Abstract
BackgroundPlant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.ResultsThe genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.ConclusionsThe genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1632-z) contains supplementary material, which is available to authorized users.
Highlights
Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR)
General genome characteristics Sequencing of the genomes of WCS358 from the P. putida group, and WCS374 and WCS417 from the P. fluorescens group was carried out at the Beijing Genome Institute (Beijing, China)
We identified 11 putative effectors for WCS417 and 15 putative effectors for WCS374 (Additional file 8: Table S3), whereas not a single putative effector could be identified in WCS358
Summary
Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). Among the group of plant growth-promoting rhizobacteria (PGPR), the genus Pseudomonas is strongly represented This genus comprises over one hundred species of aerobic bacteria that belong to the γ subclass of the Proteobacteria [12]. Some Pseudomonas spp. are plant pathogenic, many have been found to protect plants by antagonizing soil-borne pathogens through competition for nutrients, production of antimicrobial compounds, or by eliciting a systemic immune response that is effective against a broad spectrum of pathogens, called induced systemic resistance (ISR) [11, 13]. Mutualistic root-colonizing Pseudomonas spp. emerged as important players in disease-suppressive soils [7, 14,15,16], and served as model PGPR in research toward understanding how non-symbiotic root-associated bacteria protect plants against pests and diseases [11, 17]
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