Mohamed Adam Mohamed Abdou Institut für Epidemiologie und Pathogendiagnostik Root-knot nematodes: abundance in organic farming, diff erentiation among populations, microbes attached to juveniles in soil, and bacterial antagonists Dissertationen aus dem Julius Kühn-Institut Julius Kühn-Institut Bundesforschungsinstitut für Kulturpfl anzen Kontakt: Mohamed Adam Mohamed Abdou Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen (JKI) Institut für Epidemiologie und Pathogendiagnostik Messeweg 11/12 38104 Braunschweig Germany Von der Fakultät Architektur, Bauingenieurwesen und Umweltwissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte Dissertation Die Schriftenreihe ,,Dissertationen aus dem Julius Kühn-lnstitut" veröffentlicht Doktorarbeiten, die in enger Zusammenarbeit mit Universitäten an lnstituten des Julius Kühn-lnstituts entstanden sind Der Vertrieb dieser Monographien erfolgt über den Buchhandel (Nachweis im Verzeichnis lieferbarer Bücher - VLB) und OPEN ACCESS im lnternetangebot www.jki.bund.de Bereich Veröffentlichungen. Wir unterstützen den offenen Zugang zu wissenschaftlichem Wissen. Die Dissertationen aus dem Julius Kühn-lnstitut erscheinen daher OPEN ACCESS. Alle Ausgaben stehen kostenfrei im lnternet zur Verfügung: http://www.jki.bund.de Bereich Veröffentlichungen We advocate open access to scientific knowledge. Dissertations from the Julius Kühn-lnstitut are therefore published open access. All issues are available free of charge under http://www.jki.bund.de (see Publications). Bibliografische Information der Deutschen Nationalbibliothek Die Deutsche Nationalbibliothek verzeichnet diese Publikation In der Deutschen Nationalbibliografie: detaillierte bibliografische Daten sind im lnternet über http://dnb.d-nb.de abrufbar. ISBN 978-3-95547-008-1 DOI 10.5073/dissjki.2014.002 Herausgeber l Editor Julius Kühn-lnstitut, Bundesforschungsinstitut für Kulturpflanzen, Quedlinburg, Deutschland Julius Kühn-lnstitut, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany © Julius Kühn-lnstitut, Bundesforschungsinstitut für Kulturpflanzen sowie der genannten Universität, 2014. Das Werk ist urheberrechtlich geschützt. Die dadurch begründeten Rechte, insbesondere die der Übersendung, des Nachdrucks, des Vortrages, der Entnahme von Abbildungen, der Funksendung, der Wiedergabe auf fotomechanischem oder ähnlichem Wege und der Speicherung in Datenverarbeitungsanlagen, bleiben, auch bei nur auszugsweiser Verwertung, vorbehalten. Root-knot nematodes: abundance in organic farming, differentiation among populations, microbes attached to juveniles in soil, and bacterial antagonists Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte Dissertation Von Mohamed Adam Mohamed Abdou aus Giza / Ägypten 1. Referentin: apl. Professorin Dr. Kornelia Smalla 2. Referent: Professor Dr. Dieter Jahn eingereicht am: 03.02.2014 mündliche Prüfung (Disputation) am: 01.04.2014 Druckjahr 2014 VORVERÖFFENTLICHUNGEN DER DISSERTATION Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch die Mentorin der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen 1. Adam M, Heuer H, Ramadan EM, Hussein MA, Hallmann J (2013) Occurrence of plant-parasitic nematodes in organic farming in Egypt. Int. J. Nematol. 23, 82-90. 2. Adam M, Heuer H, Hallmann J (2014) Bacterial antagonists of fungal pathogens also control root-knot nematodes by induced systemic resistance of tomato plants. PLoS ONE 9, e90402, DOI: 10.1371/journal.pone.0090402. 3. Adam M, Westphal A, Hallmann J, Heuer H (2014) Specific microbial attachment to root-knot nematodes in suppressive soil. Appl. Environ. Microbiol.80, accepted, DOI: 10.1128/AEM.03905-13. 4. Köberl M, Ramadan, EM, Adam M, Cardinale M, Hallmann J, Heuer H, Smalla K, Berg G (2013) Bacillus and Streptomyces were selected as broad- spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiology Letters 342(2): 168-178. Eingereichte Manuskript 1. Adam M, Hallmann J, Heuer H (2014) Differentiation of Meloidogyne incognita Populations based on PCR-DGGE. Submitted to J. Nematol. Tagungsbeiträge 1. Adam, M., Westphal, A., Hallmann, J. and Heuer, H. (2013). Specific microbial attachment to root-knot nematodes in suppressive soil. (Oral VORVERÖFFENTLICHUNGEN DER DISSERTATION presentation) Annual meeting of the DPG Nematology working group, 12-13 March 2013, Syngenta breeding center, Bad Salzuflen, Germany. 2. Adam, M., Hallmann, J. and Heuer, H. (2012). Microbial communities associated with juveniles of Meloidogyne spp. in soil. (Poster) Nachwuchswissenschaftlerforum / Young Scientists Meeting, Julius Kühn- Institut, 4-6 December 2012, Quedlinburg, Germany. 