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Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz

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Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean Manuel MARTINS Examinateur Dr. Yves JOUANNEAU Présidant du jury Dr. Roberto GEREMIA Directeur Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) 2 Remerciements Je voudrais remercier les membres du jury, Messieurs et Mesdames Thierry Heulin, Christian Jeanthoneulin, Jean Manuel Martins, Sylvie Nazaret et Yves Jouanneau pour avoir accepté de juger mon travail de thèse. Cette thèse n’aurait pas vu le jour sans la confiance et les conseils avisés de mon directeur de recherche, Roberto Geremia, Je voudrais le remercier pour cela ainsi que pour son soutien tout au long de ces années. Ma reconnaissance s’adresse aussi à Philippe Choler d’avoir toujours été disponible à répondre à mes questions. C’était grâce à lui que j’ai fait la connaissance avec l’écosystème alpin. Je remercie également mes collègues Armelle, Sylvie et Tarafa qui m’ont encouragée à continuer et finir cette recherche. Je n’oublierai jamais les beaux jours que j’ai passés à leurs côtés. Je tiens également à remercier très chaleureusement à Lucie pour ses remarques pertinentes. Je remercie tous les professeurs, chercheurs et post-docs particulièrement Luicle Sage, Sebastien Lavergne, Jérôme Gury, Patrick Ravanel, Pierre Taberlet, Irène Till-Bottraud, Christiane Gallet, David Lejon et Bello pour leurs discussions scientifiques qui m’ont guidé au cours de mon travail, et toujours dans une ambiance bien sympathique. Je tiens à remercier tous mes collègues du LECA. C’est avec joie que j’ai partagé ces quatre années avec eux. Que tous mes collègues, Florence, Annelaure, Rodolph, Angélique, Mathieu, Ozgur, Asam, Claire, Carole, Christian, Margot, Alice et Olivier. LECA me manquera. 3 Merci à toutes l’équipes TDE/PEX et GPB. Cette thèse est effectuée en collaboration avec trois. Je remercie à mes chers amis iraniens particulièrement Shokooh, Shadi et Maryam pour tous les fantastiques moments passés ensemble et de m’avoir encouragé à continuer mon chemin. Je vais également remercier à deux mes amies iranien au LECA Hamid et saeid pour leurs qualités humaines extraordinaires. Je ne saurais jamais exprimer ma reconnaissance à mon époux Mohsen, qui m’a accompagné pendant les douze ans de notre vie commune. Son amour et son aides me encourage tout ces années. Je remercie ma chère fille, Negar qui a pu supporter notre séparation et m’a exprimé ses chagrins avec ses dessins. Mes derniers remerciements, mais pas les moindres vont à mes parents qui ont été mes meilleurs enseignants, et auxquels je dois tout ce que j’ai actuellement. 4 Sommaire CHAPITRE 1 : Introduction ___________________________________ 9 Background and objective of the thesis _______________________________11 Thesis content and structure _______________________________________13 The challenge of environmental microbiology _________________________14 Microbial ecology history __________________________________________________ 14 Bacteria ________________________________________________________________ 14 Bacterial genetic diversity__________________________________________________ 14 Bacterial roles in nature ___________________________________________________ 15 Bacterial Diversity ______________________________________________16 Importance of bacterial diversity in ecosystem__________________________________ 16 Factors important on bacterial diversity ______________________________________ 17 Abiotic factors_______________________________________________________________ 17 Biotic factors________________________________________________________________ 17 Measurement of bacterial diversity___________________________________________ 18 Measurements of taxonomic distinctness ______________________________________ 19 The species equal to OUT __________________________________________________ 21 How to assess microbial diversity?___________________________________________ 21 Traditional methods __________________________________________________________ 21 Culture-independent method ___________________________________________________ 22 Importance of soil _______________________________________________29 The spatial distribution patterns of micro-organisms_____________________________ 29 The temporal distribution patterns of micro-organisms ___________________________ 30 Alpine ecosystem ________________________________________________32 Definition_______________________________________________________________ 32 Heterogeny of the alpine stage ______________________________________________ 32 The history of bacterial characterization in artico-alpine _________________________ 34 Phenotypic characterization and adaptation to cold condition _____________________ 34 Bacterial diversity in cold environment _______________________________________ 35 Bacterial diversity and structure based on culture __________________________________________ 35 Bacterial diversity and structure based on method molecular _________________________________ 36 CHAPITR 2: Effet des régimes d’enneigement sur la diversité et relative abondance de la communauté bactérienne des sols alpins 39 Contexte général ________________________________________________41 Objectifs de l’étude ______________________________________________42 5 Article I: Microbial diversity in alpine tundra soils correlates with snow cover dynamics ______________________________________________________44 Principaux résultats et discussion___________________________________55 CHAPITRE 3: Effet des régimes d’enneigement sur la structure phylogénétique des communautés bactériennes des sols alpins __ 59 Contexte général ________________________________________________61 Objectifs de l’étude ______________________________________________64 Article II: Snow cover dynamics and phylogenetic structure of bacterial communities in alpine tundra soils __________________________________67 Abstract ________________________________________________________________ 68 Introduction_____________________________________________________________ 69 Material and Methods _____________________________________________________ 71 Study site, sample collection and bacterial ssu sequences _____________________________ 71 Sequence data treatment_______________________________________________________ 71 Statistical Analysis ___________________________________________________________ 72 Results _________________________________________________________________ 74 Comparison of bacterial communities using taxonomic information_____________________ 74 Comparison of bacterial communities using phylogenetic information___________________ 74 Distribution of bacterial groups at finer taxonomic scale _____________________________ 75 Discussion ______________________________________________________________ 76 Conclusion______________________________________________________________ 79 Acknowledgements _______________________________________________________ 80 References ______________________________________________________________ 81 Principaux résultats et discussion___________________________________96 CHAPITRE 4 : Effet des régimes d’enneigement sur la richesse des espèces bactériennes cultivables des sols alpins _________________ 99 Contexte général _______________________________________________101 Objectifs de l’étude _____________________________________________102 Article III: Phylogenetic diversity of cultivable bacteria in soils of temperate alpine tundra __________________________________________________103 Abstract _______________________________________________________________ 104 Introduction____________________________________________________________ 105
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