Nitrification plays an important role in the soil nitrogen cycle. Here, we conducted an experiment in three different soil types (red soil, black soil, and alluvial soil) to evaluate the response of nitrifiers and nitrification to manure fertilizers. We found that long-term manure fertilization altered the soil physicochemical properties, increased soil organic matter and NO₃^－-N concentrations, and decreased NH₄⁺-N concentrations. Both ammonia and nitrite oxidation potential were higher in the manured soils than those in the control soils. Long-term manure fertilization markedely increased the abundance of nitrifiers and the abundance of the complete ammonia oxidation (comammox) amoA gene copy number ranged from 0.78 × 10⁶ to 2.18 × 10⁶ g⁻¹ dry soil, which was lower than that of canonical nitrifiers including ammonia‐oxidizing archaea, ammonia‐oxidizing bacteria, and nitrite‐oxidizing bacteria (NOB). The community composition of NOB and comammox was affected by both soil type and manure fertilizer. Soil NH₄⁺-N concentration and total carbon content were the factors that were most strongly correlated with the microbial community composition. Manure fertilizers promoted the coupling linkages among soil Nitrobacter, Nitrospira, and comammox communities and created a more closely linked microbial community. The results suggest that long-term inputs of manure to agricultural soils influence the structure of NOB and increase nitrification rates.

硝化作用在土壤氮循环中起着重要作用。在这里，我们在三种不同的土壤类型（红壤，黑土和冲积土）中进行了一项实验，以评估硝化剂和硝化作用对肥料的响应。我们发现长期施肥改变了土壤的理化性质，增加了土壤有机质和NO ₃ ^－ -N的浓度，并降低了NH ₄ ⁺ -N的浓度。肥料土壤中的氨和亚硝酸盐氧化电位均高于对照土壤。长期施肥显着增加了硝化器的丰度和完全氨氧化（comammox）amoA基因拷贝数的丰度，范围为0.78×10⁶至2.18×10 ⁶ g ^-1干燥土壤，低于包括氨氧化古细菌，氨氧化细菌和亚硝酸盐氧化细菌（NOB）的标准硝化器。NOB和comammox的群落组成均受土壤类型和肥料的影响。土壤NH ₄ ⁺ -N浓度和总碳含量是与微生物群落组成最密切相关的因素。粪便肥料促进土壤之间的耦合关联硝化，硝化，以及comammox社区，并建立了更紧密联系的微生物社区。结果表明，长期向农业土壤中输入肥料会影响NOB的结构并增加硝化率。