3. Adam, M., Hallmann, J. and Heuer, H. (2012). Bacterial soil isolates with antagonistic activity against the root-knot nematode Meloidogyne incognita. (Poster) 58th Deutsche Pflanzenschutztagung "Pflanzenschutz – alternativlos", 10- 14 September, Braunschweig, Germany 4. Adam, M., Hallmann, J. and Heuer, H. (2012). Microbial communities associated with juveniles of Meloidogyne spp. in soil. (Poster) 14th International Symposium on Microbial Ecology 19-24 August 2012 Copenhagen, Denmark. 5. Adam, M., Hallmann, J. and Heuer, H. (2011). Microbial communities associated with juveniles of Meloidogyne spp. in soil. (Poster) Annual meeting of the DPG Nematology working group Ak-free living nematodes, Wageningen, Netherlands. ACKNOWLEDGMENTS Acknowledgments First of all, praise is due to almighty ALLAH for all he has given me, his compassion and mercifulness to allow me accomplishing this thesis. I would like to express my deep appreciation and gratitude to Dr. Holger Heuer, Julius Kühn-Institut (JKI), Institute for Epidemiology and Pathogen Diagnostics (EP), for his direct supervision and the continuous support of my Ph.D study and research. His enthusiasm and integral view on research, esteemed guidance, invaluable help, fruitful suggestions and friendly affection throughout the course of my work, made me possible to endure this thesis. I would like to express my special appreciation and thanks to Dr. Johannes Hallmann Julius Kühn- Institut (JKI), Institute for Epidemiology and Pathogen Diagnostics for giving me the opportunity to join the Nematology group in EP-institute, for the valuable supervision, encouragement, insightful comments, valuable suggestions and ideas, constructive criticism, dedicated effort in reviewing this thesis and for the time throughout this research work. I would like to express my deep gratitude and respect to Professor Dr. Kornelia Smalla Julius Kühn- Institut (JKI), Institute for Epidemiology and Pathogen Diagnostics (EP), whose advice and insight was invaluable to me. I also would like to thank her for providing me the facilities and labs, for being an open person to ideas, and for encouraging and helping me to shape my interest and ideas. I would like to thank strongly my examination committee, Prof. Dr. Dirk Selmar and Prof. Dr. Dieter Jahn from the Technical University of Braunschweig; for devoting their time to read, review and evaluate this work. ACKNOWLEDGMENTS My deep thanks goes to Mrs Elvira Woldt for training me at the beginning of my PhD work on how to use all molecular tools and providing fruitful suggestions for solving technical problems. I would also like to thank my colleagues in the Smalla group. All of them were always helpful and cooperative. Particularly, I would like to thank Doreen Babin for being a great reliable person to whom I could always talk about my problems. Additionally, I especially thank Susanne Schreiter for soil sampling and Guo-Chun Ding for help with the analysis of pyrosequencing data. I am so grateful to the Egyptian Government, Ministry of Higher Education, for the financial support offered to me to undertake this research work in Germany. I need to thank the Egyptian Cultural Office in Berlin for their support. I would like to thank all Egyptian and Arabic friends in Braunschweig for their kind inspiration, supports and, most important, their friendship. Finally, I would like to thank my parents, sisters and brothers for their great care, trust, affection, and love. Special thanks to every member of my great family. My deep gratitude is due to my dear wife Nariman for her continuous support and perseverance during the last 4 years. I would like also to express my thanks to my daughter Salma and my sons Adam and Omar who are a constant source of happiness in my life. I dedicate this thesis to my late mother and my father, who will always be in my heart. Mohamed Adam Braunschweig, January 2014 TABLE OF CONTANTS Table of contents Publication and conference contributions Acknowledgments Summary Zusammenfassung Chapter I General introduction and thesis outline 1 Chapter II Occurrence of plant-parasitic nematodes in organic 33 farming in Egypt Chapter III Differentiation of Meloidogyne incognita populations 51 based on PCR-DGGE Chapter IV Specific microbial attachment to root-knot nematodes 70 in suppressive soil Chapter V Bacterial antagonists of fungal pathogens also control 103 root-knot nematodes Chapter VI Main findings, general conclusion and future perspectives 140 SUMMARY SUMMARY Two surveys were conducted to determine