DNA stable isotope probing revealed no incorporation of 13CO2 into comammox Nitrospira but ammonia-oxidizing archaea in a subtropical acid soil

The recently discovered complete ammonia oxidizers (comammox Nitrospira) challenged our concept of the whole nitrification process, i.e., ammonia oxidation catalyzed by autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB), followed by the oxidation of nitrite to nitrate. However, the relative contributions of different ammonia oxidizers to soil nitrification are poorly understood. Soil samples were collected from five land use types (i.e., cropland, grassland, bushland, transition land, and forest land) from a subtropical soil in Yunnan Province, Southwest China. The quantitative distribution of comammox Nitrospira, AOA and AOB in soils was firstly investigated using the QPCR approach and three of which (cropland, transition land and forest land) with pH below 6 were further examined using DNA stable isotope probing approach with 13CO2. Clone library combined with sequencing was applied to detect the phylogenetic information of active microbial groups. The results showed that the amoA gene abundance of ammonia oxidizers except AOB was significantly lower in croplands than other land uses. Based on the 13CO2 labeling method, AOA, rather than AOB or comammox Nitrospira, was found to incorporate 13CO2 into their genomes during the incubation in cropland and transition land but not in forest land, suggesting the dominant role of AOA in ammonia oxidation. Phylogenetic analysis of the active AOA group revealed that autotrophic AOA community was mainly affiliated with the cluster of Nitrososphaera in transition land, whereas Nitrososphaera, Nitrosopumilus, and Nitrosotalea in cropland. These findings suggested niche differentiation of AOB, AOA, and comammox Nitrospira in the subtropical acid soil with different land uses, and AOA played a more important role in nitrification process of this acid soil.