S. G. Acinas and J. Anton, Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA, Appl Environ Microbiol, vol.65, issue.2, pp.514-522, 1999.

J. Aislabie and A. K. Bej, Microbial degradation of quinoline and methylquinolines, Appl Environ Microbiol, vol.56, issue.2, pp.345-351, 1990.

H. J. Anders and A. Kaetzke, Taxonomic Position of Aromatic-Degrading Denitrifying Pseudomonad Strains K 172 and KB 740 and Their Description as New Members of the Genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., Respectively, Members of the Beta Subclass of the Proteobacteria, International Journal of Systematic Bacteriology, vol.45, issue.2, pp.327-333, 1995.
DOI : 10.1099/00207713-45-2-327

G. Antranikian and C. E. Vorgias, Extreme Environments as a Resource for Microorganisms and Novel Biocatalysts, Adv Biochem Eng Biotechnol, vol.96, pp.219-262, 2005.
DOI : 10.1007/b135786

W. Arber and S. Linn, DNA Modification and Restriction, Annual Review of Biochemistry, vol.38, issue.1, pp.467-500, 1969.
DOI : 10.1146/annurev.bi.38.070169.002343

A. Ardura and S. Planes, Beyond Biodiversity: Fish Metagenomes, PLoS ONE, vol.10, issue.3, p.22592, 2011.
DOI : 10.1371/journal.pone.0022592.t003
URL : https://hal.archives-ouvertes.fr/hal-00655348

M. Bagdasarian and R. Lurz, Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas, Gene, vol.16, pp.1-3, 1981.

Y. Bai and Q. Sun, Quinoline biodegradation and its nitrogen transformation pathway by a Pseudomonas sp. strain, Biodegradation, vol.16, issue.6, pp.335-344, 2010.
DOI : 10.1007/s10532-009-9304-9

R. C. Barrick and E. T. Furlong, Hydrocarbon and azaarene markers of coal transport to aquatic sediments, Environmental Science & Technology, vol.18, issue.11, pp.846-854, 1984.
DOI : 10.1021/es00129a008

K. Benzerara and N. Menguy, Nanoscale detection of organic signatures in carbonate microbialites, Proceedings of the National Academy of Sciences, vol.103, issue.25, pp.9440-9445, 2006.
DOI : 10.1073/pnas.0603255103
URL : https://hal.archives-ouvertes.fr/hal-00105486

X. Bian and F. Huang, through Red/ET Recombineering, ChemBioChem, vol.138, issue.13, pp.1946-1952, 2012.
DOI : 10.1002/cbic.201200310

B. Liu and F. Z. , Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison, FEMS Microbiology Ecology, vol.55, issue.2, p.13, 2006.
DOI : 10.1111/j.1574-6941.2005.00033.x

A. W. Bird and A. Erler, High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes, Nature Methods, vol.14, issue.1, pp.103-109, 2012.
DOI : 10.1038/nature03502

B. Jimenez and M. , Treatment of irritable bowel syndrome with probiotics. An etiopathogenic approach at last?, Rev Esp Enferm Dig, vol.101, issue.8, pp.553-564, 2009.

M. Blase and C. Bruntner, Cloning, expression, and sequence analysis of the three genes encoding quinoline 2-oxidoreductase, a molybdenum-containing hydroxylase from Pseudomonas putida 86, J Biol Chem, vol.271, issue.38, pp.23068-23079, 1996.

M. Boll, Dearomatizing Benzene Ring Reductases, Journal of Molecular Microbiology and Biotechnology, vol.10, issue.2-4, 2005.
DOI : 10.1159/000091560

M. Boll and G. Fuchs, Benzoyl-Coenzyme A Reductase (Dearomatizing), a Key Enzyme of Anaerobic Aromatic Metabolism. ATP Dependence of the Reaction, Purification and Some Properties of the Enzyme from Thauera Aromatica Strain K172, European Journal of Biochemistry, vol.165, issue.3, pp.921-933, 1995.
DOI : 10.1006/abio.1976.9999

M. Boll and G. Fuchs, EPR and Mossbauer Studies of Benzoyl-CoA Reductase, Journal of Biological Chemistry, vol.275, issue.41, pp.31857-31868, 2000.
DOI : 10.1074/jbc.M001508200

M. Bonkowski and J. Roy, Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms, Oecologia, vol.13, issue.2, pp.232-240, 2005.
DOI : 10.1007/s00442-004-1790-1

J. Borneman and E. W. Triplett, Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation, 1997.

D. A. Bossio and K. M. Scow, Determinants of Soil Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on Phospholipid Fatty Acid Profiles, Microbial Ecology, vol.36, issue.1, pp.1-12, 1998.
DOI : 10.1007/s002489900087

