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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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2
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Ferreiro MD, Gallegos MT. Distinctive features of the Gac-Rsm pathway in plant-associated Pseudomonas. Environ Microbiol 2021; 23:5670-5689. [PMID: 33939255 DOI: 10.1111/1462-2920.15558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 02/04/2023]
Abstract
Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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3
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Zboralski A, Filion M. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Comput Struct Biotechnol J 2020; 18:3539-3554. [PMID: 33304453 PMCID: PMC7711191 DOI: 10.1016/j.csbj.2020.11.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.
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Affiliation(s)
- Antoine Zboralski
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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4
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Harrison E, Hall JPJ, Brockhurst MA. Migration promotes plasmid stability under spatially heterogeneous positive selection. Proc Biol Sci 2019; 285:rspb.2018.0324. [PMID: 29794045 DOI: 10.1098/rspb.2018.0324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
Bacteria-plasmid associations can be mutualistic or antagonistic depending on the strength of positive selection for plasmid-encoded genes, with contrasting outcomes for plasmid stability. In mutualistic environments, plasmids are swept to high frequency by positive selection, increasing the likelihood of compensatory evolution to ameliorate the plasmid cost, which promotes long-term stability. In antagonistic environments, plasmids are purged by negative selection, reducing the probability of compensatory evolution and driving their extinction. Here we show, using experimental evolution of Pseudomonas fluorescens and the mercury-resistance plasmid, pQBR103, that migration promotes plasmid stability in spatially heterogeneous selection environments. Specifically, migration from mutualistic environments, by increasing both the frequency of the plasmid and the supply of compensatory mutations, stabilized plasmids in antagonistic environments where, without migration, they approached extinction. These data suggest that spatially heterogeneous positive selection, which is common in natural environments, coupled with migration helps to explain the stability of plasmids and the ecologically important genes that they encode.
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Affiliation(s)
- Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 1AE, UK
| | - James P J Hall
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
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5
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Stevenson C, Hall JPJ, Brockhurst MA, Harrison E. Plasmid stability is enhanced by higher-frequency pulses of positive selection. Proc Biol Sci 2019; 285:rspb.2017.2497. [PMID: 29321301 PMCID: PMC5784203 DOI: 10.1098/rspb.2017.2497] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/01/2017] [Indexed: 11/22/2022] Open
Abstract
Plasmids accelerate bacterial adaptation by sharing ecologically important traits between lineages. However, explaining plasmid stability in bacterial populations is challenging owing to their associated costs. Previous theoretical and experimental studies suggest that pulsed positive selection may explain plasmid stability by favouring gene mobility and promoting compensatory evolution to ameliorate plasmid cost. Here we test how the frequency of pulsed positive selection affected the dynamics of a mercury-resistance plasmid, pQBR103, in experimental populations of Pseudomonas fluorescens SBW25. Plasmid dynamics varied according to the frequency of Hg2+ positive selection: in the absence of Hg2+ plasmids declined to low frequency, whereas pulses of Hg2+ selection allowed plasmids to sweep to high prevalence. Compensatory evolution to ameliorate the cost of plasmid carriage was widespread across the entire range of Hg2+ selection regimes, including both constant and pulsed Hg2+ selection. Consistent with theoretical predictions, gene mobility via conjugation appeared to play a greater role in promoting plasmid stability under low-frequency pulses of Hg2+ selection. However, upon removal of Hg2+ selection, plasmids which had evolved under low-frequency pulse selective regimes declined over time. Our findings suggest that temporally variable selection environments, such as those created during antibiotic treatments, may help to explain the stability of mobile plasmid-encoded resistance.
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Affiliation(s)
- Cagla Stevenson
- Department of Biology, University of York, York YO10 5DD, UK .,Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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6
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Liu Y, Wang Z, Bilal M, Hu H, Wang W, Huang X, Peng H, Zhang X. Enhanced Fluorescent Siderophore Biosynthesis and Loss of Phenazine-1-Carboxamide in Phenotypic Variant of Pseudomonas chlororaphis HT66. Front Microbiol 2018; 9:759. [PMID: 29740409 PMCID: PMC5924801 DOI: 10.3389/fmicb.2018.00759] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/04/2018] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas chlororaphis HT66 is a plant-beneficial bacterium that exhibits wider antagonistic spectrum against a variety of plant pathogenic fungi due to its main secondary metabolite, i.e., phenazine-1-carboxamide (PCN). In the present study, a spontaneous phenotypic variant designated as HT66-FLUO was isolated from the fermentation process of wild-type HT66 strain. The newly isolated phenotypic variant was morphologically distinct from the wild-type strain such as larger cell size, semi-transparent, non-production of PCN (Green or yellow crystals) and enhanced fluorescence under UV light. The whole-genome, RNA-sequencing, and phenotypic assays were performed to identify the reason of phenotypic variation in HT66-FLUO as compared to the HT66. Transcriptomic analysis revealed that 1,418 genes, representing approximately 22% of the 6393 open reading frames (ORFs) had undergone substantial reprogramming of gene expression in the HT66-FLUO. The whole-genome sequence indicated no gene alteration in HT66-FLUO as compared to HT66 according to the known reference sequence. The levels of global regulatory factor gacA and gacS expression were not significantly different between HT66 and HT66-FLUO. It was observed that overexpressing gacS rather than gacA in HT66-FLUO can recover switching of the variant to HT66. The β-galactosidase (LacZ) activity and qRT-PCR results indicate the downregulated expression of rsmX, rsmY, and rsmZ in HT66-FLUO as compared to HT66. Overexpressing three small RNAs in HT66-FLUO can revert switching of colony phenotype toward wild-type HT66 up to a certain degree, restore partial PCN production and reduces the fluorescent siderophores yield. However, the origin of the spontaneous phenotypic variant was difficult to be determined. In conclusion, this study helps to understand the gene regulatory effect in the spontaneous phenotypic variant.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huasong Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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7
