The active role of comammox Nitrospira in nitrification in acidic orchard soils revealed by DNA-SIP

The recently discovered complete ammonia oxidizers (comammox Nitrospira) have fundamentally changed the perceptions of two-step nitrification. Previous studies suggest that comammox Nitrospira may outcompete canonical ammonia oxidizers under ammonia-limited conditions (e.g., acidic soils). However, there is no convincing evidence that links comammox Nitrospira activity to nitrification in acidic soils. Here, we report the relative contributions of ammonia-oxidizing bacteria (AOB), archaea (AOA), and comammox Nitrospira to nitrification in four orchard soils with different ages (5Y, 10Y, 20Y, and 30Y) and one adjacent natural forest soil (NF) in China. DNA-based stable-isotope probing demonstrated that both AOA and AOB assimilated (CO2)-C-13 in the nonacidic NF, 5Y, and 10Y soils, although a small shift from the light fractions to heavy fractions was observed for comammox Nitrospira clade A in the 10Y soil. Comammox Nitrospira clade A rather than AOA and AOB was labeled by (CO2)-C-13 in strongly acidic 30Y soil. In strongly acidic 20Y soil, comammox Nitrospira clade A was much more heavily labeled than AOB. These results suggest the different contributions of ammonia oxidizers to nitrification in orchard soils with different ages and a greater functional importance of comammox Nitrospira than canonical ammonia oxidizers in ammonia oxidation in the tested strongly acidic orchard soils.