Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18

Abstract

BackgroundOur previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa, but there are several unusual phenotypic features. This study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.ResultsThe complete M18 genome is composed of a single chromosome of 6,327,754 base pairs containing 5684 open reading frames. Seven genomic islands, including two novel prophages and five specific non-phage islands were identified besides the conserved P. aeruginosa core genome. Each prophage contains a putative chitinase coding gene, and the prophage II contains a capB gene encoding a putative cold stress protein. The non-phage genomic islands contain genes responsible for pyoluteorin biosynthesis, environmental substance degradation and type I and III restriction-modification systems. 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 M18 genome may contribute to the relative genome stability. Although the M18 genome is most closely related to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible to several antimicrobial agents and easier to be erased in a mouse acute lung infection model than the strain LESB58. The whole M18 transcriptomic analysis indicated that 10.6% of the expressed genes are temperature-dependent, with 22 genes up-regulated at 28°C in three non-phage genomic islands and one prophage but none at 37°C.ConclusionsThe P. aeruginosa strain M18 has evolved its specific genomic structures and temperature dependent expression patterns to meet the requirement of its fitness and competitiveness under selective pressures imposed on the strain in rhizosphere niche.

From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens

“…Considering core genome based phylogeny, the strain LESB58 hypervirulent for CF patients is the closest relative to the rhizosphere strain M18 [25]. However, dominant epidemic clones have been associated to CF.…”

Phenazines in the Environment: Microbes, Habitats, and Ecological Relevance

“…1 and 4), and most genomic differences are confined to accessory regions that account for less than 10 % of the ORFs present. Strain M18 was more susceptible than the virulent strain LESB58 to several antimicrobial agents applied against P. aeruginosa in clinical settings and was more readily cleared than LESB58 from the lungs in the acute mouse infection model (Wu et al 2011). Comparative transcriptome analyses of M18 and PAO1 grown at 28°C (''rhizosphere temperature'') and 37°C (''human temperature'') revealed that M18-induced more genes at 37°C than at 28°C and conversely, that more genes were induced in PAO1 at 28°C than at 37°C, consistent with gene mobilization in both strains to adapt to stresses associated with temperature-shifted growth (Wu et al 2012).…”

Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens

“…For example, Wu et al (2011) identified the genomic differences between the MBCA P. aeruginosa M18 and certain P. aeruginosa strains, which are human pathogens. They underlined the genetic distance and the lack of genes involved in human pathogenicity in the MBCA strain, prerequisites for any plant protection product registration.…”

“…The MBCA transcriptome studies have been particularly useful in terms of providing a better understanding of how these MBCAs act and of the complex gene regulation sustaining the effect of the MBCA on the pathogenesis. More specifically the results highlighted genes involved in niche adaptation, competition for nutrients and space (Adomas et al 2006;Wu et al 2011), the complex interplay and synchronization of gene transcription needed for efficient mycoparasitism (Reithner et al 2011) and the more comprehensive understanding of the cell physiology sustaining mycoparasitism (Seidl et al 2009) or the kinetics of MBCA-pathogen interactions (Barret et al 2009a, b). The plant transcriptome studies have identified the plant defense pathways stimulated by the MBCA against the plant pathogen.…”