D. Boyd and D. S. Weiss, Towards Single-Copy Gene Expression Systems Making Gene Cloning Physiologically Relevant: Lambda InCh, a Simple Escherichia coli Plasmid-Chromosome Shuttle System, Journal of Bacteriology, vol.182, issue.3, pp.842-847, 2000.
DOI : 10.1128/JB.182.3.842-847.2000

C. Brack and H. Eberle, A map of the sites on bacteriophage PM2 DNA for the restriction endonucleases HindIII and HpaII, Journal of Molecular Biology, vol.104, issue.1, pp.305-309, 1976.
DOI : 10.1016/0022-2836(76)90016-4

F. J. Brockman and B. A. Denovan, Isolation and characterization of quinoline-degrading bacteria from subsurface sediments, Appl Environ Microbiol, vol.55, issue.4, pp.1029-1032, 1989.

A. Buchan and M. Alber, Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S???23S intergenic spacer region, FEMS Microbiology Ecology, vol.35, issue.3, pp.313-321, 2001.
DOI : 10.1016/S0168-6496(01)00109-X

B. Carl and A. Arnold, Sequence and transcriptional analysis of a gene cluster of Pseudomonas putida 86 involved in quinoline degradation, Gene, vol.331, pp.177-188, 2004.
DOI : 10.1016/j.gene.2004.02.020

B. Carl and S. Fetzner, Transcriptional Activation of Quinoline Degradation Operons of Pseudomonas putida 86 by the AraC/XylS-Type Regulator OxoS and Cross-Regulation of the PqorM Promoter by XylS, Applied and Environmental Microbiology, vol.71, issue.12, pp.8618-8626, 2005.
DOI : 10.1128/AEM.71.12.8618-8626.2005

M. Carmona and M. T. Zamarro, Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View, Microbiology and Molecular Biology Reviews, vol.73, issue.1, pp.71-133, 2009.
DOI : 10.1128/MMBR.00021-08

D. M. Carter and C. M. Radding, The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease, J Biol Chem, vol.246, issue.8, pp.2502-2512, 1971.

E. Cassuto and C. M. Radding, Mechanism for the Action of ?? Exonuclease in Genetic Recombination, Nature New Biology, vol.229, issue.1, pp.13-16, 1971.
DOI : 10.1038/newbio229013a0

Y. Chai and S. Shan, Heterologous Expression and Genetic Engineering of the Tubulysin Biosynthetic Gene Cluster Using Red/ET Recombineering and Inactivation Mutagenesis, Chemistry & Biology, vol.19, issue.3, pp.361-371, 2012.
DOI : 10.1016/j.chembiol.2012.01.007

Y. P. Chao and C. J. Chiang, Stringent Regulation and High-Level Expression of Heterologous Genes in Escherichia coli Using T7 System Controllable by the araBAD Promoter, Biotechnology Progress, vol.18, issue.2, pp.394-400, 2002.
DOI : 10.1021/bp0101785

F. Chen and M. Cui, Biodegradation of quinoline by freely suspended and immobilized cells of Comamonas sp. strain Q10, The Journal of General and Applied Microbiology, vol.49, issue.2, pp.123-128, 2003.
DOI : 10.2323/jgam.49.123

R. E. Cobb and H. Zhao, Direct cloning of large genomic sequences, Nature Biotechnology, vol.30, issue.5, pp.405-406
DOI : 10.1093/nar/gkn991

R. E. Cobb and H. Zhao, Direct cloning of large genomic sequences, Nature Biotechnology, vol.30, issue.5, pp.405-406, 2012.
DOI : 10.1093/nar/gkn991

N. Costantino and D. L. Court, Enhanced levels of ?? Red-mediated recombinants in mismatch repair mutants, Proceedings of the National Academy of Sciences, vol.100, issue.26, pp.15748-15753, 2003.
DOI : 10.1073/pnas.2434959100

M. G. Cottingham, Genetic Manipulation of Poxviruses Using Bacterial Artificial Chromosome Recombineering, Methods Mol Biol, vol.890, pp.37-57, 2012.
DOI : 10.1007/978-1-61779-876-4_3

M. T. Cottrell and L. A. Waidner, Bacterial diversity of metagenomic and PCR libraries from the Delaware River, Environmental Microbiology, vol.28, issue.12, pp.1883-1895, 2005.
DOI : 10.1111/j.1462-2920.2005.00762.x

D. Court, S. J. Thomason, and L. , Genetic Engineering Using Homologous Recombination, Annual Review of Genetics, vol.36, issue.1, p.28, 2002.
DOI : 10.1146/annurev.genet.36.061102.093104

D. L. Court and S. Swaminathan, Mini-??: a tractable system for chromosome and BAC engineering, Gene, vol.315, pp.63-69, 2003.
DOI : 10.1016/S0378-1119(03)00728-5

D. Cowan and Q. Meyer, Metagenomic gene discovery: past, present and future, Trends in Biotechnology, vol.23, issue.6, pp.321-329, 2005.
DOI : 10.1016/j.tibtech.2005.04.001

F. Crescitelli, Effects of oxine, carbostyril and quinoline on frog nerve, Am J Physiol, vol.163, issue.1, pp.197-200, 1950.