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Secondary Metabolism and Interspecific Competition Affect Accumulation of Spontaneous Mutants in the GacS-GacA Regulatory System in Pseudomonas protegens. mBio 2018; 9:mBio.01845-17. [PMID: 29339425 PMCID: PMC5770548 DOI: 10.1128/mbio.01845-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Secondary metabolites are synthesized by many microorganisms and provide a fitness benefit in the presence of competitors and predators. Secondary metabolism also can be costly, as it shunts energy and intermediates from primary metabolism. In Pseudomonas spp., secondary metabolism is controlled by the GacS-GacA global regulatory system. Intriguingly, spontaneous mutations in gacS or gacA (Gac− mutants) are commonly observed in laboratory cultures. Here we investigated the role of secondary metabolism in the accumulation of Gac− mutants in Pseudomonas protegens strain Pf-5. Our results showed that secondary metabolism, specifically biosynthesis of the antimicrobial compound pyoluteorin, contributes significantly to the accumulation of Gac− mutants. Pyoluteorin biosynthesis, which poses a metabolic burden on the producer cells, but not pyoluteorin itself, leads to the accumulation of the spontaneous mutants. Interspecific competition also influenced the accumulation of the Gac− mutants: a reduced proportion of Gac− mutants accumulated when P. protegens Pf-5 was cocultured with Bacillus subtilis than in pure cultures of strain Pf-5. Overall, our study associated a fitness trade-off with secondary metabolism, with metabolic costs versus competitive benefits of production influencing the evolution of P. protegens, assessed by the accumulation of Gac− mutants. Many microorganisms produce antibiotics, which contribute to ecologic fitness in natural environments where microbes constantly compete for resources with other organisms. However, biosynthesis of antibiotics is costly due to the metabolic burdens of the antibiotic-producing microorganism. Our results provide an example of the fitness trade-off associated with antibiotic production. Under noncompetitive conditions, antibiotic biosynthesis led to accumulation of spontaneous mutants lacking a master regulator of antibiotic production. However, relatively few of these spontaneous mutants accumulated when a competitor was present. Results from this work provide information on the evolution of antibiotic biosynthesis and provide a framework for their discovery and regulation.
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8
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Jousset A, Eisenhauer N, Merker M, Mouquet N, Scheu S. High functional diversity stimulates diversification in experimental microbial communities. SCIENCE ADVANCES 2016; 2:e1600124. [PMID: 27386573 PMCID: PMC4928988 DOI: 10.1126/sciadv.1600124] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/03/2016] [Indexed: 05/30/2023]
Abstract
There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.
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Affiliation(s)
- Alexandre Jousset
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Straße 28, 37073 Göttingen, Germany
- Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Monika Merker
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Straße 28, 37073 Göttingen, Germany
| | - Nicolas Mouquet
- Institut des Sciences de l’Evolution, UMR 5554, CNRS, Université Montpellier 2, CC 065, Place Eugène Bataillon, 34095 Montpellier, Cedex 05, France
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université Montpellier, CC 093, FR-34095 Montpellier, Cedex 5, France
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Straße 28, 37073 Göttingen, Germany
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9
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Harrison E, Dytham C, Hall JPJ, Guymer D, Spiers AJ, Paterson S, Brockhurst MA. Rapid compensatory evolution promotes the survival of conjugative plasmids. Mob Genet Elements 2016; 6:e1179074. [PMID: 27510852 PMCID: PMC4964889 DOI: 10.1080/2159256x.2016.1179074] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 12/14/2022] Open
Abstract
Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome.
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Affiliation(s)
| | - Calvin Dytham
- Department of Biology, University of York , York, UK
| | | | - David Guymer
- Department of Biology, University of York , York, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool , Liverpool, UK
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10
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Song C, Kidarsa TA, van de Mortel JE, Loper JE, Raaijmakers JM. Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility. Environ Microbiol 2016; 18:3453-3465. [PMID: 26945503 DOI: 10.1111/1462-2920.13288] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/02/2016] [Indexed: 11/28/2022]
Abstract
Swarming motility is a flagella-driven multicellular behaviour that allows bacteria to colonize new niches and escape competition. Here, we investigated the evolution of specific mutations in the GacS/GacA two-component regulatory system in swarming colonies of Pseudomonas protegens Pf-5. Experimental evolution assays showed that repeated rounds of swarming by wildtype Pf-5 drives the accumulation of gacS/gacA spontaneous mutants on the swarming edge. These mutants cannot swarm on their own because they lack production of the biosurfactant orfamide A, but they do co-swarm with orfamide-producing wildtype Pf-5. These co-swarming assays further demonstrated that ΔgacA mutant cells indeed predominate on the edge and that initial ΔgacA:wildtype Pf-5 ratios of at least 2:1 lead to a collapse of the swarming colony. Subsequent whole-genome transcriptome analyses revealed that genes associated with motility, resource acquisition, chemotaxis and efflux were significantly upregulated in ΔgacA mutant on swarming medium. Moreover, transmission electron microscopy showed that ΔgacA mutant cells were longer and more flagellated than wildtype cells, which may explain their predominance on the swarming edge. We postulate that adaptive evolution through point mutations is a common feature of range-expanding microbial populations and that the putative fitness benefits of these mutations during dispersal of bacteria into new territories are frequency-dependent.
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Affiliation(s)
- Chunxu Song
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands.,Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Teresa A Kidarsa
- Agricultural Research Service, US Department of Agriculture, Corvallis, OR, 97330, USA
| | - Judith E van de Mortel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Joyce E Loper
- Agricultural Research Service, US Department of Agriculture, Corvallis, OR, 97330, USA
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands. .,Microbial Biotechnology Department, Institute of Biology (IBL), Leiden University, Leiden, The Netherlands.
