Abstract Complete ammonia oxidizers (comammox Nitrospira) were recently discovered to be capable of oxidizing ammonia and nitrite in a single microorganism, which refutes the long-held paradigm that nitrification required two distinct groups of microbes. However, the niche differentiation of comammox Nitrospira and their co-occurrence with ammonia-oxidizing archaea (AOA) and bacteria (AOB) remain elusive in different soil aggregates. Here, we investigated how 27-year application of mineral and/or organic fertilizers affects comammox Nitrospira, AOA and AOB in aggregates from an Ultisol. Aggregate sizes significantly influenced the community structure of AOA and AOB, rather than comammox Nitrospira. However, organic fertilizers had a greater role in mediating the community structure of comammox Nitrospira, AOA, and AOB than aggregate sizes. Comammox Nitrospira clade A dominated in the tested soils, while pig manure application significantly increased the relative abundance of clade B, especially in microaggregates. Comammox Nitrospira had more co-occurrence links with AOA than with AOB, indicating that comammox Nitrospira may share more similar ecological niches with AOA than with AOB. The co-ocurrence links between comammox Nitrospira and AOA were more intensive in microaggregates than in macroaggregates, supporting their similar oligotrophic lifestyles. However, comammox Nitrospira also co-occurred with AOB, despite the frequency was much lower than that with AOA, indicating that some comammox Nitrospira could share niches with AOB, especially in macroaggregates. Together, these results suggest that comammox Nitrospira could co-occur with both AOA and AOB, although they were more likely to co-occur with AOA than with AOB, particularly in microaggregates of the soils. These findings advance our understanding of the ecology and physiology of comammox Nitrospira in microhabitats of agricultural soils.

中文翻译：

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27 年施肥后土壤团聚体中 comammox Nitrospira 和经典氨氧化剂的生态位分化

摘要 最近发现完全氨氧化剂 (comammox Nitrospira) 能够在单个微生物中氧化氨和亚硝酸盐，这驳斥了长期存在的硝化需要两组不同微生物的范式。然而，comammox Nitrospira 的生态位分化及其与氨氧化古菌 (AOA) 和细菌 (AOB) 的共存在不同土壤团聚体中仍然难以捉摸。在这里，我们调查了 27 年施用矿物和/或有机肥料如何影响来自 Ultisol 的聚集体中的 comammox Nitrospira、AOA 和 AOB。聚集体大小显着影响 AOA 和 AOB 的群落结构，而不是 comammox Nitrospira。然而，有机肥料在调节硝化螺旋藻、AOA 和 AOB 群落结构方面的作用比聚集体尺寸更大。Comammox Nitrospira 进化枝 A 在测试土壤中占主导地位，而猪粪施用显着增加了进化枝 B 的相对丰度，尤其是在微团聚体中。Comammox Nitrospira 与 AOA 的共生联系比 AOB 多，表明 Comammox Nitrospira 与 AOA 的生态位可能比与 AOB 更相似。comammox Nitrospira 和 AOA 之间的共生联系在微团聚体中比在大团聚体中更加密集，支持它们类似的贫营养生活方式。然而，comammox Nitrospira 也与 AOB 共同发生，尽管频率远低于 AOA，表明一些 comammox Nitrospira 可以与 AOB 共享生态位，尤其是在大团聚体中。总之，这些结果表明 comammox Nitrospira 可能与 AOA 和 AOB 同时发生，尽管它们更可能与 AOA 一起发生而不是与 AOB 一起发生，尤其是在土壤的微团聚体中。这些发现促进了我们对农业土壤微生境中硝化螺旋藻生态学和生理学的理解。