The microbiology of acidic mine waters, Research in Microbiology, vol.154, issue.7, pp.466-473, 2003. ,
DOI : 10.1016/S0923-2508(03)00114-1
Microbiology of a wetland ecosystem constructed to remediate mine drainage from a heavy metal mine, Science of The Total Environment, vol.338, issue.1-2, pp.53-66, 2005. ,
DOI : 10.1016/j.scitotenv.2004.09.005
Mediation of arsenic oxidation by Thiomonas sp. in acid-mine drainage (Carnoules, France), Journal of Applied Microbiology, vol.6, issue.3, pp.492-499, 2003. ,
DOI : 10.1126/science.1072896
An arsenic(III)-oxidizing bacterial population: selection, characterization, and performance in reactors, Journal of Applied Microbiology, vol.6, issue.4, pp.656-667, 2002. ,
DOI : 10.1023/A:1009255012328
Arsenite oxidation by a chemoautotrophic moderately acidophilic Thiomonas sp.: from the strain isolation to the gene study, Environmental Microbiology, vol.173, issue.0, pp.228-237, 2008. ,
DOI : 10.1023/A:1009255012328
URL : https://hal.archives-ouvertes.fr/hal-00281294
Oxidation of iron, sulfur and arsenic in mine waters and mine wastes: an important role of novel Thiomonas spp Biohydrometallurgy: a sustainable technology in evolution, pp.639-646, 2004. ,
Phylogeny of Thiobacillus cuprinus and Other Mixotrophic Thiobacilli: Proposal for Thiomonas gen. nov., International Journal of Systematic Bacteriology, vol.47, issue.2, pp.522-528, 1997. ,
DOI : 10.1099/00207713-47-2-522
Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes, BMC Microbiology, vol.9, issue.1, p.127, 2009. ,
DOI : 10.1186/1471-2180-9-127
URL : https://hal.archives-ouvertes.fr/hal-00512152
Oxidation of arsenite by Thiomonas strains and characterization of Thiomonas arsenivorans sp. nov., Antonie van Leeuwenhoek, vol.12, issue.1, pp.99-108, 2006. ,
DOI : 10.1007/s10482-005-9013-2
Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.56, issue.11, pp.2553-2557, 2006. ,
DOI : 10.1099/ijs.0.64299-0
Novel acidophiles isolated from moderately acidic mine drainage waters, Hydrometallurgy, vol.71, issue.1-2, pp.139-148, 2003. ,
DOI : 10.1016/S0304-386X(03)00150-6
Bacterial immobilization and oxidation of arsenic in acid mine drainage (Carnoul??s creek, France), Water Research, vol.37, issue.12, pp.2929-2936, 2003. ,
DOI : 10.1016/S0043-1354(03)00080-0
Sequencing the species pan-genome, Nature Reviews Microbiology, vol.8, issue.4, pp.258-259, 2009. ,
DOI : 10.1038/nrmicro2123
Genomic islands: tools of bacterial horizontal gene transfer and evolution, FEMS Microbiology Reviews, vol.33, issue.2, pp.376-393, 2009. ,
DOI : 10.1111/j.1574-6976.2008.00136.x
Role of Staphylococcal Phage and SaPI Integrase in Intra- and Interspecies SaPI Transfer, Journal of Bacteriology, vol.189, issue.15, pp.5608-5616, 2007. ,
DOI : 10.1128/JB.00619-07
Horizontal Transfer of the High-Pathogenicity Island of Yersinia pseudotuberculosis, Journal of Bacteriology, vol.187, issue.10, pp.3352-3358, 2005. ,
DOI : 10.1128/JB.187.10.3352-3358.2005
Unusual Integrase Gene Expression on the clc Genomic Island in Pseudomonas sp. Strain B13, Journal of Bacteriology, vol.185, issue.15, pp.4530-4538, 2003. ,
DOI : 10.1128/JB.185.15.4530-4538.2003
Pathogenicity Islands and the Evolution of Microbes, Annual Review of Microbiology, vol.54, issue.1, pp.641-679, 2000. ,
DOI : 10.1146/annurev.micro.54.1.641
Comparative genomics: the bacterial pan-genome, Current Opinion in Microbiology, vol.11, issue.5, pp.472-477, 2008. ,
DOI : 10.1016/j.mib.2008.09.006
The microbial pan-genome, Current Opinion in Genetics & Development, vol.15, issue.6, pp.589-594, 2005. ,
DOI : 10.1016/j.gde.2005.09.006
Microbial diversity and the genetic nature of microbial species, Nature Reviews Microbiology, vol.71, pp.431-440, 2008. ,
DOI : 10.1038/nrmicro1872
The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity, Science, vol.323, issue.5915, pp.741-746, 2009. ,
DOI : 10.1126/science.1159388
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome", Proceedings of the National Academy of Sciences, vol.102, issue.39, pp.13950-13955, 2005. ,