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11
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Mitri S, Foster KR. Pleiotropy and the low cost of individual traits promote cooperation. Evolution 2016; 70:488-94. [DOI: 10.1111/evo.12851] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/08/2015] [Accepted: 12/16/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Sara Mitri
- Department of Fundamental Microbiology; University of Lausanne; Lausanne Switzerland
| | - Kevin R. Foster
- Department of Zoology; University of Oxford; Oxford UK
- Oxford Centre for Integrative Systems Biology; University of Oxford; Oxford UK
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12
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Harrison E, Guymer D, Spiers AJ, Paterson S, Brockhurst MA. Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum. Curr Biol 2015; 25:2034-9. [PMID: 26190075 DOI: 10.1016/j.cub.2015.06.024] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/25/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1, 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4-6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7-15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful.
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Affiliation(s)
- Ellie Harrison
- Department of Biology, University of York, York YO10 5DD, UK
| | - David Guymer
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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13
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de Oliveira GB, Favarin L, Luchese RH, McIntosh D. Psychrotrophic bacteria in milk: How much do we really know? Braz J Microbiol 2015; 46:313-21. [PMID: 26273245 PMCID: PMC4507522 DOI: 10.1590/s1517-838246220130963] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/19/2014] [Indexed: 02/07/2023] Open
Abstract
The occurrence of psychrotrophic bacteria in raw milk is studied worldwide due to the difficulties associated with controlling their growth during cold storage and the consequent negative effects upon fluid milk or dairy products. Among the psychrotrophic bacteria, the genus Pseudomonas (represented primarily by P. fluorescens) has been highlighted as the cause of numerous defects in dairy products. In light of its perceived predominance, this species has frequently been chosen as a model organism to assess the effects of psychrotrophic bacteria on milk or to evaluate the efficacy of control measures. However, recent findings derived from the application of molecular biological techniques have exposed a number of deficiencies in our knowledge of the biology of milk-associated psychrotrophs. Furthermore, it has been revealed that microbe to microbe communication plays a significant role in determining both the identities and the extent to which different groups of microbes develop during cold storage. The application of molecular identification methods has exposed errors in the classification of members of the genus Pseudomonas isolated from cold stored milk and has stimulated a reevaluation of the presumed status of P. fluorescens as the predominant milk-associated psychrotrophic species. This article presents a succinct review of data from studies on psychrotrophic bacteria in milk, some of which contest established theories in relation to the microbiology of cold stored raw milk, and poses the question: how much do we really know?
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Affiliation(s)
- Gislene B de Oliveira
- Universidade Federal Rural do Rio de Janeiro, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Luciana Favarin
- Universidade Federal Rural do Rio de Janeiro, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Rosa H Luchese
- Universidade Federal Rural do Rio de Janeiro, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil, Ciência e Tecnologia de Alimentos, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Douglas McIntosh
- Universidade Federal Rural do Rio de Janeiro, Parasitologia Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil, Parasitologia Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
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14
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Evolutionary history predicts the stability of cooperation in microbial communities. Nat Commun 2014; 4:2573. [PMID: 24113642 DOI: 10.1038/ncomms3573] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/09/2013] [Indexed: 11/08/2022] Open
Abstract
Cooperation fundamentally contributes to the success of life on earth, but its persistence in diverse communities remains a riddle, as selfish phenotypes rapidly evolve and may spread until disrupting cooperation. Here we investigate how evolutionary history affects the emergence and spread of defectors in multispecies communities. We set up bacterial communities of varying diversity and phylogenetic relatedness and measure investment into cooperation (proteolytic activity) and their vulnerability to invasion by defectors. We show that evolutionary relationships predict the stability of cooperation: phylogenetically diverse communities are rapidly invaded by spontaneous signal-blind mutants (ignoring signals regulating cooperation), while cooperation is stable in closely related ones. Maintenance of cooperation is controlled by antagonism against defectors: cooperators inhibit phylogenetically related defectors, but not distant ones. This kin-dependent inhibition links phylogenetic diversity and evolutionary dynamics and thus provides a robust mechanistic predictor for the persistence of cooperation in natural communities.
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Sall KM, Casabona MG, Bordi C, Huber P, de Bentzmann S, Attrée I, Elsen S. A gacS deletion in Pseudomonas aeruginosa cystic fibrosis isolate CHA shapes its virulence. PLoS One 2014; 9:e95936. [PMID: 24780952 PMCID: PMC4004566 DOI: 10.1371/journal.pone.0095936] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/30/2014] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa, a human opportunistic pathogen, is capable of provoking acute and chronic infections that are associated with defined sets of virulence factors. During chronic infections, the bacterium accumulates mutations that silence some and activate other genes. Here we show that the cystic fibrosis isolate CHA exhibits a unique virulence phenotype featuring a mucoid morphology, an active Type III Secretion System (T3SS, hallmark of acute infections), and no Type VI Secretion System (H1-T6SS). This virulence profile is due to a 426 bp deletion in the 3′ end of the gacS gene encoding an essential regulatory protein. The absence of GacS disturbs the Gac/Rsm pathway leading to depletion of the small regulatory RNAs RsmY/RsmZ and, in consequence, to expression of T3SS, while switching off the expression of H1-T6SS and Pel polysaccharides. The CHA isolate also exhibits full ability to swim and twitch, due to active flagellum and Type IVa pili. Thus, unlike the classical scheme of balance between virulence factors, clinical strains may adapt to a local niche by expressing both alginate exopolysaccharide, a hallmark of membrane stress that protects from antibiotic action, host defences and phagocytosis, and efficient T3S machinery that is considered as an aggressive virulence factor.
