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Pantoea Spp: a New Bacterial Threat to Rice Production in Sub-Saharan Africa

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Pantoea Spp: a New Bacterial Threat to Rice Production in Sub-Saharan Africa Pantoea spp : a new bacterial threat to rice production in sub-Saharan Africa Kossi Kini To cite this version: Kossi Kini. Pantoea spp : a new bacterial threat to rice production in sub-Saharan Africa. Botan- ics. Université Montpellier; AfricaRice (Abidjan), 2018. English. NNT : 2018MONTG015. tel- 02868182v2 HAL Id: tel-02868182 https://tel.archives-ouvertes.fr/tel-02868182v2 Submitted on 16 Jun 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. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En ÉVOLUTION DES SYSTÈMES INFECTIEUX École doctorale GAIA (N°584) Unité Mixte de recherche IPME Interactions Plantes-Microorganismes-Environnement (IRD, CIRAD, UM) Pantoea spp: a new bacterial threat for rice production in sub-Saharan Africa. Présentée par par Kossi KINI Le 22 Mai 2018 Sous la direction de Ralf KOEBNIK et Drissa SILUÉ Devant le jury composé de : RAPPORT DE GESTION Ralf KOEBNIK, Directeur de Recherche, IRD Directeur de thèse 2015 Drissa SILUÉ, Chargé de Recherche, AfricaRice Co directeur de thèse Claude BRAGARD, Professeur des Universités, UCL Rapporteur Marie-Agnès JACQUES, Directrice de Recherche, INRA Présidente du jury Monique ROYER, Cadre Scientifique, CIRAD Examinatrice Alice BOULANGER, Directrice de Recherche, INRA Examinatrice Kossi KINI PhD manuscript 22/05/2018 i Kossi KINI PhD manuscript 22/05/2018 Résumé Parmi les 24 espèces de Pantoea décrites jusqu'à présent, cinq ont été signalées jusqu'à 46 fois dans 21 pays comme phytopathogènes d'au moins 31 cultures. En effet, P. ananatis et P. agglomerans ont été signalés comme bactéries phytopathogènes pour au moins dix cultures économiquement importantes, y compris le riz. Récemment, le Centre du Riz pour l'Afrique et ses partenaires ont soupçonné la présence d'une bactérie émergente qui cause la bactériose du riz dans plusieurs pays africains. L'agent causal a été confirmé comme appartenant au genre Pantoea . Les objectifs de notre projet de thèse étaient (i) d'améliorer la collection d’isolats d'AfricaRice par de nouvelles collections (ii) de développer des outils de diagnostic et de génotypage. Nos résultats ont montré que les bactéries capables de produire des symptômes flétrissement bactérien du riz en Afrique forment un complexe d'espèces composé principalement de P. ananatis , P. stewartii et P. agglomerans . Différents types d'outils de diagnostic et de caractérisations ont ensuite été développés et validés. Les résultats de l'utilisation de ces outils ont permis de mettre en évidence la présence de ce complexe bactérien dans plusieurs pays africains et ont fourni des détails sur sa structuration géographique. En effet, nous avons diagnostiqué un complexe d'espèces bactériennes, phytopathogènes du riz dans 11 pays africains (Bénin, Burkina Faso, Burundi, Ghana, Côte d'Ivoire, Mali, Niger, Nigeria, Sénégal, Tanzanie, Togo). En plus, nous avons analysé trois génomes de P. ananatis africains puis développé, évalué et validé des outils d'analyse VNTR à locus multiples. Les résultats ont fourni un aperçu des relations phylogénétiques qui existent entre les souches de P. ananatis isolées du riz et les souches provenant d'autres sources (plantes, animaux et environnement). En effet, les résultats préliminaires ont montré que plusieurs souches de P. ananatis isolées du riz en Afrique, en Asie et en Europe étaient phylogénétiquement liées et formaient un groupe qui les différenciait de P. ananatis d'autres sources. En conclusion, les résultats de ce projet de thèse constituent une base solide pour de futures études de Pantoea spp.en Afrique. ii Kossi KINI PhD manuscript 22/05/2018 Abstract Among the 24 species of Pantoea described so far, five have been reported up to 46 times in 21 countries as phytopathogens of at least 31 crop plants. Indeed, P. ananatis and P. agglomerans have been reported as phytopathogenic bacteria for at least ten economically important crops, including rice. Recently, Africa Rice Center and its partners have suspected the presence of an emerging bacterium that causes rice bacterial blight in several African countries. The causal agent has been confirmed as belonging to the genus Pantoea . The objectives of our thesis project were (i) to improve the collection of existing AfricaRice isolates through new collections, and (ii) to develop diagnostic and genotyping tools. Our results showed that bacteria capable of producing bacterial blight symptoms of rice in Africa form a species complex composed mainly of P. ananatis , P. stewartii and P. agglomerans . Various types of diagnostic tools were developed and validated. The results obtained using these tools helped to point out the presence of this bacterial complex in several African