DOI : 10.1073/pnas.0506758102
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus, PLoS Genet, vol.3, 2007. ,
Genomic Islands and the Ecology and Evolution of Prochlorococcus, Science, vol.311, issue.5768, pp.1768-1770, 2006. ,
DOI : 10.1126/science.1122050
Homologous Recombination in Agrobacterium: Potential Implications for the Genomic Species Concept in Bacteria, Molecular Biology and Evolution, vol.26, issue.1, pp.167-176, 2009. ,
DOI : 10.1093/molbev/msn236
URL : https://hal.archives-ouvertes.fr/halsde-00526076
Life in extreme environments, Nature, vol.409, issue.6823, pp.1092-1101, 2001. ,
DOI : 10.1038/35059215
Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool, FEMS Microbiology Reviews, vol.31, issue.4, pp.449-477, 2007. ,
DOI : 10.1111/j.1574-6976.2007.00074.x
Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments, Genet Mol Res, vol.2, pp.92-101, 2003. ,
Prokaryotic sulfur oxidation, Current Opinion in Microbiology, vol.8, issue.3, pp.253-259, 2005. ,
DOI : 10.1016/j.mib.2005.04.005
Sulfur Metabolism in Phototrophic Sulfur Bacteria, Adv Microb Physiol, vol.54, pp.103-200, 2009. ,
DOI : 10.1016/S0065-2911(08)00002-7
Cytoplasmic pH Measurement and Homeostasis in Bacteria and Archaea, Adv Microb Physiol, vol.55, pp.1-79, 2009. ,
DOI : 10.1016/S0065-2911(09)05501-5
Life in acid: pH homeostasis in acidophiles, Trends in Microbiology, vol.15, issue.4, pp.165-171, 2007. ,
DOI : 10.1016/j.tim.2007.02.005
Acid survival of Helicobacter pylori: how does urease activity trigger cytoplasmic pH homeostasis?, Trends in Microbiology, vol.10, issue.2, pp.70-74, 2002. ,
DOI : 10.1016/S0966-842X(01)02287-9
A biological role for prokaryotic ClC chloride channels, Nature, vol.136, issue.6908, pp.715-718, 2002. ,
DOI : 10.1073/pnas.120163297
A bacterial view of the periodic table: genes and proteins for toxic inorganic ions, Journal of Industrial Microbiology & Biotechnology, vol.300, issue.11-12, pp.587-605, 2005. ,
DOI : 10.1007/s10295-005-0019-6
Multimetal resistance and tolerance in microbial biofilms, Nature Reviews Microbiology, vol.5, issue.12, pp.928-938, 2007. ,
DOI : 10.1038/nrmicro1774
A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments, PLoS Genetics, vol.73, issue.4, 2007. ,
DOI : 10.1371/journal.pgen.0030053.st004
URL : https://hal.archives-ouvertes.fr/halsde-00230447
Genes and Enzymes Involved in Bacterial Oxidation and Reduction of Inorganic Arsenic, Applied and Environmental Microbiology, vol.71, issue.2, pp.599-608, 2005. ,
DOI : 10.1128/AEM.71.2.599-608.2005
As(III) and Sb(III) Uptake by GlpF and Efflux by ArsB in Escherichia coli, Journal of Biological Chemistry, vol.279, issue.18, pp.18334-18341, 2004. ,
DOI : 10.1074/jbc.M400037200
Modulation of DNA repair processes by arsenic and selenium compounds, Toxicology, vol.193, issue.1-2, pp.161-169, 2003. ,
DOI : 10.1016/j.tox.2003.08.004
Induction of oxidative DNA damage by arsenite and its trivalent and pentavalent methylated metabolites in cultured human cells and isolated DNA, Carcinogenesis, vol.24, issue.5, pp.967-974, 2003. ,
DOI : 10.1093/carcin/bgg018
Structural and mechanistic determinants of c-di-GMP signalling, Nature Reviews Microbiology, vol.1, issue.10, pp.724-735, 2009. ,
DOI : 10.1038/nrmicro2203
Principles of c-di-GMP signalling in bacteria, Nature Reviews Microbiology, vol.178, issue.4, pp.263-273, 2009. ,
DOI : 10.1038/nrmicro2109
Shaping bacterial genomes with integrative and conjugative elements, Research in Microbiology, vol.155, issue.5, pp.376-386, 2004. ,
DOI : 10.1016/j.resmic.2004.01.012
Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, Proceedings of the National Academy of Sciences, vol.99, issue.19, pp.12391-12396, 2002. ,
DOI : 10.1073/pnas.182380799
Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray, Journal of Bacteriology, vol.186, issue.12, pp.3911-3921, 2004. ,
DOI : 10.1128/JB.186.12.3911-3921.2004
Bacillus subtilis Genome Diversity, Journal of Bacteriology, vol.189, issue.3, pp.1163-1170, 2007. ,