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Affiliation(s)
- Khady Mayebine Sall
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
- CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France
- UJF-Grenoble 1, Grenoble, France
- CEA, DSV/iRTSV, Grenoble, France
| | - Maria Guillermina Casabona
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
- CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France
- UJF-Grenoble 1, Grenoble, France
- CEA, DSV/iRTSV, Grenoble, France
| | - Christophe Bordi
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR 7255 CNRS - Aix Marseille University, Marseille, France
| | - Philippe Huber
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
- CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France
- UJF-Grenoble 1, Grenoble, France
- CEA, DSV/iRTSV, Grenoble, France
| | - Sophie de Bentzmann
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR 7255 CNRS - Aix Marseille University, Marseille, France
| | - Ina Attrée
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
- CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France
- UJF-Grenoble 1, Grenoble, France
- CEA, DSV/iRTSV, Grenoble, France
| | - Sylvie Elsen
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
- CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France
- UJF-Grenoble 1, Grenoble, France
- CEA, DSV/iRTSV, Grenoble, France
- * E-mail:
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Abstract
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.
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Stallforth P, Brock DA, Cantley AM, Tian X, Queller DC, Strassmann JE, Clardy J. A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene. Proc Natl Acad Sci U S A 2013; 110:14528-33. [PMID: 23898207 PMCID: PMC3767522 DOI: 10.1073/pnas.1308199110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria's host is a "farmer" clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer's spore production and depresses a nonfarmer's spore production. Genome sequence and phylogenetic analyses identify a derived point mutation in the food strain that generates a premature stop codon in a global activator (gacA), encoding the response regulator of a two-component regulatory system. Generation of a knockout mutant of this regulatory gene in the nonfood bacterial strain altered its secondary metabolite profile to match that of the food strain, and also, independently, converted it into a food source. These results suggest that a single mutation in an inedible ancestral strain that served a protective role converted it to a "domesticated" food source.
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Affiliation(s)
- Pierre Stallforth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; and
| | - Debra A. Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Alexandra M. Cantley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; and
| | - Xiangjun Tian
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; and
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Wang D, Lee SH, Seeve C, Yu JM, Pierson LS, Pierson EA. Roles of the Gac-Rsm pathway in the regulation of phenazine biosynthesis in Pseudomonas chlororaphis 30-84. Microbiologyopen 2013; 2:505-24. [PMID: 23606419 PMCID: PMC3684763 DOI: 10.1002/mbo3.90] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 02/02/2023] Open
Abstract
The GacS/GacA two-component regulatory system activates the production of secondary metabolites including phenazines crucial for biological control activity in Pseudomonas chlororaphis 30-84. To better understand the role of the Gac system on phenazine regulation, transcriptomic analyses were conducted by comparing the wild-type strain to a gacA mutant. RNA-seq analysis identified 771 genes under GacA control, including many novel genes. Consistent with previous findings, phenazine biosynthetic genes were significantly downregulated in a gacA mutant. The transcript abundances of phenazine regulatory genes such as phzI, phzR, iopA, iopB, rpoS, and pip also were reduced. Moreover, the transcript abundance of three noncoding RNAs (ncRNAs) including rsmX, rsmY, and rsmZ was significantly decreased by gacA mutation consistent with the presence of consensus GacA-binding sites associated with their promoters. Our results also demonstrated that constitutive expression of rsmZ from a non-gac regulated promoter resulted in complete restoration of N-acyl-homoserine lactone (AHL) and phenazine production as well as the expression of other gac-dependent secondary metabolites in gac mutants. The role of RsmA and RsmE in phenazine production also was investigated. Overexpression of rsmE, but not rsmA, resulted in decreased AHL and phenazine production in P. chlororaphis, and only a mutation in rsmE bypassed the requirement for GacA in phenazine gene expression. In contrast, constitutive expression of the phzI/phzR quorum sensing system did not rescue phenazine production in the gacA mutant, indicating the direct posttranscriptional control by Gac on the phenazine biosynthetic genes. On the basis of these results, we propose a model to illustrate the hierarchic role of phenazine regulators modulated by Gac in the control of phenazine production. The transcriptomic analysis also was used to identify additional genes regulated by GacA that may contribute to the biological control capability of strain 30-84.
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Affiliation(s)
- Dongping Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2133, USA
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Grenga L, Gervasi F, Paolozzi L, Scortichini M, Ghelardini P. Characterisation of the MutS and MutL Proteins from the Pseudomonas avellanae Mismatch Repair (MMR) System. Open Microbiol J 2012; 6:45-52. [PMID: 22670163 PMCID: PMC3367300 DOI: 10.2174/1874285801206010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/13/2012] [Accepted: 02/20/2012] [Indexed: 11/22/2022] Open
Abstract
The identification and analysis of the Pseudomonas avellanae mismatch repair system (MMR) were performed via sequencing and cloning the mutS and mutL genes and then analyzing the characteristics of the corresponding proteins studying their function and biological role in an E. coli heterologous system. In these studies, the P. avellanae MutS and MutL proteins were shown to localise at the nucleoid level, in a MutS-dependent manner as far as MutL is concerned, and were also able to complement the defect observed in both the mutS and mutL knockout strains of E. coli. In addition, their ability to form both homo and heterodimers between each other was shown by using the prokaryotic two-hybrid assay. Our results represent a first step to elucidate the MMR mechanism in plant pathogenic pseudomonads since the MMR genes were identified in P. syringae pathovars but there was no evidence on their action as effective repair products.
