Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species

Abstract

Streptomyces bacteria are ubiquitous in soils and are well known for producing secondary metabolites, including antimicrobials. Increasingly, they are being isolated from plant roots, and several studies have shown they are specifically recruited to the rhizosphere and the endosphere of the model plant Arabidopsis thaliana Here, we test the hypothesis that Streptomyces bacteria have a beneficial effect on A. thaliana growth and could potentially be used as plant probiotics. To do this, we selectively isolated streptomycetes from surface-washed A. thaliana roots and generated high-quality genome sequences for five strains, which we named L2, M2, M3, N1, and N2. Reinfection of A. thaliana plants with L2, M2, and M3 significantly increased plant biomass individually and in combination, whereas N1 and N2 had a negative effect on plant growth, likely due to their production of polyene natural products which can bind to phytosterols and reduce plant growth. N2 exhibits broad-spectrum antimicrobial activity and makes filipin-like polyenes, including 14-hydroxyisochainin which inhibits the take-all fungus, Gaeumannomyces graminis var. tritici N2 antifungal activity as a whole was upregulated ∼2-fold in response to indole-3-acetic acid (IAA), suggesting a possible role during competition in the rhizosphere. Furthermore, coating wheat seeds with N2 spores protected wheat seedlings against take-all disease. We conclude that at least some soil-dwelling streptomycetes confer growth-promoting benefits on A. thaliana, while others might be exploited to protect crops against disease.IMPORTANCE We must reduce reliance on agrochemicals, and there is increasing interest in using bacterial strains to promote plant growth and protect against disease. Our study follows up reports that Arabidopsis thaliana specifically recruits Streptomyces bacteria to its roots. We test the hypotheses that they offer benefits to their A. thaliana hosts and that strains isolated from these plants might be used as probiotics. We isolated Streptomyces strains from A. thaliana roots and genome sequenced five phylogenetically distinct strains. Genome mining and bioassays indicated that all five have plant growth-promoting properties, including production of indole-3-acetic acid (IAA), siderophores, and aminocyclopropane-1-carboxylate (ACC) deaminase. Three strains significantly increased A. thaliana growth in vitro and in combination in soil. Another produces potent filipin-like antifungals and protected germinating wheat seeds against the fungal pathogen Gaeumannomyces graminis var. tritici (wheat take-all fungus). We conclude that introducing Streptomyces strains into the root microbiome provides significant benefits to plants.

Keywords: Arabidopsis; Streptomyces; plant-microbe interactions; wheat.

FIG 1

Confocal laser scanning microscopy images of A. thaliana rhizoplane colonization by eGFP-tagged Streptomyces strains 3 days after inoculation. (A and B) A. thaliana roots (red) colonized by eGFP-tagged Streptomyces coelicolor M145 (green), which is a known root endophyte and was used as a control (67). (C and D) A. thaliana roots (red) colonized by eGFP-tagged Streptomyces strain M3 which was isolated in this study (green).

FIG 2

Violin plots showing the biomass of Arabidopsis thaliana plants grown on agar plates following inoculation with sequenced Streptomyces isolates. Biomass (dry weight in grams) was measured 16 days after inoculation. Sterile plants were grown as a control. N = 16 plants per treatment. Box plots show the locations of the medians and quartiles, with whiskers reaching to 1.5 times the interquartile range. ♦, mean values. The width of the outer shaded area illustrates the proportion of the data located there (the kernel probability density). Groups labeled with different lowercase letters have a significantly different plant biomass (P < 0.05 in Tukey’s HSD tests).

FIG 3

Violin plots demonstrating the total dry weight of A. thaliana plants grown in Levington’s F2 compost from seeds inoculated with spores of Actinovate, L2, M2, M3, N1, and N2 or a mixture of L2, M2, and M3 Streptomyces spores. Dry weight is shown in grams. Sterile seeds were grown as a control. N = 8 replicate plants per treatment. Box plots show the locations of the medians and quartiles, with whiskers reaching to 1.5 times the interquartile range. ♦, mean values. The width of the outer shaded area illustrates the proportion of data located there (the kernel probability density). Groups labeled with different lowercase letters differ significantly in plant biomass (P < 0.05 in Tukey’s HSD tests).

FIG 4

(A) Three biological replicates of strain N2 (center) growing on minimal medium agar that has been overlaid with soft LB agar inoculated with Candida albicans. (B) Same as for panel A but the minimal medium agar contains 0.1 mg ml⁻¹ of indole-3-acetic acid. This experiment was repeated 4 times (each time with 3 replicates), with consistent results. Bars, 2 cm.

FIG 5

Structures of filipin III, pentamycin, and 14-hydroxyisochainin.

FIG 6

Inhibition of G. graminis var. tritici in wheat seedlings. Germinating wheat seeds (W) are either sterile (A) or inoculated with a spore preparation of Streptomyces isolate N2 (B), growing next to a plug of G. graminis var. tritici, the take-all fungus (P). G. graminis is prevented from growing toward inoculated seeds, as demonstrated by the zone of inhibition (marked with arrowheads). Bars, 5 mm.

FIG 7

(Top) The effect of Streptomyces strain N2 on wheat plant infection severity by G. graminis var. tritici. Infections were scored after 3 weeks of growth. N2 control, seeds coated in N2 spores/no G. graminis; sterile control, sterile seeds/no G. graminis; N2/fungus, seeds coated in N2 spores grown in the presence of G. graminis; sterile seeds/fungus, sterile seeds grown in the presence of G. graminis. N = 25 plants per treatment group; error bars represent standard errors. Wheat plants were grown from sterile seeds in the presence of G. graminis var. tritici (A), from seeds inoculated with N2 spores, in the presence of G. graminis var. tritici (B), from sterile seeds, no G. graminis var. tritici (C), or from seeds coated with N2 spores, no G. graminis var. tritici (D). Bars, 2 cm.