DOCSLIB.ORG

Genes Expressed by the Biological Control Bacterium Pseudomonas Protegens Pf-5 on Seed Surfaces Under the Control of the Global Regulators Gaca and Rpos

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genes Expressed by the Biological Control Bacterium Pseudomonas Protegens Pf-5 on Seed Surfaces Under the Control of the Global Regulators Gaca and Rpos bs_bs_banner Environmental Microbiology (2013) 15(3), 716–735 doi:10.1111/1462-2920.12066 Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS Teresa A. Kidarsa,1 Brenda T. Shaffer,1 biosynthetic gene expression profiles. Future studies Neal C. Goebel,2 Daniel P. Roberts,3 evaluating biological control mechanisms can now Jeffrey S. Buyer,3 Aaron Johnson,4 focus on genes expressed by Pf-5 on seed surfaces, Donald Y. Kobayashi,5 T. Mark Zabriskie,2 the habitat where the bacterium interacts with seed- Ian Paulsen6 and Joyce E. Loper1* infecting pathogens to suppress seedling diseases. 1USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA. Introduction 2Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA. The soil bacterium Pseudomonas protegens Pf-5 (for- 3USDA-ARS Sustainable Agricultural Systems merly Pseudomonas fluorescens Pf-5; Ramette et al., Laboratory, Beltsville, MD, USA. 2011) colonizes the surfaces of seeds and roots and can 4J. Craig Venter Institute, Rockville, MD, USA. protect plants from infection by certain soil-borne fungal, 5Department of Plant Biology and Pathology, Rutgers oomycete and bacterial plant pathogens (Howell and University, New Brunswick, NJ, USA. Stipanovic, 1979; 1980; Xu and Gross, 1986; Kraus and 6Department of Chemistry and Biomolecular Sciences, Loper, 1992; Pfender et al., 1993; Rodriguez and Pfender, Macquarie University, Sydney, NSW, Australia. 1997; Sharifi-Tehrani et al., 1998). Secondary metabolite production is an important contributing factor for the bio- logical control of many plant diseases by Pseudomonas Summary spp. (Haas and Keel, 2003; Rezzonico et al., 2007; Gene expression profiles of the biological control Weller et al., 2007), and Pf-5 produces a spectrum of strain Pseudomonas protegens Pf-5 inhabiting pea secondary metabolites with antibiotic activity, including seed surfaces were revealed using a whole-genome 2,4-diacetylphloroglucinol (DAPG), pyoluteorin, pyrrolni- oligonucleotide microarray. We identified genes trin, hydrogen cyanide, rhizoxin analogues and orfamide expressed by Pf-5 under the control of two global A (Howell and Stipanovic, 1979; 1980; Nowak-Thompson regulators (GacA and RpoS) known to influence bio- et al., 1994; Gross et al., 2007; Loper et al., 2008). A logical control and secondary metabolism. Transcript similar suite of antibiotics is produced by the biological levels of 897 genes, including many with unknown control strain CHA0, which is closely related to Pf-5 (Haas functions as well as those for biofilm formation, cyclic and Keel, 2003). Antibiotic production by strains Pf-5 and diguanylate (c-di-GMP) signalling, iron homeostasis CHA0 is regulated at multiple levels, including by the and secondary metabolism, were influenced by one Gac/Rsm signal transduction pathway (Lapouge et al., s or both regulators, providing evidence for expression 2008) and the stationary-phase sigma factor RpoS (s ; of these genes by Pf-5 on seed surfaces. Comparison Sarniguet et al., 1995; Heeb et al., 2005). of the GacA and RpoS transcriptomes defined for Pf-5 In the Gac/Rsm signal transduction pathway, GacA acts grown on seed versus in broth culture overlapped, as a positive transcriptional regulator of genes encoding but most genes were regulated by GacA or RpoS the small regulatory RNAs, RsmX, RsmY and RsmZ under only one condition, likely due to differing levels (Heeb et al., 2002; Valverde et al., 2003; Kay et al., 2005). of expression in the two conditions. We quantified These small RNAs sequester the RNA-binding proteins secondary metabolites produced by Pf-5 and gacA RsmA and RsmE, relieving translational repression of and rpoS mutants on seed and in culture, and found genes having upstream binding sites for these repressor that production profiles corresponded generally with proteins (Valverde et al., 2003; Kay et al., 2005). GacA also has extensive effects on the transcriptome of Pseu- domonas spp.: transcript levels of nearly 10% of the Received 15 June, 2012; revised 20 October, 2012; accepted 22 November, 2012. *For correspondence. E-mail Joyce.Loper@ protein-encoding genes in the Pf-5 genome are influ- ars.usda.gov; Tel. (+1) 541 738 4057; Fax (+1) 541 738 4025. enced by GacA (Hassan et al., 2010), although this is Published 2012. This article is a U.S. Government work and is in the public domain in the USA. GacA and RpoS regulation of Pf-5 genes on seeds 717 likely due largely to indirect regulation via other genes and also may influence the expression of biocontrol traits under translational regulation by the Gac/Rsm pathway, by bacteria on the seed surface. Indeed, the availability as in Pseudomonas aeruginosa (Brencic and Lory, 2009). and composition of carbon and other nutrients are major Among the many genes regulated by GacA and its factors influencing antibiotic production by P. protegens cognate sensor kinase GacS are those required for pro- Pf-5 and CHA0 (Nowak-Thompson et al., 1994; Kraus duction of secondary metabolites and secreted exoen- and Loper, 1995; Duffy and Défago, 1999; Haas and Keel, zymes, such as chitinase and the AprA protease 2003; Haas and Défago, 2005; Valverde and Haas, 2008; (Lapouge et al., 2008; Hassan et al., 2010). Humair et al., 2009). The RpoS sigma factor directs RNA polymerase to pro- The primary focus of this work was to identify genes moters of certain genes transcribed in response to stress expressed under the control of GacA and RpoS by P. pro- or during the transition to stationary phase (Hengge- tegens Pf-5 inhabiting seed surfaces. Because both GacA Aronis, 2002), directly or indirectly regulating the expres- and RpoS influence biological control by Pseudomonas sion of a large set of genes having diverse functions spp., the GacA and RpoS transcriptomes of Pf-5 inhabit- (Schuster et al., 2004; Battesti et al., 2011). An rpoS ing the spermosphere are expected to include genes con- mutant of Pf-5 shows reduced tolerance to oxidative and tributing to biological control. We defined and compared osmotic stress, as well as to freezing, starvation, UV the GacA and RpoS transcriptomes of Pf-5 grown in irradiation and desiccation (Sarniguet et al., 1995; Stock- culture and on seed surfaces. While many genes were well and Loper, 2005). RpoS has differential effects on regulated by GacA and RpoS both in culture and on seed secondary metabolite production in Pf-5, with an rpoS surfaces, the majority of genes were regulated signifi- mutant of Pf-5 overproducing pyoluteorin and DAPG, cantly under only one condition, thus greatly expanding while failing to produce pyrrolnitrin (Pfender et al., 1993; the list of genes known to be under the control of these Sarniguet et al., 1995). global regulators. This study provides evidence for the Both the Gac/Rsm system and RpoS affect the ability of expression of hundreds of genes by Pf-5 inhabiting seed Pf-5 or CHA0 to act as biological control agents. gacS, surfaces and highlights GacA- and RpoS-regulated genes gacA, rsmX, rsmY or rsmZ mutants of CHA0 are deficient that could contribute to biological control of seed-infecting in biological control of several plant diseases (Schmidli- pathogens. Sacherer et al., 1997; Valverde et al., 2003; Zuber et al., 2003; Kay et al., 2005). An rpoS mutant of Pf-5 showed Results and discussion enhanced biological control of postemergence damping- off of cucumber caused by Pythium ultimum (Sarniguet The major goal of our study was to determine the effects et al., 1995), but a reduced ability to inhibit Pyrenophora of GacA and RpoS on gene expression of Pf-5 grown on tritici-repentis in wheat straw (Pfender et al., 1993). seed surfaces. We assessed the transcriptomes of Pf-5 Because the Gac/Rsm system and RpoS have such and gacA and rpoS mutants on surface-sterilized pea broad effects on the physiology of the bacterium, it is seed, as well as the chemical composition of the pea seed unclear whether their influence on biological control is exudate (Table S1). Initial experiments showed that the mediated solely through changes in secondary metabolite population size of Pf-5 increased rapidly in the first 24 h production versus other important traits, such as the following seed inoculation (from ~ 107 cfu per seed to ability to efficiently colonize seed or root surfaces. ~ 108 cfu per seed), whereas minimal additional growth To effect biological control of seed-infecting pathogens, occurred in the subsequent 24 h period. Our observation Pf-5 must express genes needed to suppress target that the population size of Pf-5 on seed surfaces