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Affiliation(s)
- Lucia Grenga
- Dipartimento di Biologia, Università di Roma Tor Vergata, Italy
| | - Fabio Gervasi
- Unità di Ricerca per la Frutticoltura, C.R.A. Caserta, Italy
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20
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Marchand S, De Block J, De Jonghe V, Coorevits A, Heyndrickx M, Herman L. Biofilm Formation in Milk Production and Processing Environments; Influence on Milk Quality and Safety. Compr Rev Food Sci Food Saf 2012. [DOI: 10.1111/j.1541-4337.2011.00183.x] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Wei Q, Tarighi S, Dötsch A, Häussler S, Müsken M, Wright VJ, Cámara M, Williams P, Haenen S, Boerjan B, Bogaerts A, Vierstraete E, Verleyen P, Schoofs L, Willaert R, De Groote VN, Michiels J, Vercammen K, Crabbé A, Cornelis P. Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa. PLoS One 2011; 6:e29276. [PMID: 22195037 PMCID: PMC3240657 DOI: 10.1371/journal.pone.0029276] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 11/23/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Small colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch. METHODOLOGY/PRINCIPAL FINDINGS One SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10(-5) on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS). Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM), the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAO-SCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexAB-oprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels. CONCLUSIONS By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the Pseudomonas quinolone signal quorum sensing system.
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Affiliation(s)
- Qing Wei
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Saeed Tarighi
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andreas Dötsch
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Twincore, Center for Experimental and Clinical Infection Research, Helmholtz Center for Infection Research and the Medical School Hannover, Hannover, Germany
| | - Mathias Müsken
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Twincore, Center for Experimental and Clinical Infection Research, Helmholtz Center for Infection Research and the Medical School Hannover, Hannover, Germany
| | - Victoria J. Wright
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Miguel Cámara
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paul Williams
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Steven Haenen
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Bart Boerjan
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Annelies Bogaerts
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Evy Vierstraete
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Peter Verleyen
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Ronnie Willaert
- Structural Biology Brussels, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Jan Michiels
- Centre of Microbial and Plant Genetics, K.U. Leuven, Heverlee, Belgium
| | - Ken Vercammen
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Aurélie Crabbé
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, Arizona, United States of America
| | - Pierre Cornelis
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- * E-mail:
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22
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Spontaneous Gac mutants of Pseudomonas biological control strains: cheaters or mutualists? Appl Environ Microbiol 2011; 77:7227-35. [PMID: 21873476 DOI: 10.1128/aem.00679-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Bacteria rely on a range of extracellular metabolites to suppress competitors, gain access to resources, and exploit plant or animal hosts. The GacS/GacA two-component regulatory system positively controls the expression of many of these beneficial external products in pseudomonad bacteria. Natural populations often contain variants with defective Gac systems that do not produce most external products. These mutants benefit from a decreased metabolic load but do not appear to displace the wild type in nature. How could natural selection maintain the wild type in the presence of a mutant with enhanced growth? One hypothesis is that Gac mutants are "cheaters" that do not contribute to the public good, favored within groups but selected against between groups, as groups containing more mutants lose access to ecologically important external products. An alternative hypothesis is that Gac mutants have a mutualistic interaction with the wild type, so that each variant benefits by the presence of the other. In the biocontrol bacterium Pseudomonas chlororaphis strain 30-84, Gac mutants do not produce phenazines, which suppress competitor growth and are critical for biofilm formation. Here, we test the predictions of these alternative hypotheses by quantifying interactions between the wild type and the phenazine- and biofilm-deficient Gac mutant within growing biofilms. We find evidence that the wild type and Gac mutants interact mutualistically in the biofilm context, whereas a phenazine-defective structural mutant does not. Our results suggest that the persistence of alternative Gac phenotypes may be due to the stabilizing role of local mutualistic interactions.
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Romanowski A, Migliori ML, Valverde C, Golombek DA. Circadian variation in Pseudomonas fluorescens (CHA0)-mediated paralysis of Caenorhabditis elegans. Microb Pathog 2011; 50:23-30. [DOI: 10.1016/j.micpath.2010.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 09/15/2010] [Accepted: 09/20/2010] [Indexed: 11/17/2022]
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Sperandio D, Rossignol G, Guerillon J, Connil N, Orange N, Feuilloley MGJ, Merieau A. Cell-associated hemolysis activity in the clinical strain of Pseudomonas fluorescens MFN1032. BMC Microbiol 2010; 10:124. [PMID: 20416103 PMCID: PMC2871272 DOI: 10.1186/1471-2180-10-124] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 04/24/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND MFN1032 is a clinical Pseudomonas fluorescens strain able to grow at 37 degrees C. MFN1032 cells induce necrosis and apoptosis in rat glial cells at this temperature. This strain displays secretion-mediated hemolytic activity involving phospholipase C and cyclolipopeptides. Under laboratory conditions, this activity is not expressed at 37 degrees C. This activity is tightly regulated and is subject to phase variation. RESULTS We found that MFN1032 displays a cell-associated hemolytic activity distinct from the secreted hemolytic activity. Cell-associated hemolysis was expressed at 37 degrees C and was only detected in vitro in mid log growth phase in the presence of erythrocytes. We studied the regulation of this activity in the wild-type strain and in a mutant defective in the Gac two-component pathway. GacS/GacA is a negative regulator of this activity. In contrast to the Pseudomonas fluorescens strains PfO-1 and Pf5, whose genomes have been sequenced, the MFN1032 strain has the type III secretion-like genes hrcRST belonging to the hrpU operon. We showed that disruption of this operon abolished cell-associated hemolytic activity. This activity was not detected in P.fluorescens strains carrying similar hrc genes, as for the P. fluorescens psychrotrophic strain MF37. CONCLUSIONS To our knowledge this the first demonstration of cell-associated hemolytic activity of a clinical strain of Pseudomonas fluorescens. Moreover, this activity seems to be related to a functional hrpU operon and is independent of biosurfactant production. Precise link between a functional hrpU operon and cell-associated hemolytic activity remains to be elucidated.
