Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots

Abstract

Several bacterial strains of the Pseudomonas genus provide plant growth stimulation, plant protection against pests or bioremediation. Among these bacteria, P. fluorescens Pf29Arp reduces the severity of take-all, a disease caused by the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In this study, we obtained a draft genome of Pf29Arp and subsequent comparative genomic analyses have revealed that this bacterial strain is closely related to strains of the 'P. brassicacearum-like' subgroup including P. brassicacearum ssp. brassicacearum NFM421 and P. fluorescens F113. Despite an overall chromosomal organization similar to these strains, a number of features including antibiotic synthesis gene clusters from secondary metabolism are not found in the Pf29Arp genome. But Pf29Arp possesses different protein secretion systems including type III (T3SS) and type VI (T6SS) secretion systems. Pf29Arp is the first Pseudomonas sp. strain described with four T6SS clusters (cluster I, II, III and IV). In addition, some protein-coding genes involved in the assembly of these secretion systems are basally expressed during Pf29Arp colonization of healthy wheat roots and display different expression patterns on necrotized roots caused by Ggt. These data suggest a role of T3SS and T6SS in the Pf29Arp adaptation to different root environments.

Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans

“…The Hrp1 family is the most common T3SS found among P. fluorescens strains (46)(47)(48)(49)(50). The Hrp (hypersensitivity response and pathogenicity) system triggers the hypersensitivity defense response in resistant plants, while leading to disease in susceptible plants, and was first described for P. syringae (148).…”

“…The activity and functionality of the Hrp1 system have been worked out for only a couple of the strains in which it has been found. The Hrp1 T3SS of P. fluorescens Pf29Arp, a strain known for its ability to reduce the severity of wheat take-all, shows activity during the colonization of wheat rhizospheres (46). The homologous Hrp1 T3SS in strain SBW25 is induced during sugar beet rhizosphere colonization (154) and can induce a hypersensitive response in tobacco (47,155).…”

“…P. fluorescens has been studied most widely as an environmental microbe, most notably for its role in promoting plant health via a number of encoded antimicrobial mechanisms (25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38). However, P. fluorescens also possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts, including production of bioactive secondary metabolites (26-30, 33, 39-42), siderophores (43)(44)(45), and a type III secretion system (46)(47)(48)(49)(50)(51), the ability to form biofilms (20,(52)(53)(54)(55)(56), and the plasticity of some strains to adapt to growth at higher temperature (53,(57)(58)(59).…”

Genetics and Functional Genomics of the Pseudomonas fluorescens Group

“…A simpler and more accessible procedure is to generate a tree using housekeeping genes. Figure 5.1 shows a phylogenetic tree which was generated from concatenation of four housekeeping genes (rpoD, gltA, Marchi et al (2013) gyrB, and gapA). The topology is consistent with that generated by Marchi et al (2013) using the core genome (Marchi et al 2013), indicating that new isolates can be placed into the phylogeny based on housekeeping genes with a relatively high degree of confidence.…”

“…Figure 5.1 shows a phylogenetic tree which was generated from concatenation of four housekeeping genes (rpoD, gltA, Marchi et al (2013) gyrB, and gapA). The topology is consistent with that generated by Marchi et al (2013) using the core genome (Marchi et al 2013), indicating that new isolates can be placed into the phylogeny based on housekeeping genes with a relatively high degree of confidence. In this chapter, we will discuss multiple species within the ''Pseudomonas fluorescens complex'' including the recently renamed P. protegens Pf-5 and members of the closely related P. brassicacearum, P. synxantha, and P. chlororaphis.…”