Comparison of the effects of quinone imine, dicyandiamide (DCD) and nitrapyrin on target and non-target microbial groups under contrasting soil pH

Dicyandiamide (DCD) and nitrapyrin (NP) are established nitrification inhibitors (NIs). Ethoxyquin was proposed as a novel potential NI, acting through its oxidation derivative quinone imine (QI). To date we still know little about the specific activity of these NIs on the different ammonia-oxidizing microbes (AOM) like bacteria (AOB), archaea (AOA) and complete ammonia-oxidation bacteria (CAOB) under soil conditions. Even less are known about the off-target effects of these NIs on the soil microbiota. We determined the impact of DCD, NP and QI applied at two doses, representing the agriculturally recommended (low) and 5-15 times higher (high), on the function, diversity, and dynamics of target (AOM), functionally associated (nitrite-oxidizing bacteria (NOB), and off-target prokaryotic and fungal microbial communities in two agricultural soils of contrasting pH (acidic vs. alkaline). DCD was more persistent than NP and QI and showed a dose-dependent dissipation pattern with higher persistence in the alkaline soil. The low dose of all NIs successfully inhibited nitrification in the alkaline, but not in the acidic soil, where consistent inhibition was observed only at the high dose rates. DCD and QI were more efficient than NP in inhibiting nitrification in the acidic soil, while in the alkaline soil QI was less efficient than DCD and NP. This was attributed to the higher activity of QI towards AOA prevailing in the acidic soil, as verified by q-PCR and RT-q-PCR, unlike AOB whose abundance and transcriptional activity was less affected by both QI dose rates. A dose-dependent effect of the NIs on the dynamics of NOB was observed in the alkaline soil, with Nitrobacter being more susceptible than Nitrospira. Amplicon sequencing revealed a significant and uniform effect of all NIs on the AOB community in both soils, unlike AOA which were less responsive. QI was the sole NI that perturbated the bacterial and fungal community in both soils, inducing dose-dependent shifts in the abundance of microbes associated with key soil functions within and beyond N cycling, implying for possible effects on the soil ecosystem homeostasis. Our findings improve our understanding of the interactions of NIs with the soil microbial community beyond target organisms and lay the basis for a thorough consideration of the effects of NIs on soil microbiota.