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Affiliation(s)
- Daniel Sperandio
- Laboratory of cold microbiology signals and the microenvironment, LMDF-SME, UPRES EA 4312, University of Rouen, 55 rue Saint Germain, 27000 Evreux, France
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25
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Workentine ML, Harrison JJ, Weljie AM, Tran VA, Stenroos PU, Tremaroli V, Vogel HJ, Ceri H, Turner RJ. Phenotypic and metabolic profiling of colony morphology variants evolved fromPseudomonas fluorescensbiofilms. Environ Microbiol 2010; 12:1565-77. [DOI: 10.1111/j.1462-2920.2010.02185.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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The Legionella pneumophila LetA/LetS two-component system exhibits rheostat-like behavior. Infect Immun 2010; 78:2571-83. [PMID: 20351136 DOI: 10.1128/iai.01107-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When confronted with metabolic stress, replicative Legionella pneumophila bacteria convert to resilient, infectious cells equipped for transmission. Differentiation is promoted by the LetA/LetS two-component system, which belongs to a family of signal-transducing proteins that employ a four-step phosphorelay to regulate gene expression. Histidine 307 of LetS was essential to switch on the transmission profile, but a threonine substitution at position 311 (T311M) suggested a rheostat-like function. The letS(T311M) bacteria resembled the wild type (WT) for some traits and letS null mutants for others, whereas they displayed intermediate levels of infectivity, cytotoxicity, and lysosome evasion. Although only 30 to 50% of letS(T311M) mutants became motile, flow cytometry determined that every cell eventually activated the flagellin promoter to WT levels, but expression was delayed. Likewise, letS(T311M) mutants exhibited delayed induction of RsmY and RsmZ, regulatory RNAs that relieve CsrA repression of transmission traits. Transcriptional profile analysis revealed that letS(T311M) mutants expressed the flagellar regulon and multiple other transmissive-phase loci at a higher cell density than the WT. Accordingly, we postulate that the letS(T311M) mutant may relay phosphate less efficiently than the WT LetS sensor protein, leading to sluggish gene expression and a variety of phenotypic profiles. Thus, as first described for BvgA/BvgS, rather than acting as on/off switches, this family of two-component systems exhibit rheostat activity that likely confers versatility as microbes adapt to fluctuating environments.
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Rossignol G, Sperandio D, Guerillon J, Duclairoir Poc C, Soum-Soutera E, Orange N, Feuilloley M, Merieau A. Phenotypic variation in the Pseudomonas fluorescens clinical strain MFN1032. Res Microbiol 2009; 160:337-44. [DOI: 10.1016/j.resmic.2009.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/10/2009] [Accepted: 04/14/2009] [Indexed: 12/20/2022]
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Hagen MJ, Stockwell VO, Whistler CA, Johnson KB, Loper JE. Stress tolerance and environmental fitness of Pseudomonas fluorescens A506, which has a mutation in RpoS. PHYTOPATHOLOGY 2009; 99:679-688. [PMID: 19453226 DOI: 10.1094/phyto-99-6-0679] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Establishment of suppressive populations of bacterial biological control agents on aerial plant surfaces is a critical phase in biologically based management of floral diseases. Periodically, biocontrol agents encounter inhospitable conditions for growth on plants; consequently, tolerance of environmental stresses may contribute to their fitness. In many gram-negative bacteria, including strains of Pseudomonas spp., the capacity to survive environmental stresses is influenced by the stationary phase sigma factor RpoS. This study focused on the role of RpoS in stress response and epiphytic fitness of Pseudomonas fluorescens A506, a well-studied bacterial biological control agent. We detected a frameshift mutation in the rpoS of A506 and demonstrated that the mutation resulted in a truncated, nonfunctional RpoS. Using site-directed mutagenesis, we deleted a nucleotide from rpoS, which then encoded a full-length, functional RpoS. We compared the stress response and epiphytic fitness of A506 with derivative strains having the functional full-length RpoS or a disrupted, nonfunctional RpoS. RpoS had little effect on stress response of A506 and no consistent influence on epiphytic population size of A506 on pear or apple leaves or flowers. Although the capacity of strain A506 to withstand exposure to environmental stresses was similar to that of other fluorescent pseudomonads, this capacity was largely independent of rpoS.
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Affiliation(s)
- Mary J Hagen
- Department of Botany, Oregon State University, Corvallis 97331, USA
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Jousset A, Rochat L, Péchy-Tarr M, Keel C, Scheu S, Bonkowski M. Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters. ISME JOURNAL 2009; 3:666-74. [DOI: 10.1038/ismej.2009.26] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Barret M, Frey-Klett P, Boutin M, Guillerm-Erckelboudt AY, Martin F, Guillot L, Sarniguet A. The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp. THE NEW PHYTOLOGIST 2009; 181:435-447. [PMID: 19121038 DOI: 10.1111/j.1469-8137.2008.02675.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In soil, some antagonistic rhizobacteria contribute to reduce root diseases caused by phytopathogenic fungi. Direct modes of action of these bacteria have been largely explored; however, commensal interaction also takes place between these microorganisms and little is known about the influence of filamentous fungi on bacteria. An in vitro confrontation bioassay between the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) and the biocontrol bacterial strain Pseudomonas fluorescens Pf29Arp was set up to analyse bacterial transcriptional changes induced by the fungal mycelium at three time-points of the interaction before cell contact and up until contact. For this, a Pf29Arp shotgun DNA microarray was constructed. Specifity of Ggt effect was assessed in comparison with one of two other filamentous fungi, Laccaria bicolor and Magnaporthe grisea. During a commensal interaction, Ggt increased the growth rate of Pf29Arp. Before contact, Ggt induced bacterial genes involved in mycelium colonization. At contact, genes encoding protein of stress response and a patatin-like protein were up-regulated. Among all the bacterial genes identified, xseB was specifically up-regulated at contact by Ggt but down-regulated by the other fungi. Data showed that the bacterium sensed the presence of the fungus early, but the main gene alteration occurred during bacterial-fungal cell contact.
