DOCSLIB.ORG

Real-Time PCR Detection of Pseudomonas Cichorii, the Causal Agent of Midrib Rot in Lettuce

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Real-Time PCR Detection of Pseudomonas Cichorii, the Causal Agent of Midrib Rot in Lettuce Faculty of Sciences Department of Biochemistry, Physiology and Microbiology Laboratory of Microbiology-Ghent Academic year 2006-2007 Thesis submitted to obtain the degree of Master of Science in ‘Applied Microbial Systematics’ Real-Time PCR detection of Pseudomonas cichorii, the causal agent of midrib rot in lettuce Ines Verbaendert Promotor: Dr J. Heyrman Co-promotor: Prof. Dr. P. De Vos DANKWOORD Zonder de steun en hulp van een aantal mensen zou ik deze scriptie niet kunnen gerealiseerd hebben. Daarom een kleine attentie voor hen op papier, want hun advies en goede raad was zéér welkom! Dr. Jeroen Heyrman en Caroline, merci voor alle tijd die jullie hebben gestoken in het aanleren van alle technieken die ik nodig had om deze scriptie tot een goed einde te brengen en voor alle advies die ik van jullie gekregen heb! Jeroen , bedankt ook voor de uurtjes denkwerk en lees- en verbeterwerk die ik u heb aangedaan! Prof. P. De Vos wil ik heel hartelijk bedanken voor de kans die ik gekregen heb om een tijdje deel uit te maken van het Laboratorium voor Microbiologie. Kim, Emly, Caroline, An, Jeroen A., Liesbeth, Karen: de sfeer was schitterend! Ik voelde mij na een paar dagen echt op mijn gemak tussen jullie en ik wil jullie bedanken voor alle aanmoedigingen, hulp en het beantwoorden van de meest onmogelijke vragen. En als laatste wil ik mijn ouders bedanken. Na 6 jaar studeren, zijn ze nog steeds geïnteresseerd in de dingen waar ik mee bezig ben en ik vind het magnifiek dat ze mij nog een jaartje extra wilden ondersteunen om daarna ‘de grote mensenwereld’ in te stappen! Dankuwel! Ines, mei 2007 2 3 Content Dankwoord Index 1. ABSTRACT 8 2. INTRODUCTION 9 2.1. INTRODUCTION TO THE PROJECT 9 2.2. OBJECTIVE OF THE THESIS 10 3. OVERVIEW OF LITERATURE 11 3.1. PSEUDOMONAS CICHORII AS A PLANT PATHOGEN 11 3.1.1. THE HOST RANGE OF P. CICHORII 11 3.1.2. THE INFECTION MODE OF P. CICHORII 11 3.1.3. THE SOURCE OF P. CICHORII 14 3.2. (QUANTITATIVE) REAL‐TIME PCR 15 3.2.1. INTRODUCTION 15 3.2.2. PCR AMPLIFICATION 15 3.2.3. REAL‐TIME MONITORING OF PCR 16 3.2.3.1. Quantification and characterisation 16 3.2.3.2. Detection formats: fluorescence reporters 17 3.2.3.3. Instrumentation of real‐time PCR 19 3.2.4. OPTIMISATION OF REAL‐TIME PCR 20 3.2.5. APPLICATIONS OF REAL‐TIME PCR 20 4. MATERIALS AND METHODS 22 4.1. STRAINS 22 4.1.1. ORIGIN OF THE STRAINS 22 4.1.2. LONG‐TERM PRESERVATION OF THE STRAINS 22 4.2. DNA EXTRACTION 23 4.2.1. QUALITY CONTROL AND STORAGE OF DNA 24 4.2.1.1. Assessment of fragmentation 25 4.2.1.2. Concentration and purity assessment 26 4.3. GRADIENT PCR 28 4.3.1. PCR REACTION 28 4.3.2. GEL ELECTROPHORESIS 29 4.4. PCR 29 4.5. REAL‐TIME PCR ASSAYS 30 4.5.1. INTRODUCTION 30 4.5.2. REAL TIME PCR DEVELOPMENT 32 4 4.5.2.1. Optimisation of the PCR conditions 33 4.5.2.2. Further optimisation 35 4.5.2.3. Exclusivity 36 4.5.2.4. Inclusivity 37 