M. Cui, Microbial Metabolism of Quinoline by Comamonas sp., World Journal of Microbiology and Biotechnology, vol.20, issue.6, 2004.
DOI : 10.1023/B:WIBI.0000043149.61562.3f

M. Cui, Microbial Metabolism of Quinoline by Comamonas sp., World Journal of Microbiology and Biotechnology, vol.20, issue.6, 2004.
DOI : 10.1023/B:WIBI.0000043149.61562.3f

M. Cui and F. Chen, Cometabolic biodegradation of quinoline's derivatives by a quinoline-degrading bacteria: Comamonas sp. strain Q10, The Journal of General and Applied Microbiology, vol.49, issue.6, pp.351-355, 2003.
DOI : 10.2323/jgam.49.351

D. 'hondt, S. , and A. J. Spivack, Subseafloor sedimentary life in the South Pacific Gyre, Proceedings of the National Academy of Sciences, vol.106, issue.28, pp.11651-11656, 2009.
DOI : 10.1073/pnas.0811793106

P. Dabert and S. D. Ehrlich, Chi sequence protects against RecBCD degradation of DNA in vivo., Proceedings of the National Academy of Sciences, vol.89, issue.24, pp.12073-12077, 1992.
DOI : 10.1073/pnas.89.24.12073

G. Dai and S. Kim, Development of a bacterial artificial chromosome (BAC) recombineering procedure using galK-untranslated region (UTR) for the mutation of diploid genes, Journal of Virological Methods, vol.182, issue.1-2, pp.18-26, 2012.
DOI : 10.1016/j.jviromet.2012.02.010

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.6640-6645, 2000.
DOI : 10.1073/pnas.120163297

S. Datta and N. Costantino, A set of recombineering plasmids for gram-negative bacteria, Gene, vol.379, pp.109-115, 2006.
DOI : 10.1016/j.gene.2006.04.018

S. Datta and N. Costantino, Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages, Proceedings of the National Academy of Sciences, vol.105, issue.5, pp.1626-1631, 2008.
DOI : 10.1073/pnas.0709089105

J. G. De-boer and B. W. Glickman, The lacI gene as a target for mutation in transgenic rodents and Escherichia coli, Genetics, vol.148, issue.4, pp.1441-1451, 1998.

T. O. Delmont and E. Prestat, Structure, fluctuation and magnitude of a natural grassland soil metagenome, The ISME Journal, vol.64, issue.9, pp.1677-1687, 2012.
DOI : 10.1038/nrmicro2119
URL : https://hal.archives-ouvertes.fr/hal-00747243

T. O. Delmont and P. Robe, Accessing the Soil Metagenome for Studies of Microbial Diversity, Applied and Environmental Microbiology, vol.77, issue.4, pp.1315-1324, 2011.
DOI : 10.1128/AEM.01526-10
URL : https://hal.archives-ouvertes.fr/hal-00579312

T. O. Delmont and P. Robe, Metagenomic comparison of direct and indirect soil DNA extraction approaches, Journal of Microbiological Methods, vol.86, issue.3, pp.397-400, 2011.
DOI : 10.1016/j.mimet.2011.06.013
URL : https://hal.archives-ouvertes.fr/hal-00629399

N. A. Desai and V. Shankar, Single-strand-specific nucleases, FEMS Microbiology Reviews, vol.26, issue.5, pp.457-491, 2003.
DOI : 10.1111/j.1574-6976.2003.tb00626.x

I. B. Dodd and K. E. Shearwin, Revisited gene regulation in bacteriophage ??, Current Opinion in Genetics & Development, vol.15, issue.2, pp.145-152, 2005.
DOI : 10.1016/j.gde.2005.02.001

L. Donald, A. B. Court, and S. L. Adhya, A New Look at Bacteriophage Genetic Networks, Journal of Bacteriology, vol.189, issue.?0062, p.7

A. Duran and M. Gryzenhout, AFLP analysis reveals a clonal population of Phytophthora pinifolia in Chile, Fungal Biology, vol.114, issue.9, pp.746-752, 2010.
DOI : 10.1016/j.funbio.2010.06.008

P. G. Egland and C. S. Harwood, BadR, a new MarR family member, regulates anaerobic benzoate degradation by Rhodopseudomonas palustris in concert with AadR, an Fnr family member, J Bacteriol, vol.181, issue.7, pp.2102-2109, 1999.