reaches pathogens, as well as those required for growth and sur- carrying capacity at 24 h after the onset of seed imbibition vival in the spermosphere, the region of the soil under the is consistent with the temporal pattern of pea seed exu- influence of seeds. The main energy source in the sper- dation, as the highest levels of exudation occur during the mosphere is reduced carbon released from germinating initial hours after the onset of imbibition, with exudation seeds in the form of exudate (Nelson, 2004). Propagules diminishing 24 h after sowing (Roberts et al., 1999; 2000). of many fungal and oomycete plant pathogens can remain Preliminary reverse-transcriptase real-time PCR (RT- dormant in the soil for months or years but germinate qPCR) analysis showed that wild-type and mutant bacte- quickly in response to seed exudates, producing mycelia ria grown on seed surfaces for 24 h displayed expression that can infect seeds. Consequently, the spermosphere is differences in genes previously found to be regulated by often the initial point of interaction between pathogens GacA or RpoS in culture, including genes involved in the infecting seeds and biological control microorganisms and production of secondary metabolites (data not shown).
Load more

Recommended publications
  • Pseudomonas Fluorescens 2P24 Yang Zhang1†, Bo Zhang1†, Haiyan Wu1, Xiaogang Wu1*, Qing Yan2* and Li-Qun Zhang3*
    Zhang et al. BMC Microbiology (2020) 20:191 https://doi.org/10.1186/s12866-020-01880-x RESEARCH ARTICLE Open Access Pleiotropic effects of RsmA and RsmE proteins in Pseudomonas fluorescens 2P24 Yang Zhang1†, Bo Zhang1†, Haiyan Wu1, Xiaogang Wu1*, Qing Yan2* and Li-Qun Zhang3* Abstract Background: Pseudomonas fluorescens 2P24 is a rhizosphere bacterium that produces 2,4-diacetyphloroglucinol (2,4-DAPG) as the decisive secondary metabolite to suppress soilborne plant diseases. The biosynthesis of 2,4-DAPG is strictly regulated by the RsmA family proteins RsmA and RsmE. However, mutation of both of rsmA and rsmE genes results in reduced bacterial growth. Results: In this study, we showed that overproduction of 2,4-DAPG in the rsmA rsmE double mutant influenced the growth of strain 2P24. This delay of growth could be partially reversal when the phlD gene was deleted or overexpression of the phlG gene encoding the 2,4-DAPG hydrolase in the rsmA rsmE double mutant. RNA-seq analysis of the rsmA rsmE double mutant revealed that a substantial portion of the P. fluorescens genome was regulated by RsmA family proteins. These genes are involved in the regulation of 2,4-DAPG production, cell motility, carbon metabolism, and type six secretion system. Conclusions: These results suggest that RsmA and RsmE are the important regulators of genes involved in the plant- associated strain 2P24 ecologic fitness and operate a sophisticated mechanism for fine-tuning the concentration of 2,4-DAPG in the cells. Keywords: Pseudomonas fluorescens, RsmA/RsmE, 2,4-DAPG, Biofilm, Motility Background motility [5], the formation of biofilm [6], and the production Bacteria use a complex interconnecting mechanism to of secondary metabolites and virulence factors [7, 8].
    [Show full text]
  • Competence Genes in Pseudomonas Protegens
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.01.407551; this version posted April 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Experimental evolution-driven identification of Arabidopsis rhizosphere 2 competence genes in Pseudomonas protegens 3 Running title: Pseudomonas protegens adaptation to the rhizosphere 4 Erqin Li1,†, #,*, Hao Zhang1,*, Henan Jiang1, Corné M.J. Pieterse1, Alexandre Jousset2, Peter 5 A.H.M. Bakker1, Ronnie de Jonge1,† 6 7 1Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 8 Padualaan 8, 3584 CH, Utrecht, The Netherlands 9 2Ecology and Biodiversity, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 10 3584 CH, Utrecht, The Netherlands. 11 12 *E.L. and H.Z. contributed equally to this article. The author order was determined by 13 contribution to writing the manuscript. 14 15 †Corresponding authors: Ronnie de Jonge ([email protected]), Erqin Li ([email protected]). 16 #Current address: Freie Universität Berlin, Institut für Biologie, Dahlem Center of Plant Sciences, 17 Plant Ecology, Altensteinstr. 6, D-14195, Berlin, Germany 18 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.01.407551; this version posted April 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.
