| Pseudomonas sp. M18was first isolated from sweet melon rhizosphere in Shanghaisuburb in1996, and has effective biocontrol ability with highly yield ofphenazine-1-carboxylic acid and pyoluteorin. Shengqin antibiotic produced by the strainM18has been applied in Chinese plant protection for helping to ensure the food safety ofChina. Previous works from our group found that the genetic background of strain M18ismost close to Pseudomonas aeruginosa, but also with several unique phenotype and generegulation pattern. Therefore, it is important to clarify the genetic composition thebiocontrol strain Pseudomoans sp. M18.Through the prospects of genome, phenotype, transcriptome and function of genomicisland, we analyzed the genomic features of strain M18, the modification of transcriptomein response to the environmental stress and the function of specific genomic island (GI), toexplore the reasons of the excellent biocontrol ability and unique genome structure of thestrain M18. The results are as follows:Firstly, the complete genome of strain M18was sequenced using next generationsequencing technology. The M18genome is composed of a single chromosome of6,327,754bp containing5684coding genes and80RNA genes. Based on the higher than90%of genome similarity with the available genomes of P. aeruginosa, the strain M18isnow designated as Pseudomonas aeruginosa strain M18. Compared with other P.aeruginosa strains, the fewest number (3) of insertion sequences and the most number (3) of clustered regularly interspaced short palindromic repeats in M18genome maycontribute to the relative genome stability. Furthermore, the accessory genome of strainM18including two novel prophages and five specific non-phage islands were identified. Itcontains genes responsible for restriction-modification systems, pyoluteorin biosynthesis,glycosylation modification and environmental substance degradation. The M18genomealso carries biosynthesis gene clusters of five types of biocontrol related secondarymetabolites.Secondly, comparing the sequence of virulence gene and antibiotic resistance gene inP. aeruginosa M18and its close related hyper virulence strain LESB58, we found that thedifference in several virulence genes between two strains, but less difference in theantibiotic resistance genes located in core genome between two strains. After competitiveactivity in mouse lung model and MIC tests, we found that the strain M18is moresusceptible to several antimicrobial agents and easier to be erased in a mouse acute lunginfection model than the strain LESB58. The results suggested that environmental selectivepressure has a huge influence on the genotype and phenotype of different P. aeruginosastrains.Thirdly, using customer-desigened DNA chip technology, this study measured thetranscriptome modifactions of rhizosphere strain M18and model clinical isolate PAO1atdifferent typical niche temperatures (28℃for rhizosphere,37℃for human body). Thecomparative results showed that the transcriptome at two typical temperatures showed thesignificant temperature-dependent differences compared with that of the genome structure.The specific induced genes at non-originating growth temperature of the each strain areevidently more than those of the induced genes at originating growth temperature.Furthermore, we found that22genes up-regulated at28°C in three GIs and one prophagebut none at37°C of rhizosphere strain M18, suggesting that the expression of accessorygenome is important in environmental adaption of bacteria. Fourthly, rhizosphere originated P. aeruginosa strain M18carries two full subunitrestriction and modification system located in two specific genomic island MGI-I andMGI-II. But, there is no complete RM system in close related strain. Therefore, this studyfirstly demonstrated that the two GI are newly introduced in M18genome. Then, after geneknock out experiment, the results showed that RM system can restrict exogenous DNAentering host cell via transformation and conjunction to prevent the foreign geneticmaterial enter bacteria cell. The results indicted the important function of RM genomicisland in shaping the genome structure of strain M18to stable the genome under theenvironmental selective pressure.In conclusion, this study systematically analyzed the genome, temperature-dependenttranscriptome, related phenotype, and further investigated the important role of M18strainspecific GI in shaping the genome structure. The results indicated that the P. aeruginosastrain M18has evolved its specific genomic structures and temperature dependentexpression patterns to meet the requirement of fitness and competitiveness under selectivepressures imposed on the strain in rhizosphere niche.
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