4.5.2.5. Analytical sensitivity (work range) 37 4.5.2.6. Analytical specificity 38 4.5.2.7. TaqMan probe 39 5. RESULTS AND DISCUSSION 40 5.1. CONVENTIONAL PCR 40 5.2. REAL‐TIME PCR 42 5.2.1. SYBR GREEN I 42 5.2.1.1. Optimisation MgCl2 concentration 42 5.2.1.2. Optimisation temperature‐time profile 45 5.2.1.3. Optimisation of the primer concentration 50 5.2.1.4. Further optimisation 51 5.2.1.5. Exclusivity 53 5.2.1.6. Inclusivity 56 5.2.1.7. Analytical sensitivity (work range) 57 5.2.1.8. Analytical specificity 64 5.2.2. ROCHE‐ AND SIGMA‐ KIT FOR REAL‐TIME PCR 66 5.2.3. DEVELOPMENT AND PRELIMINARY TESTING OF A TAQMAN PROBE 67 5.2.3.1. Reverse probe 67 5.2.3.2. Forward probe 68 6. CONCLUDING REMARKS 70 7. REFERENCES 72 List with used abbreviations Addendum 5 List of figures FIGURE 1: Midrib rot (left) of green house grown lettuce(right) FIGURE 2: Type III secretion structure of P. syringae FIGURE 3: HrcR, hrcS and hrcT of P. syringae pv. syringae FIGURE 4: The PCR temperature cycle FIGURE 5: Quantification of Microcystis aeruginosa PCC 7820 using real‐time PCR FIGURE 6: The chemical structure of SYBR Green I FIGURE 7: The TaqMan probe fluorescent chemistry FIGURE 8: Conventional PCR (segment of photographs) FIGURE 9: Amplification curves of the optimisation of the MgCl2 concentration for primer couple F1‐R1 and P. cichorii strain LMG 8401 FIGURE 10: Amplification curves of the optimisation of the MgCl2 concentration for primer couple F1‐R1 and P. cichorii strain LMG 2162T FIGURE 11: Melting curves of the optimisation of the MgCl2 concentration for primer couple F1‐R1 and P. cichorii strain LMG 2162T FIGURE 12: Amplification curves of the optimisation of the MgCl2 concentration for primer couple F1‐R1 and P. syringae strain LMG 2352T FIGURE 13: Amplification curves of the optimisation of the MgCl2 concentration for primer couple F2‐R1 and P. cichorii strain LMG 8401 FIGURE 14: Amplification curves of the optimisation of the MgCl2 concentration for primer couple F2‐R1 and P. cichorii strain LMG 2162T FIGURE 15: Amplification curves of the optimisation of the annealing temperature for primer couple F2‐R1 (0.5µM) and three P. cichorii strains FIGURE 16: Amplification curves of the optimisation of the annealing temperature for primer couple F2‐R1 (0.5µM) and two non‐P. cichorii strains FIGURE 17: Melting curves of the optimisation of the annealing temperature for primer couple F2‐R1 (0.5µM) and two non‐P. cichorii strains FIGURE 18: Melting curves of the optimisation of the annealing temperature: 60°C FIGURE 19: Melting curves of the optimisation of the annealing temperature: 62°C FIGURE 20: Melting curves of the optimisation of the annealing temperature: 64°C FIGURE 21: Amplification curves of the optimisation of the annealing time for P. cichorii LMG 2162T and P. cichorii R‐25254 FIGURE 22: Comparison of primer couples F1‐R1 and F2‐R1 with the initial optimised PCR conditions FIGURE 23: Further optimisation of the primer concentration with primer couple F2‐R1 and P. cichorii strains LMG 2162T, R‐25254 and LMG 8401 FIGURE 24: Further optimisation of the annealing temperature by raising