The aim of this study was to understand how the application of decomposed stubble return (DSR), a type of bio-organic fertilization, affects soil microbial communities under crop rotation. The changes in microbial composition and diversity related to DSR were investigated based on metagenomic sequencing and comparative analysis of two groups of soil samples after a 3-year tomato-pepper-papaya rotation: the DSR and no-DSR (i.e., without DSR) groups, with the soils before crop rotation as the control group. Inter-group comparisons of the crop performance (growth and yield) and physicochemical soil properties (pH value, nutrient elements, and heavy metals) were also conducted to reveal the effects of DSR application on the soil. The relative abundance of bacteria was higher than 90% in all soil samples. Proteobacteria and Actinobacteria in the DSR group and Proteobacteria and Firmicutes in the no-DSR group, whereas Acidobacteria and Proteobacteria in the control, were the two most abundant phyla. The abundance of Proteobacteria decreased, whereas that of Actinobacteria increased, in the DSR-amended soil compared to the no-DSR soil. At genus level, Acidobacterium dominated in the control and genera Pseudomonas, Burkholderia, and Bacillus in the no-DSR group, while Burkholderia, Pseudomonas, and Bacillus in the DSR-amended soil comprised the majority of their microbiomes. The DSR soil had higher microbial diversity and relative abundance of Ascomycota fungi than the no-DSR group after the crop rotation. Along with higher diversity of microbial community, more favorable soil pH, better crop growth, higher crop yields, higher abundance of soil nutrient elements, and lower accumulation of heavy metals in the soil were found in the DSR group compared to the no-DSR one. Furthermore, the DSR soil had more similarities with the control than with the No-DSR soil, in aspects of microbial composition and microbe-derived potential gene functions. It was indicated that decomposed stubble return may improve soil conditions or prevent them from degradation incurred by long-term crop cultivation. It was suggested that the application of the compost derived from fermented post-harvest plant residue may be a general strategy for developing more sustainable agricultural systems.

本研究的目的是了解腐熟茬还田（DSR）（一种生物有机肥）的应用如何影响轮作下的土壤微生物群落。通过宏基因组测序和对番茄-辣椒-木瓜轮作三年后两组土壤样品的比较分析，研究了与 DSR 相关的微生物组成和多样性的变化：DSR 组和无 DSR 组，以轮作前土壤为对照组。还对作物性能（生长和产量）和土壤理化性质（pH 值、营养元素和重金属）进行了组间比较，以揭示 DSR 施用对土壤的影响。所有土壤样品中细菌相对丰度均高于90%。DSR 组中的变形菌门和放线菌门以及无 DSR 组中的变形菌门和厚壁菌门以及对照组中的酸杆菌门和变形菌门是两个最丰富的门。与无 DSR 土壤相比，DSR 改良土壤中变形菌丰度下降，而放线菌丰度增加。在属水平上，酸杆菌在对照和无 DSR 组中的假单胞菌属、伯克霍尔德氏菌属和芽孢杆菌属中占主导地位，而 DSR 修正土壤中的伯克霍尔德氏菌属、假单胞菌属和芽孢杆菌属构成了其大部分微生物组。轮作后，DSR 土壤比无 DSR 组具有更高的微生物多样性和子囊菌门真菌的相对丰度。与无 DSR 组相比，DSR 组微生物群落多样性更高，土壤 pH 值更有利，作物生长更好，作物产量更高，土壤营养元素丰度更高，土壤中重金属积累更低。此外，DSR土壤在微生物组成和微生物来源的潜在基因功能方面与对照土壤比No-DSR土壤有更多相似性。研究表明，腐熟的残茬还田可以改善土壤状况或防止长期作物种植造成的土壤退化。有人建议，使用来自发酵的收获后植物残渣的堆肥可能是发展更可持续农业系统的总体策略。