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Affiliation(s)
- M Barret
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - P Frey-Klett
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - M Boutin
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - A-Y Guillerm-Erckelboudt
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - F Martin
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - L Guillot
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
| | - A Sarniguet
- INRA, Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P 'Biologie des Organismes et des Populations Appliquée à la Protection des Plantes', 35653 Le Rheu, France;INRA, UMR 1136 INRA-Nancy Université'Interactions Arbres/Microorganismes', 54280 Champenoux, France;IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes, France
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Valverde C, Haas D. Small RNAs Controlled by Two-Component Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:54-79. [DOI: 10.1007/978-0-387-78885-2_5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Mulyukin AL, Kozlova AN, El’-Registan GI. Properties of the phenotypic variants of Pseudomonas aurantiaca and P. fluorescens. Microbiology (Reading) 2008. [DOI: 10.1134/s0026261708060052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Phase and antigenic variation mediated by genome modifications. Antonie van Leeuwenhoek 2008; 94:493-515. [DOI: 10.1007/s10482-008-9267-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2008] [Accepted: 07/09/2008] [Indexed: 11/26/2022]
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Abstract
Among the many bacteria present on and around the root, Pseudomonas bacteria are (among) the best root colonizers and therefore very suitable to apply for beneficial purposes. In this chapter, we discuss the possibilities to use such bacteria for the following purposes: fertilization of the plant, stimulation of plant growth and yield, reduction of plant stress, and reduction of plant diseases. This research was supported by numerous grants, especially from the Dutch Organization for scientific research (NWO), EET, the European Commission and INTAS.
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A LysR-type transcriptional regulator in Burkholderia cenocepacia influences colony morphology and virulence. Infect Immun 2007; 76:38-47. [PMID: 17967860 DOI: 10.1128/iai.00874-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Burkholderia cenocepacia strain K56-2 typically has rough colony morphology on agar medium; however, shiny colony variants (shv) can appear spontaneously. These shv all had a minimum of 50% reduction in biomass formation and were generally avirulent in an alfalfa seedling infection model. Three shv-K56-2 S15, K56-2 S76, and K56-2 S86-were analyzed for virulence in a chronic agar bead model of respiratory infection and, although all shv were able to establish chronic infection, they produced significantly less lung histopathology than the rough K56-2. Transmission electron microscopy revealed that an extracellular matrix surrounding bacterial cells was absent or reduced in the shv compared to the rough wild type. Transposon mutagenesis was performed on the rough wild-type strain and a mutant with an insertion upstream of ORF BCAS0225, coding for a putative LysR-type regulator, exhibited shiny colony morphology, reduced biofilm production, increased N-acyl homoserine lactone production, and avirulence in alfalfa. The rough parental colony morphotype, biofilm formation, and virulence in alfalfa were restored by providing BCAS0225 in trans in the BCAS0225::pGSVTp-luxCDABF mutant. Introduction of BCAS0225 restored the rough morphotype in several shv which were determined to have spontaneous mutations in this gene. In the present study, we show that the conversion from rough wild type to shv in B. cenocepacia correlates with reduced biofilm formation and virulence, and we determined that BCAS0225 is one gene involved in the regulation of these phenotypes.
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Costa R, Gomes NCM, Krögerrecklenfort E, Opelt K, Berg G, Smalla K. Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses. Environ Microbiol 2007; 9:2260-73. [PMID: 17686023 DOI: 10.1111/j.1462-2920.2007.01340.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis.
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Affiliation(s)
- Rodrigo Costa
- Federal Biological Research Centre for Agriculture and Forestry (BBA), Messeweg 11/12, D-38104 Braunschweig, Germany
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Martínez-Granero F, Rivilla R, Martín M. Rhizosphere selection of highly motile phenotypic variants of Pseudomonas fluorescens with enhanced competitive colonization ability. Appl Environ Microbiol 2006; 72:3429-34. [PMID: 16672487 PMCID: PMC1472367 DOI: 10.1128/aem.72.5.3429-3434.2006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenotypic variants of Pseudomonas fluorescens F113 showing a translucent and diffuse colony morphology show enhanced colonization of the alfalfa rhizosphere. We have previously shown that in the biocontrol agent P. fluorescens F113, phenotypic variation is mediated by the activity of two site-specific recombinases, Sss and XerD. By overexpressing the genes encoding either of the recombinases, we have now generated a large number of variants (mutants) after selection either by prolonged laboratory cultivation or by rhizosphere passage. All the isolated variants were more motile than the wild-type strain and appear to contain mutations in the gacA and/or gacS gene. By disrupting these genes and complementation analysis, we have observed that the Gac system regulates swimming motility by a repression pathway. Variants isolated after selection by prolonged cultivation formed a single population with a swimming motility that was equal to the motility of gac mutants, being 150% more motile than the wild type. The motility phenotype of these variants was complemented by the cloned gac genes. Variants isolated after rhizosphere selection belonged to two different populations: one identical to the population isolated after prolonged cultivation and the other comprising variants that besides a gac mutation harbored additional mutations conferring higher motility. Our results show that gac mutations are selected both in the stationary phase and during rhizosphere colonization. The enhanced motility phenotype is in turn selected during rhizosphere colonization. Several of these highly motile variants were more competitive than the wild-type strain, displacing it from the root tip within 2 weeks.
