Canonical ammonia oxidizers, rather than comammox Nitrospira, dominated autotrophic nitrification during the mineralization of organic substances in two paddy soils

Abstract

Chemoautotrophic canonical ammonia-oxidizers and complete ammonia oxidizers (comammox) are responsible for ammonia oxidation, which is the rate-limiting step of nitrification in terrestrial ecosystems. However, the relative importance of autotrophic nitrification and the related active nitrifiers during mineralization of organic substances with different C/N ratios have not been fully elucidated to date. In this study, ¹⁵N tracing and ¹³CO₂-DNA-based stable isotope probing (DNA-SIP) techniques were employed to investigate the responses of soil nitrification processes and the active nitrifying phylotypes in acidic and neutral paddy soils with amendment of glutamine (Gln) or rice straw with low C/N (LS) or high C/N (HS). Acetylene (C₂H₂) was utilized to differentiate autotrophic and heterotrophic nitrification. The results indicated that C₂H₂ completely blocked the production of ¹⁵NO₃− in Gln and LS treatments, implying the predominance of autotrophic nitrification with the N derived from the mineralization of Gln and LS. Neither ¹⁵NH4+ nor ¹⁵NO3− was detected in the HS-amended soils, suggesting that NH₄+ derived from organic N mineralization was immobilized immediately by microorganisms. In the DNA-SIP microcosms, the abundance of ammonia-oxidizing bacteria (AOB) in the unamended control (CK), Gln and LS treatments of acidic paddy soil increased by 22.1-, 71.9- and 27.6-fold, respectively. A significantly larger proportion of Nitrosospira-like AOB, rather than ammonia-oxidizing archaea (AOA) and comammox Nitrospira, was labelled by ¹³CO₂, indicating that AOB made a stronger contribution to autotrophic nitrification in acidic paddy soil. The active nitrification of neutral paddy soil was predominated by AOA affiliated with the Nitrososphaera viennensis lineage in the CK and LS microcosms but by Nitrosospira-like AOB in the Gln microcosm. These results suggest the significance of autotrophic nitrification catalysed by canonical ammonia oxidizers, rather than comammox, during the mineralization of organic substances with low C/N in paddy soils.