G. Eller and M. Kruger, Comparing field and microcosm experiments: a case study on methano- and methylo-trophic bacteria in paddy soil, FEMS Microbiology Ecology, vol.51, issue.2, pp.279-291, 2005.
DOI : 10.1016/j.femsec.2004.09.007

H. M. Ellis and D. Yu, High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides, Proceedings of the National Academy of Sciences, vol.98, issue.12, pp.6742-6746, 2001.
DOI : 10.1073/pnas.121164898

T. Feher and I. Karcagi, Scarless Engineering of the Escherichia coli Genome, Methods Mol Biol, vol.416, pp.251-259, 2008.
DOI : 10.1007/978-1-59745-321-9_16

K. Gerdes and F. W. Bech, Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon, EMBO J, vol.5, issue.8, pp.2023-2029, 1986.

K. Gerdes and L. K. Poulsen, The hok killer gene family in gram-negative bacteria, New Biol, vol.2, issue.11, pp.946-956, 1990.

D. C. Gillan and A. G. Speksnijder, Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA, Appl Environ Microbiol, vol.64, issue.9, pp.3464-3472, 1998.

B. Gomez-villalba and C. Calvo, TGGE analysis of the diversity of ammonia-oxidizing and denitrifying bacteria in submerged filter biofilms for the treatment of urban wastewater, Applied Microbiology and Biotechnology, vol.173, issue.2, pp.393-400, 2006.
DOI : 10.1007/s00253-005-0272-7

A. Gomtsyan and E. K. Bayburt, Novel Transient Receptor Potential Vanilloid 1 Receptor Antagonists for the Treatment of Pain:?? Structure???Activity Relationships for Ureas with Quinoline, Isoquinoline, Quinazoline, Phthalazine, Quinoxaline, and Cinnoline Moieties, Journal of Medicinal Chemistry, vol.48, issue.3, pp.744-752, 2005.
DOI : 10.1021/jm0492958

D. J. Grant and T. R. , Degradation of quinoline by a soil bacterium, Microbios, vol.15, pp.61-62, 1976.

W. D. Grant and S. Heaphy, Metagenomics and recovery of enzyme genes from alkaline saline environments, Environmental Technology, vol.51, issue.10, pp.1135-1143, 2010.
DOI : 10.1021/ja809461u

L. M. Guzman and D. Belin, Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter., Journal of Bacteriology, vol.177, issue.14, pp.4121-4130, 1995.
DOI : 10.1128/jb.177.14.4121-4130.1995

J. Handelsman, Metagenomics: Application of Genomics to Uncultured Microorganisms, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.669-685, 2004.
DOI : 10.1128/MMBR.68.4.669-685.2004

J. Handelsman and M. R. Rondon, Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products, Chemistry & Biology, vol.5, issue.10, pp.245-249, 1998.
DOI : 10.1016/S1074-5521(98)90108-9

T. Harmer and M. Wu, The role of rigidity in DNA looping-unlooping by AraC, Proceedings of the National Academy of Sciences, vol.98, issue.2, pp.427-431, 2001.
DOI : 10.1073/pnas.98.2.427

C. R. Harwood, Bacillus subtilis and its relatives: molecular biological and industrial workhorses, Trends in Biotechnology, vol.10, issue.7, pp.247-256, 1992.
DOI : 10.1016/0167-7799(92)90233-L

T. Hashimoto-gotoh and F. C. Franklin, Specific-purpose plasmid cloning vectors I. Low copy number, temperature-sensitive, mobilization-defective pSC101-derived containment vectors, Gene, vol.16, issue.1-3, pp.1-3, 1981.
DOI : 10.1016/0378-1119(81)90079-2

D. Heintz and S. Gallien, Differential Membrane Proteome Analysis Reveals Novel Proteins Involved in the Degradation of Aromatic Compounds in Geobacter metallireducens, Molecular & Cellular Proteomics, vol.8, issue.9, pp.2159-2169, 2009.
DOI : 10.1074/mcp.M900061-MCP200

K. Hirao and Y. Shinohara, Carcinogenic activity of quinoline on rat liver, Cancer Res, vol.36, issue.2, p.329, 1976.

R. H. Hoess and A. Wierzbicki, spacer region in PI site-specific recombination, Nucleic Acids Research, vol.14, issue.5, pp.2287-2300, 1986.
DOI : 10.1093/nar/14.5.2287

S. M. Hollenback and S. Lyman, Recombineering-Based Procedure for Creating BAC Transgene Constructs for Animals and Cell Lines, Curr Protoc Mol Biol Chapter, vol.20, issue.23, p.14, 2011.
DOI : 10.1002/0471142727.mb2314s95

L. B. Jensen and J. L. Ramos, A substrate-dependent biological containment system for Pseudomonas putida based on the Escherichia coli gef gene, Appl Environ Microbiol, vol.59, issue.11, pp.3713-3717, 1993.

