Use of In Vivo Expression Technology To Identify Genes Important in Growth and Survival of
            <i>Pseudomonas fluorescens</i>
            Pf0-1 in Soil: Discovery of Expressed Sequences with Novel Genetic Organization

Silby, Mark W.; Levy, Stuart B.

doi:10.1128/jb.186.21.7411-7419.2004

Cited by 87 publications

(106 citation statements)

References 43 publications

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“…Lugtenberg and Dekkers (21) have shown that utilization of organic acids by P. fluorescens is the nutritional basis governing the ability of this organism to colonize tomato roots. Genes in pseudomonads encoding proteins with functions in nutrient acquisition and in energy generation are up-regulated in the rhizosphere or when bacteria were exposed to the soil environment as revealed by in vivo expression technology-based approaches (22,23). Differences in expression of these genes in response to the var.…”

Section: Resultsmentioning

confidence: 99%

“…In vivo expression technology is now established as a method of analyzing bacterial gene expression in the rhizosphere as an approach for the identification of genes involved in microbe-plant interactions (22,23,29,35). One clear advantage of in vivo expression technology is that investigations are carried out in the appropriate environment in the organism of interest; there is no extrapolation from in vitro model systems.…”

Section: Evaluation and Comparison With Other Techniques To Study Rhizo-mentioning

confidence: 99%

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Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions

Mark

Dow

Kiely

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

226

166

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Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.Pseudomonas ͉ Rhizosphere colonization

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Section: Resultsmentioning

confidence: 99%

Section: Evaluation and Comparison With Other Techniques To Study Rhizo-mentioning

confidence: 99%

Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions

Mark

Dow

Kiely

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

226

166

View full text Add to dashboard Cite

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“…Mutants were constructed using the gene splicing by overlap extension method (48) and homologous recombination as previously outlined (49). Primers complimentary to regions flanking the targeted gene were used to monitor the proper replacement with the mutant constructs by PCR, and confirmed by sequencing both template strands.…”

Section: Methodsmentioning

confidence: 99%

Importance of positioning for microbial evolution

Kim

Racimo

Schluter

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

144

207

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Microbes commonly live in dense surface-attached communities where cells layer on top of one another such that only those at the edges have unimpeded access to limiting nutrients and space. Theory predicts that this simple spatial effect, akin to plants competing for light in a forest, generates strong natural selection on microbial phenotypes. However, we require direct empirical tests of the importance of this spatial structuring. Here we show that spontaneous mutants repeatedly arise, push their way to the surface, and dominate colonies of the bacterium Pseudomonas fluorescens Pf0-1. Microscopy and modeling suggests that these mutants use secretions to expand and push themselves up to the growth surface to gain the best access to oxygen. Physically mixing the cells in the colony, or introducing space limitations, largely removes the mutant's advantage, showing a key link between fitness and the ability of the cells to position themselves in the colony. We next follow over 500 independent adaptation events and show that all occur through mutation of a single repressor of secretions, RsmE, but that the mutants differ in competitiveness. This process allows us to map the genetic basis of their adaptation at high molecular resolution and we show how evolutionary competitiveness is explained by the specific effects of each mutation. By combining population level and molecular analyses, we demonstrate how living in dense microbial communities can generate strong natural selection to reach the growing edge.bacteria | biofilm | experimental evolution | social interaction

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“…Genes were deleted from the P. fluorescens Pf0-1 genome by SOE-PCR (Horton et al, 1989) and allele exchange using suicide plasmid pSR47s (Matthews and Roy, 2000) as described previously (Silby and Levy, 2004). Two of the deletion mutants obtained, Pfl01_3463-66 (bases 3947327-3952129) and Pfl01_3655-59 (bases 4136447-4143889), were used for comparison of antibiotic production with the wild-type strain.…”

Section: Extraction Of Antimicrobial Compoundsmentioning

confidence: 99%

Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors

et al. 2011

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The ability of soil bacteria to successfully compete with a range of other microbial species is crucial for their growth and survival in the nutrient-limited soil environment. In the present work, we studied the behavior and transcriptional responses of soil-inhabiting Pseudomonas fluorescens strain Pf0-1 on nutrient-poor agar to confrontation with strains of three phylogenetically different bacterial genera, that is, Bacillus, Brevundimonas and Pedobacter. Competition for nutrients was apparent as all three bacterial genera had a negative effect on the density of P. fluorescens Pf0-1; this effect was most strong during the interaction with Bacillus. Microarray-based analyses indicated strong differences in the transcriptional responses of Pf0-1 to the different competitors. There was higher similarity in the gene expression response of P. fluorescens Pf0-1 to the Gram-negative bacteria as compared with the Gram-positive strain. The Gram-negative strains did also trigger the production of an unknown broad-spectrum antibiotic in Pf0-1. More detailed analysis indicated that expression of specific Pf0-1 genes involved in signal transduction and secondary metabolite production was strongly affected by the competitors' identity, suggesting that Pf0-1 can distinguish among different competitors and fine-tune its competitive strategies. The results presented here demonstrate that P. fluorescens Pf0-1 shows a species-specific transcriptional and metabolic response to bacterial competitors and provide new leads in the identification of specific cues in bacteria-bacteria interactions and of novel competitive strategies, antimicrobial traits and genes.

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Use of In Vivo Expression Technology To Identify Genes Important in Growth and Survival of Pseudomonas fluorescens Pf0-1 in Soil: Discovery of Expressed Sequences with Novel Genetic Organization

Cited by 87 publications

References 43 publications

Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions

Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions

Importance of positioning for microbial evolution

Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors

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