The newly-discovered complete ammonia-oxidizing bacteria (comammox) doubts our inherent understanding of nitrification. Herein, we study communities of comammox, ammonia-oxidizing bacteria (AOB) and archaea (AOA) in Mollisol after a 30-year fertilization history with four treatments: chemical nitrogen (N) and potassium (K) fertilizers (NK); chemical N, phosphorus (P), and K fertilizers (NPK); chemical NPK fertilizers plus organic manure (NPKM); and a control without fertilizers (CK). Compared with CK, chemical fertilizer treatments (NK and NPK) significantly reduced AOA amoA gene abundance and increased AOB and comammox amoA gene abundances. The highest values of AOA and AOB amoA gene abundances were found in the NPKM treatment and the highest value of comammox amoA gene abundance was observed in the NK treatment. The application of combined NPK and organic manure (NPKM) significantly increased AOA, AOB, and comammox amoA gene abundances compared to CK. Long-term chemical fertilization decreased the diversity of comammox community; whereas, the application of combined NPK with organic manure (NPKM) restored it to levels comparable to CK. Long-term fertilization management altered the community structure of comammox based on principal coordinate analysis (PCoA). Soil pH and NH₄⁺-N concentration were the key factors affecting soil abundance and community structure of comammox. This study demonstrates the different responses of comammox community and canonical ammonia oxidizers to long-term fertilization practices in Mollisol.

新发现的完全氨氧化细菌（comammox）怀疑我们对硝化作用的内在理解。在此，我们通过化学氮 (N) 和钾 (K) 肥料 (NK) 四种处理，研究了经过 30 年施肥历史的 Mollisol 中的 comammox、氨氧化细菌 (AOB) 和古菌 (AOA) 群落；化学氮、磷 (P) 和钾肥 (NPK)；化学 NPK 肥料加有机肥 (NPKM)；和不施肥的对照 (CK)。与CK相比，化肥处理（NK和NPK）显着降低了AOA amoA基因丰度，增加了AOB和comammox amoA基因丰度。AOA 和 AOB amoA的最高值在 NPKM 处理中发现了基因丰度，在 NK 处理中观察到comammox amoA基因丰度的最高值。与 CK 相比，NPK 和有机肥 (NPKM) 的组合施用显着增加了 AOA、AOB 和 comammox amoA基因丰度。长期化肥降低了comammox群落的多样性；而结合施用 NPK 与有机肥 (NPKM) 将其恢复到与 CK 相当的水平。基于主坐标分析 (PCoA) 的长期施肥管理改变了 comammox 的群落结构。土壤 pH 值和 NH ₄ ⁺-N浓度是影响comammox土壤丰度和群落结构的关键因素。这项研究证明了 comammox 群落和典型氨氧化剂对 Mollisol 中长期施肥实践的不同反应。