the temperature again up to 64°C for a range of Pseudomonas strains FIGURE 25: The exclusivity assay (amplification curves) 6 FIGURE 26: The exclusivity assay (melting curves) Pcichrc 2007‐03‐22A FIGURE 27: The exclusivity assay (melting curves) Pcichrc 2007‐03‐22B FIGURE 28: The exclusivity assay (melting curves) Pcichrc 2007‐03‐22C FIGURE 29: The exclusivity assay (melting curves) Pcichrc 2007‐03‐26 FIGURE 30: The inclusivity assay (amplification curves) FIGURE 31: The inclusivity assay (melting curves) FIGURE 32: Amplification curves of a dilution series of P. cichorii LMG 2162T FIGURE 33: Melting curves of a dilution series of P. cichorii LMG 2162T FIGURE 34: Amplification curves of a dilution series of P. cichorii R‐25254 FIGURE 35: Melting curves of a dilution series of P. cichorii R‐25254 FIGURE 36: Amplification curves of a dilution series of P. cichorii R‐31877 FIGURE 37: Melting curves of a dilution series of P. cichorii R‐31877 FIGURE 38: Analytical sensitivity of the SYBR Green I assay determined with serial dilutions of P. cichorii LMG T 2162 genomic DNA using primer couple F2‐R1 FIGURE 39: Analytical sensitivity of the SYBR Green I assay determined with serial dilutions of P. cichorii R‐ 25254 genomic DNA using primer couple F2‐R1 FIGURE 40: Analytical sensitivity of the SYBR Green I assay determined with serial dilutions of P. cichorii R‐ 31877 genomic DNA using primer couple F2‐R1 FIGURE 41: Analytical specificity for strain P. mediterranea LMG 23075T at a dilution of 108 and 107 (amplification curves) FIGURE 42: Analytical specificity for strain P. mediterranea LMG 23075T at a dilution of 102 (amplification curves) FIGURE 43: Analytical specificity for strain P. mediterranea LMG 23075T at a dilution of 102 and 108 FIGURE 44: Amplification curves of F1‐Rprobe0 for five P. cichorii strains (Pcichrc 2007‐03‐09) FIGURE 45: Amplification curves for F1‐Rprobe for P. cichorii (Pcichrc 2007‐04‐17) FIGURE 46: Amplification curves for F1‐Rprobe with additional P. cichorii strains (Pcichrc 2007‐04‐19D) FIGURE 47: Amplification curves for Fprobe‐R1 for P. cichorii strains (Pcichrc 2007‐04‐17) FIGURE 48: Amplification curves for Fprobe‐R1 at 65°C for 8 P. cichorii strains 7 1. ABSTRACT The incidence of bacterial soft rot in salad vegetables caused by Pseudomonas has increased from a rather sporadic to a chronic problem in Flanders and it currently represents a serious threat for the production sector. Early detection of the sources of introduction can guide the implementation of appropriate measures to prevent or counter infections of salad vegetables with P. cichorii. The goal of this study was to participate in the development and mainly in the optimisation of a specific real- time PCR-detection system targeting P. cichorii hrp/hrc genes in order to allow for fast detection of infection at an early stage of the crop. Construction of primers for rapid detection of P. cichorii was already performed. The primers although still had to be extensively tested for: (1) exclusivity (2) inclusivity (3) analytical specificity (4) analytical sensitivity and (5) reproducibility.
