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Réseaux D'interactions, Biodiversité Et Services Éco-Systémiques En Milieu Agricole

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Réseaux D'interactions, Biodiversité Et Services Éco-Systémiques En Milieu Agricole Réseaux d’interactions, biodiversité et services éco-systémiques en milieu agricole : que nous apprennent les coléoptères carabiques ? Stefaniya Kamenova To cite this version: Stefaniya Kamenova. Réseaux d’interactions, biodiversité et services éco-systémiques en milieu agri- cole : que nous apprennent les coléoptères carabiques ?. Biodiversité et Ecologie. Université de Poitiers, 2013. Français. tel-01076147 HAL Id: tel-01076147 https://tel.archives-ouvertes.fr/tel-01076147 Submitted on 13 Feb 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. THESE Pour l'obtention du grade de DOCTEUR DE L'UNIVERSITÉ DE POITIERS UFR des Sciences Fondamentales et Appliquées Centre d'Etudes Biologiques de Chizé – CEBC Institut de Génétique, Environnement et Protection des Plantes - IGEPP (Diplôme National - Arrêté du 7 août 2006) École doctorale : Sciences pour l'Environnement - Gay Lussac Secteur de recherche : Biologie de l'Environnement, des Populations, Ecologie Présentée par: Stefaniya KAMENOVA Réseaux d’interactions, biodiversité et services éco-systémiques en milieu agricole : que nous apprennent les coléoptères carabiques ? Directeur de thèse : Vincent Bretagnolle Co-directeur : Manuel Plantegenest Soutenue le 13 décembre 2013 devant la Commission d’Examen François Pompanon Maître de conférences-Université de Grenoble Rapporteur Philippe Tixier Chercheur-CIRAD Rapporteur David Bohan Directeur de recherche-INRA Examinateur Pierre Franck Chargé de recherche-INRA Examinateur Frédéric Grandjean Professeur-Université de Poitiers Examinateur Anne Le Ralec Professeur-Agrocampus Ouest Rennes Examinateur Bertrand Gauffre Chargé de recherche-INRA Co-directeur Manuel Plantegenest Professeur-Agrocampus Ouest Rennes Co-Directeur Table des matières REMERCIEMENTS INTRODUCTION ET PROBLÉMATIQUE ............................................................................. 1 1) Le contexte général de l’agriculture moderne ................................................. 1 1.1) Vers un nouveau paradigme de l’agriculture ............................................ 2 1.2) Biodiversité et services éco-systémiques en milieu agricole .................... 3 1.3) Le contrôle biologique : la biodiversité pour la protection des cultures ..... 7 2) Ecologie des communautés et mécanismes à l’origine de la biodiversité ........ 9 2.1) Concepts théoriques ................................................................................ 9 2.2) Des concepts à l’application: les apports de l’écologie des communautés à la gestion des espaces agricoles ........................................... 10 3) De nouveaux outils pour l’étude de la biodiversité : barcoding et nouvelles technologies de séquençage haut-débit .............................................................. 12 3.1) Barcoding moléculaire ou 15 000 taxonomistes à perpétuité pour décrire la biodiversité? .................................................................................................... 12 3.2) Extension de la définition de barcoding: métabarcoding ........................ 14 4) Modèle d’étude : la communauté des coléoptères carabiques en milieu agricole ............................................................................................................... 17 4.1) Présentation générale et bilan des connaissances ................................ 17 4.2) Comportement alimentaire et potentiel de régulation ............................. 23 4.3) Coexistence et interactions interspécifiques .......................................... 23 5) Objectifs de la thèse et démarche générale .................................................. 25 CHAPITRE 1 : Mise au point méthodologique pour la caractérisation moléculaire du régime alimentaire des coléoptères carabiques par séquençage haut-débit ............ 27 1) Présentation générale des méthodes pour l’étude du régime alimentaire en écologie ............................................................................................................... 27 1.1) Les méthodes classiques ......................................................................... 27 1.2) Les méthodes moléculaires ...................................................................... 28 2) Problématique générale et démarche méthodologique ................................. 33 2.1) Matériel & Méthode ............................................................................... 33 2.2) Résultats ............................................................................................... 40 2.3) Discussion & Perspectives..................................................................... 47 3) ARTICLE: Molecular high-throughput characterization of plant consumption in insect generalist predators .................................................................................. 53 4) Annexe Chapitre 1 ........................................................................................ 80 CHAPITRE 2 : Etude des relations trophiques et des mécanismes de coexistence chez les coléoptères carabiques : une approche isotopique ............................................ 89 1) Les isotopes stables : trente ans au service des écologistes ........................ 89 1.1) Présentation et intérêt général de la technique ...................................... 89 1.2) Principes de base et sources de variations ............................................ 90 1.3) Mises en gardes méthodologiques ........................................................ 92 2) Questions de recherche et stratégie d’analyse ............................................. 93 2.1) Problématique de recherche .................................................................. 93 2.2) Problématique méthodologique ............................................................. 94 3) ARTICLE: Resource overlapping and resource partitioning in carabid beetles, a community-scale stable isotope analysis ........................................................... 102 4) Conclusion générale ................................................................................... 122 5) Annexe Chapitre 2 ...................................................................................... 123 CHAPITRE 3 : Aspects comportementaux de la différentiation de niche et mécanismes de coexistence chez les coléoptères carabiques ................................................... 126 1) ARTICLE: Behavioral-driven micro-scale niche differentiation in carabid beetles (Coleoptera: Carabidae) .................................................................................... 127 2) Conclusion générale ................................................................................... 147 CHAPITRE 4 : Caractérisation moléculaire haut-débit du régime alimentaire des coléoptères carabiques en milieu agricole ............................................................. 148 1) Introduction ................................................................................................. 148 2) Matériel & Méthode..................................................................................... 149 2.1) Evaluation in silico des amorces métabarcoding .................................... 149 2.2) Echantillonnage ...................................................................................... 149 2.3) Choix des individus ................................................................................. 150 2.4) Constitution de la base de référence ...................................................... 150 2.5) Séquençage haut-débit .......................................................................... 151 2.6) Analyses ................................................................................................. 153 3) Résultats .................................................................................................... 153 3.1) Evaluation in silico des amorces métabarcoding .................................... 153 3.2) Echantillonnage et choix des individus ................................................... 154 3.3) Constitution de la base de référence ...................................................... 155 3.4) Séquençage ........................................................................................... 158 4) Discussion .................................................................................................. 165 5) Annexe 1 Chapitre 4: Evaluation par PCR in silico des amorces universelles COI et 16S ........................................................................................................ 167 6) Annexe 2 Chapitre 4: Identification taxonomique des spécimens séquencés pour la base de référence barcoding locale. ...................................................... 171 DISCUSSION GÉNÉRALE ET PERSPECTIVES ............................................................... 181 1) Bilan des résultats produits dans le cadre de cette thèse ........................... 181 2) Discussion: données de la littérature et perspectives .................................. 184 2.1) Questions de recherche ........................................................................
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