Cropping system history and crop rotation phase drive the abundance of soil denitrification genes nirK, nirS and nosZ in conventional and organic grain agroecosystems

While nitrogen fertilizers have helped increase crop yields substantially, they have also contributed to several environmental problems, including an increasing atmospheric concentration of nitrous oxide (N2O), a green-house gas (GHG) and catalyst of stratospheric ozone decay. The dominant source of atmospheric N2O in many agricultural soils is denitrification, a process carried out by soil microbes containing the genes for nitrate reductase (Nar), nitrite reductase (Nir), nitric oxide reductase (Nor) and/or nitrous oxide reductase (Nos). We monitored the abundance of soil nirK, nirS, and nosZ genes during the summer growing season. We sampled replicated field plots from a long-term agricultural research site that includes agroecosystems with com/soybean/wheat/legume rotations: two tilled-organic systems (Org3 and Org6), and two conventional systems, one using a chisel plow for primary tillage (CT) and one using no-tillage (NT). We demonstrate that nirK copy number in soil was affected primarily by the phase of the crop rotation and secondarily by time of year, regardless of cropping system. In contrast, nosZ gene copy number was primarily driven by cropping system. Soil N2O emissions during the sampling period were highest in Org3 and lowest in NT. However, gene quantities did not correspond to N2O emissions patterns, indicating that quantitative PCR of key denitrification genes measured at the temporal resolution reported here is not a good predictor of soil N2O emissions. These results, nonetheless, show that cropping system management can affect microbial community composition, gene quantity of nir and nos genes and N2O emissions. We found cropping system and time of year captured variation in gene abundance among microbial denitrifier populations in these agricultural soils.