School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.
China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA, 5064, Australia.
Genome Biol. 2020 Apr 6;21(1):89. doi: 10.1186/s13059-020-01999-0.
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.
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.
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.
土壤环境是维持大多数陆生植物生命的基础，但我们对土壤中多样化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（即碎屑区）中的土壤微生物，很可能对植物的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。了解碎屑区的微生物宏基因组及其对农业管理（如轮作和土壤耕作）的响应，对于提高全球粮食产量至关重要。
本研究基于作物土壤中活-死根际生态位，建立了一个深入的土壤微生物基因目录。碎屑区微生物组比植物类型更能调节根际微生物组的组成和功能：在存在腐烂根系（DR）系统的情况下，小麦和鹰嘴豆的根际微生物组具有同源性（65-87%的相似度），但在耕作破坏 DR 时则具有异质性（3-24%的相似度）。当根际和碎屑区的微生物组在 DR 存在下相互作用时，根际微生物组会显著降解植物根系分泌物，并且与膜转运蛋白、碳水化合物和氨基酸代谢相关的基因得到富集。
本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。研究结果表明，碎屑区微生物组在决定发育中根系的宏基因组方面发挥了作用。通过土壤管理对根微生物功能的改变最终可以控制植物的健康、生产力和粮食安全。
