Characterization of microbial communities in Technosols constructed for industrial wastelands restoration Farhan Hafeez To cite this version: Farhan Hafeez. Characterization of microbial communities in Technosols constructed for industrial wastelands restoration. Agricultural sciences. Université de Bourgogne, 2012. English. NNT : 2012DIJOS029. tel-00859362 HAL Id: tel-00859362 https://tel.archives-ouvertes.fr/tel-00859362 Submitted on 7 Sep 2013 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. Ecole Doctorale Environnements-Santé-STIC-E2S UMR 1347 Agroecology INRA/ Université de Bourgogne/AgroSup Dijon THÈSE Pour obtenir le grade de Docteur de l’Université de Bourgogne Discipline: Sciences Vie Spécialité : Ecologie Microbienne Par Farhan HAFEEZ Le 06 Septembre 2012 Characterization of microbial communities in Technosols constructed for industrial wastelands restoration Directeur de thèse Laurent PHILIPPOT Co-directeur de thèse Fabrice MARTIN-LAURENT E. BENIZRI Professeur, Université de Lorraine, INRA , Nancy Rapporteur F. DOUAY Enseignant-Chercheur , Groupe ISA, Lille Rapporteur J. GUZZO Professeur, Université de Bourgogne, Dijon Examinateur C. SCHWARTZ Professeur, Université de Lorraine, INRA, Nancy Examinateur L. PHILIPPOT Directeur de Recherche, INRA, Dijon Directeur de thèse F. MARTIN-LAURENT Directeur de Recherche, INRA, Dijon Co-directeur de thèse Dedication I dedicate this dissertation to my family, who always motivated and encouraged me to fulfill my dreams, and especially…. to my mother for her unconditional love to my Father who is no more with us, but still live and walk beside us everyday, ‘unseen, unheard, but always near, still loved, still missed…. 2 Acknowledgements Acknowledgements It is only just to mention the fact that it would not have been possible to write this Doctoral Thesis without the support and help of many good people around me, to only some of whom a particular mentioning is possible in this humble gratitude. First and foremost, I pay utmost gratitude to my supervisor Dr. Laurent Philippot, whose encouragement, and radiant guidance made this thesis a reality. He served as an inspiration to me as I hurdle all the obstacles in the completion of this research work. His undying efforts and experience paved my way through the difficult and tiresome path of research. Despite his tight schedules, he always provided me substantial guidance and valuable suggestions throughout my PhD, and never stopped inspiring me for hard work. Without his kind supervision my thesis would have remained just a dream for me. I would like to extend my heartiest gratitude to my co-supervisor Dr. Fabrice Martin-Laurent, for his dynamic and intellectual supervision. Indeed, it was an honor for me to work under his supervision. I am thankful to him for sharing his extensive experience and knowledge and appreciate his support throughout my time here. I am grateful for his keen interest in my research work and constructive suggestions which served as a beacon of guidance for me. I wish to extend my thanks to Dr. Philippe Lemanceau, director of Agroécologie (INRA, Dijon) for welcoming me and providing me with a great opportunity to work in this prestigious research laboratory. I express my feelings of most sincere gratitude and devout appreciations to all the jury members, Emile Benizri, Francis Douay, Jean Guzzo and Christophe Schwartz for taking out time from their busy schedules in accepting and evaluating my research work and for the comments and suggestions that will help to improve the quality of this work and also my approach towards the overall research work. I share the credit of my work with Jean Claude Germon, Aymé Spor and Romain Barnard for their thoughtful comments and valuable suggestions in the thesis write-up. I thank Chris for helping in PDA data analyses and especially Aymé for the assistance in statistical analyses. I would like to extend gratitude to Christophe Schwartz and Alain Brauman for taking out time as the members of ‘Comité de Pilotage’ and for their valuable suggestions. Thanks also to Jérôme Cortet and Geoffroy Sere for time to time assistance and useful discussions which helped me to understand the work on Technosols. My deepest thanks to Jérémie, David, Marie-Christine and Florian for their valuable assistance and help to learn various methods I needed to perform. I am grateful to Nadine, Marion, Frederique, Géraldine, Abdel, Najoi, Chloé, Ines, Fiona, Aude, Anthony, Irène, Koki, and all other fellow research members at INRA, Dijon