W. Jianlong and Q. Xiangchun, Microbial degradation of quinoline by immobilized cells of Burkholderia pickettii, Water Research, vol.36, issue.9, pp.2288-2296, 2002.
DOI : 10.1016/S0043-1354(01)00457-2

J. Jose and R. Giridhar, Heavy metal pollution exerts reduction/adaptation in the diversity and enzyme expression profile of heterotrophic bacteria in Cochin estuary, India, Environmental Pollution, vol.159, issue.10, pp.2775-2780, 2011.
DOI : 10.1016/j.envpol.2011.05.009

D. F. Juang and P. C. Yang, Effects of microbial species, organic loading and substrate degradation rate on the power generation capability of microbial fuel cells, Biotechnology Letters, vol.10, issue.11, pp.2147-2160, 2011.
DOI : 10.1007/s10529-011-0690-9

M. Kaebernick and E. Dittmann, Multiple Alternate Transcripts Direct the Biosynthesis of Microcystin, a Cyanobacterial, Applied and Environmental Microbiology, vol.68, issue.2, pp.449-455, 2002.
DOI : 10.1128/AEM.68.2.449-455.2002

H. Y. Kahng and J. J. Kukor, Characterization of strain HY99, a novel microorganism capable of aerobic and anaerobic degradation of aniline, FEMS Microbiology Letters, vol.190, issue.2, pp.215-221, 2000.
DOI : 10.1111/j.1574-6968.2000.tb09289.x

J. P. Kaiser and Y. Feng, Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions, Microbiol Rev, vol.60, issue.3, pp.483-498, 1996.

G. Karakousis and N. Ye, The beta protein of phage ?? binds preferentially to an intermediate in DNA renaturation, Journal of Molecular Biology, vol.276, issue.4, pp.721-731, 1998.
DOI : 10.1006/jmbi.1997.1573

A. E. Karu and Y. Sakaki, The gamma protein specified by bacteriophage gamma. Structure and inhibitory activity for the recBC enzyme of Escherichia coli, J Biol Chem, vol.250, issue.18, pp.7377-7387, 1975.

C. Kato and M. H. Qureshi, Pressure response in deep-sea piezophilic bacteria, J Mol Microbiol Biotechnol, vol.1, issue.1, pp.87-92, 1999.

K. Kawaguchi and Y. Shinoda, sp. strain TS-6 capable of aerobic and anaerobic degradation of aromatic compounds, FEMS Microbiology Letters, vol.257, issue.2, pp.208-213, 2006.
DOI : 10.1111/j.1574-6968.2006.00165.x

T. J. Kelly, H. O. Jr, and . Smith, A restriction enzyme from Hemophilus influenzae, Journal of Molecular Biology, vol.51, issue.2, pp.393-409, 1970.
DOI : 10.1016/0022-2836(70)90150-6

C. Kessler and V. Manta, Specificity of restriction endonucleases and DNA modification methyltransferases ??? a review (edition 3), Gene, vol.92, issue.1-2, pp.1-248, 1990.
DOI : 10.1016/0378-1119(90)90486-B

S. Kim and H. G. Dallmann, tau couples the leading-and lagging-strand polymerases at the Escherichia coli DNA replication fork, J Biol Chem, vol.271, issue.35, pp.21406-21412, 1996.

K. Sergueev, D. Y. , S. Austin, and D. Court, Cell toxicity caused by products of the pLoperon of bacteriophage lambda, Gene, vol.272, issue.12, p.9, 2001.

S. Knudsen and P. Saadbye, Development and testing of improved suicide functions for biological containment of bacteria, Appl Environ Microbiol, vol.61, issue.3, pp.985-991, 1995.

S. A. Kools and B. Ferwerda, MICROBIAL RESPONSES TO ZINC IN SOIL MICROCOSMS WITH AND WITHOUT A NATURAL ASSEMBLAGE OF ENCHYTRAEIDS, Environmental Toxicology and Chemistry, vol.24, issue.9, pp.2178-2184, 2005.
DOI : 10.1897/04-661R.1

H. Kopecka and J. Hillova, Effect of restriction endonucleases on infectivity of Rous sarcoma virus DNA, Nature, vol.391, issue.5563, pp.72-74, 1976.
DOI : 10.1038/262072a0

J. W. Kung and C. Loffler, Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases, Proceedings of the National Academy of Sciences, vol.106, issue.42, pp.17687-17692, 2009.
DOI : 10.1073/pnas.0905073106
URL : https://hal.archives-ouvertes.fr/hal-00455814

L. Snyder and K. M. , The rex genes of bacteriophage lambda can inhibit cell function without phage superinfection, Gene, vol.81, issue.1, pp.17-24, 1989.
DOI : 10.1016/0378-1119(89)90332-6

C. Lacroix and D. Giovannini, FLP/FRT-mediated conditional mutagenesis in pre-erythrocytic stages of Plasmodium berghei, Nature Protocols, vol.19, issue.9, pp.1412-1428, 2011.
DOI : 10.1073/pnas.76.9.4350

