THESE Anne POSTEC DiversitÃƒÂ© de populations microbiennes ...

More documents

Recommendations

Info

Résultats - Chapitre 3 Grote, R., Li, L. N., Tamaoka, J., Kato, C., Horikoshi, K. & Antranikian, G. (1999). Thermococcus siculi sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Okinawa Trough. Extremophiles 3, 55-62. Harmsen, H. J. M., Prieur, D. & Jeanthon, C. (1997). Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations. Appl. Environ. Microbiol. 63, 2876-2883. Head, I. M., Saunders, J. R. & Pickup, R. W. (1998). Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microbial Ecology 35, 1 - 21. Huber, J. A., Butterfield, D. A. & Baross, J. A. (2002). Temporal Changes in Archaeal Diversity and Chemistry in a Mid-Ocean Ridge Subseafloor Habitat. Appl. Environ. Microbiol. 68, 1585-1594. Huber, J. A., Butterfield, D. A. & Baross, J. A. (2003). Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiology Ecology 43, 393-409. López-García, P., Duperron, S., Philippot, P., Foriel, J., Susini, S. and Moreira, D. (2003). Bacterial diversity in hydrothermal sediment and epsilon-proteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5, 961-976. Marteinsson, V., Birrien, J., Reysenbach, A., Vernet, M., Marie, D., Gambacorta, A., Messner, P., Sleytr, U. & Prieur, D. (1999). Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Bacteriol 49, 351-359. Miroshnichenko, M. L., L'Haridon, S., Nercessian, O., Antipov, A. N., Kostrikina, N. A., Tindall, B. J., Schumann, P., Spring, S., Stackebrandt, E., Bonch-Osmolovskaya, E. A. & Jeanthon, C. (2003a). Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 53, 1143-1148. Miroshnichenko, M. L., L'Haridon, S., Schumann, P., Spring, S., Bonch-Osmolovskaya, E. A., Jeanthon, C. & Stackebrandt, E. (2004). Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 54, 41-45. Miroshnichenko, M. L., Slobodkin, A. I., Kostrikina, N. A., L'Haridon, S., Nercessian, O., Spring, S., Stackebrandt, E., Bonch-Osmolovskaya, E. A. & Jeanthon, C. (2003b). Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 53, 1637-1641. Moussard, H., L'Haridon, S., Tindall, B. J., Banta, A., Schumann, P., Stackebrandt, E., Reysenbach, A.-L. & Jeanthon, C. (2004). Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 54, 227-233. Muyzer, G., De Waal, E. C. & Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction- amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700. Muyzer, G. & Smalla, K. (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73, 127-141. Nercessian, O., Reysenbach, A.-L., Prieur, D. & Jeanthon, C. (2003). Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13°N). Environ. Microbiol. 5, 492-502. O'Brien, D., Carton, M., Eardly, D. & Patching, J. W. (1998). In situ filtration and preliminary molecular analysis of microbial biomass from the Rainbow hydrothermal plume at 36[deg]15'N on the Mid-Atlantic Ridge. Earth and Planetary Science Letters 157, 223-231. Pace, N. R., Stahl, D. A., Lane, D. J. & Olsen, G. J. (1986). The analysis of natural microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology 9, 1-55. Pikuta, E. V., Hoover, R. B., Marsic, D., Beg, A. K. & Garriott, O. K. (non publié, 2004). Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. 196
Résultats - Chapitre 3 Pledger, R. J. & Baross, J. A. (1991). Preliminary description and nutritional characterization of a chemoorganotrophic archaeobacterium growing at temperature up to 110°C isolated from a submarine hydrothermal vent environment. J. Gen. Microbiol. 137, 203-211. Postec, A., Le Breton, C., Fardeau, M.-L., Lesongeur, F., Pignet, P., Querellou, J., Ollivier, B. & Godfroy, A. (2005). Marinitoga hydrogenitolerans sp. nov., a novel member of the order Thermotogales isolated from a black smoker chimney on the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 55, 1217-1221. Postec, A., Pignet, P., Cueff-Gauchard, V., Schmitt, A., Querellou, J. & Godfroy, A. (2005a). Optimisation of growth conditions for continuous culture of the hyperthermophilic archaeon Thermococcus hydrothermalis and development of sulphur-free defined and minimal media. Research in Microbiology 156, 82-87. Postec, A., Urios, L., Lesongeur, L., Ollivier, B., Querellou, J. & Godfroy, A. (2005b). Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting the deep-sea hydrothermal ecosystems. Current microbiology 50, 1-7. Raven, N., Ladwa, N. & Sharp, R. (1992). Continuous culture of the hyperthermophilic archaeum Pyrococcus furiosus. Appl. Microbiol. Biotechnol. 38, 263-267. Raven, N. D. H. & Sharp, R. J. (1997). Development of defined and minimal media for the growth of the hyperthermophilic archaeon Pyrococcus furiosus Vc1. FEMS Microbiol. Lett. 146, 135-141. Reysenbach, A.-L., Longnecker, K. & Kirshtein, J. (2000). Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic ridge hydrothermal vent. Appl. Environ. Microbiol. 66, 3798-3806. Schrenk, M. O., Kelley, D. S., Delaney, J. R. & Baross, J. A. (2003). Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl. Environ. Microbiol. 69, 3580-3592. Sharp, R. J. & Raven, N. D. H. (1997). Isolation and growth of hyperthermophiles, p. 23-51. In P. M. Rhodes and P. F. Stanbury (ed.), Applied Microbial Physiology : A practical approach. IRL Press, Oxford University press. Suzuki, M. & Giovannoni, S. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625-630. Takai, K. & Horikoshi, K. (1999). Genetic Diversity of Archaea in Deep-Sea Hydrothermal Vent Environments. Genetics 152, 1285-1297. Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. (2001). Distribution of Archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 3618-3629. Theron, J. & Cloete, T. E. (2000). Molecular Techniques for Determining Microbial Diversity and Community Structure in Natural Environments. Critical Reviews in Microbiology 26, 37- 57. Thompson, J., Higgins, D. & Gibson, T. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680. Urios, L., Cueff-Gauchard, V., Pignet, P., Postec, A., Fardeau, M.-L., Ollivier, B. & Barbier, G. (2004). Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol 54, 1953- 1957. Vetriani, C., Speck, M. D., Ellor, S. V., Lutz, R. A. & Starovoytov, V. (2004). Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 54, 175-181. Voordeckers, J. W., Starovoytov, V. & Vetriani, C. (sous presse, 2005). Caminibacter mediatlanticus sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. Int. J. Syst. Evol. Microbiol. 197
Page 1:
UNIVERSITE DE PROVENCE (AIX-MARSEIL
Page 4 and 5:
phylogénie, à Valérie Cueff-Gauc
Page 6 and 7:
5 Méthodes pour décrire et accéd
Page 8 and 9:
Chapitre III : Diversité microbien
Page 11 and 12:
Introduction bibliographique Table
Page 13 and 14:
Résultats et discussion 1 Chapitre
Page 15 and 16:
Introduction générale C’est en
Page 17:
Introduction bibliographique
Page 20 and 21:
Introduction bibliographique manife
Page 22 and 23:
Introduction bibliographique Tablea
Page 24 and 25:
Introduction bibliographique 1.3 Le
Page 26 and 27:
Introduction bibliographique 2 Faun
Page 28 and 29:
Introduction bibliographique Figure
Page 30 and 31:
Introduction bibliographique 3 Les
Page 32 and 33:
Introduction bibliographique denses
Page 34 and 35:
Introduction bibliographique Un aut
Page 36 and 37:
Introduction bibliographique incult
Page 38 and 39:
Introduction bibliographique 3.3 Di
Page 40 and 41:
Introduction bibliographique 3.4.2
Page 42 and 43:
Tableau 4 : Bacteria associées aux
Page 44 and 45:
Page 46 and 47:
Page 48 and 49:
Tableau 5 : Archaea associées aux
Page 50 and 51:
Introduction bibliographique 3.5 Le
Page 52 and 53:
Introduction bibliographique L’en
Page 54 and 55:
Introduction bibliographique Figure
Page 56 and 57:
Introduction bibliographique Tablea
Page 58 and 59:
Introduction bibliographique impliq
Page 60 and 61:
Introduction bibliographique ouvre
Page 62 and 63:
Introduction bibliographique 5 Mét
Page 64 and 65:
Introduction bibliographique b) Les
Page 66 and 67:
Introduction bibliographique 5.2 L
Page 68 and 69:
Introduction bibliographique - la s
Page 70 and 71:
Introduction bibliographique laquel
Page 72 and 73:
