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Functional Diversity of Marine Protists in Coastal Ecosystems Pierre Ramond

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Functional Diversity of Marine Protists in Coastal Ecosystems Pierre Ramond Functional Diversity of Marine Protists in Coastal Ecosystems Pierre Ramond To cite this version: Pierre Ramond. Functional Diversity of Marine Protists in Coastal Ecosystems. Oceanography. Sorbonne Université, 2018. English. NNT : 2018SORUS210. tel-02495684 HAL Id: tel-02495684 https://tel.archives-ouvertes.fr/tel-02495684 Submitted on 2 Mar 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. Sorbonne Université Ecole doctorale 227 Sciences de la Nature et de l'Homme - Evolution et Ecologie UPMC-CNRS Adaptation et Diversité en Milieu Marin - (UMR 7144), équipe EPEP, Station Biologique de Roscoff Ifremer – Centre de Brest, équipe DYNECO/PELAGOS Diversité Fonctionnelle des Protistes Marins dans l’Ecosystème Côtier Par Pierre Ramond Thèse de doctorat d’Ecologie et Evolution Dirigée par Colomban de Vargas, Raffaele Siano et Marc Sourisseau Dans le but d’obtenir le grade de Docteur de Sorbonne Université Présentée et soutenue publiquement le 19 Octobre 2018, devant un jury composé de : Pr. Elena Litchman Michigan State University, USA Rapporteur Pr. Christine Paillard Institut universitaire européen de la mer, Brest, France Rapporteur Dr. Ramiro Logares Institut de Ciències del Mar, CSIC, Barcelona, Espagne Examinateur Dr. Valérie David Université de Bordeaux, France Examinateur Pr. Eric Thiébaut Station Biologique de Roscoff, France Examinateur “imagining for a moment that we understand the many complex contingencies on which the existence of each species depends.” Charles Darwin Remerciements Il convient tout d’abord de remercier la Région Bretagne (50%) et l’Ifremer (50%) qui cofinancent ce projet de thèse, ainsi que François Lallier et Cédric Bacher pour leurs accueils respectifs au sein de l’UMR 7144 (‘Adaptation and Diversity in the Marine Environment’) et de l’unité Dyneco de l’Ifremer. Plus que des remerciements je souhaite adresser mes sincères amitiés aux superviseurs de cette thèse. Colomban, merci pour tes échanges francs et ouverts, ton mime de la nage des dinoflagellés lors d’une de nos premières rencontres restera à jamais gravé dans mon esprit et alimentera encore longtemps mes soirées dansantes. Marc, je pense avoir compris un peu mieux la physique de l’océan à tes côtés et surtout son effet sur le plancton, en travaillant avec toi j’ai eu l’impression d’être mis sur un pied d’égalité, merci pour ça, cela m’a donné une plus grande confiance en moi. Raffaele, merci pour tout. Merci de m’avoir parfaitement intégré dès mon arrivée, merci de ton enthousiasme et de ton encadrement tout au long de cette thèse, merci pour ta curiosité et ta confiance, enfin merci pour nos discussions sans fin sur le travail et sur mon avenir. Je vous souhaite le meilleur à tous et j’espère vous recroiser si l’opportunité professionnelle, ou autre, se présente. Je remercie l’ensemble des membres de mon jury de thèse de me faire l’honneur d’évaluer ce travail de thèse et de l’intérêt qu’ils ont manifesté à l’égard de son sujet. Merci à Elena Litchman et Christine Paillard d’avoir accepté le rôle de rapporteur de cette thèse, merci à Ramiro Logares, Valérie David et Eric Thiébaut d’avoir accepté le rôle d’examinateur. Je tiens également à remercier les membres du comité de suivi de cette thèse, Sakina-Dorothée Ayata, Laurent Memery, Télésphore Sime-Ngando et Frédérique Viard. Sakina, merci pour ton retour sur la partie statistique de notre premier chapitre. Laurent, merci pour ta franchise inébranlable. Télésphore, merci pour ta pédagogie et ton intérêt. Frédérique, merci d’avoir posé un visage humain sur l’administration de l’université. D’autres membres extérieurs doivent également être remerciés pour leur contribution, notamment Eric Thiébaut pour son retour sur l’écologie fonctionnelle, Stéphane Audic pour le travail bio-informatique, Nathalie Simon et Fabienne Rigaut-Jalabert pour le jeu de données de la série d’Astan ainsi que pour leur retour sur le premier chapitre, Nicolas Henry pour son retour sur le second chapitre, et Cédric Berney pour ses apports à notre choix de traits fonctionnels. Je souhaite remercier ici aussi l’ensemble des membres et directeurs des projets DAOULEX, DYNAPSE, PELGAS, PHYTEC, IPARO, MINISCOPE et M2BIPAT sans qui notre jeu de données n’aurait pu exister. Un remerciement plus particulier va à l’égard d’Eric Machu pour les données issues des campagnes du Sénégal. Je remercie plus spécialement encore l’ensemble de la team M2BIPAT, qui m’a donné accès aux données