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

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.

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization

“…We have seen that Kaistobacter was significantly increased in bulk soil, whereas Flavobacterium, Rhizobium or Devosia were overrepresented in the rhizosphere, and Sphingomonas in rhizosphere and root endosphere. Kaistobacter has been described as one of the most abundant bacterial genera in soil globally (Delgado-Vaquerizo et al, 2018), including those from wheat crops (Schlatter et al, 2019;Zhou et al, 2020). It is not surprising the abundance of Rhizobium and Devosia close to the root system as they are rhizobacteria with a symbiotic lifestyle with plants (Zhou et al, 2020).…”

“…Kaistobacter has been described as one of the most abundant bacterial genera in soil globally (Delgado-Vaquerizo et al, 2018), including those from wheat crops (Schlatter et al, 2019;Zhou et al, 2020). It is not surprising the abundance of Rhizobium and Devosia close to the root system as they are rhizobacteria with a symbiotic lifestyle with plants (Zhou et al, 2020). In addition, it has been reported the use of antagonistic Sphingomonas for the biological control of wheat pathogens (Wachowska et al, 2013).…”

Mechanisms in plant growth‐promoting rhizobacteria that enhance legume–rhizobial symbioses

“…The rhizosphere is an important soil chemical and ecological zone close to the roots of plants where substantial plant–microbe interactions occur (Zhou et al . 2020). Some of the bacteria in the rhizosphere are able to promote plant growth and protect plants from biotic and abiotic stresses are known as plant growth‐promoting rhizobacteria (PGPR; Berg 2009).…”

Phospholipid signaling pathway in Capsicum chinense suspension cells as a key response to consortium infection

“…The roots of plants establish a relationship with the microorganisms present in the rhizosphere. These interactions can involve either beneficial or pathogenic microorganisms [ 24 , 25 ]. Both types of interactions trigger a complex response that determine the success of pathogenic proliferation and development in the plant.…”