countries. Moreover, it provided details on its geographical structure. As a result, we diagnosed a bacterial species complex, which is phytopathogenic of rice in 11 African countries (Benin, Burkina Faso, Burundi, Ghana, Ivory Coast, Mali, Niger, Nigeria, Senegal, Tanzania, Togo). In addition, we analyzed three genomes of African P. ananatis and developed, evaluated, and validated Multiple Locus VNTR Analysis (MLVA) tools. The data provided insights into the phylogenetic and phylogenomic relationships that exist between P. ananatis strains isolated from rice and strains from other sources (plants, animals and environment). Indeed, preliminary results showed that several strains of P. ananatis isolated from rice in Africa, Asia and Europe were phylogenetically linked and formed a group that differentiated them from P. ananatis from other sources. In conclusion, the results of this thesis project lay a solid foundation for the future studies of Pantoea spp.in Africa. iii Kossi KINI PhD manuscript 22/05/2018 Acknowledgements This project was carried out in sandwich program with a collaboration between Africa Rice Cotonou (Benin) and Research Institute for Development (IRD) Montpellier (France). As such, I would like to give thanks to the management of the two institutes and their directors for having offered me good conditions to work. This project was realized with the financial support of IRD's Research Allocation for Southern Thesis program (ARTS) and International Foundation for Science (IFS) grants. We thank the first officials of ARTS and IFS for their financial support. I would like to give thanks to the President of the jury and all its members for agreeing to evaluate this thesis. Special thanks go to: Þ Dr Valérie VERDIER for allowing me to join her team: Interaction Plantes Microorganismes Environment (IPME). Þ The management of IPME for all the given services and support. Þ The Presidency of Montpellier’s university and the direction of the Doctoral School GAIA for having allowed me to register at UM as PhD student. At the end of this project, I was convinced that thise thesis was far from being a solitary work. It represents a long-term job, and is, therefore, the thread of a slice of life during its duration. Briefly, I couldn't have done this doctoral work without the support of a broad number of people whose generosity, good humor and interest in our thesis allowed me to progress in this delicate "apprentice researcher phase" THANKS, to Ralf KOEBNIK and Drissa SILUE, my two thesis co-supervisors who form a complementary duet, which made our thesis a completed work. Without your involvement and dedication in obtaining this scholarship for my thesis, I do not know what my wife will, my children and I would have been right now. As a Christian, I request every time that God provides you an excellent health and long life. With Drissa, I have understood what the following expressions mean: Producing results by being able to work autonomously under pressure, resistant to stress, be tactful and diplomatic in the exercise of your duties. With Ralf, I have understood what lies behind the expressions, demonstrating initiative and liking teamwork, having the ability to plan, organize and put in place effective working procedures, work with flexibility, while having the attention to detail and rigor in the accomplishment of his work. For this reason, during this project, I immersed myself in these expressions and made them my work and life mottoes. I sincerely thank the members of my thesis Committee, who during the three years, were the lighthouse that guided our ship aboard port. Special thanks to Christian Vernière, my Reference for the ED GAIA, for his advice and for sharing his experience with us. I would like to thank all the members of my two teams (GTIPP of UMR IPME in Montpellier in France and the Phytopathology Lab of Africa Rice Cotonou Benin) who allowed me spend these pleasant years in the laboratory. Thank also to all the staff (researcher, engineers, iv Kossi KINI PhD manuscript 22/05/2018 technicians, observers, trainees ...) for their help and their kindness. I extend sincere thanks to the other PhD students and MSc students from both teams. I know, I'm not the most available friend and the most smiling because of the experiences during this thesis but you supported my moods, my awkwardness, the problems and incomprehension generated during all these years. At IRD Montpellier, I address a special thanks to Boris, Emmanuel, Servane, and Charlotte for the discussions and the practical advises. Thanks to Sandrine and Florence for their kindness and availability. To other PhD students and postdocs, past and present, who are: Céline, Mathilde, Tu, Hinda, Alvaro, Jonathan, Taca, Kader, Ganna some thanks for your presence and smiles. I thank all the permanent members of the GTIPP team for their availability.
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