    [Show full text]
  • Evolutionary Patchwork of an Insecticidal Toxin
    Ruffner et al. BMC Genomics (2015) 16:609 DOI 10.1186/s12864-015-1763-2 RESEARCH ARTICLE Open Access Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus Beat Ruffner1, Maria Péchy-Tarr2, Monica Höfte3, Guido Bloemberg4, Jürg Grunder5, Christoph Keel2* and Monika Maurhofer1* Abstract Background: Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. Results: Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. Conclusions: Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.
    [Show full text]
  • Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
    Downloaded from orbit.dtu.dk on: Oct 01, 2021 Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter? Özen, Asli Ismihan; Ussery, David Published in: Microbial Ecology in Health & Disease Link to article, DOI: 10.1007/s00248-011-9914-8 Publication date: 2012 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Özen, A. I., & Ussery, D. (2012). Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter? Microbial Ecology in Health & Disease, 63(2), 239-248. https://doi.org/10.1007/s00248-011-9914-8 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Microb Ecol (2012) 63:239–248 DOI 10.1007/s00248-011-9914-8 MINIREVIEWS Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter? Asli I. Özen & David W. Ussery Received: 7 November 2010 /Accepted: 13 July 2011 /Published online: 3 August 2011 # The Author(s) 2011.
    [Show full text]
  • Download Article (PDF)
    Biologia 66/2: 288—293, 2011 Section Cellular and Molecular Biology DOI: 10.2478/s11756-011-0021-6 The first investigation of the diversity of bacteria associated with Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) Hacer Muratoglu, Zihni Demirbag &KazimSezen* Karadeniz Technical University, Faculty of Arts and Sciences, Department of Biology, 61080 Trabzon, Turkey; e-mail: [email protected] Abstract: Colorado potato beetle, Leptinotarsa decemlineata (Say), is a devastating pest of potatoes in North America and Europe. L. decemlineata has developed resistance to insecticides used for its control. In this study, in order to find a more effective potential biological control agent against L. decemlineata, we investigated its microbiota and tested their insecticidal effects. According to morphological, physiological and biochemical tests as well as 16S rDNA sequences, microbiota was identified as Leclercia adecarboxylata (Ld1), Acinetobacter sp. (Ld2), Acinetobacter sp. (Ld3), Pseudomonas putida (Ld4), Acinetobacter sp. (Ld5) and Acinetobacter haemolyticus (Ld6). The insecticidal activities of isolates at 1.8×109 bacteria/mL dose within five days were 100%, 100%, 35%, 100%, 47% and 100%, respectively, against the L. decemlineata larvae. The results indicate that Leclercia adecarboxylata (Ld1) and Pseudomonas putida (Ld4) isolates may be valuable potential biological control agents for biological control of L. decemlineata. Key words: Leptinotarsa decemlineata; 16S rDNA; microbiota; insecticidal activity; microbial control. Abbreviations: ANOVA, one-way analysis of variance; LSD, least significant difference; PBS, phosphate buffer solution. Introduction used because of marketing concerns and limited num- ber of transgenic varieties available. Also, recombinant Potato is an important crop with ∼4.3 million tons defence molecules in plants may affect parasitoids or of production on 192,000 hectares of growing area predators indirectly (Bouchard et al.