M. Larentis and A. Alfreider, Comparative evaluation of prokaryotic 16S rDNA clone libraries and SSCP in groundwater samples, Journal of Basic Microbiology, vol.59, issue.3, pp.330-335, 2011.
DOI : 10.1002/jobm.201000295

P. C. Lau and R. W. Rowsome, Comparative nucleotide sequences encoding the immunity proteins and the carboxyl-terminal peptides of colicins E2 and E3, Nucleic Acids Research, vol.12, issue.22, pp.8733-8745, 1984.
DOI : 10.1093/nar/12.22.8733

E. J. Lavoie and A. Shigematsu, Tumor-initiating activity of quinoline and methylated quinolines on the skin of SENCAR mice, Cancer Letters, vol.22, issue.3, pp.269-273, 1984.
DOI : 10.1016/0304-3835(84)90162-9

E. C. Lee and D. Yu, A Highly Efficient Escherichia coli-Based Chromosome Engineering System Adapted for Recombinogenic Targeting and Subcloning of BAC DNA, Genomics, vol.73, issue.1, pp.56-65, 2001.
DOI : 10.1006/geno.2000.6451

N. Lee, Molecular aspects of ara regulation, p.22, 1980.

N. Lee and C. Francklyn, Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter., Proceedings of the National Academy of Sciences, vol.84, issue.24, pp.8814-8818, 1987.
DOI : 10.1073/pnas.84.24.8814

B. Lesic, Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa, BMC Molecular Biology, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2199-9-20

X. T. Li and N. Costantino, Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli, Nucleic Acids Research, vol.31, issue.22, pp.6674-6687, 2003.
DOI : 10.1093/nar/gkg844

D. J. Licht, Transformation of indole and quinoline by Desulfobacterium indolicum, Applied Microbiology and Biotechnology, vol.42, issue.7, 1997.

R. B. Lobell and R. F. Schleif, DNA looping and unlooping by AraC protein, Science, vol.250, issue.4980, pp.528-532, 1990.
DOI : 10.1126/science.2237403

C. Loffler and K. Kuntze, Occurrence, genes and expression of the W/Se-containing class II benzoyl-coenzyme A reductases in anaerobic bacteria, Environmental Microbiology, vol.21, issue.3, pp.696-709, 2011.
DOI : 10.1111/j.1462-2920.2010.02374.x

Y. Mao and X. Zhang, Versatile aromatic compound-degrading capacity and microdiversity of Thauera strains isolated from a coking wastewater treatment bioreactor, Journal of Industrial Microbiology & Biotechnology, vol.64, issue.2, pp.927-934, 2010.
DOI : 10.1007/s10295-010-0740-7

M. Maresca and A. Erler, Single-stranded heteroduplex intermediates in ?? Red homologous recombination, BMC Molecular Biology, vol.11, issue.1, p.54, 2010.
DOI : 10.1186/1471-2199-11-54

L. J. Marinelli and G. F. Hatfull, Recombineering, Bacteriophage, vol.148, issue.1, pp.5-14, 2012.
DOI : 10.1146/annurev.micro.112408.134233
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357384

J. T. Martinsohn and M. Radman, The ?? Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome Mosaicism, PLoS Genetics, vol.97, issue.5, p.1000065, 2008.
DOI : 10.1371/journal.pgen.1000065.s008
URL : https://hal.archives-ouvertes.fr/inserm-00496049

H. Masai and Y. Kaziro, Definition of oriR, the minimum DNA segment essential for initiation of R1 plasmid replication in vitro., Proceedings of the National Academy of Sciences, vol.80, issue.22, pp.6814-6818, 1983.
DOI : 10.1073/pnas.80.22.6814

H. Masaki and T. Ohta, A plasmid region encoding the active fragment and the inhibitor protein of colicin E3-CA38, FEBS Letters, vol.72, issue.1, pp.129-132, 1982.
DOI : 10.1016/0014-5793(82)81087-9

T. Mechichi and E. Stackebrandt, Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov., Archives of Microbiology, vol.178, issue.1, pp.26-35, 2002.
DOI : 10.1007/s00203-002-0422-6

A. Mehta, R. P. Leite, and . Jr, Assessment of the genetic diversity of Xylella fastidiosa isolated from citrus in Brazil by PCR-RFLP of the 16S rDNA and 16S-23S intergenic spacer and rep-PCR fingerprinting, Antonie van Leeuwenhoek, vol.79, issue.1, pp.53-59, 2001.
DOI : 10.1023/A:1010219811555

N. M. Mesbah and J. Wiegel, Life at Extreme Limits, Annals of the New York Academy of Sciences, vol.281, issue.1, pp.44-57, 2008.
DOI : 10.1196/annals.1419.028