Introduction bibliographique Des t
Page 74 and 75:
Introduction bibliographique consti
Page 76 and 77:
Introduction bibliographique l’é
Page 78 and 79:
Introduction bibliographique L’am
Page 80 and 81:
Introduction bibliographique ou par
Page 82 and 83:
Introduction bibliographique matric
Page 84 and 85:
Introduction bibliographique Le but
Page 86 and 87:
Introduction bibliographique très
Page 89:
Matériel et Méthodes
Page 92 and 93:
Matériel et méthodes Une cheminé
Page 94 and 95:
Matériel et méthodes - par filtra
Page 96 and 97:
Matériel et méthodes 2.3 Culture
Page 98 and 99:
Matériel et méthodes D’autres t
Page 100 and 101:
Matériel et méthodes L’étanch
Page 102 and 103:
Matériel et méthodes 2.3.3 Condit
Page 104 and 105:
Matériel et méthodes cellules ont
Page 106 and 107:
Matériel et méthodes 2.4.3 Techni
Page 108 and 109:
Matériel et méthodes 3 Techniques
Page 110 and 111:
Matériel et méthodes ‣ Le cycle
Page 112 and 113:
Matériel et méthodes 3.3 Extracti
Page 114 and 115:
Matériel et méthodes 0,8 mm) intr
Page 116 and 117:
Matériel et méthodes β-galactosi
Page 118 and 119:
Matériel et méthodes fluorochrome
Page 120 and 121:
Matériel et méthodes 3.7.2 Métho
Page 122 and 123:
Matériel et méthodes 3.8 Hybridat
Page 124 and 125:
Matériel et méthodes 4 Descriptio
Page 126 and 127:
Matériel et méthodes coloration
Page 128 and 129:
Matériel et méthodes 4.4 Caracté
Page 130 and 131:
Matériel et méthodes après 8 h e
Page 133:
Chapitre 1 Diversité microbienne d
Page 136 and 137:
Résultats - Chapitre 1 1 Diversit
Page 138 and 139:
Résultats - Chapitre 1 Tableau 1 :
Page 140 and 141:
Résultats - Chapitre 1 d’inculti
Page 142 and 143:
Résultats - Chapitre 1 Tableau 2 :
Page 144 and 145:
Résultats - Chapitre 1 Beaucoup de
Page 146 and 147:
Résultats - Chapitre 1 Cheminée '
Page 148 and 149:
Résultats - Chapitre 1 Cheminée '
Page 151:
Résultats - Chapitre 2 Afin d’ac
Page 154 and 155:
146 Résultats - Chapitre 2
Page 156 and 157: 148 Résultats - Chapitre 2
Page 161 and 162: Résultats complémentaires - Chapi
Page 175: Résultats complémentaires - Chapi
Page 179: Résultats - Chapitre 3 Afin de pou
Page 182 and 183: Résultats - Chapitre 3 Summary The
Page 184 and 185: Résultats - Chapitre 3 present stu
Page 186 and 187: Résultats - Chapitre 3 Nucleic aci
Page 188 and 189: Résultats - Chapitre 3 Analyses of
Page 190 and 191: Résultats - Chapitre 3 while the n
Page 192 and 193: Résultats - Chapitre 3 µm) occurr
Page 194 and 195: Résultats - Chapitre 3 the optimal
Page 196 and 197: Résultats - Chapitre 3 thermophili
Page 198 and 199: Résultats - Chapitre 3 Conclusion
Page 200 and 201: Résultats - Chapitre 3 Table 2. Id
Page 202 and 203: Résultats - Chapitre 3 100 70 60 1
Page 204 and 205: Résultats - Chapitre 3 Figure 3. W
Page 208 and 209: Résultats - Chapitre 3 Wery, N., C
Page 211: Résultats - Chapitre 4 Une nouvell
Page 221: Discussion générale
Page 224 and 225: Discussion générale Les Thermococ
Page 226 and 227: Discussion générale est la seule
Page 228 and 229: Discussion générale ε Proteobact
Page 230 and 231: Discussion générale Figure 5 : Po
Page 233 and 234: Conclusion et perspectives Les cond
Page 235 and 236: Conclusion et perspectives Les tech
Page 237: Bibliographie
Page 240 and 241: Bibliographie Baross, J. & Deming,
Page 242 and 243: Bibliographie Felsentein, J. (1981)
Page 244 and 245: Bibliographie J Jannasch, H. W. & W
Page 246 and 247: Bibliographie Marteinsson, V. T., B
Page 248 and 249: Bibliographie Raguénès, G., Chris
Page 250 and 251: Bibliographie Takai, K., Sugai, A.,
Page 253: Annexes
Page 256 and 257:
Annexe 2 Protocole de clonage (kit
Page 258 and 259:
Annexe 3 Caractérisation d’une n
Page 261 and 262:
241 Annexe 4
Page 263 and 264:
243 Annexe 4
Page 265 and 266:
245 Annexe 4
Page 267 and 268:
247 Annexe 5
Page 269 and 270:
249 Annexe 5
Page 271 and 272:
251 Annexe 5
Page 274:
Diversité de populations microbien
show all

THESE Anne POSTEC DiversitÃƒÂ© de populations microbiennes ...

Create successful ePaper yourself

Delete template?

Save as template?