Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome

Abstract

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialised 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 colonised more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonisation 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. ImportanceStreptomyces bacteria are ubiquitous in soil but their role as rhizobacteria is less well studied. Our recent work demonstrated that streptomycetes isolated from A. thaliana roots can promote growth and protect against disease across plant species and that plant growth hormones can modulate the production of bioactive specialised metabolites by these strains. Here we used 13CO2 DNA stable isotope probing to identify which bacteria feed on plant metabolites in the A. thaliana rhizosphere and, for the first time, in the endosphere. We found that Streptomyces species are outcompeted for these metabolites by faster growing proteobacteria and instead likely subsist on more complex organic material such as cellulose derived from plant cell material that is shed from the roots. This work thus reveals the "winners and losers" in the battle between soil bacteria for plant metabolites and could inform the development of methods to apply streptomycetes as plant growth-promoting agents.