H. Mizoguchi and K. Tanaka-masuda, K-12 Chromosome, Bioscience, Biotechnology, and Biochemistry, vol.71, issue.12, pp.2905-2911, 2007.
DOI : 10.1271/bbb.70274

D. Mora and G. Ricci, 16S-23S rRNA intergenic spacer region sequence variation in Streptococcus thermophilus and related dairy streptococci and development of a multiplex ITS-SSCP analysis for their identification, Microbiology, vol.149, issue.3, pp.807-813, 2003.
DOI : 10.1099/mic.0.25925-0

J. A. Mosberg and C. J. Gregg, Improving Lambda Red Genome Engineering in Escherichia coli via Rational Removal of Endogenous Nucleases, PLoS ONE, vol.7, issue.9, p.44638, 2012.
DOI : 10.1371/journal.pone.0044638.s002

J. A. Mosberg and M. J. Lajoie, Lambda Red Recombineering in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate, Genetics, vol.186, issue.3, pp.791-799, 2010.
DOI : 10.1534/genetics.110.120782

K. Muniyappa and C. M. Radding, The homologous recombination system of phage lambda. Pairing activities of beta protein, J Biol Chem, vol.261, issue.16, pp.7472-7478, 1986.

K. C. Murphy, Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme., Journal of Bacteriology, vol.173, issue.18, pp.5808-5821, 1991.
DOI : 10.1128/jb.173.18.5808-5821.1991

K. C. Murphy, Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli, J Bacteriol, vol.180, issue.8, pp.2063-2071, 1998.

K. C. Murphy and K. G. Campellone, PCR-mediated gene replacement in Escherichia coli, Gene, vol.246, issue.1-2, pp.321-330, 2000.
DOI : 10.1016/S0378-1119(00)00071-8

R. Musiol and J. Jampilek, Investigating biological activity spectrum for novel quinoline analogues, Bioorganic & Medicinal Chemistry, vol.15, issue.3, pp.1280-1288, 2007.
DOI : 10.1016/j.bmc.2006.11.020

R. Musiol and D. Tabak, Investigating biological activity spectrum for novel quinoline analogues 2: Hydroxyquinolinecarboxamides with photosynthesis-inhibiting activity, Bioorganic & Medicinal Chemistry, vol.16, issue.8, pp.4490-4499, 2008.
DOI : 10.1016/j.bmc.2008.02.065

M. H. Nicolaisen and N. B. Ramsing, Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria, Journal of Microbiological Methods, vol.50, issue.2, pp.189-203, 2002.
DOI : 10.1016/S0167-7012(02)00026-X

C. Nithya and S. K. Pandian, Evaluation of Bacterial Diversity in Palk Bay Sediments Using Terminal-Restriction Fragment Length Polymorphisms (T-RFLP), Applied Biochemistry and Biotechnology, vol.48, issue.6, pp.1763-1777, 2012.
DOI : 10.1007/s12010-012-9578-y

D. Noble, Genes and causation, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.317, issue.5839, pp.3001-3015, 1878.
DOI : 10.1126/science.1141807

M. Normand-bayle and C. Benard, New HIV-1 replication inhibitors of the styryquinoline class bearing aroyl/acyl groups at the C-7 position: Synthesis and biological activity, Bioorganic & Medicinal Chemistry Letters, vol.15, issue.18, pp.4019-4022, 2005.
DOI : 10.1016/j.bmcl.2005.06.036
URL : https://hal.archives-ouvertes.fr/hal-00258372

P. Normand, P. C. Nesme, and X. , ITS analysis of prokaryotes, Molecular Microbial Ecology Manual, vol.3, 1996.

V. V. Nosikov and E. A. Braga, Protection of particular cleavage sites of restriction endonucleases by distamycin A and actinomycin D, Nucleic Acids Research, vol.3, issue.9, pp.2293-2301, 1976.
DOI : 10.1093/nar/3.9.2293

O. 'loughlin and E. J. , Isolation, characterization, and substrate utilization of a quinoline-degrading bacterium, International Biodeterioration & Biodegradation, vol.38, issue.2, 1996.

A. A. Ogunjobi and O. E. Fagade, Comparative analysis of genetic variation among Xanthomonas axonopodis pv manihotis isolated from the western states of Nigeria using RAPD and AFLP, Indian Journal of Microbiology, vol.142, issue.10, pp.132-138, 2010.
DOI : 10.1007/s12088-010-0037-6

C. S. Oie and C. E. Albaugh, Benzoate and salicylate degradation by Halomonas campisalis, an alkaliphilic and moderately halophilic microorganism, Water Research, vol.41, issue.6, pp.1235-1242, 2007.
DOI : 10.1016/j.watres.2006.12.029

B. Ollivier and P. Caumette, Anaerobic bacteria from hypersaline environments, Microbiol Rev, vol.58, issue.1, pp.27-38, 1994.