    [Show full text]
  • Diverse Environmental Pseudomonas Encode Unique Secondary Metabolites That Inhibit Human Pathogens
    DIVERSE ENVIRONMENTAL PSEUDOMONAS ENCODE UNIQUE SECONDARY METABOLITES THAT INHIBIT HUMAN PATHOGENS Elizabeth Davis A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2017 Committee: Hans Wildschutte, Advisor Ray Larsen Jill Zeilstra-Ryalls © 2017 Elizabeth Davis All Rights Reserved iii ABSTRACT Hans Wildschutte, Advisor Antibiotic resistance has become a crisis of global proportions. People all over the world are dying from multidrug resistant infections, and it is predicted that bacterial infections will once again become the leading cause of death. One human opportunistic pathogen of great concern is Pseudomonas aeruginosa. P. aeruginosa is the most abundant pathogen in cystic fibrosis (CF) patients’ lungs over time and is resistant to most currently used antibiotics. Chronic infection of the CF lung is the main cause of morbidity and mortality in CF patients. With the rise of multidrug resistant bacteria and lack of novel antibiotics, treatment for CF patients will become more problematic. Escalating the problem is a lack of research from pharmaceutical companies due to low profitability, resulting in a large void in the discovery and development of antibiotics. Thus, research labs within academia have played an important role in the discovery of novel compounds. Environmental bacteria are known to naturally produce secondary metabolites, some of which outcompete surrounding bacteria for resources. We hypothesized that environmental Pseudomonas from diverse soil and water habitats produce secondary metabolites capable of inhibiting the growth of CF derived P. aeruginosa. To address this hypothesis, we used a population based study in tandem with transposon mutagenesis and bioinformatics to identify eight biosynthetic gene clusters (BGCs) from four different environmental Pseudomonas strains, S4G9, LE6C9, LE5C2 and S3E10.
    [Show full text]
  • Gene Regulation by a Novel Two-Component System Conserved Among Gammaproteobacteria Kristin M
    Northern Michigan University NMU Commons All NMU Master's Theses Student Works 8-2015 Gene Regulation by a Novel Two-Component System Conserved Among Gammaproteobacteria Kristin M. Jacob Northern Michigan University, [email protected] Follow this and additional works at: https://commons.nmu.edu/theses Part of the Microbiology Commons Recommended Citation Jacob, Kristin M., "Gene Regulation by a Novel Two-Component System Conserved Among Gammaproteobacteria" (2015). All NMU Master's Theses. 66. https://commons.nmu.edu/theses/66 This Open Access is brought to you for free and open access by the Student Works at NMU Commons. It has been accepted for inclusion in All NMU Master's Theses by an authorized administrator of NMU Commons. For more information, please contact [email protected],[email protected]. GENE REGULATION BY A NOVEL TWO-COMPONENT SYSTEM CONSERVED AMONG γ-PROTEOBACTERIA By Kristin M. Jacob THESIS Submitted to Northern Michigan University In partial fulfillment of the requirements For the degree of MASTERS OF BIOLOGY Office of Graduate Education and Research August 2015 SIGNATURE APPROVAL FORM Title of Thesis: Gene Regulation by a Novel Two-Component System Conserved Among γ-Proteobacteria. This thesis by Kristin Jacob is recommended for approval by the student’s Thesis Committee and Department Head in the Department of Biology and by the Assistant Provost of Graduate Education and Research. ____________________________________________________________ Committee Chair: Dr. Josh Sharp Date ____________________________________________________________ First Reader: Dr. Erich Ottem Date ____________________________________________________________ Second Reader: Dr. Donna Becker Date ____________________________________________________________ Department Head: Dr. John Rebers Date ____________________________________________________________ Dr. Brian D. Cherry Date Assistant Provost of Graduate Education and Research ABSTRACT GENE REGULATION BY A NOVEL TWO-COMPONENT SYSTEM CONSERVED AMONG γ-PROTEOBACTERIA By Kristin M.
    [Show full text]
  • Aquatic Microbial Ecology 80:15
    The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package.
    [Show full text]
  • High Quality Draft Genome Sequences of Pseudomonas Fulva DSM
    Peña et al. Standards in Genomic Sciences (2016) 11:55 DOI 10.1186/s40793-016-0178-2 EXTENDED GENOME REPORT Open Access High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains Arantxa Peña1, Antonio Busquets1, Margarita Gomila1, Magdalena Mulet1, Rosa M. Gomila2, T. B. K. Reddy3, Marcel Huntemann3, Amrita Pati3, Natalia Ivanova3, Victor Markowitz3, Elena García-Valdés1,4, Markus Göker5, Tanja Woyke3, Hans-Peter Klenk6, Nikos Kyrpides3,7 and Jorge Lalucat1,4* Abstract Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T.Allthreegenomesarecomparableinsize(4.6–4.9 Mb), with 4,119–4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to- genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex. Keywords: Genomic Encyclopedia of Type Strains (GEBA), One Thousand Microbial Genomes Project (KMG-I), P.
