Different ammonia oxidizers are responsible for nitrification in two neutral paddy soils

Human intervention in agriculture, such as farming and fertilization, could result in major changes of ammonia availability that shapes niche-specific occupied communities of soil ammonia oxidizers. The aim of this study was to investigate nitrification and active ammonia oxidizers in N-rich and N-limited soils, which were induced by different management practices. Here, we used DNA-based stable isotope probing (DNA-SIP) microcosm to decipher active ammonia-oxidizing archaea (AOA) and bacteria (AOB) phylotypes involved in ammonia oxidation in the cultivated and uncultivated soils. The results showed that net nitrification rate in the cultivated soil was significantly higher than in the uncultivated soil (6.19 and 1.40 mg N kg(-1) dry soil d(-1), respectively). Growth of soil AOB and AOA during incubation occurred in the cultivated soil, while in the uncultivated soil, only AOA significantly increased after 56 days. Combining DNA-SIP and sequencing results, we gathered evidence of ammonia oxidation by Nitrososphaera-like AOA, in addition to active AOB, within the classic Nitrosospira group in the cultivated soil. For the uncultivated soil, ammonia oxidation was driven by Nitrososphaera-like and Nitrosopumilus-like AOA, rather than AOB. Our results demonstrate the potential of ammonium concentration for shaping the communities of active AOA and AOB, which imply that ammonia-dependent "diversification" may be important strategies for niche differentiation of sympatric AOA/AOB under different field management conditions.