sur le front tidal de la mer d’Iroise qui constitue un chapitre entier de ma thèse. Un grand merci à Louis Marie et Laurent Memery pour l’organisation des campagnes de l’été 2016, ces campagnes ont été formatrices dans ma vision de l’échantillonnage de l’écosystème marin. Merci à Sarah Romac et Sophie Schmitt pour m’avoir appris les rudiments de la génétique en laboratoire. Sarah, merci beaucoup pour ta pédagogie et ta disponibilité pour discuter des manips. Sophie, merci de m’avoir accompagné dans ces manips mais aussi dans les campagnes M2BIPAT, avant tout merci pour ta bonne humeur constante. Merci à Cecilia Teillet pour son stage de M2, ce n’était pas un stage facile mais tu n’as pas démérité, j’espère que tout va pour le mieux. Merci à l’ensemble de l’équipe Dyneco pelagos, quel plaisir de travailler dans une si bonne ambiance ! J’ai pu participer à de superbes débats tout au long de cette thèse, sur la monde de la recherche avec un peu tout le monde, j’en ai appris plus au sujet de l’évolution au contact de Mickael et Gabriel ou sur la physique et la modelo avec Martin et Marc. J’ai aussi participé à des débats beaucoup moins sérieux avec Marie, Julien, Sophie, Florian, Agnès et tant d’autres… j’ai attaché de l’importance à toutes ces petites routines et discussions (aussi sérieuses parfois), j’y ai trouvé un grand réconfort, un soutien nécessaire et une amitié sincère. Merci. Mes salutations distinguées à tous mes frères et sœurs d’armes, en benthos : Thibault, Vincent, Auri… euh Dr Jones, et en pelagos : Laurie, Tristan, Sam. Un merci tout particulier à Bastien et Louise, je vous sais tristes de ne pas pouvoir venir à ma soutenance mais votre présence tout au long de ma thèse a surement été bien plus importante. Je passe aussi un petit coucou à tous les post-doc, et autres, qui sont passé par le labo : Tania, Clémence, Kim, Margaux et plus récemment Malwenn, Stéphane, Aurore, Cécile et Gaspard, merci de votre solidarité. Gabriel, j’ai la vague impression que nous avons mûri ensemble ces trois ans, je te vois finir ta thèse et rajouter ce truc sur la dispersion à la dernière minute, ce mec… promis, je passerai à Murat, bien que je doute encore de l’existence d’une zone habitée dans la Creuse. Je remercie également l’ensemble de l’équipe de volley de l’ASCI, parce que esta noche : ‘ganamos’, ‘galapagos’, ‘albatros’, ‘Ser Davos’… et bien entendu le fameux : ‘ça glisse’. Merci aussi à l’équipe d’escalade pour son super investissement et sa pédagogie. Un remerciement plus informel revient à notre magnifique Equipe de France de Football, qui je le rappel est CHAMPIONNE DU MONDE **. Enfin merci à ma famille, à mes amis loin chez moi, et à Johanne, pour leurs soutiens, je vous aime. Un remerciement tout spécial à mon grand-père Momo, merci de t’être intéressé à chaque fois qu’on a pu discuter de mon travail, j’espère avoir porté fièrement l’adage familial : « têtu comme un Ramond ». Table of Contents INTRODUCTION .................................................................................................................. 1 1) Preamble: Ecology .................................................................................................. 2 2) Marine Protistan Diversity ...................................................................................... 5 3) Marine Protistan Ecology: State of the Art ........................................................... 11 a) Everything is everywhere but the environment selects ................................................................. 11 b) Redfield Ratio ............................................................................................................................... 13 c) Trophic Ecology ............................................................................................................................ 14 d) Competitive Exclusion and the Paradox of the Plankton .............................................................. 15 e) Plankton species successions and ecosystem maturity ................................................................. 16 f) The microbial loop ........................................................................................................................ 17 g) Transitions in pelagic ecosystems ................................................................................................. 22 h) Neutral theory and dispersal .......................................................................................................... 23 i) Conclusion ....................................................................................................................................
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