Autotrophic archaeal nitrification is preferentially stimulated by rice callus mineralization in a paddy soil

Aims Previous studies suggest that organic carbon (C) and nitrogen (N) can stimulate soil nitrification, but whether autotrophic or heterotrophic nitrification is stimulated and who are active nitrifiers for the nitrification activity is still in debate. We elucidated which nitrification dominated and the active nitrifiers during the decomposition of rice callus. Methods N-15-labeled callus and acetylene (C2H2) inhibition were used to explore the autotrophic or heterotrophic nitrification during the decomposition of callus and DNA-based stable isotope probing (SIP) and high-throughput sequencing were used to investigate the active nitrifiers. Results Autotrophic nitrification dominated the nitrification activity, driven by oxidation of ammonia (NH3) produced from mineralization of the callus-derived organic N. Callus significantly stimulated nitrification activity, which was paralleled by changes in the abundance and community composition of AOA. DNA-SIP further demonstrated that the active AOA outnumbered their bacterial counterparts in the C-13-DNA from the soil with callus amendment. Phylogenetic analysis revealed the functional importance of soil fosmid 29i4-like and 54d9-like AOA within soil group 1.1b during the active nitrification with callus cells. Conclusions NH3 released from the mineralization of callus was the main substrate for autotrophic nitrification and preferentially stimulated the growth of AOA within group 1.1b in the paddy soil.