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Type: Journal article
Title: The preceding root system drives the composition and function of the rhizosphere microbiome
Author: Zhou, Y.
Coventry, D.
Gupta, V.
Fuentes, D.
Merchant, A.
Kaiser, B.
Li, J.
Wei, Y.
Liu, H.
Wang, Y.
Gan, S.
Denton, M.D.
Citation: Genome Biology, 2020; 21(1):89-1-89-19
Publisher: Springer Nature
Issue Date: 2020
ISSN: 1474-760X
Statement of
Yi Zhou, David R. Coventry, Vadakattu V.S.R. Gupta, David Fuentes, Andrew Merchant, Brent N. Kaiser, Jishun Li, Yanli Wei, Huan Liu, Yayu Wang, Shuheng Gan, and Matthew D. Denton
Abstract: 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.
Keywords: Soil microbiome; metagenome; tillage; agricultural system; root
Rights: © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated in a credit line to the data.
DOI: 10.1186/s13059-020-01999-0
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Appears in Collections:Agriculture, Food and Wine publications
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