Background The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. Results This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65–87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3–24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. Conclusions The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

中文翻译：

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前面的根系统驱动根际微生物组的组成和功能


背景土壤环境负责维持大多数陆地植物的生命，但令人惊讶的是，我们对土壤中不同微生物群落所发挥的重要功能知之甚少。栖息在腐烂根系通道（碎屑圈）中的土壤微生物可能对植物生长和健康至关重要，因为这些通道是新根生长的首选位置。了解碎屑圈的微生物宏基因组，以及它如何响应作物轮作和土壤耕作等农业管理，对于提高全球粮食生产至关重要。结果本研究根据耕作土壤中的活腐烂根际生态位建立了深入的土壤微生物基因目录。碎屑球微生物组比植物类型更大程度地调节根际微生物组的组成和功能：小麦和鹰嘴豆的根际微生物组在存在腐烂根 (DR) 系统的情况下是同质的（65-87% 相似性），但它们是异质的（3 –24% 相似性），其中 DR 因耕作而中断。当根际和碎屑圈的微生物群在 DR 存在下相互作用时，根际微生物群对植物根系分泌物进行显着降解，并且与膜转运蛋白、碳水化合物和氨基酸代谢相关的基因被富集。结论该研究描述了高质量土壤微生物宏基因组的多样性和功能能力。结果证明了碎屑球微生物组在确定发育中的根系统的宏基因组中的贡献。通过土壤管理改变根部微生物功能最终可以控制植物健康、生产力和粮食安全。