DOI : 10.1128/JB.01343-06
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797320
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics, International Journal of Systematic and Evolutionary Microbiology, vol.37, issue.4, pp.463-464, 1987. ,
DOI : 10.1099/00207713-37-4-463
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries, Functional & Integrative Genomics, vol.54, issue.5, pp.165-185, 2006. ,
DOI : 10.1007/s10142-006-0027-2
Comparative Genomic Analyses of the Vibrio Pathogenicity Island and Cholera Toxin Prophage Regions in Nonepidemic Serogroup Strains of Vibrio cholerae, Applied and Environmental Microbiology, vol.69, issue.3, pp.1728-1738, 2003. ,
DOI : 10.1128/AEM.69.3.1728-1738.2003
A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus, Molecular Microbiology, vol.24, issue.4, pp.1145-1157, 2007. ,
DOI : 10.1111/j.1365-2958.2006.05570.x
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion, Microbiology and Molecular Biology Reviews, vol.68, issue.3, pp.560-602, 2004. ,
DOI : 10.1128/MMBR.68.3.560-602.2004
Run-Off Replication of Host-Adaptability Genes Is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii, PLoS Genetics, vol.187, issue.3, 2009. ,
DOI : 10.1371/journal.pgen.1000546.s005
Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria, Current Biology, vol.18, issue.6, pp.442-448, 2008. ,
DOI : 10.1016/j.cub.2008.02.067
Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates, Environmental Microbiology, vol.51, issue.10, pp.1505-1513, 2005. ,
DOI : 10.1046/j.1462-2920.2003.00403.x
Phage-Mediated Intergeneric Transfer of Toxin Genes, Science, vol.323, issue.5910, pp.139-141, 2009. ,
DOI : 10.1126/science.1164783
Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence, Cellular Microbiology, vol.63, issue.12, pp.2377-2386, 2008. ,
DOI : 10.1111/j.1462-5822.2008.01187.x
: from DNA donation to homologous recombination, Molecular Microbiology, vol.6, issue.2, pp.376-385, 2006. ,
DOI : 10.1111/j.1365-2958.2005.04964.x
Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiology Reviews, vol.33, issue.3, pp.539-571, 2009. ,
DOI : 10.1111/j.1574-6976.2009.00169.x
Phenotypic switching of Thiobacillus ferrooxidans., Journal of Bacteriology, vol.170, issue.9, pp.3915-3923, 1988. ,
DOI : 10.1128/jb.170.9.3915-3923.1988
Novel acidophiles isolated from moderately acidic mine drainage waters, Hydrometallurgy, vol.71, issue.1-2, pp.139-148, 2003. ,
DOI : 10.1016/S0304-386X(03)00150-6
Thiobacillus perometabolis nov. sp., a non-autotrophic thiobacillus, Archiv f???r Mikrobiologie, vol.11, issue.1-3, pp.218-225, 1967. ,
DOI : 10.1007/BF00406335
The Quantitative Measurement of DNA Hybridization from Renaturation Rates, European Journal of Biochemistry, vol.94, issue.1, pp.133-142, 1970. ,
DOI : 10.1016/0003-2697(60)90025-7
Studies on the spectrophotometric determination of DNA hybridization from renaturation rates, Systematic and Applied Microbiology, vol.4, issue.2, pp.184-192, 1983. ,
DOI : 10.1016/S0723-2020(83)80048-4
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data, Bioinformatics, vol.21, issue.23, pp.4209-4215, 2005. ,
DOI : 10.1093/bioinformatics/bti711
MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006. ,
DOI : 10.1093/nar/gkj406
A new nonlinear normalization method for reducing variability in DNA microarray experiments, Genome Biol, vol.3, pp.48-89, 2002. ,
Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, vol.5, issue.4, pp.557-572, 2004. ,
DOI : 10.1093/biostatistics/kxh008
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches, Nucleic Acids Research, vol.28, issue.15, pp.2919-2926, 2000. ,
DOI : 10.1093/nar/28.15.2919
L'analyse des correspondances, 1984. ,
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes, Nucleic Acids Research, vol.14, issue.13, pp.5125-5143, 1986. ,
DOI : 10.1093/nar/14.13.5125
Use and misuse of correspondence analysis in codon usage studies, Nucleic Acids Research, vol.30, issue.20, pp.4548-4555, 2002. ,
DOI : 10.1093/nar/gkf565
URL : https://hal.archives-ouvertes.fr/hal-00427295