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Control of Phytopathogenic Microorganisms with Pseudomonas Sp. and Substances and Compositions Derived Therefrom

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(19) TZZ Z_Z_T (11) EP 2 820 140 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A01N 63/02 (2006.01) A01N 37/06 (2006.01) 10.01.2018 Bulletin 2018/02 A01N 37/36 (2006.01) A01N 43/08 (2006.01) C12P 1/04 (2006.01) (21) Application number: 13754767.5 (86) International application number: (22) Date of filing: 27.02.2013 PCT/US2013/028112 (87) International publication number: WO 2013/130680 (06.09.2013 Gazette 2013/36) (54) CONTROL OF PHYTOPATHOGENIC MICROORGANISMS WITH PSEUDOMONAS SP. AND SUBSTANCES AND COMPOSITIONS DERIVED THEREFROM BEKÄMPFUNG VON PHYTOPATHOGENEN MIKROORGANISMEN MIT PSEUDOMONAS SP. SOWIE DARAUS HERGESTELLTE SUBSTANZEN UND ZUSAMMENSETZUNGEN RÉGULATION DE MICRO-ORGANISMES PHYTOPATHOGÈNES PAR PSEUDOMONAS SP. ET DES SUBSTANCES ET DES COMPOSITIONS OBTENUES À PARTIR DE CELLE-CI (84) Designated Contracting States: • O. COUILLEROT ET AL: "Pseudomonas AL AT BE BG CH CY CZ DE DK EE ES FI FR GB fluorescens and closely-related fluorescent GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO pseudomonads as biocontrol agents of PL PT RO RS SE SI SK SM TR soil-borne phytopathogens", LETTERS IN APPLIED MICROBIOLOGY, vol. 48, no. 5, 1 May (30) Priority: 28.02.2012 US 201261604507 P 2009 (2009-05-01), pages 505-512, XP55202836, 30.07.2012 US 201261670624 P ISSN: 0266-8254, DOI: 10.1111/j.1472-765X.2009.02566.x (43) Date of publication of application: • GUANPENG GAO ET AL: "Effect of Biocontrol 07.01.2015 Bulletin 2015/02 Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere (73) Proprietor: Marrone Bio Innovations, Inc. Using T-RFLP and DGGE", PLOS ONE, vol. 7, no. Davis, CA 95618 (US) 2, 16 February 2012 (2012-02-16), page e31806, XP55202957, DOI: 10.1371/journal.pone.0031806 (72) Inventors: • Hoda H El-Hendawy ET AL: "The biological • ASOLKAR, Ratnakar control of soft rot disease in melon caused by Davis, CA 95618 (US) Erwinia carotovora subsp. carotovora using • CORDOVA-KREYLOS, Ana Lucia Pseudomonas fluorescens", Microbial. Res., 1 Davis, CA 95618 (US) April 1998 (1998-04-01), pages 55-60, • TODD, Carly XP55202977, Retrieved from the Internet: Sacramento, CA 95814 (US) URL:http://ac.els-cdn.com/S094450139880021 9/1-s2.0-S0944501398800219-main.pdf?_tid=2 (74) Representative: Hertin und Partner 9b841f6-2bc9-11e5-a6d3-00000aacb35e&acdnat Rechts- und Patentanwälte PartG mbB =1437058049_03b92932b00a0e422f7be3e586fcf Kurfürstendamm 54/55 0 3b [retrieved on 2015-07-16] 10707 Berlin (DE) (56) References cited: KR-B1- 0 130 075 US-A1- 2010 266 717 US-B1- 6 194 194 US-B1- 6 194 194 Note: Within nine months of the publication of the mention of the grant of the European patent in the European Patent Bulletin, any person may give notice to the European Patent Office of opposition to that patent, in accordance with the Implementing Regulations. Notice of opposition shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention). EP 2 820 140 B1 Printed by Jouve, 75001 PARIS (FR) (Cont. next page) EP 2 820 140 B1 • S Schmoock ET AL: "Biological control of apple • ALBAN RAMETTE ET AL: "sp. nov., widespread scab and fire blight by the application of the plant-protecting bacteria producing the non-pathogenic bacterium Pseudomonas biocontrol compounds fluorescens