Objectives Delaying urea hydrolysis is an effect way to reduce soil nitrogen (N) losses. We compared the inhibition effects of natural urease inhibitor allicin (DATS) with chemical urease inhibitor N-butylthiophosphoryl triamine (NBPT) by investigating the urea hydrolysis rate, nitrification and ammonia volatilization, as well as the gene abundance and community structure of key microbes for urea hydrolysis and nitrification.

Methods An aerobic incubation experiment was conducted. Urea was added into the calcareous soil, then eight treatments were set up, including no inhibitor control (CK), adding NBPT at rate of 1% of N dosage (NBPT), and adding DATS at rates of 5%, 10%, 20%, 30%, 50% and 100% N dosages, respectively. The incubation lasted for 28 days, and soil urea-N, NH₄⁺-N, NO₃⁻-N contents as well as ammonia volatilization rates were determined regularly, soil gene abundances and community structures of ureC, AOA and AOB were determined using fluorogenic quantitative PCR and high-throughput sequencing.

Results NBPT and DATS demonstrated significant inhibition of urea hydrolysis within 21 and 14 days, respectively, with average inhibition rates of 42.18% for NBPT and 5.37% to 7.54% for six dosages of DATS. During the incubation period, NBPT reduced total ammonia volatilization by 91.91% (P<0.001), while DATS reduced it by 19.74% to 26.17% (P<0.05). There was no significant difference in the inhibition of urea hydrolysis, nitrification and ammonia volatilization among six dosages of DATS. Both NBPT and DATS significantly decreased the average gene abundances of urea-decomposing bacteria (ureC) and ammonia-oxidizing bacteria (AOB). NBPT exhibited stronger inhibition of ureC and AOB abundances than DATS, whereas less inhibition of ammonia-oxidizing archaea (AOA) abundance than DATS. NBPT increased the relative abundances of Burkholderia and Ralstonia within the dominant ureC community, while decreasing the relative abundances of Cupriavidus and Variovorax. The impact of DATS on the dominant population within the ureC community was opposite to that of NBPT. Both NBPT and DATS reduced the relative abundance of Nitrososphaera, the dominant community within AOA, with DATS showing a greater reduction. They also reduced the relative abundance of Nitrosospira, the dominant community within AOB, but only NBPT showed a significant reduction. The addition of DATS and NBPT increased the diversity of the ureC and AOA communities, but decreased the diversity of the AOB community. The impact of NBPT on the diversity of the AOB community was greater than that of DATS. NBPT significantly altered the community structure of both ureC and AOB, while DATS significantly altered the community structure of AOA. Association analysis revealed that soil pH and nitrate (NO₃⁻-N) content significantly influenced the community structure of ureC, while soil urea-N, NH₄⁺-N and NO₃⁻-N contents significantly influenced the community structure of AOB.

Conclusions Both DATS and NBPT inhibited urea hydrolysis, nitrification and significantly reduced ammonia volatilisation by suppressing the abundance and altering their community structure of ureC, AOA and AOB in calcareous soils. The inhibition of soil urea hydrolysis and nitrification and the effects of DATS on ureC and AOB community structure were smaller than those of NBPT, but the effects on AOA community structure were larger than those of NBPT.