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.
Highlights
Our previously published reports have described an effective biocontrol agent named Pseudomonas sp
We first provide the evidence to show that the secondary metabolites produced from the strain M18 have strong effective inhibitory activity against the growth of the Mycosphaerella melonis mycelium plug on a potato dextrose agar (PDA) plate (Figure 1A) and therapeutic anti-fungal effect on the sweat melon plant with full recovery of the plant infected by the M. melonis fungus two days after the culture of 108 CFU/ml of the strain M18 that was sprayed on the infected sweat melon stem (Figure 1B and 1C)
Global alignments were performed by the MUMer software [29], and the results showed that the large segment inversion of the chromosome by recombination between the rrnA and rrnB genes was found in the M18 genome, as well as in other P. aeruginosa strains LESB58, PA14 and PA7 (Figure 3B) in comparison with that in PAO1 genome sequenced by the Seattle consortium [23]
Summary
Our 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. Published work from our group has described an effective biocontrol strain M18 that was isolated from sweet melon rhizosphere in Shanghai suburb in 1996 [1]. This strain has been named as the Pseudomonas sp. In a more recent study, we demonstrated the negative effect of the QscR regulator on PCA production, but not on Plt in the strain M18 [4]. The interrelationship between the QS las and rhl system in strain M18 are different from that in strain P. aeruginosa PAO1 [15]
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