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Affiliation(s)
- Francisco Martínez-Granero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, Spain
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38
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van den Broek D, Bloemberg GV, Lugtenberg B. The role of phenotypic variation in rhizosphere Pseudomonas bacteria. Environ Microbiol 2006; 7:1686-97. [PMID: 16232284 DOI: 10.1111/j.1462-2920.2005.00912.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Colony phase variation is a regulatory mechanism at the DNA level which usually results in high frequency, reversible switches between colonies with a different phenotype. A number of molecular mechanisms underlying phase variation are known: slipped-strand mispairing, genomic rearrangements, spontaneous mutations and epigenetic mechanisms such as differential methylation. Most examples of phenotypic variation or phase variation have been described in the context of host-pathogen interactions as mechanisms allowing pathogens to evade host immune responses. Recent reports indicate that phase variation is also relevant in competitive root colonization and biological control of phytopathogens. Many rhizospere Pseudomonas species show phenotypic variation, based on spontaneous mutation of the gacA and gacS genes. These morphological variants do not express secondary metabolites and have improved growth characteristics. The latter could contribute to efficient root colonization and success in competition, especially since (as shown for one strain) these variants were observed to revert to their wild-type form. The observation that these variants are present in rhizosphere-competent Pseudomonas bacteria suggests the existence of a conserved strategy to increase their success in the rhizosphere.
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Affiliation(s)
- Daan van den Broek
- Leiden University, Institute of Biology, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, the Netherlands.
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Kassab DM, Roane TM. Differential responses of a mine tailings Pseudomonas isolate to cadmium and lead exposures. Biodegradation 2006; 17:379-87. [PMID: 16477362 DOI: 10.1007/s10532-005-9010-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Accepted: 08/04/2005] [Indexed: 10/25/2022]
Abstract
We examined cadmium and lead resistance in Pseudomonas sp. S8A, an isolate obtained from mine tailings-contaminated soil. Resistant to soluble metal concentrations up to 200 mg l(-1) cadmium and 300 mg l(-1) lead, S8A produced both exopolymer and biosurfactant. Upon growth, this pseudomonad diverged into two morphologically distinct colony subtypes; small and round or large and flat. In the presence of lead and in the no metal control the large morphotype appeared only in late stationary phase. With cadmium the large morphotype appeared immediately following exposure. Results show that the large morphotype produced greater amounts of surfactant than the small morphotype, suggesting a unique subpopulation response to cadmium toxicity. Results also indicate that an unidentified 28 kDa protein was expressed following exposure to >10 mg l(-1) cadmium. This study demonstrates new links between surfactant production, differential subpopulation response and metal exposure.
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Affiliation(s)
- Duried M Kassab
- Department of Biology, University of Colorado at Denver, Denver, USA
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40
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Berg G, Eberl L, Hartmann A. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 2005; 7:1673-85. [PMID: 16232283 DOI: 10.1111/j.1462-2920.2005.00891.x] [Citation(s) in RCA: 333] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
During the last years, the number of human infections caused by opportunistic pathogens has increased dramatically. One natural reservoir of opportunistic pathogens is the rhizosphere, the zone around roots that is influenced by the plant. Due to a high content of nutrients, this habitat is a 'microbial hot-spot', where bacterial abundances including those with strong antagonistic traits are enhanced. Various bacterial genera, including Burkholderia, Enterobacter, Herbaspirillum, Ochrobactrum, Pseudomonas, Ralstonia, Staphylococcus and Stenotrophomonas, contain root-associated strains that can encounter bivalent interactions with both plant and human hosts. Mechanisms responsible for colonization of the rhizosphere and antagonistic activity against plant pathogens are similar to those responsible for colonization of human organs and tissues, and pathogenicity. Multiple resistances against antibiotics are not only found with clinical strains but also with strains isolated from the rhizosphere. High competition, the occurrence of diverse antibiotics in the rhizosphere, and enhanced horizontal gene transfer rates in this microenvironment appear to contribute to the high levels of natural resistances. While opportunistic bacteria from the rhizosphere have some properties in common, each of these emerging pathogens has its own features, which are discussed in detail for Burkholderia, Ochrobactrum and Stenotrophomonas.
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Affiliation(s)
- Gabriele Berg
- University of Rostock, Department of Life Sciences, Institute of Microbiology, Albert-Einstein-Strasse 3, D-18051 Rostock, Germany.
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van den Broek D, Chin-A-Woeng TFC, Bloemberg GV, Lugtenberg BJJ. Role of RpoS and MutS in phase variation of Pseudomonas sp. PCL1171. Microbiology (Reading) 2005; 151:1403-1408. [PMID: 15870450 DOI: 10.1099/mic.0.27777-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas sp. strain PCL1171 undergoes reversible colony phase variation between opaque phase I and translucent phase II colonies, which is dependent on spontaneous mutations in the regulatory genes gacA and gacS. Mutation of the mutS gene and constitutive expression of rpoS increases the frequency at which gac mutants appear 1000- and 10-fold, respectively. Experiments were designed to study the relationship between gacS, rpoS and mutS. These studies showed that (i) a functional gac system is required for the expression of rpoS, (ii) RpoS suppresses the expression of mutS and therefore increases the frequency of gac mutants, and (iii) upon mutation of rpoS and gacS, the expression of mutS is increased. Mutation of gacS abolishes suppression of mutS expression in stationary growth, suggesting that additional gac-dependent factors are involved in this suppression. In conclusion, inefficient mutation repair via MutS, of which the expression is influenced by gacA/S itself and by rpoS in combination with other factors, contributes to the high frequency of mutations accumulating in gacA/S. The role of RpoS in the growth advantage of a gac mutant was analysed, and mutation of rpoS only reduced the length of the lag phase, but did not affect the growth rate, suggesting a role for both RpoS and a reduction of metabolic load in the growth advantage of a gac mutant.
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Affiliation(s)
- Daan van den Broek
- Institute of Biology, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Thomas F C Chin-A-Woeng
- Institute of Biology, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Guido V Bloemberg
- Institute of Biology, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Ben J J Lugtenberg
- Institute of Biology, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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