Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome

Abstract

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonized more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonization by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions

“…On the contrary, binary plant-bacteria interactions (positive, neutral, negative) were better predictors of SynCom’s effects on plants. Using the 13 C DNA Stable Isotope Probing technique, Worsley et al [ 203 ] demonstrated that several Pseudomonadota genera incorporated 13 C from PRE components when Arabidopsis is grown on compost.…”

Endophytism: A Multidimensional Approach to Plant–Prokaryotic Microbe Interaction

“… Saleh et al (2020) reported that citric acid, a root exudate of Brachypodium distachyon , acting as a strong chemoattractant for PGP bacterial strains. The hypothesis of Streptomyces species being attracted by the root exudates was tested and confirmed by Worsley et al (2021) on the root exudates of Arabidopsis thaliana . The study demonstrated that phytohormone, salicylate, plays a specific role in this process.…”

Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum

“…Many of the biomarkers, including for Bacillus, Pseudomonas, Agrobacterium, Gemmatimonas, Enterobacter, Streptomyces, Devosia, Ensifer, Acinetobacter, Halomonas, Brevundimonas, Mesorhizobium, and Burkholderia, are known as beneficial microbes for plants, and these microbes may help to maintain plant hormone balance, control root development, facilitate nutrition acquisition, and prevent disease in the plant host [42,44,[51][52][53][54][55]. Several studies have reported that Streptomycetes are abundant inside of the roots of Arabidopsis thaliana [56] where they can have beneficial effects on growth [57] or protect plants against biotic and abiotic stressors [58,59].…”