Differentiation of individual clusters of comammox Nitrospira in an acidic Ultisol following long-term fertilization

The newly discovered comammox Nitrospira has fundamentally overturned the perception of labor division in nitrification and attracted growing interests in the niche preferences of comammox Nitrospira in soils. Here, we investigated the abundance and community structure of comammox Nitrospira in an acidic Ultisol which received the fertilizers continuously for 32 years. Fertilization treatments included chemical nitrogen (N), phosphorus (P), and potassium (K) fertilizers (NPK), NP, NK, PK, and NPK plus peanut straw, rice straw, radish residue or pig manure. Our results revealed that comammox Nitrospira were undetectable in the NK, which was excluded from further analysis. Compared with NPK, NPK plus pig manure significantly increased the abundance of comammox Nitrospira clade A, while the other treatments did not. Available P was the most important factor positively associated with the abundance of clade A. In contrast, soil pH was the best predictor for the variation of comammox Nitrospira community structure, which was distinctly separated by three groups: PK, NPK plus pig manure and the other treatments. Four comammox Nitrospira clusters were identified: clades A.2.1, A.2.2, B.1, and B.2. Of these clusters, clade A.2.1 accounted for 100% of the comammox Nitrospira sequences in NPK, whereas PK and NPK plus pig manure increased the relative abundance of clades A.2.2, B.1, and B.2. The relative abundance of clade A.2.1 was negatively correlated to soil pH, while that of clade A.2.2 showed an opposite trend, indicating the potential niche differentiation of clade A in the soils. Moreover, clade B.1 were more abundant in NPK plus pig manure soils while clade B.2 favored growth in PK, suggesting their different niche preferences. Together, we provide novel evidence for the niche differentiation of individual clusters of comammox Nitrospira clades A and B in an acidic agricultural soil, which was fundamental to the sustainable management of microbial N cycle.