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.

粮食系统需要变得更加可持续。有必要调查更好地解决可持续性问题的农业管理组成部分。长期轮作被认为是对环境友好的，但是，在覆盖作物和肥料的有机作物以及具有不同氮肥率的常规作物下，长期轮作如何影响土壤微生物群落尚知之甚少。我们分别在 2013 年和 2018 年开始和结束时检查了五场作物轮作中土壤细菌和真菌群落的组成和多样性。我们的分析显示细菌和真菌多样性在轮作结束时增加在所有有机处理和低至中等氮肥量（每公顷 20-100 kg 氮）的常规处理中。不添加氮的常规处理降低了细菌和真菌的多样性。150 公斤/公顷的氮肥只降低了细菌多样性，而对真菌多样性的影响是中性的。轮作显着增加了参与硝化和反硝化的细菌类群的相对丰度。在真菌功能组中，在轮作期间，尤其是在增加覆盖作物的情况下，致病功能组的相对丰度下降，而菌根组的相对丰度增加。我们的结果表明，在构建土壤微生物群落方面，轮作可能优于种植系统。轮作显着增加了参与硝化和反硝化的细菌类群的相对丰度。在真菌功能组中，在轮作期间，尤其是在增加覆盖作物的情况下，致病功能组的相对丰度下降，而菌根组的相对丰度增加。我们的结果表明，在构建土壤微生物群落方面，轮作可能优于种植系统。轮作显着增加了参与硝化和反硝化的细菌类群的相对丰度。在真菌功能组中，在轮作期间，尤其是在增加覆盖作物的情况下，致病功能组的相对丰度下降，而菌根组的相对丰度增加。我们的结果表明，在构建土壤微生物群落方面，轮作可能优于种植系统。