Contrasting seasonal response of comammox Nitrospira and canonical ammonia oxidizers in two paddy soils

The discovery of comammox Nitrospira fundamentally changed our perspective of the traditional concept of soil nitrification and has expanded our understanding of the diversity of nitrifying microorganisms. However, the significance and the relative contribution of comammox to nitrification in soil remains poorly understood. Two paddy soils collected in January (winter, nitrification almost stopped) and June (summer, nitrification occurred quickly and at high rates) in 2021 were analyzed for nitrification rates. In situ active nitrifiers were identified by quantifying the amoA gene and transcript abundance to distinguish the relative importance of Ammonia Oxidizing Archaea (AOA), Ammonia Oxidizing Bacteria (AOB) and commomox Nitrospira Clade A and Clade B to ammonia oxidation. Both amoA gene abundance and transcript abundance for comammox were high even in January when nitrification almost stopped and did not increase significantly in summer when nitrification occurred at high rates. On the contrary, AOB transcriptional activity showed a consistent pattern with nitrification, with the amoA gene expression being low for AOB in winter when nitrification almost stopped and increased two orders of magnitudes in summer when nitrification occurred quickly. AOB showed a much higher transcription ratio than AOA. These results indicated that AOB basically drives ammonia oxidation in these paddy soils, and comammox Nitrospira adapts better to low temperature conditions than AOA and AOB. Furthermore, soil water content was identified to be an important factor in shaping comammox clade A activity, but not clade B in these two neutral paddy soils.