Load more

Recommended publications
  • Pseudomonas Cichorii
    Plant Pathology Bulletin 15:275-285, 2006 Pseudomonas cichorii 1 1 1, 2 1 2 [email protected] 95 12 02 2006 Pseudomonas cichorii 15 275-285 60 (RAPD) Pseudomonas cichorii (Swingle) Stapp 1,100 bp Topo pCR®II-TOPO Pseudomonas cichorii SfL1/SfR2 (polymerase chain reaction, PCR) 379 bp 6 21 SfL1 / SfR2 P. cichorii DNA 5~10 pg 5.5~9 (P. cichorii) 10 6 cfu/ml 10 5~10 8 cfu/ml SfL1/ SfR2 P. cichorii 3 - 4 hr SfL1/SfR2 P. cichorii PCR Pseudomonas cichorii (3) (Swingle) Stapp P. cichorii (10) (13) (lettuce) (10) (27) (15) (33) (cabbage) (celery) (tomato) (14) (chrysanthemum) (16) (geranium) (16) (dwarf schefflera) (11) (sunflower) (22) (magnolia) (19) (5, 10) (5) (3) ( polymerase chain reaction PCR) (20) RFLP ( 276 15 4 2006 restriction fragment length polymorphism) AFLP RAPD PCR (amplified fragment length polymorphism) RAPD Table 1. Bacterial isolates used in experiments of RAPD (random amplified polymorphic DNA) (17, 18, 32) and PCR. Bacterium Strain Pseudomonas Burkholderia andropogonis Pan1 Pseudomonas B. caryophylli Tw7, Tw9 syringae pv. cannabina efe gene DNA B. gladioli pv. gladioli Bg ETH1 ETH2 ETH3 P. syringae pv. Erwinia carotovora subsp. carotovora Zan01~15 Ech10~22 cannabina P. syringae pv. glycinea P. syringae pv. Erwinia chrysanthemi Sr53~56 (24) phaseolicola P. Pantoea agglomerans Yx5, Yx7 syringae pv. atropurpurea cfl gene DNA Pseudomonas aeruginosa Pae Primer 1 Primer 2 P. syringae pv. glycinea P. P. cichorii Sf syringae pv. maculicola P. syringae pv. tomato P. fluorescens Pf (8) (30) P. putida Pu P. syringae pv. atropurpurea P. P. syringae pv.
    [Show full text]
  • Archaea, Bacteria and Termite, Nitrogen Fixation and Sustainable Plants Production
    Sun W et al . (2021) Notulae Botanicae Horti Agrobotanici Cluj-Napoca Volume 49, Issue 2, Article number 12172 Notulae Botanicae Horti AcademicPres DOI:10.15835/nbha49212172 Agrobotanici Cluj-Napoca Re view Article Archaea, bacteria and termite, nitrogen fixation and sustainable plants production Wenli SUN 1a , Mohamad H. SHAHRAJABIAN 1a , Qi CHENG 1,2 * 1Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing 100081, China; [email protected] ; [email protected] 2Hebei Agricultural University, College of Life Sciences, Baoding, Hebei, 071000, China; Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei 071000, China; [email protected] (*corresponding author) a,b These authors contributed equally to the work Abstract Certain bacteria and archaea are responsible for biological nitrogen fixation. Metabolic pathways usually are common between archaea and bacteria. Diazotrophs are categorized into two main groups namely: root- nodule bacteria and plant growth-promoting rhizobacteria. Diazotrophs include free living bacteria, such as Azospirillum , Cupriavidus , and some sulfate reducing bacteria, and symbiotic diazotrophs such Rhizobium and Frankia . Three types of nitrogenase are iron and molybdenum (Fe/Mo), iron and vanadium (Fe/V) or iron only (Fe). The Mo-nitrogenase have a higher specific activity which is expressed better when Molybdenum is available. The best hosts for Rhizobium legumiosarum are Pisum , Vicia , Lathyrus and Lens ; Trifolium for Rhizobium trifolii ; Phaseolus vulgaris , Prunus angustifolia for Rhizobium phaseoli ; Medicago, Melilotus and Trigonella for Rhizobium meliloti ; Lupinus and Ornithopus for Lupini, and Glycine max for Rhizobium japonicum . Termites have significant key role in soil ecology, transporting and mixing soil. Termite gut microbes supply the enzymes required to degrade plant polymers, synthesize amino acids, recycle nitrogenous waste and fix atmospheric nitrogen.
    [Show full text]
  • Comparative Genomic Analysis of Three Pseudomonas
    microorganisms Article Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column Ashish Pathak 1, Paul Stothard 2 and Ashvini Chauhan 1,* 1 Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA; [email protected] 2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-850-412-5119; Fax: +1-850-561-2248 Abstract: The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because Citation: Pathak, A.; Stothard, P.; of their immense metabolic and ecological potential. To obtain a comprehensive understanding on Chauhan, A. Comparative Genomic this aspect, we previously reported on the isolation and preliminary genomic characterization of Analysis of Three Pseudomonas Species three Pseudomonas species isolated from minced oyster tissue (P.
