Responses of ammonia-oxidizers and comammox to different long-term fertilization regimes in a subtropical paddy soil

Abstract Nitrogen, including ammonium, is an essential nutrient for plant growth and heavily applied in agricultural systems via fertilization. Nitrification is a two-step microbiologically-mediated process in which ammonium is first oxidized to nitrite and then subsequently to nitrate. The objective of this study was to determine the influence of variable long-term (28 years) fertilization on the potential nitrification rate (PNR) and three prokaryotic groups involved in this process: (1) ammonium-oxidizing bacteria (AOB), (2) ammonium-oxidizing archaea (AOA), and (3) recently discovered bacteria with the capacity to perform complete nitrification (comammox). Fertilization treatments included urea ((NH 2 ) 2 CO) only (N), urea ((NH 2 ) 2 CO) + potassium sulfate (K 2 SO 4 ) (NK), urea ((NH 2 ) 2 CO) +calcium superphosphate (CaP 2 H 4 O 8 ) +potassium sulfate (K 2 SO 4 ) (NPK), and a control with no N. The PNR increased with N fertilization, indicating that N application accelerated soil nitrification. The lower AOB abundance, the highest AOA/AOB ratios and lower PNR were observed in the NK treatment compared to N and NPK treatments, suggesting that AOB may be the key driver of nitrification in this soil. Comammox had higher amoA gene abundance (2.72 × 10 7 gene copies g −1 to 2.35 × 10 8 gene copies g −1 dry soil) than AOB and AOA for all treatments. The abundance of comammox clade A (7.38 × 10 7 gene copies g −1 -2.35 × 10 8 gene copies g −1 dry soil) was significantly higher than for comammox clade B (5.66 × 10 6 gene copies g −1 -1.42 × 10 7 gene copies g −1 dry soil), and based on high abundance values, we suppose that comammox are non-negligible contributors to soil nitrification resulting from responsiveness to N fertilization.