for their affectionate attitude, valuable suggestions and best cooperation throughout my stay in the lab. I feel privileged to have worked in the cooperative and encouraging environment of this laboratory, which enabled me to succeed in my research endeavors. I cannot forget the invaluable support of Sabir especially during my early days in the lab. I owe my deepest gratitude to the Higher Education Commission (HEC) Pakistan, and the Doctoral School of the University of Burgundy (France) for their financial and academic sponsorship of my PhD. Thanks to SFERE also. This PhD was part of the ‘Biotechnosol program’ coordinated by Dr J. Cortet, carried out as part of the Gessol program ‘Fonctions environnementales des sols et gestion du patrimoine sol’ funded by the French Ministry of Ecology in cooperation with the ADEME. I would like to thank the technical staff of the 3 Acknowledgements Laboratoire Sols et Environnement, as well as the GISFI. I extend my gratitude to all the individuals and organizations that have directly or indirectly helped me throughout my work. To HEC thank you again for providing me an opportunity to carry on my doctoral studies in France by awarding me the PhD scholarship grants. I am indebted to my longtime friends who deserve recognition here for their friendship, those in Pakistan including Baqa, Maqshoof, Danish, Khuram, Iftikhar, Malik, Fani, Imran, Asif, Shakil and Usman and also those in Dijon including Anees, Ashfaque, Sabir, Amjad, Hamid, Ali, Farasat, Sajjad, Atif, Abid, Ahmed, Ahsan, and Shamsheer for their enthusiastic attitude, and moral support during my entire academic pursuit. Time spent in Dijon will be remembered for ages (Sajjad and Atif can better express). Again, I would like to thank all other friends in France and in Pakistan with whom I had a nice time. Finally, thanks to my family, for their love, support, prayers for me and encouragement over the years throughout my studies. No acknowledgements could ever adequately express my obligations to my affectionate and adoring parents, brothers and sisters for their amicable attitude and love, mellifluous affections, inspiration, well wishing and keen interest which hearten me to achieve success in every sphere of life. I cannot find words in acknowledging that all the credit goes to my beloved father, who is no more with us but without his support, the present distinction would have been merely a dream. Sweet memories of my loving father are always encouraging me in hard and harsh times. Last but by no means the least, I praise God Almighty whose blessings and glory flourished my thoughts and Who gave me courage and health to finalize my study. FARHAN HAFEEZ 4 Résumé Résumé L'augmentation de la dégradation des sols et ses conséquences sur les services écosystémiques nécessite le développement de stratégies de restauration de ces sols. La constitution de Technosols, résultant de l’assemblage de sols pollués et de déchet industriels, est une approche innovatrice pouvant à la fois permettre de restaurer les sols et de recycler des sous- produits industriels. Des études récentes ont mis en évidence que les Technosols pouvaient assurer des services écosystémiques tels que la production primaire. Toutefois, notre connaissances des autres services écosystémiques rendus par les Technosols tels que les cycles biogéochimiques est limitée. En raison de la contribution significative des communautés microbiennes aux cycles biogéochimiques dans les sols, l’objectif de ce travail de thèse était l’effet du type de Technosol sur les communautés microbiennes et plus particulièrement les communautés fonctionnelles impliquées dans le cycle de l’azote. Dans ce contexte, (i) la densité et la diversité de la communauté bactérienne totale, (ii) la densité de la communauté crenarchéenne ainsi que (iii) la densité et les activités des communautés nitrifiante et dénitrifiante ont été étudiées dans deux types de Technosols différents. Les résultats obtenus montrent que la diversité et la composition de la communauté bactérienne des deux Technosols n'étaient pas significativement différentes entre elles, et similaires à celles de ‘sols naturels’, les Proteobacteria étant le phylum dominant (50-80%). La densité de la communauté bactérienne oxydant l’ammonium était non seulement plus importante que celle des crenarcheae qui oxyde l’ammonium, mais est également corrélée avec l'activité potentielle de nitrification suggérant ainsi que les bactéries sont responsables de l’oxydation de l’ammonium dans les Technosols.