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Thesis Reference Thesis Role of phototrophic sulfur bacteria from the chemocline in the primary production of Lake Cadagno STORELLI, Nicola Abstract Phototrophic sulfur bacteria are important for primary production in many stratified lakes. In Lake Cadagno, these bacteria greatly contribute to the total primary production with high values of CO2 fixation both in the presence and absence of light. The small-celled PSB Candidatus “Thiodictyon syntrophicum” Cad16T was the strongest CO2 assimilator and used as model organism. The draft genome sequence of strain Cad16T revealed the presence of two RuBisCO genes (cbbL and cbbM), which were deferentially expressed. 2D-DIGE analysis showed the presence of 23 protein spots up-regulated in the light, and 17 in the dark. Among the 23 protein spots that were up-regulated in the light, three are involved in the storage mechanism that produces granules of poly(3-hydroxybutyrate) from an excess of reducing power and carbon compounds. Among the 17 protein spots up-regulated in the dark, three were found to be part of the autotrophic dicarboxylate-hydroxybutyrate (DC/HB) cycle. Reference STORELLI, Nicola. Role of phototrophic sulfur bacteria from the chemocline in the primary production of Lake Cadagno. Thèse de doctorat : Univ. Genève, 2014, no. Sc. 4646 URN : urn:nbn:ch:unige-349153 DOI : 10.13097/archive-ouverte/unige:34915 Available at: http://archive-ouverte.unige.ch/unige:34915 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de botanique et biologie végétale Dr. Xavier Perret Unité de microbiologie Dr. Mauro Tonolla Role of Phototrophic Sulfur Bacteria from the Chemocline in the Primary Production of Lake Cadagno THÈSE présentée à la Faculté des sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie par Nicola Storelli de Losone (TI) Thèse n° 4646 GENÈVE Atelier de reprographie ReproMail 2014 ii PUBLISHED PAPERS †Peduzzi S., †Storelli N., Welsh A., Peduzzi R., Hahn D., Perret X., Tonolla M. (2012) Candidatus "Thiodictyon syntrophicum", sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp. Systematic and Applied Microbioogyl 35, 139-144. (DOI: 10.1016/j.syapm.2012.01.001). †: equally contributed. Storelli N., Peduzzi S., Saad M., Frigaard N-U., Perret X., Tonolla M. (2013) CO2 assimilation in the chemocline of Lake Cadagno is dominated by a few types of phototrophic purple sulfur bacteria. FEMS Microbiology Ecology 84(2), 421-432. (DOI: 10.1111/1574-6941.12074). Storelli N., Peduzzi S., Saad M., Frigaard N-U., Perret X., Tonolla M. (2014). Autotrophic carbon dioxide assimilation mechanism in the dark disclosed by proteome analysis of the purple sulfur bacterium Candidatus “Thiodictyon syntrophicum” strain Cad16T. EuPA Open Proteomics 2, 17-30 (DOI: http://dx.doi.org/10.1016/j.euprot.2013.11.010). iii iv REMERCIEMENTS En premier lieu je tiens à remercier mon directeur de thèse CC Dr. Mauro Tonolla et co- directeur MER Dr. Xavier Perret de m’avoir permis d’entreprendre ce projet à l’Université de Genève, et au Laboratoire d’écologie microbienne de Bellinzona. Merci également au Prof. Michel Goldschmidt-Clermont professeur responsable pour cette thèse. Un remerciement spécial va au Professeur associé. Niels-Ulrik Frigaard pour avoir accepté de faire partie du jury de thèse et au Dr. Maged Saad pour son soutien scientifique tout au long de ce travail. Leur aide et leur expérience ont joué un rôle fondamental dans la réussite de cette thèse. J’aimerais remercier tous les collaboratrices et les collaborateurs de l'ICM, en particulier le groupe du Laboratoire de Biosécurité et le groupe du Laboratoire d'Ecologie Microbienne pour leur aide. Un grand merci encore au Dr. Maged Saad pour avoir partagé ses connaissances sur la protéomique, au Dr. Sandro Peduzzi et au Dr. Paola Gandolfi-Decristophoris pour l’aide au niveau de la cultivation des microorganismes anaerobiques, et au Dr. Valeria Guidi, à Francesco Danza, à Anna Mariotti-Nessurini et au Dr. Damiana Ravasi pour toutes les discussions intéressantes que nous avons eues au cours de ces années. Ma reconnaissance s’adresse également aux personnes que j’ai connues et m’ont gentiment aidé lors de mes sejours en Danmark à l’Université de Copenhague (Biocenter Department of Biology Section for marine biology): Carina Holkenbrink, Jørgen Deiker Petersen, Chizuko Sakamoto, Bjørn Sindballe Broberg, Tonny D. Hansen; et dans les laboratoires de l’Unité de Microbiologie à Geneve: Dr. Cristina Andrés-Barrao, Dr. Antoine Huyghe, Natalia Giot, Coralie Fumeaux, Dr. Nadia Bakkou, Anissa Ravez, Vanesa Miguelez De La Torre. Je remercie la Fondation du Centre de Biologie Alpine de Piora et son président Prof. Dr. R. Peduzzi pour