Seasonal dynamics of prokaryotic nitrogen cycling genes in cropland soils: Effects of soil texture, tillage, and environmental factors

In cropland, prokaryotic microbiomes mediate the biogeochemical cycling of nitrogen (N), which is typically supplied at large amounts for plant growth promotion. While genes encoding for key enzymes of the N cycle in soil have been identified, little is known about their seasonal variation along cropping cycles. Here, we followed over a period of two years at 2-week intervals with quantitative PCR the abundance of seven N-functional genes on three neighboring fields at an operational farm in Northern Germany. The fields differed in soil texture (clay or loam) and soil management (soil conservation vs. conventional tillage). Total N (TN) was the main factor driving temporal dynamics of all seven N-functional genes, while total carbon, temperature, fertilization events and soil tillage were less important. Precipitation, and thus soil moisture, negatively affected gene abundances, and this effect was more pronounced in loam than in clay. Clear differences could be detected for the abundance of archaeal and bacterial amoA and also, though less stringent, for nirS/K but not for nosZI/nosZII . The contrasting responses of the two former suggests distinct preferences in response to different textures and tillage regimes. Overall, this study demonstrates that in cropland, the seasonal dynamics of N functional genes depends on the TN contents, which is variable in response to soil moisture, texture and tillage. The coexistence of alternative prokaryotic genes encoding for the same enzymatic reactions reflects their specific adaptations to different environmental conditions, which can result in high, but also low correlations between them. • Microbial N-functional genes quantified at 2-week intervals for 2 years in cropland. • Irrespective of tillage and soil texture N was the primary driver of gene abundance. • Precipitation reduced N-functional genes more strongly in loam as compared to clay. • Bacterial and archaeal amoA genes with distinct responses to clay/loam and tillage. • nirS and nirK with different responses to soil texture and tillage regimes.