Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome

Abstract

The roots of plants have the ability to influence its surrounding microbiology, the so-called rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals. Here we report how these phytochemicals could modulate the microbial composition of a soil in the absence of the plant. For this purpose, root exudates of Arabidopsis were collected and fractionated to obtain natural blends of phytochemicals at various relative concentrations that were characterized by GC-MS and applied repeatedly to a soil. Soil bacterial changes were monitored by amplifying and pyrosequencing the 16 S ribosomal small subunit region. Our analyses reveal that one phytochemical can culture different operational taxonomic units (OTUs), mixtures of phytochemicals synergistically culture groups of OTUs, and the same phytochemical can act as a stimulator or deterrent to different groups of OTUs. Furthermore, phenolic-related compounds showed positive correlation with a higher number of unique OTUs compared with other groups of compounds (i.e. sugars, sugar alcohols, and amino acids). For instance, salicylic acid showed positive correlations with species of Corynebacterineae, Pseudonocardineae and Streptomycineae, and GABA correlated with species of Sphingomonas, Methylobacterium, Frankineae, Variovorax, Micromonosporineae, and Skermanella. These results imply that phenolic compounds act as specific substrates or signaling molecules for a large group of microbial species in the soil.

FIGURE 1.

Soil microbiome sequencing data of treatments and controls analyzed by principal component analyses at phyla levels (A) and genus levels (B). Whole, whole exudates; Chloro, CHCl₃ fraction; EtoAc, ethyl acetate fraction; Water, water fraction; Nothing, nothing added in the soil; Water ctrl, water control; EtoAc ctrl, ethyl acetate control; CHCl₃ Ctrl, chloroform control.

FIGURE 2.

Cluster analysis of the soil microbiome sequencing data of controls and treatments by Ward method. Whole, whole exudates; Chloro, CHCl₃ fraction; EtoAc, ethyl acetate fraction; Water, water fraction; Nothing, nothing added in the soil; Water ctrl, water control; EtoAc ctrl, ethyl acetate control; CHCl₃ Ctrl, chloroform control.

FIGURE 3.

Relative abundance (%) of the major bacterial phyla present in the treatments and controls revealed by pyrosequencing.

FIGURE 4.

Flow diagram indicating the shared and unique OTUs present in controls and treatments. Controls (A) and treatments (B) are shown. Overall, 138 OTUs were shared by controls, and 11 OTUs were shared by treatments. The number of OTUs unique to a particular control or treatment is represented inside the shaded box, and the number of OTUs shared between the controls and treatments is represented in the intersections.

FIGURE 5.

Taxonomic to phenotypic mapping based on the biotic habitat. Graph illustrates the number of sequence reads present in the controls and treatments. Symbiotic bacteria (A) and free-living bacteria (B) are shown. The bars with different letters are significantly different (p value < 0.05) from one another.

FIGURE 6.

Taxonomic to phenotypic mapping based on the metabolism of specific microbial groups. The graph illustrates the number of sequence reads present in the controls and treatments. Carbon fixation (A), nitrite reducing (B), and atrazine degradation (C) are shown. The bars with different letters are significantly different (p value < 0.05) from one another.