le soutien et la mise à disposition des infrastructures nécessaires aux travaux sur le lac de Cadagno ainsi que la Fédération des sociétés européennes de microbiologie (FEMS) et la Societé de Microbiologie Suisse (SMS/SGM) en particulier son ancien president Professeur Dr. Dieter Haas pour le soutien financier pendant mon sejour en Danmark. Je tiens enfin à exprimer mon immense gratitude à Alice Benzoni et ma famille pour m’avoir continuellement soutenu durant cette période. v vi TABLE OF CONTENTS REMERCIEMENTS ................................................................................................................... iv SUMMARY ................................................................................................................................... x RÉSUMÉ...................................................................................................................................... xii ABBREVIATIONS .................................................................................................................... xvi LIST OF TABLES AND FIGURES .......................................................................................... xx 1. INTRODUCTION ..................................................................................................................... 2 1.1. Meromixis ........................................................................................................................... 2 1.1.1. The crenogenic meromictic Lake Cadagno .................................................................. 4 1.1.2. Biota of the Lake Cadagno............................................................................................ 6 1.2. Phototrophic sulfur bacteria ............................................................................................... 8 1.2.1. The sulfur cycle ............................................................................................................. 8 1.2.2. Ecological distribution of phototrophic sulfur bacteria .............................................. 10 1.2.3. Photosynthetic inorganic carbon fixation in PSB and GSB ........................................ 11 1.2.4. Phototrophic sulfur bacteria in the Lake Cadagno ...................................................... 15 1.3. Proteomics ......................................................................................................................... 19 1.3.1. Techniques for separating proteins ............................................................................. 19 1.3.2. Protein identification using mass spectrometry .......................................................... 20 1.4. Aims of the PhD thesis ..................................................................................................... 21 2. RESEARCH PAPER 1 ........................................................................................................... 24 CO2 assimilation in the chemocline of Lake Cadagno is dominated by a few types of phototrophic purple sulfur bacteria ...................................................................................... 24 2.1. Supporting information ................................................................................................... 40 SM1. Recipe of trace elements SL10 and SL12. .................................................................. 40 SM2. Dissolved inorganic carbon (DIC) and pH from dialysis bags. .................................. 41 SM3. Genome analysis. ........................................................................................................ 42 References supporting information ....................................................................................... 43 3. RESEARCH PAPER 2 ........................................................................................................... 48 vii Candidatus “Thiodictyon syntrophicum”, sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp. ......................................................................................... 48 3.1. Supplementary material S1 (Material and methods) .................................................... 58 Enrichment and cultivation of strain Cad16T ........................................................................ 58 Phyologenetic analysis with 16S rRNA ................................................................................ 58 MALDI-TOF MS analysis .................................................................................................... 58 Pigment analysis ...................................................................................................................
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