Abstract Soil microbiomes play an integral role in agricultural production systems. Understanding of the complex microbial community structure and responses to conventional compared to organic cropping systems is crucial for sustainable production and ecosystems health. This study investigated soil microbial community structure responses based on a four year long field experiment. Bacterial communities characterizing conventional and organic cropping systems were evaluated using Illumina MiSeq high-throughput sequencing targeting the V4-V5 variable region of the 16S rRNA gene. Soil bacterial community structure showed a cropping system dependant distribution, with nitrogen cycling taxa (Bacillus, Niastella, Kribbella, and Beijerinckia) dominant in conventional cropping systems, while carbon cycling taxa (Dokdonella, Caulobacter, Mathylibium, Pedobacter, Cellulomonas and Chthoniobacter and Sorangium) were abundant in organic cropping systems. Functional prediction of the bacterial biomes showed conventional cropping systems to harbour a community adapted to carbon-limited environments, with organic cropping systems dominated by those involved in the degradation of complex organic compounds. These findings suggest the existence of niche specific communities and functional specialization between cropping systems with potential use in soil management through selective promotion of organisms beneficial to soil health.

中文翻译：

---

传统和有机种植系统土壤的细菌群落动态和功能分析

摘要 土壤微生物组在农业生产系统中发挥着不可或缺的作用。与有机种植系统相比，了解复杂的微生物群落结构和对传统种植系统的反应对于可持续生产和生态系统健康至关重要。本研究基于为期四年的田间试验调查了土壤微生物群落结构响应。使用针对 16S rRNA 基因 V4-V5 可变区的 Illumina MiSeq 高通量测序来评估表征传统和有机种植系统的细菌群落。土壤细菌群落结构呈现种植系统依赖性分布，氮循环类群（芽孢杆菌、尼亚斯特拉菌、Kribbella 和 Beijerinckia）在常规种植系统中占主导地位，而碳循环类群（Dokdonella、Caulobacter、Mathylibium、Pedobacter、Cellulomonas、Chthoniobacter 和 Sorangium）在有机种植系统中含量丰富。细菌生物群落的功能预测表明，传统的种植系统包含一个适应碳限制环境的群落，有机种植系统由参与复杂有机化合物降解的系统主导。这些发现表明，通过选择性促进有益于土壤健康的生物体，在土壤管理中具有潜在用途的种植系统之间存在生态位特定群落和功能专业化。以参与复杂有机化合物降解的有机种植系统为主。这些发现表明，通过选择性促进有益于土壤健康的生物体，在土壤管理中具有潜在用途的种植系统之间存在生态位特定群落和功能专业化。以参与复杂有机化合物降解的有机种植系统为主。这些发现表明，通过选择性促进有益于土壤健康的生物体，在土壤管理中具有潜在用途的种植系统之间存在生态位特定群落和功能专业化。