The application of organic matter to agricultural land is an efficient way to maintain soil eco-sustainability through the mediation of the soil-dwelling microbiome. Despite their important role in soil health, trait-based changes within cross-kingdom microbial communities following organic fertilization in soils are still poorly characterized. Here, shotgun metagenomic sequencing was used to examine microbial taxonomic and functional composition when subjected to a fertilization gradient, in which increasing amounts of cow manure have been continuously applied to paddy lands over 8 years. Organic fertilization did not have significant effects on the richness and diversity of soil microbial communities (bacteria, archaea, or fungi), nor the overall archaeal or fungal community compositions. However, bacterial communities were highly responsive to the fertilization gradient, and a unidirectional and progressive shift was observed. Notably, over 95% of bacterial taxa showing significant changes in relative abundances could be classified as copiotrophic taxa, such as those assigned to the Proteobacteria and Actinobacteria; in contrast, those in non-fertilized soils were mostly assigned to Acidobacteria, which is an oligotrophic group. Coupled with these changes, indices such as the decreased ratios of unclassified bacterial taxa to the total taxa with fertilization provided both direct and indirect lines of evidence for shifts towards a higher proportion of microbes with a copiotrophic lifestyle in fertilized soils compared with controls. Besides, the relative abundances of functional genes responsible for nutrient cycles (e.g., nitrate and sulfur reduction) as well as the degradation of complex organic compounds (e.g., lignin) were generally enriched with fertilization compared with the controls, implying a potential for preferentially enhanced nutrient biogeochemical processes with the higher proportion of copiotrophic microbes in fertilized soils. The present work helps to identify trait-based shifts in cross-kingdom soil microbial communities under organic fertilization, for the better evaluation of sustainable eco-agricultural management from a microbial community viewpoint.

有机质在农田中的应用是通过土壤微生物群落的调节来维持土壤生态可持续性的有效方式。尽管它们在土壤健康中发挥着重要作用，但在土壤中有机施肥后跨界微生物群落内基于性状的变化仍然没有得到很好的表征。在这里，使用鸟枪宏基因组测序来检查在施肥梯度下微生物分类和功能组成，其中越来越多的牛粪已连续应用于稻田超过 8 年。有机施肥对土壤微生物群落（细菌、古细菌或真菌）的丰富度和多样性没有显着影响，对整个古细菌或真菌群落组成也没有显着影响。然而，细菌群落对受精梯度高度敏感，并观察到单向和渐进的变化。值得注意的是，超过 95% 的细菌分类群显示出相对丰度的显着变化，可以归类为营养型分类群，例如分配给变形菌和放线菌；相比之下，未施肥土壤中的那些大多属于酸杆菌，这是一个寡营养组。与这些变化相结合，诸如未分类细菌分类群与施肥总分类群的比率降低等指标提供了直接和间接证据，表明与对照相比，在受精土壤中，具有营养生活方式的微生物比例更高。此外，与对照相比，负责营养循环（例如硝酸盐和硫还原）以及复杂有机化合物（例如木质素）降解的功能基因的相对丰度通常在施肥中富集，这意味着有可能优先增强养分生物地球化学过程与施肥土壤中营养微生物的比例较高。