Bk3 to the leaf surface", Orgprints, 1 2,4-diacetylphloroglucinol and pyoluteorin", January 2008 (2008-01-01), pages 306-309, SYSTEMATIC AND APPLIED MICROBIOLOGY, XP55202966, Retrieved from the Internet: vol. 34, no. 3, 9 March 2011 (2011-03-09), pages URL:http://orgprints.org/13736/1/306-309.p df 180-188, XP028192238, ISSN: 0723-2020, DOI: [retrieved on 2015-07-16] 10.1016/J.SYAPM.2010.10.005 [retrieved on • STOCKWELL ET AL: "Using Pseudomonas spp. 2011-02-15] for Integrated Biological Control", • DATABASECA [Online] CHEMICAL ABSTRACTS PHYTOPATHOLOGY, AMERICAN SERVICE, COLUMBUS, OHIO, US; 16 December PHYTOPATHOLOGICAL SOCIETY, US, vol. 97, 1 1998 (1998-12-16), AL-SHIBIB, A. ET AL: February 2007 (2007-02-01), pages 244-249, "Antimicrobial activity of pyoverdin", XP008166405, ISSN: 0031-949X XP002742574, retrieved from STN Database • JI P ET AL: "Integrated biological control of accession no. 1998:787676 & AL-SHIBIB, A. ET bacterial speck and spot of tomato under field AL: "Antimicrobial activity of pyoverdin", conditions using foliar biological control agents BULLETIN OF PHARMACEUTICAL SCIENCES, and plant growth-promoting rhizobacteria", ASSIUT UNIVERSITY , 21(1), 37-40 CODEN: BIOLOGICAL CONTROL, SAN DIEGO, CA, US, BPAUEC; ISSN: 1110-0052, 1998, vol. 36, no. 3, 1 March 2006 (2006-03-01), pages • DATABASECA [Online] CHEMICAL ABSTRACTS 358-367, XP024905380, ISSN: 1049-9644, DOI: SERVICE, COLUMBUS, OHIO, US; 30 October 10.1016/J.BIOCONTROL.2005.09.003 [retrieved 2000 (2000-10-30), WANG, CHUNXIA ET AL: on 2006-03-01] "Effect of transferring • M.A.A Seleim ET AL: "biological control of 1-aminocyclopropane-1-carboxylic acid (ACC) bacterialwilt of tomato by plant growth promoting deaminase genes into Pseudomonas rhizobacteria",plant pathology journal, 1 January fluorescens strain CHAO and its gacA derivative 2011 (2011-01-01), pages 146-153, XP55039810, CHA96 on their growth-promoting and Retrieved from the Internet: disease-suppressive capacities", XP002742582, URL:http://docsdrive.com/pdfs/ansinet/ppj/ retrieved from STN Database accession no. 2011/146-153.pdf [retrieved on 2012-10-02] 2000:760346 & WANG, CHUNXIA ET AL: "Effect • MATHIYAZHAGAN KAVINO ET AL: "Induction of of transferring systemic resistance in banana (Musa spp.) 1-aminocyclopropane-1-carboxylic acid (ACC) against Banana bunchy top virus (BBTV) by deaminase genes into Pseudomonas combining chitin with root-colonizing fluorescens strain CHAO and its gacA derivative Pseudomonas fluorescens strain CHA0", CHA96 on their growth-promoting and EUROPEAN JOURNAL OF PLANT PATHOLOGY, disease-suppressive capacities", CANADIAN KLUWER ACADEMIC PUBLISHERS, DO, vol. 120, JOURNAL OF MICROBIOLOGY , 46(10), 898-907 no. 4, 1 November 2007 (2007-11-01), pages CODEN: CJMIAZ; ISSN: 0008-4166, 2000, DOI: 353-362, XP019572197, ISSN: 1573-8469 10.1139/W00-071 • MUHAMMAD NADEEM HASSAN ET AL: • RAMETTE, ALBAN ET AL.: ’Pseudomonas "Suppression of red rot caused by protegens sp. nov., widespread plant -protecting Colletotrichum falcatum on sugarcane plants bacteria producing he biocontrol compounds using plant growth-promoting rhizobacteria", 2,4-diacetylphlo- roglucinol and pyoluteorin’ BIOCONTROL, KLUWER ACADEMIC SYSTEMATIC AND APPLIED MICROBIOLOGY PUBLISHERS, DO, vol. 55, no. 4, 24 February 2010 vol. 4, no. 3, 09 March 2011, pages 180 - 188, (2010-02-24), pages531-542, XP019813323, ISSN: XP028192238 1573-8248 • MOLLOY, DANIEL P. ET AL.: ’Overview of a novel • DON CRONIN ET AL: "Ecological interaction of a greentechnology: Biological control ofzebra and biocontrol Pseudomonas fluorescens strain quaggamussels with Pseudomonas fluorescens’ producing 2,4-diacetylphloroglucinol with the BACTERIAL PROJECT OVERVIEW 24 August soft rot potato pathogen Erwinia carotovora 2007, pages 1 - 9, XP055159308 subsp. atroseptica", FEMS MICROBIOLOGY ECOLOGY, vol. 23, no. 2, 17 June 1997 (1997-06-17), pages 95-106, XP55203668, ISSN: 0168-6496, DOI: 10.1111/j.1574-6941.1997.tb00394.x 2 EP 2 820 140 B1 Description TECHNICAL FIELD 5 [0001] Compositions and methods for controlling phytopathogenic microorganisms, particularly bacteria and fungi, obtained from Pseudomonas sp, particularly, Pseudomonas protogens ATCC 55799 are provided. BACKGROUND 10 [0002] Plant pathogens are responsible for significant losses in agricultural production. Diseases in plants may be caused by bacteria, fungi or viruses. [0003] Most bacterial plantdiseases can be controlled with a combination of host resistance,cultural practices, chemical and biological control. [0004] Several strains of Pseudomonas have previously demonstrated biocontrol properties (see for example, Dowling 15 and O’Gara, 1994, for discussion of antifungal and antibacterial properties; Keel et al., 1992, for discussion of antibacterial properties, US Patent No. 5,622,846, 5,552,315, Ramette et al., 2011). However, there is no clear understanding re- garding the mechanisms of pathogen control. Some theories include the induction of systemic resistance in the host plant, competition with the plant pathogens or the productions of antagonistic compounds against the plant pathogens. [0005] Pseudomonas strain CL145A has been isolated from water samples and has a demonstrated ability to control 20 mollusks (see, for example, see Molloy, D. P. US Patent No. 6,194,194, issued February 27, 2001 and US Patent Application Pub. No. 20100266717). [0006] Wang, Chunxia et al. disclose the "Effect of transferring 1-aminocyclopropane-1-carboxylic acid (ACC) deam- inase genes into Pseudomonas fluorescens strain CHAO and its gacA derivative CHA96 on their growth-promoting and disease-suppressive capacities" in the Canadian Journal of Microbiology. 25 SUMMARY OF THE INVENTION [0007] Provided are isolated compounds and compositions obtained from Pseudomonas ATCC 55799 having anti- microbial properties and particularly, antibacterial properties and antifungal properties. 30 [0008] Disclosed herein are compounds derived from Pseudomonas species that have the following characteristics: (a) is obtainable from a Pseudomonas species, particularly, a Pseudomonas species which produces at least one compound that controls zebra, quagga and golden mussels; (b) modulates one or more species of phytopathogenic
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    Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels Cyril Zappelini To cite this version: Cyril Zappelini. Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels. Sciences agricoles. Université Bourgogne Franche- Comté, 2018. Français. NNT : 2018UBFCD057. tel-01902775 HAL Id: tel-01902775 https://tel.archives-ouvertes.fr/tel-01902775 Submitted on 23 Oct 2018 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. UNIVERSITÉ DE BOURGOGNE FRANCHE-COMTÉ École doctorale Environnement-Santé Laboratoire Chrono-Environnement (UMR UFC/CNRS 6249) THÈSE Présentée en vue de l’obtention du titre de Docteur de l’Université Bourgogne Franche-Comté Spécialité « Sciences de la Vie et de l’Environnement » ÉTUDE DES COMMUNAUTES MICROBIENNES RHIZOSPHERIQUES DE LIGNEUX INDIGENES DE SOLS ANTHROPOGENIQUES, ISSUS D’EFFLUENTS INDUSTRIELS Présentée et soutenue publiquement par Cyril ZAPPELINI Le 3 juillet 2018, devant le jury composé de : Membres du jury : Vera SLAVEYKOVA (Professeure, Univ. de Genève) Rapporteure Bertrand AIGLE (Professeur, Univ. de Lorraine) Rapporteur & président du jury Céline ROOSE-AMSALEG (IGR, Univ. de Rennes) Examinatrice Karine JEZEQUEL (Maître de conférences, Univ. de Haute Alsace) Examinatrice Nicolas CAPELLI (Maître de conférences HDR, UBFC) Encadrant Christophe GUYEUX (Professeur, UBFC) Co-directeur de thèse Michel CHALOT (Professeur, UBFC) Directeur de thèse « En vérité, le chemin importe peu, la volonté d'arriver suffit à tout.
  • Microorganisms-08-01166-V3.Pdf

    Microorganisms-08-01166-V3.Pdf

    microorganisms Article Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene Léa Girard 1 ,Cédric Lood 1,2 , Hassan Rokni-Zadeh 3, Vera van Noort 1,4, Rob Lavigne 2 and René De Mot 1,* 1 Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium; [email protected] (L.G.); [email protected] (C.L.); [email protected] (V.v.N.) 2 Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; [email protected] 3 Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran; [email protected] 4 Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, The Netherlands * Correspondence: [email protected]; Tel.: +32-16329681 Received: 23 June 2020; Accepted: 28 July 2020; Published: 31 July 2020 Abstract: The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or engaging in more laborious and costly approaches. The rpoD gene, like the 16S rRNA gene, is included in most MLSA procedures and has already been suggested for the rapid identification of certain groups of Pseudomonas. However, a comprehensive overview of the rpoD-based phylogenetic relationships within the Pseudomonas genus is lacking. In this study, we present the rpoD-based phylogeny of 217 type strains of Pseudomonas and defined a cutoff value of 98% nucleotide identity to differentiate strains at the species level.
  • The Ever-Expanding Pseudomonas Genus: Description of 43

    The Ever-Expanding Pseudomonas Genus: Description of 43

    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 14 July 2021 doi:10.20944/preprints202107.0335.v1 Article The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas Putida Group Léa Girard1+, Cédric Lood1,2+, Monica Höfte3, Peter Vandamme4, Hassan Rokni-Zadeh5, Vera van Noort1,6, Rob Lavigne2*, René De Mot1,* 1 Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Aren- berg 20, 3001 Leuven, Belgium; [email protected] (L.G.), [email protected] (C.L.), [email protected] (V.v.N.) 2 Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; [email protected] 3 Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 4 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; [email protected] 5 Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran; [email protected] 6 Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, The Netherlands + The authors contributed equally to this work. * Correspondence: [email protected], +3216379524; [email protected] ; Tel.: +3216329681 Abstract: The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution.