The preceding root system drives the composition and function of the rhizosphere microbiome

Yi Zhou,Huan Liu,David R Coventry,Yayu Wang,Yanli Wei,Vadakattu V S R Gupta,Matthew D Denton,Brent N Kaiser,Andrew Merchant,Shuheng Gan,David Fuentes,Jishun Li

doi:10.1186/s13059-020-01999-0

Abstract

BackgroundThe 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.ResultsThis 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.ConclusionsThe 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.

Highlights

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
The existence of the decaying root (DR) and its physiochemical properties was the key factor evaluated for its effect in influencing the rhizosphere microbiome structure and function of the living roots compared with the non-DR control
The separation was reliant on plant type whereas under non-sterilised conditions, the plant type effect was stronger for −DR but not for +DR (Fig. 1a)

Summary

Introduction

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. The composition and function of the rhizosphere microbiome have been evaluated using reconstructed soils in controlled conditions [19,20,21] and in on-farm environments [22, 23]. Crop management practices such as tillage, residue retention and crop rotation are crucial components in the functioning of an agroecosystem, but are often neglected when studying the dynamics of rhizosphere microbiota, in particular during the establishment of rhizosphere microbial communities in early seedling growth phases in no-till or disrupted soil profiles. In view of the significant influence that the detritusphere (soil surrounding the decaying root from the previous crop) can have on soil microbial communities, it is hypothesised that early seedling rhizosphere communities would be influenced by the detritusphere microbiomes

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Discussion

Conclusion