Original articlenirS- and nirK-type denitrifier communities are differentially affected by soil type, rice cultivar and water management

•The nirK:nirS gene abundance ratio was higher in samples taken at flower primordium.•The nirS communities were more sensitive than nirK communities to the studied factors.•Soil type was the most important analyzed factor shaping nirS communities.•The rice cultivar affected some OTUs but did not influence the community structure.

Denitrification is one of the main biological sources of N2O, a greenhouse gas. In paddies, water flooding provides anaerobic soil conditions that can boost denitrification. In this work, the influences of rice cultivar, water management and soil type on the abundance and community structure of denitrifying bacteria were evaluated; nirS and nirK-type denitrifiers were considered separately. Two microcosm experiments were performed, and the abundance and community structure for both nitrite reductase genes were assessed using qPCR and T-RFLP, respectively. In the first experiment, two rice cultivars and two water managements were evaluated; in the second experiment, two soils, which mainly differed in their organic matter content, and two flooding times were evaluated. The results show that sampling time was the main factor driving nirS and nirK abundances. The nirK:nirS ratio, recently proposed as an indicator of the soil N2O emission potential, was higher in samples taken at the flower primordium stage of rice in both experiments, suggesting that this stage could be a hot moment for N2O emissions. Soil type was the main factor influencing the nirS community structure, while it had no effect on nirK communities. Although the nirK community structure was not affected by cultivar or soil type, statistical analysis showed that some T-RFs were associated with each cultivar or soil type, indicating that these factors exerted effects on certain subsets of the denitrifying population rather than the whole community. The community structure of nirS-type denitrifiers was more sensitive to the analyzed factors than the nirK-type, and soil type was the main factor that influenced this community structure.