Niche differentiation of comammox Nitrospira and canonical ammonia oxidizers in soil aggregate fractions following 27-year fertilizations

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.