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Thèse D'antoine Gazaix THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE MONTPELLIER En Ecologie et Biodiversité École doctorale GAIA Unité de recherche Centre d’Ecologie Fonctionnelle et Evolutive Ecologie des Lythrum annuels des mares temporaires méditerranéennes. Applications à la conservation de L. thesioides dans les Costières de Nîmes. Présentée par Antoine Gazaix Le 13 décembre 2019 Sous la direction de John Thompson et Patrick Grillas RAPPORT DE GESTION 2015 Devant le jury composé de Anne Bonis, CR CNRS, Université Clermont Auvergne Rapportrice Frédéric Bioret PR, Université de Bretagne Occidentale Rapporteur Ana Rodrigues, DR, CNRS Examinatrice, Présidente du Jury Bruno Colas, PR, AgroParisTech Examinateur Frédéric Médail, PR, Aix Marseille Université Examinateur John Thompson, DR, CNRS Directeur Patrick Grillas, Directeur scientifique, Tour du Valat Directeur Résumé Les communautés de plantes des mares temporaires méditerranéennes sont caractérisées par la dominance des espèces annuelles, avec une banque de graines persistante, dont la germination est associée aux alternances d’inondation et d’assèchement. Bien que de petites tailles et irrégulièrement distribuées dans les paysages, elles possèdent une flore riche. Elles ont cependant été particulièrement détruites et dégradés, et de nombreuses espèces inféodées à cet habitat sont aujourd’hui rares et menacées. Parmi elles, six espèces annuelles du genre Lythrum sont présentes dans le sud de la France, dont Lythrum thesioides. Cette espèce supposée éteinte en Europe au milieu du XX° siècle, a été redécouverte successivement à partir de 1998 dans 3 mares temporaires méditerranéennes de France. Les objectifs de cette thèse sont (1) de caractériser les niches écologiques de ces six espèces et (2) d’utiliser cette connaissance pour proposer des actions de gestion pertinentes pour leur conservation, notamment pour L. thesioides. La première étape a été de clarifier la distribution de ces 6 espèces annuelles dans la région méditerranéenne et particulièrement celle de Lythrum thesioides. Ce travail s’est accompagné d’une étude phylogénétique des relations entre les six espèces et 13 autres du genre Lythrum. La comparaison des niches de régénération a ensuite illustré l’importance de plusieurs variables environnementales pour la germination, et principalement la température optimale de germination qui était différente entre les espèces et particulièrement élevée pour L. thesioides. L’étude des micro-niches des plantes adultes a enfin démontré une différentiation franche entre les espèces en termes de propriété du sol, et dans une moindre mesure, de présence et phénologie de la communauté végétale compagne. La combinaison des résultats de ce travail, caractérisant une niche écologique originale pour L. thesioides, a enfin été utilisée pour alimenter des propositions de gestion, composée de plusieurs scénarios pour la conservation de L. thesioides dans sa principale population dans le sud de la France. Abstract The vegetation of Mediterranean temporary pools is characterized by the dominance of annual species with a perennial seed bank whose germination is cued with cyclic flooding and drying. Although small in size and patchy in the landscape they have a riche flora. They have however suffered much from habitat loss and degradation and many species specialized to this habitat have become rare and endangered. Among these species are found six annual Lythrum species in the South of France. The objectives of this thesis were to quantify the ecological niche of these species in order to inform management action for their conservation. Management of these ecosystems and species conservation depend on knowledge the ecology of regeneration and survival in the changing environment of this ecosystem. The first step here was to clarify the distribution of the six species in the Mediterranean region and in particular L. thesioides, a species thought to be extinct in the wild and rediscovered in three Mediterranean temporary pools in France since 1998, two of which are still visible. This was accompanied by a phylogenetic study of the relationships among these six species and 13 other species in the genus studied previously. Comparison of the regeneration niche illustrated the importance of several variables for germination, principally the optimal temperature that was different among the species and in particular for the very rare L. thessioides. Examination of the micro-niche of adult plants also revealed a clear differentiation of the species in terms of soil properties and less notably the presence and phenology of associated species. The combined results of this work have been used in the construction of a management action plan composed of several scenarios for the conservation of L. thessioides at its primary site of occurrence in the South of France. Remerciements Tout d’abord, afin notamment de leurs permettre l’économie de la lecture de cette partie, je souhaite remercier l’ensemble de mon jury de thèse, les deux rapporteurs