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Foraminifera Thesis New insights into the diversity of deep-sea benthic foraminifera LECROQ, Béatrice Abstract Les foraminifères benthiques sont une composante majeure des fonds océaniques. Leur importance dans le cycle du carbone est largement reconnue et ils sont couramment utilisés en paléocéanographie en tant que marqueurs des changements climatiques. Cependant, nos connaissances croissantes à leur sujet nous dévoilent peu à peu que ce vaste phylum retient encore quelques secrets, notamment quant à sa diversité et à la distribution géographique de ses espèces. Dans cette thèse sont décrits deux nouveaux genres de foraminifères agglutinés : Capsammina patelliformis et Shinkaiya lindsayi. Leur morphologies, spectaculairement différentes, illustrent parfaitement l'étendue de la richesse des foraminifères monothalames. Comme d'autres xenophyophores, S. lindsayi présente un réseau interne de conglomérats digestifs (stercomata) mais se distingue aussi par l'absence de cristaux de barite dans son cytoplasme. Des analyses élémentaires ont révélé que ce foraminifère géant (8 cm de diamètre) concentrait de grandes quantités de métaux, dont l'uranium, à l'intérieur de ses stercomata, contribuant ainsi [...] Reference LECROQ, Béatrice. New insights into the diversity of deep-sea benthic foraminifera. Thèse de doctorat : Univ. Genève, 2009, no. Sc. 4106 URN : urn:nbn:ch:unige-39568 DOI : 10.13097/archive-ouverte/unige:3956 Available at: http://archive-ouverte.unige.ch/unige:3956 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de Zoologie et Biologie Animale Professeur Jan PAWLOWSKI New Insights Into The Diversity Of Deep-sea Benthic Foraminifera THÈSE présentée à la Faculté des Sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie par Béatrice Lecroq de Roquebrune Cap Martin (France) Thèse N °°° 4106 Lausanne Reprographie de l’ EPFL 2009 ii Je dédie cette thèse à l’église de Ruminghem qui a prié une nuit entière pour moi lors de mes difficiles premiers jours… et surtout, à celui qui leur a répondu. iii First of all, I would like to thank all the members of my thesis jury: Dr Tomas Cedhagen, Dr Andrew John Gooday, Dr Hiroshi Kitazato, and Dr Purificación López-García. iv Remerciements J’ai le sentiment d’avoir été extrêmement privilégiée tout au long de ma vie, en ne faisant rien pour le mériter réellement. Sans que cela ne puisse jamais compenser tout ce qui m’a été donné, j’aimerais dire merci, plusieurs fois merci, aux personnes qui m’ont aidée ou encouragée… A Jan, pour m’avoir fait confiance. A Jackie (chan), la meilleure de tout l’étage (pas sûre que tu me revoies près de la frontière alors n’oublies pas que tu restes quand même dans mon cœur). Aux gars de l’autre coté du couloir : Fabien, Loic et Thierry qui a pseudopodé ma life (on aurait quand même pu sortir plus souvent ensemble, désolée, c’est un peu ma faute…). A José, pour ses grandes qualités et pour tout ce qu’il m’a transmis. Aux petits nouveaux : Cyril, Michael (courage, merci pour votre gentillesse, et bonne chance, Cyril, pour le dessin). Aux anciens : Quique (futur éleveur de crabes phosphorescents des iles Tonga), Cédric, Ben, David, Xavier, Patrick, Délia, Yurika et mon dive body préféré : Fred (salut Fred ;) ). Au vénérable Juan (merci pour tes précieuses corrections et tes questions toujours pertinentes lors des lab meetings !), à Ilham (Shokran, passes à la maison quand tu viendras voir Rime), Slim (merci pour tes encouragements qui m’ont énormément touchée, j’espère que l’on se reverra), Raphael, Aurélia, Anouchka, et la douce Yamila. Au professeur Bény qui aime tant les petits poulpes à la niçoise, M. Wuest. A Jacqueline, Roland, Frank et André. A Wanda, Yvan, Anne, Lisbeth, Virginie (la furieuse pilote de rallye des champs) et Kevin. Au Dr Peck et à Benjamin (merci pour ton éternel sourire qui réchauffe le cœur). A Tomohiko qui fait glisser ses claquettes, à Patrick qui a tort (et que je vais humilier bientôt au Poker), à Julien, la belle Chen-Da et Luca (c’est bête que l’on ne soit devenus amis que maintenant !). A Wojciech. A Giovanni (spetacollo !). A toutes les bonnes rencontres de missions ou de meetings. De ORI, Arctowski, Ferraz (spécialement à Janaina), Polarstern, Hakuho Maru, Tansei Maru, Håkon Mosby, Téthys II. A Pedro. Aux grands Thierry et Pierre (un jour je vivrai à Marseille et je mangerai des trucs bons, comme vous ...). A Juljiana, Edu, Asma, Raphaella, Ludwig (j’espère que tu es en train de chauffer les pistes à Thonon). A Antoine, Charly (le nain) et Blujita. A toute l’équipe du Lausanne Water Polo (un de plus !!!). A mes amis que je garderai toute ma vie ! Caro-ling-ling-Bambou ( !!! love you baby !!! ), Tao (le saaaage, le jazz man, le lionceau, mon ami…), Pop’eye (prête pour la course j’espère), la Cantunette des bois (ah, qu’est ce que je vais faire sans toi ?), A Carl (Bombyx des), Lanou et son petit Gabriel (merci de m’être restée fidèle), Alex Pardo (la manatee), Mu (la fée végétale, acidulée et pétillante), Scully (revival), Mulder, Pablo et Salvia (« you know my friends, if you have some neurones….. »), Daphné (mon inséparable sœur ennemie), Jose et Catherine, Chloé, Patricia, Sandra, Gwen, Manon-lolola (courage), Rudy et Mariana, Sarah, Maria et Montse. A Yuuka. A Miško et Nena. A Nina, reine des fleurs. A ma famille: papa (j’espère que tu es fier de moi), ma petite maman chérie, ma sœur l’endive, Lilou, anounette (je t’aime). A Pépé et mémé (mon refuge), Jean Luc et maintenant aussi…………ZIGI, Gabibone et Gordana. Au Baron de Münchausen, à Kuro et Shiro A Davor (ti i ja) v vi Résumé Les foraminifères benthiques sont une composante majeure des fonds océaniques. Leur importance dans le cycle du carbone est largement reconnue et ils sont couramment utilisés en paléocéanographie en tant que marqueurs des changements climatiques. Cependant, nos connaissances croissantes à leur sujet nous dévoilent peu à peu que ce vaste phylum retient encore quelques secrets, notamment quant à sa diversité et à la distribution géographique de ses espèces. Dans cette thèse sont décrits deux nouveaux genres de foraminifères agglutinés : Capsammina patelliformis et Shinkaiya lindsayi . Leur morphologies, spectaculairement différentes, illustrent parfaitement l’étendue de la richesse des foraminifères monothalames. Comme d’autres xenophyophores, S. lindsayi présente un réseau interne de conglomérats digestifs (stercomata) mais se distingue aussi par l’absence de cristaux de barite dans son cytoplasme. Des analyses élémentaires ont révélé que ce foraminifère géant (8 cm de diamètre) concentrait de grandes quantités de métaux, dont l’uranium, à l’intérieur de ses stercomata, contribuant ainsi à modifier la composition chimique du sédiment. En recherchant l’origine moléculaire des komokiacés Septuma ocotillo et Normanina conferta , nous avons révélé involontairement une importante faune eucaryotique associée à leurs tests branchus. Cette étude a mis en évidence une richesse dissimulée à l’intérieur des tests de foraminifères ou dans le sédiment. Il semble plausible que des foraminifères nus ou de petite taille soient particulièrement difficile à observer au microscope, échappant ainsi aux études passées. Pour cette raison, afin d’améliorer notre connaissance de ce phylum, nous avons également appliqué les dernières techniques moléculaires de séquençage massif à des extractions globales d’ADN provenant d’échantillons environnementaux. Dans cette optique, nous avons parcouru les régions variables du « SSU rDNA » de différents foraminifères à la recherche du meilleur « code barre » potentiel. L’hélice 37 (région I), ayant présenté une excellente résolution aux plus bas niveaux taxonomiques, a été choisie pour tester cette approche. Nous avons donc séquencé massivement quatre échantillons de sédiment dont l’ADN global a été amplifié sélectivement pour les foraminières. Un fragment extrêmement court de cette région (36 pb) a été analysé par le séquenceur Solexa nous permettant d’identifier un grand nombre de phylotypes avec une résolution satisfaisante. Quelques séquences sont cependant restées sans attribution car trop éloignées de tous taxa connus. Nous suspectons que beaucoup de ces phylotypes sont en faite encore inconnus de la science, et que la diversité des foraminifères, en particulier celle des monothalames, est grandement sous estimée. Finallement, nous nous sommes intéréssés à trois espèces communes de foraminifères calcaires ayant une distribution particulièrement étendue : Epistominella exigua , Oridorsalis umbonatus et Cibicides wuellerstorfi . Nos analyses phylogénétiques basées sur le SSU partiel et l’ITS de ces espèces révélèrent un flux de gènes entre les populations des deux régions polaires. Cette étude a été généralisée dans le dernier article de cette thèse en incluant des analyses de spécimens de E. exigua provenant de l’océan pacifique. L’analyse génétique des populations de cette espèce, basée sur les séquences de l’ITS montre effectivement une homogénéité globale, confirmant qu’au moins un foraminifère benthique d’océan profond pourrait avoir une dispersion mondiale. De plus, l’analyse phylogénétique d’espèces sœurs d’ E. exigua indique que la crypticité de ce genre décroîtrait avec la profondeur. vii Abstract Benthic foraminifera are major components of the deep-sea bottoms and especially of the abyssal plains. Because of their value as paleoceanographic proxies and their importance in the carbon cycle, they have
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