THESE Anne POSTEC DiversitÃƒÂ© de populations microbiennes ...

More documents

Recommendations

Info

Résultats - Chapitre 3 Conclusion Continuous enrichment culture performed in gas-lift bioreactor was shown to be an improved method to expand our view of the cultivable microbial community inhabiting deep-sea hydrothermal black smokers. The microbial diversity detected in traditional batch enrichment cultures in vials was lower than that obtained from the bioreactor. All the sequences retrieved in this study, archaeal or bacterial, obtained from cultures in vials or in the bioreactor, were related to cultured microorganisms originating from deep-sea hydrothermal environments. Molecular methods to assess the microbial diversity gave important data to guide the isolation of new prokaryotic strains as shown in this study. Without change in the experimental conditions, whole-cell hybridization analysis and data from the clone libraries revealed a clear evolution of the community structure, indicating a dynamics among the cultivated microbial community. Thanks to the continuous culture in bioreactor, it was possible to maintain in culture heterotrophic strains and autotrophic strains for several weeks. This was an unexpected result considering the organic rich medium supplied and indicated that metabolic products of the heterotrophs helped to support the growth of the autotrophic populations. The extended duration of culture in the bioreactor allowed cells to interact primarily by means of end products of primary metabolism (fermentative pathway) that are released and taken up. These interactions could be important factors permitting the growth of as-yet uncultivated microorganisms. The impact of the environment on a microbial community might be very intense in deep-sea hydrothermal systems, since steep physico-chemical gradients are expected to exist, in the range approximately of 350°C at pH3 to 4°C at pH7 in the case of a black smoker investigated (Charlou, et al. 2002). The gas-lift bioreactor combined with the use of molecular tools to monitor the microbial population structure could be used to investigate the effect of environmental perturbations on the microbial community composition. Acknowledgements The authors want to thank P.M. Sarradin, chief scientist of the ATOS cruise, as well as the captain and crew of the Atalante and the Victor team. This work was supported by Ifremer, European VENTOX Program and Région Bretagne. We also wish to thank Dr C. L. Van Dover for her helpful reading of the manuscript. 188
Résultats - Chapitre 3 Table 1. Distribution and phylogenetic affiliations of archaeal and bacterial 16S rDNA sequences (≥ 97% similarity in each phylotype) retrieved from enrichment cultures in the bioreactor at 60°C. Representative clones were completely sequenced, and the sequence types deposited in GenBank appear in bold. Sample Phylogenetic affiliation Representative clones T7 Thermococcales A704- A710- A712- A715- A730-A732- A737-A739 T28 Thermococcales A800-A811- A816-A817 T7 Clostridiales 775-700-725- 728-750-770- Thermotogales 716-705-706- 709-724-768 Deferribacterales 737-711-740- 754-769 T28 Clostridiales Thermotogales Deferribacterales Thermodesulfobacter iales 813-874 805-802-822- 823-832 840-812-821- 825-868-884-893 820-829-856 850-816-858 Number of clones Closest match organism a identity a 76 Thermococcus siculi (AY099185) 98% 71 Thermococcus siculi (AY099185) 98% 38 29 9 5 35 12 17 3 Caminicella sporogenes (AJ320233) Marinitoga camini (AJ250439) Deferribacter abyssi (AJ515882) Caminicella sporogenes (AJ320233) Marinitoga camini (AJ250439) Thermosipho MV1063 (AJ419874) Deferribacter abyssi (AJ515882) Thermodesulfatator indicus (AF393376) a Based on BLAST search (http://www.ncbi.nlm.nih.gov/BLAST). GenBank accession numbers are in brackets. 97% 94% 98% 97% 95% 99% 98% 96% 189
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 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 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 206 and 207: Résultats - Chapitre 3 Grote, R.,
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?