    [Show full text]
  • Entomopathogenic Nematode-Associated Microbiota: from Monoxenic Paradigm to Pathobiome Jean-Claude Ogier, Sylvie Pages, Marie Frayssinet, Sophie Gaudriault
    Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome Jean-Claude Ogier, Sylvie Pages, Marie Frayssinet, Sophie Gaudriault To cite this version: Jean-Claude Ogier, Sylvie Pages, Marie Frayssinet, Sophie Gaudriault. Entomopathogenic nematode- associated microbiota: from monoxenic paradigm to pathobiome. Microbiome, BioMed Central, 2020, 8 (1), pp.1-17. 10.1186/s40168-020-00800-5. hal-02503304 HAL Id: hal-02503304 https://hal.archives-ouvertes.fr/hal-02503304 Submitted on 9 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Ogier et al. Microbiome (2020) 8:25 https://doi.org/10.1186/s40168-020-00800-5 RESEARCH Open Access Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome Jean-Claude Ogier†, Sylvie Pagès†, Marie Frayssinet and Sophie Gaudriault* Abstract Background: The holistic view of bacterial symbiosis, incorporating both host and microbial environment, constitutes a major conceptual shift in studies deciphering host-microbe interactions. Interactions between Steinernema entomopathogenic nematodes and their bacterial symbionts, Xenorhabdus, have long been considered monoxenic two partner associations responsible for the killing of the insects and therefore widely used in insect pest biocontrol.
    [Show full text]
  • Ferric-Pyoverdine Recognition by Fpv Outer Membrane Proteins of Pseudomonas Protegens Pf-5
    Ferric-Pyoverdine Recognition by Fpv Outer Membrane Proteins of Pseudomonas protegens Pf-5 Sierra L. Hartney,a* Sylvie Mazurier,b Maëva K. Girard,c Samina Mehnaz,d Edward W. Davis II,e Harald Gross,c* Philippe Lemanceau,b Joyce E. Lopera,e Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USAa; INRA, UMR 1347 Agroécologie, Dijon, Franceb; Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germanyc; Department of Biological Sciences, Forman Christian College University, Lahore, Pakistand; United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon, USAe Downloaded from The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyo- chelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 also utilizes ferric complexes of some pyoverdines produced by other strains of Pseudomonas spp. as sources of iron. Previously, phylogenetic analysis of the 45 TonB-dependent outer membrane proteins in Pf-5 indicated that six are in a well-supported clade with ferric-pyoverdine re- ceptors (Fpvs) from other Pseudomonas spp. We used a combination of phylogenetics, bioinformatics, mutagenesis, pyoverdine structural determinations, and cross-feeding bioassays to assign specific ferric-pyoverdine substrates to each of the six Fpvs of Pf-5. We identified at least one ferric-pyoverdine that was taken up by each of the six Fpvs of Pf-5. Functional redundancy of the http://jb.asm.org/ Pf-5 Fpvs was also apparent, with some ferric-pyoverdines taken up by all mutants with a single Fpv deletion but not by a mutant having deletions in two of the Fpv-encoding genes.
    [Show full text]
  • Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas Taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease
    International Journal of Molecular Sciences Article Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease Wen-Jen Chen 1, Tzu-Yen Kuo 1, Chun-Yi Chen 1, Feng-Chia Hsieh 2 , Yu-Liang Yang 1 , Je-Ruei Liu 1,3 and Ming-Che Shih 1,* 1 Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; [email protected] (W.-J.C.); [email protected] (T.-Y.K.); [email protected] (C.-Y.C.); [email protected] (Y.-L.Y.); [email protected] (J.-R.L.) 2 Biopesticide Division, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung 41358, Taiwan; [email protected] 3 Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan * Correspondence: [email protected] Received: 23 September 2020; Accepted: 13 November 2020; Published: 16 November 2020 Abstract: The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P.
    [Show full text]