Substituting chemical fertilizer with organic fertilizer is an important agricultural practice that improves crop yields but also affects soil biogeochemical cycling. To explore the effects of organic fertilizer on soil properties and bacterial community structure and diversity, a long-term field experiment (2011–2017) was conducted in a wheat–rice rotation system with four treatments: control (CK, no fertilizer), chemical fertilizer only (NPK), substitution of 50% of chemical nitrogen (N) fertilizer with organic fertilizer (NPKM), and substitution of 100% of chemical N fertilizer with organic fertilizer (OM). Results showed that, crop yields (wheat and rice) from 2011–2017 were highest in NPKM. Combined with α-diversity analysis, long-term application of NPK led to a decrease in soil bacterial diversity. However, soil bacterial community richness (Ace and Chao1 indices) increased in NPKM in the wheat season, as well as in OM in the rice season. Compared with NPK, organic fertilizer inputs (NPKM and OM) increased microbial biomass carbon and abundance of dominant bacteria (Acidobacteria, Anaerolineaceae, and Nitrospira) in both crop seasons. In NPK, relative abundance of Rhodanobacter increased significantly in the wheat season because of low soil pH. Bacterial community composition and structure were similar between NPKM and OM in the wheat season. Redundancy analysis further found that soil pH (R² = 0.735, P = 0.013) co-varied with the bacterial community structure in the wheat season. In the rice season, relative abundance of Nitrospira increased significantly in NPKM, which could generate large amounts of nitrate nitrogen (NO₃⁻-N), and then increase risks of N₂O emissions and NO₃⁻-N leaching in paddies. Overall, partial substitution of chemical fertilizer with organic fertilizer was optimal to increase crop yields and recover soil bacterial diversity in the wheat–rice rotation, and greater substitution with organic fertilizer in combination with chemical fertilizer is recommended only for rice seasons.

以有机肥替代化肥是一种重要的农业实践，可以提高作物产量，但也会影响土壤生物地球化学循环。为了探索有机肥对土壤特性和细菌群落结构和多样性的影响，在小麦-水稻轮作系统中进行了一项长期田间试验（2011-2017），四个处理：对照（​​CK，不施肥），化学处理仅施肥（NPK），化肥（N）50%替代有机肥（NPKM），化氮（N）100%替代有机肥（OM）。结果表明，2011-2017 年作物产量（小麦和水稻）在 NPKM 中最高。结合α-多样性分析，长期施用NPK导致土壤细菌多样性下降。然而，小麦季节 NPKM 和水稻季节 OM 土壤细菌群落丰富度（Ace 和 Chao1 指数）增加。与 NPK 相比，有机肥投入（NPKM 和 OM）增加了微生物生物量碳和优势细菌的丰度（酸杆菌、厌氧菌科和硝化螺菌）在两个作物季节。在 NPK 中，由于土壤 pH 值低，小麦季节罗丹杆菌的相对丰度显着增加。小麦季节 NPKM 和 OM 之间的细菌群落组成和结构相似。冗余分析进一步发现， 小麦季节土壤pH值（R ² = 0.735，P = 0.013）与细菌群落结构共变。在稻季，NPKM中Nitrospira的相对丰度显着增加，可产生大量硝态氮（NO ₃ ^- -N），进而增加N ₂ O排放和NO的风险₃ ^- -N 在稻田中浸出。总体而言，以有机肥部分替代化肥是提高作物产量和恢复小麦 - 水稻轮作土壤细菌多样性的最佳选择，并且仅在水稻季节建议更多地使用有机肥与化肥结合使用。