Cropping systems with higher organic carbon promote soil microbial diversity

Food systems need to become more sustainable. There is a need to investigate the agricultural management components that address the sustainability better. Long crop rotations are suggested to be environmentally friendly, yet, little is known how soil microbial communities may be affected by long-term rotation under organic cropping with cover crops and manure and conventional cropping with different nitrogen rates. We examined the composition and diversity of soil bacterial and fungal communities in a five-field crop rotation at the beginning and end, respectively in 2013 and 2018. Our analysis revealed that bacterial and to a lesser extent fungal diversity increased by the end of the rotation in all organic treatments and in conventional treatments with low to medium nitrogen rate (20‐100 kg of nitrogen per hectare). Conventional treatment with no added nitrogen decreased bacterial and fungal diversity. Nitrogen rate of 150 kg/ha decreased only bacterial diversity, while the impact on fungal diversity was neutral. Crop rotation significantly increased the relative abundance of bacterial taxa involved in nitrification and denitrification. Of fungal functional groups, the relative abundance of pathogenic functional groups decreased and mycorrhizal groups increased during crop rotation and especially with added cover crops. Our results suggest that crop rotation may outperform cropping systems in structuring soil microbial communities.