Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities

Aims Soil microbiomes and their interactions with crop plants are important drivers of agricultural health and productivity. Our objective was to examine short-term responses of soil microbiota to agricultural management (i.e. cover cropping and nitrogen fertilization). Methods Following three years of cropping, soil samples were collected from replicated field plots at two southern Minnesota field sites (Lamberton and Waseca). We used amplicon-based gene sequencing (ITS2 and 16S rRNA V4) to investigate short-term soil fungal and bacterial community responses to cover crops and urea-nitrogen (N) fertilization (0, 80, 100, and 120% of recommended rates) in a corn (Zea mays)-soybean (Glycine max) cropping system planted with and without cover crops. Results We found that rates of N-fertilizer applied, more than cover crops, significantly impacted soil chemical properties at both sites. Different cropping or N fertilization treatments did not lead to strong differences in fungal or bacterial alpha (local) diversity. At both sites, cover crop was a significant predictor of fungal community compositions and specific fungal and bacterial taxa were significantly impacted by cover crops. While, N fertilization was not a strong predictor of community compositions, urea-N additions, at any rate, resulted in changes in the relative abundances of the fungal phyla Glomeromycota in addition to a number of bacterial phyla. Conclusions Our findings suggest that after three years of cropping, fungal communities respond to cover crops, while bacterial community responses may depend on soil chemical conditions.