    [Show full text]
  • Increased Moisture Content of Propagation Media Enhances Bacterial Rot of Chrysanthemum
    Table 4, Effectiveness of chemical treatments to control leaf spot of basil when applied as protectants (Table 4). No sign of caused by Pseudomonas cichorii. phytotoxicity was seen on any of the sprayed plants under conditions of this experiment. However, to our knowledge, Plant rating2 neither has EPA registered for use on basil. Chemical Greenhouse Mist chamber Literature Cited Saline control 0.0 0.5 Inoculated control 8.0 9.5 1. Chase, A. R. and D. D. Brunk. 1984. Bacterial leaf incited by Streptomycin 0.5 0.0 Pseudomonas cichorii in Schefflera arboricola and some related plants. Copper-maneb 0.5 1.0 Plant Dis. 68:73-74. 2. Crockett, J. U. and O. Tanner. 1977. The Time-Life Encyclopedia of zRating based on 0-10 where 0 = no infection, 1 = 1- and 10 Gardening, Herbs. Time-Life Books, Alexandia, VA. 90-100%. Average of 3 replications. 3. Irey, M. S. 1980. Taxonomic value of the yellow pigment of the genus Xanthomonas. M.S. Thesis, Univ. Florida, Gainesville. showed that the disease level was much higher at high 4. King, E. O., M. K. Ward, and D. E. Raney. 1954. Two simple media moisture levels than at low moisture levels even at approx for the demonstration of pyocyanin and fluorescin. J. Lab. Med. 44 imately equal temperature regimes (Table 3). This indi 301-307. 5. Klement, Z., G. L. Farkas, and I. Lovrekovich. 1964. Hypersensitive cates that high moisture levels favor severe disease de reaction induced by phytopathogenic bacteria in the tobacco leaf. velopment. Thus, keeping the foliage as dry as possible Phytopathology 54:474-477.
    [Show full text]
  • Performance Evaluation of Microbe and Plant-Mediated Processes in Phytoremediation of Toluene in Fractured Bedrock Using Hybrid Poplars
    Performance evaluation of microbe and plant-mediated processes in phytoremediation of toluene in fractured bedrock using hybrid poplars by Michael Ben-Israel A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Environmental Sciences Guelph, Ontario, Canada © Michael Ben-Israel, March, 2020 ABSTRACT PERFORMANCE EVALUATION OF MICROBE AND PLANT-MEDIATED PROCESSES IN PHYTOREMEDIATION OF TOLUENE IN FRACTURED BEDROCK USING HYBRID POPLARS Michael Ben-Israel Advisor: University of Guelph, 2020 Dr. Kari Dunfield Efficacy of hybrid poplar trees for phytoremediation of toluene in fractured bedrock aquifers is unclear and active mechanisms require validation. This multi-year field study was conducted on a pilot phytoremediation system at an urban site, implemented to address aged toluene impacts to a shallow fractured dolostone aquifer. The study aimed to establish performance by quantifying phytoremedial activities at the site. Contaminant concentrations in groundwater, soil, and soil vapour, measured in high spatial resolution, showed the main residual toluene mass is coincident with the water table and located favourably for phyto-remedial uptake and biodegradation, with shallow groundwater concentrations approaching aqueous solubility in high-impact areas. Biodegradation occurring in the vadose zone was shown through metagenomic analyses that enumerated toluene degradation genes and gene transcripts in roots and root-associated soil, and compound-specific stable isotope analysis that showed enrichment of toluene stable carbon isotopes in soil vapour. Transpiration measurement, in planta contaminant quantification, and high-throughput sequencing of microbial taxonomic genes in roots and stem tissue were employed to measure toluene uptake through phytoextraction and resolve biodegradation influences upon uptake patterns.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Understanding the Composition and Role of the Prokaryotic Diversity in the Potato Rhizosphere for Crop Improvement in the Andes
    Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Jonas Ghyselinck Dissertation submitted in fulfilment of the requirements for the degree of Doctor (Ph.D.) in Sciences, Biotechnology Promotor - Prof. Dr. Paul De Vos Co-promotor - Dr. Kim Heylen Ghyselinck Jonas – Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Copyright ©2013 Ghyselinck Jonas ISBN-number: 978-94-6197-119-7 No part of this thesis protected by its copyright notice may be reproduced or utilized in any form, or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Printed by University Press | www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. This Ph.D. work was financially supported by European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement N° 227522 Publicly defended in Ghent, Belgium, May 28th 2013 EXAMINATION COMMITTEE Prof. Dr. Savvas Savvides (chairman) Faculty of Sciences Ghent University, Belgium Prof. Dr. Paul De Vos (promotor) Faculty of Sciences Ghent University, Belgium Dr. Kim Heylen (co-promotor) Faculty of Sciences Ghent University, Belgium Prof. Dr. Anne Willems Faculty of Sciences Ghent University, Belgium Prof. Dr. Peter Dawyndt Faculty of Sciences Ghent University, Belgium Prof. Dr. Stéphane Declerck Faculty of Biological, Agricultural and Environmental Engineering Université catholique de Louvain, Louvain-la-Neuve, Belgium Dr. Angela Sessitsch Department of Health and Environment, Bioresources Unit AIT Austrian Institute of Technology GmbH, Tulln, Austria Dr.
    [Show full text]
  • 11 Microbial Communities in the Phyllosphere Johan H.J
    Biology of the Plant Cuticle Edited by Markus Riederer, Caroline Müller Copyright © 2006 by Blackwell Publishing Ltd Biology of the Plant Cuticle Edited by Markus Riederer, Caroline Müller Copyright © 2006 by Blackwell Publishing Ltd 11 Microbial communities in the phyllosphere Johan H.J. Leveau 11.1 Introduction The term phyllosphere was coined by Last (1955) and Ruinen (1956) to describe the plant leaf surface as an environment that is physically, chemically and biologically distinct from the plant leaf itself or the air surrounding it. The term phylloplane has been used also, either instead of or in addition to the term phyllosphere. Its two- dimensional connotation, however, does not do justice to the three dimensions that characterise the phyllosphere from the perspective of many of its microscopic inhab- itants. On a global scale, the phyllosphere is arguably one of the largest biological surfaces colonised by microorganisms. Satellite images have allowed a conservative approximation of 4 × 108 km2 for the earth’s terrestrial surface area covered with foliage (Morris and Kinkel, 2002). It has been estimated that this leaf surface area is home to an astonishing 1026 bacteria (Morris and Kinkel, 2002), which are the most abundant colonisers of cuticular surfaces. Thus, the phyllosphere represents a significant refuge and resource of microorganisms on this planet. Often-used terms in phyllosphere microbiology are epiphyte and epiphytic (Leben, 1965; Hirano and Upper, 1983): here, microbial epiphytes or epiphytic microorganisms, which include bacteria, fungi and yeasts, are defined as being cap- able of surviving and thriving on plant leaf and fruit surfaces. Several excellent reviews on phyllosphere microbiology have appeared so far (Beattie and Lindow, 1995, 1999; Andrews and Harris, 2000; Hirano and Upper, 2000; Lindow and Leveau, 2002; Lindow and Brandl, 2003).
    [Show full text]
  • Field Manual of Diseases on Garden and Greenhouse Flowers Field Manual of Diseases on Garden and Greenhouse Flowers
    R. Kenneth Horst Field Manual of Diseases on Garden and Greenhouse Flowers Field Manual of Diseases on Garden and Greenhouse Flowers R. Kenneth Horst Field Manual of Diseases on Garden and Greenhouse Flowers R. Kenneth Horst Plant Pathology and Plant Microbe Biology Cornell University Ithaca, NY , USA ISBN 978-94-007-6048-6 ISBN 978-94-007-6049-3 (eBook) DOI 10.1007/978-94-007-6049-3 Springer Dordrecht Heidelberg New York London Library of Congress Control Number: 2013935122 © Springer Science+Business Media Dordrecht 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, speci fi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on micro fi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied speci fi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc.
