Nitrification inhibitors impose distinct effects on comammox bacteria and canonical ammonia oxidizers under high N fertilization regimes

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The response of complete ammonia-oxidizing (comammox) bacteria to variable nitrogen (N) inputs and nitrification inhibitors (NIs) remains poorly understood. We conducted two experiments, in a soil where both clade A and B comammox Nitrospira were present, to identify the type (ammonium sulphate vs. urea) and the level of N-fertilization (0–500 mg-N-kg‐1d.w. soil) that are conducive to the growth of comammox, compared to canonical ammonia-oxidizing microorganisms (AOM), and subsequently to assess their response to three commercial (DCD, nitrapyrin, DMPP) and a new potent (ethoxyquin) NI under these favourable N fertilization regimes. The highest concentration of ammonium sulphate stimulated comammox compared to canonical AOM which showed a dose-dependent increase by both N sources. DMPP primarily, and DCD, imposed a more persistent inhibition on nitrification than nitrapyrin and ethoxyquin, a result which did not concur with the soil persistence of NIs (DMPP was the least persistent among the commercial NIs) but was mostly driven by their selective inhibitory activity on ammonia-oxidizing bacteria (AOB) that prevailed in the studied soil. The inhibition of AOB by DMPP and DCD was complemented by the proliferation of comammox and ammonia-oxidizing archaea (AOA). NIs induced significant changes on AOB and comammox communities. Comammox Nitrospira clade B were enriched by DCD and DMPP but depleted by nitrapyrin and ethoxyquin. We showed that (i) releasing comammox Nitrospira and AOA from AOB competition allows them to proliferate efficiently, even under high inorganic ammonium conditions; (ii) comammox clade B are more responsive than clade A to high inorganic N input and NIs.