fertilizer application and for reducing greenhouse gas emissions from denitrification. These findings are essential for understanding the biological mechanism of nitrogen cycling in dryland agricultural soil. Based on these findings, we may design a strategy to increase the abundance of nitrite ammonifiers in agricultural soil, which might promote DNRA metabolism to improve nitrogen retention. This strategy would ultimately enhance fertilizer use efficiency and mitigate the detrimental environmental effects of nitrogen fertilizer abuse.