Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 10:R51

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA.
Genome biology (Impact Factor: 10.81). 06/2009; 10(5). DOI: 10.1186/gb-2009-10-5-r51
Source: PubMed Central


Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species.
Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome.
P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

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    • "Second, recent studies have shown that different strains of P. fluorescens are highly diverse at the genomic level (as is true for many bacterial species, see Lukjancenko et al. 2010); the core genes shared by ten P. fluorescens strains represent only 45–52% of the total proteome of each strain (Loper et al. 2012). The remaining genes, defined as accessory genes, are absent in one or more of the ten strains (Silby et al. 2009; Loper et al. 2012). Although core genes cluster around the origin of replication , accessory genes segregate toward the replication terminus , raising the question whether this genomic architecture results from differential mutation pressure, genome-wide differences in natural selection or other factors such as conjugation/recombination . "
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    ABSTRACT: High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluorescens, and are especially elevated around the replication terminus of the genome, where strain-specific genes are found. In an effort to understand the role of genetic variation in the evolution of Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution mutation rate of 2.34 × 10(-8) per site per generation (SE: 0.01 × 10(-8)) and a small-insertion-deletion mutation rate of 1.65 × 10(-9) per site per generation (SE: 0.03 × 10(-9)). We find that the spectrum of mutations in prophage regions, which often contain virulence factors and antibiotic resistance, is highly similar to that in the intergenic regions of the host genome. Our results show that the mutation rate varies around the chromosome, with the lowest mutation rate found near the origin of replication. Consistent with observations from other studies, we find that site-specific mutation rates are heavily influenced by the immediately flanking nucleotides, indicating that mutations are context dependent. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Genome Biology and Evolution 12/2014; 7(1). DOI:10.1093/gbe/evu284 · 4.23 Impact Factor
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    • "Phylogenetic analysis of 14 sequenced Pseudomonas strains belonging to five Pseudomonas species, based on 1,705 conserved genes, indicated that P. stutzeri A1501 is somewhat distantly related to the other Pseudomonas spp. [3]. A phylogenetic tree based on concatenation of four housekeeping genes (16S rRNA, gyrB, rpoB and rpoD genes) from 107 Pseudomonas species placed type strain P. stutzeri ATCC 17588T in a separate group along with P. azotifigens, P. balearica and P. xanthomarina [2]. "
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    ABSTRACT: The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.
    PLoS ONE 09/2014; 9(9):e105837. DOI:10.1371/journal.pone.0105837 · 3.23 Impact Factor
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    • "Only a small set of 22 genes was differentially expressed in all treatments. Among these common differentially expressed genes were Pfl_0064 Catalase, an important enzyme in protecting the cell against damage by reactive oxygen species; Pfl_0157 Sulfotransferase, belonging to a group of enzymes that catalyze the transfer of a sulfo group from a donor molecule to an acceptor alcohol or amine; Pfl_2907 and Pfl_4382 Chemotaxis sensory transducer genes, genes that are important for regulation of bacterial chemotaxis, and Pfl_0623 Diguanylate cyclase (GGDEF domain), a gene that has been indicated to be responsible for the wrinkly spreader phenotype in P. fluorescens (Malone et al., 2007; Silby et al., 2009). The difference in transcriptional response of P. fluorescens to different bacterial strains appeared to reflect the composition of volatiles. "
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    ABSTRACT: There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0-1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.
    Frontiers in Microbiology 06/2014; 5:289. DOI:10.3389/fmicb.2014.00289 · 3.99 Impact Factor
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