The discovery of comammox Nitrospira has expanded our knowledge of classical labor division in nitrification and opened up new avenues to unravel the nitrification process in terrestrial ecosystems. However, the effects of fertilization and rhizosphere on comammox Nitrospira remains largely limited, especially in alkaline agricultural soils. To address this knowledge gap, the community structure of comammox Nitrospira and canonical ammonia oxidizers in the bulk and rhizosphere of an alkaline agricultural soil following 8 years of fertilizer applications was investigated. The fertilization treatments included no fertilization (CON), mineral NPK fertilizer (NPK), manure + straw (MS), NPK + manure (NPKM), NPK + manure and straw (NPKMS), and NPK + manure and straw by deep ploughing (NPKMSD). Five phylogenetic clusters of comammox Nitrospira were detected in the soil including clades A.1, A.2.1, A.2.2, A.3 and B, with A.2.1 and B as the dominant clades. Fertilization had a greater effect than rhizosphere on the community structure of comammox Nitrospira, while both fertilization and rhizosphere had no significant effect on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Compared with CON and NPK, the relative abundance of comammox Nitrospira clade A, especially clade A.2.1, increased while clade B decreased following manure applications. Soil nitrate played a critical role in driving the variation of comammox Nitrospira community structure. These findings showed novel evidence of niche specialization of comammox Nitrospira and canonical ammonia oxidizers in agricultural soils.

comammox Nitrospira的发现扩展了我们对硝化作用中经典分工的认识，并为揭示陆地生态系统中的硝化过程开辟了新途径。然而，施肥和根际对 comammox Nitrospira的影响在很大程度上仍然有限，特别是在碱性农业土壤中。为了解决这一知识差距，comammox Nitrospira的群落结构研究了施肥 8 年后碱性农业土壤的块体和根际中的典型氨氧化剂和典型氨氧化剂。施肥处理包括不施肥（CON）、矿物氮磷钾肥（NPK）、粪肥+秸秆（MS）、氮磷钾+粪肥（NPKM）、氮磷钾+粪肥和秸秆（NPKMS）、氮磷钾+粪肥和秸秆深耕（ NPKMSD）。在土壤中检测到5个comammox Nitrospira的系统发育簇，包括进化枝A.1、A.2.1、A.2.2、A.3和B，其中A.2.1和B是优势进化枝。施肥对硝螺菌群落结构的影响大于根际，而施肥和根际对氨氧化古菌（AOA）和氨氧化细菌（AOB）的群落结构没有显着影响。与CON和NPK相比，施肥后comammox Nitrospira进化枝A，尤其是进化枝A.2.1的相对丰度增加，而进化枝B减少。土壤硝酸盐在驱动comammox Nitrospira群落结构变化中发挥了关键作用。这些发现显示了农业土壤中 comammox Nitrospira和典型氨氧化剂的生态位专业化的新证据。