    [Show full text]
  • Comparative Analysis of the Core Proteomes Among The
    Diversity 2020, 12, 289 1 of 25 Article Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species‐Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis Marios Nikolaidis 1, Dimitris Mossialos 2, Stephen G. Oliver 3 and Grigorios D. Amoutzias 1,* 1 Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 2 Microbial Biotechnology‐Molecular Bacteriology‐Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; [email protected] * Correspondence: [email protected]; Tel.: +30‐2410‐565289; Fax: +30‐2410‐565290 Received: 22 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core‐orthologues. The subsequent phylogenomic analysis revealed two well‐defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus‐level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group‐specific core proteins were also identified, with P.
    [Show full text]
  • Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus Mali in Tianshan Forests
    Wild apple-associated fungi and bacteria compete to colonize the larval gut of an invasive wood-borer Agrilus mali in Tianshan forests Tohir Bozorov ( [email protected] ) Xinjiang Institute of Ecology and Geography https://orcid.org/0000-0002-8925-6533 Zokir Toshmatov Plant Genetics Research Unit: Genetique Quantitative et Evolution Le Moulon Gulnaz Kahar Xinjiang Institute of Ecology and Geography Daoyuan Zhang Xinjiang Institute of Ecology and Geography Hua Shao Xinjiang Institute of Ecology and Geography Yusufjon Gafforov Institute of Botany, Academy of Sciences of Uzbekistan Research Keywords: Agrilus mali, larval gut microbiota, Pseudomonas synxantha, invasive insect, wild apple, 16S rRNA and ITS sequencing Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-287915/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: The gut microora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of gut bacteria to address this absence of fungi in the larval gut. Results: The results demonstrated that gut bacteria were able to selectively inhibit wild apple tree-associated fungi. However, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identied.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider Et Al
    USOO7476532B2 (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider et al. (45) Date of Patent: Jan. 13, 2009 (54) MANNITOL INDUCED PROMOTER Makrides, S.C., "Strategies for achieving high-level expression of SYSTEMIS IN BACTERAL, HOST CELLS genes in Escherichia coli,” Microbiol. Rev. 60(3):512-538 (Sep. 1996). (75) Inventors: J. Carrie Schneider, San Diego, CA Sánchez-Romero, J., and De Lorenzo, V., "Genetic engineering of nonpathogenic Pseudomonas strains as biocatalysts for industrial (US); Bettina Rosner, San Diego, CA and environmental process.” in Manual of Industrial Microbiology (US) and Biotechnology, Demain, A, and Davies, J., eds. (ASM Press, Washington, D.C., 1999), pp. 460-474. (73) Assignee: Dow Global Technologies Inc., Schneider J.C., et al., “Auxotrophic markers pyrF and proC can Midland, MI (US) replace antibiotic markers on protein production plasmids in high cell-density Pseudomonas fluorescens fermentation.” Biotechnol. (*) Notice: Subject to any disclaimer, the term of this Prog., 21(2):343-8 (Mar.-Apr. 2005). patent is extended or adjusted under 35 Schweizer, H.P.. "Vectors to express foreign genes and techniques to U.S.C. 154(b) by 0 days. monitor gene expression in Pseudomonads. Curr: Opin. Biotechnol., 12(5):439-445 (Oct. 2001). (21) Appl. No.: 11/447,553 Slater, R., and Williams, R. “The expression of foreign DNA in bacteria.” in Molecular Biology and Biotechnology, Walker, J., and (22) Filed: Jun. 6, 2006 Rapley, R., eds. (The Royal Society of Chemistry, Cambridge, UK, 2000), pp. 125-154. (65) Prior Publication Data Stevens, R.C., “Design of high-throughput methods of protein pro duction for structural biology.” Structure, 8(9):R177-R185 (Sep.
    [Show full text]