Anne Bonis et Frédéric Bioret, ainsi qu’Ana Rodrigues, Bruno Colas et Frédéric Médail, pour avoir accepté d’évaluer mon travail. Evidemment, je souhaite chaleureusement remercier mes deux encadrants de thèse. Patrick Grillas, pour m’avoir fait confiance pour ce travail, et m’avoir mis les cuissardes aux pieds. John Thompson, pour ses retours immédiats à mes manuscrits balbutiants. Merci à vous deux pour votre disponibilité et les échanges réguliers que nous avons pu entretenir. Vos deux approches initialement différentes du sujet ont, je l’espère, donné naissance à une thèse originale. J’aimerais par ailleurs remercier l’ensemble des membres de mes comités de thèse : Sandrine Maurice, Eric Imbert, Pierre Olivier Cheptou, Frédéric Médail, Simonetta Bagella et Perrine Gauthier. Je souhaite également apporter mes remerciements aux financeurs de cette thèse, SNCF réseau et Oc’Via construction, la fondation Pierre Fabre et la Klorane Botanical Foundation, ainsi que l’ensemble des membres du comité de gestion de Campuget pour leur implication : Luis de Sousa (DREAL), Hortense Lebeau (Oc’Via), Violaine Bernard (SNCF Réseau), James Molina (CBNMed), Lionel Pirsoul et Mario Klesczewski (CEN L- R). Un merci tout particulier au personnel du CEN L-R pour les échanges fréquents et les quelques journées de terrain partagées. A Mario spécifiquement, merci de m’avoir initialement permis de travailler sur ce sujet. J’espère profondément que ce travail vous sera utile, à Campuget, mais également à plus large échelle. Je remercie également toutes les personnes avec qui j’ai pu collaborer et échanger pour ces travaux de thèse, notamment Marie Pierre Dubois, Claudine Montgelard et Shirley Graham pour les analyses génétiques, Shmuel Mazar pour les échanges autour des Lythrum en Israël, Attila Mesterhazy et Andrew Efremov pour les prospections kazakhs, Laila Rhazi pour les travaux autour de la germination. J’adresse également un immense merci à toutes les personnes avec qui j’ai pu faire du terrain et échanger autour de mon travail durant cette thèse, Perrine Gauthier, Virginie Pons, Emilie Luna-Laurent et Florent Sabatier. Et évidemment je n’oublie pas Hugo Fontès, le dormeur des Costières. Merci de m’avoir offert la possibilité de voir autre chose que des Lythrum pendant ces trois années ! Le temps passé à la tour du Valat a été particulièrement enrichissant à bien des égards, et je garderai longtemps en mémoire l’ambiance unique de ce lieu. Nul doute qu’il restera gravé longtemps dans mes petits papiers. Un immense merci évidemment à l’ensemble des personnes qui ont rendu mon travail plus agréable, Marie Antoinette, Jean Claude et Florence bien évidemment ! J’ai aussi une pensée pour tous ceux qui m’ont apporté un soutien et qui ont contribué à mon travail durant les trois années, alors merci à Hadrien, Charlotte, Amélie, Solène, Corentin et bien sûr Florent, et plus généralement à tous ceux qui ont donné des petits coups de main ou simplement partagé une ou plusieurs bière. La tour a été le théâtre de soirées mémorables, de moments de vie inoubliables, et de rencontres formidables, alors merci à Manon, Elie et Elise, Carole, Emeline, Hadrien, Matteo, les Thomas, Jocelyn, Clémence, Antoine, Léo, David et tous les autres que j’oublie d’avoir animé ces moments. Je ne pourrais toutefois pas terminer ce paragraphe sans citer Sam et Charlotte, qui ne sont pas innocents à l’aboutissement de ce travail. Merci de m’avoir très certainement fait découvrir le septième meilleur carnaval du monde. Cette dernière année, et les quelques courts séjours précédents au CEFE ont été l’occasion de partager un nouvel environnement. Malgré une équipe déjà soudée, je ne suis pas peu fier d’avoir réussi à intégrer le bureau 309B, je l’espère avec un certain brio. Merci à Charlotte et Marie, de m’avoir accepté dans leur cocon. Je remercie également tous ceux qui ont pu arriver par la suite et participer à l’ambiance unique de ce lieu, Marine, Edouard, Hugo, Pierre, Audrey. Mais également Clémence, dont les provisions m’ont permis de résister à la chaleur de ce dernier été de thésard. Enfin, un merci gros comme çà (#j’ai les bras écartés) pour Guillaume. Merci pour son aide à tous les niveaux, sa fougue indomptable, et son élan de générosité lorsqu’il doit fêter quelque chose au broc, qui ont beaucoup apportés à ce travail. J’espère que cette thèse sera une nouvelle occasion de développer tous ensemble, divers mouvements de gymnastiques au rockstore ! Pour finir cette parenthèse laborantine, merci également à toutes les personnes qui font vivre ce troisième étage comme aucun autre (bien que je ne sois jamais descendu pour le vérifier). Je pense à Rémi, Ana, Anne, Virginie, Simon, Camille, Elodie, Pauline, Gustave, Gaël, et évidemment Victor dont l’aide fût précieuse à bien des égards ! Evidemment, si la réussite de ce travail ne dépendait que d’un contexte professionnel favorable, mes remerciements pourraient s’arrêter là. Que nenni ! Les amis montpelliérains et d’ailleurs ont bien sûr été capitaux dans la réalisation de ce travail.
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