V. S. Panangala and V. L. Van-santen, Analysis of 16S-23S intergenic spacer regions of the rRNA operons in Edwardsiella ictaluri and Edwardsiella tarda isolates from fish, Journal of Applied Microbiology, vol.27, issue.3, pp.657-669, 2005.
DOI : 10.1001/archinte.149.1.208

H. Pearson, Genetics: What is a gene?, Nature, vol.309, issue.7092, pp.398-401, 2006.
DOI : 10.1038/441398a

D. A. Pelletier and C. S. Harwood, 2-Hydroxycyclohexanecarboxyl Coenzyme A Dehydrogenase, an Enzyme Characteristic of the Anaerobic Benzoate Degradation Pathway Used by Rhodopseudomonas palustris, Journal of Bacteriology, vol.182, issue.10, pp.2753-2760, 2000.
DOI : 10.1128/JB.182.10.2753-2760.2000

E. Pennisi, GENOMICS: DNA Study Forces Rethink of What It Means to Be a Gene, Science, vol.316, issue.5831, pp.1556-1557, 2007.
DOI : 10.1126/science.316.5831.1556

W. E. Pereira, Fate and movement of azaarenes in an aquifer contaminated by wood-treatment chemicals, Environmental Toxicology and Chemistry, vol.6, 1987.

W. E. Pereira, Microbial hydroxylation of quinoline in contaminated groundwater: evidence for incorporation of the oxygen atom of water, Appl Environ Microbiol, vol.53, 1988.

V. Pirrotta, Two restriction endonucleases from Bacillus globiggi, Nucleic Acids Research, vol.3, issue.7, pp.1747-1760, 1976.
DOI : 10.1093/nar/3.7.1747

Y. Pommier and A. A. Johnson, Integrase inhibitors to treat HIV/Aids, Nature Reviews Drug Discovery, vol.17, issue.3, pp.236-248, 2005.
DOI : 10.1038/nrd1660

K. Ponnusamy and S. Jose, Genetic diversity study of Chromobacterium violaceum isolated from Kolli hills by amplified ribosomal DNA restriction analysis (ARDRA) and random amplified polymorphic DNA (RAPD), Letters in Applied Microbiology, vol.16, issue.3, pp.341-349, 2011.
DOI : 10.1111/j.1472-765X.2011.03115.x

A. R. Poteete, Involvement of DNA replication in phage lambda Red-mediated homologous recombination, Molecular Microbiology, vol.48, issue.1, pp.66-74, 2008.
DOI : 10.1073/pnas.100127597

L. K. Poulsen and N. W. Larsen, A family of genes encoding a cell-killing function may be conserved in all Gram-negative bacteria, Molecular Microbiology, vol.246, issue.11, pp.1463-1472, 1989.
DOI : 10.1016/0378-1119(85)90120-9

D. Qiu, PBAD-Based Shuttle Vectors for Functional Analysis of Toxic and Highly Regulated Genes in Pseudomonas and Burkholderia spp. and Other Bacteria, Applied and Environmental Microbiology, vol.74, issue.23, 2008.
DOI : 10.1128/AEM.01369-08

M. L. Ranieri and K. J. Boor, Short communication: Bacterial ecology of high-temperature, short-time pasteurized milk processed in the United States, Journal of Dairy Science, vol.92, issue.10, pp.4833-4840, 2009.
DOI : 10.3168/jds.2009-2181

L. Ranjard and F. Poly, Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA), Microb Ecol, vol.39, issue.4, pp.263-272, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00427090

A. J. Roberts, How restriction enzymes became the workhorses of molecular biology, Proceedings of the National Academy of Sciences, vol.102, issue.17, 2005.
DOI : 10.1073/pnas.0500923102

R. J. Roberts, Restriction Endonuclease, CRC Critical Reviews in Biochemistry, vol.29, issue.2, pp.123-164, 1976.
DOI : 10.1016/0022-2836(75)90172-2

R. J. Roberts, How restriction enzymes became the workhorses of molecular biology, Proceedings of the National Academy of Sciences, vol.102, issue.17, pp.5905-5908, 2005.
DOI : 10.1073/pnas.0500923102

R. J. Roberts and I. F. Burgess, New head-lice treatments: hope or hype?, The Lancet, vol.365, issue.9453, pp.8-10, 2005.
DOI : 10.1016/S0140-6736(04)17677-0

E. M. Rockafellow, Is sulfur-doped TiO2 an effective visible light photocatalyst for remediation?, Applied Catalysis B: Environmental, vol.91, issue.1-2, 2009.
DOI : 10.1016/j.apcatb.2009.06.027

B. Rosche and B. Tshisuaka, 2-oxo-1,2-dihydroquinoline 8-monooxygenase: phylogenetic relationship to other multicomponent nonheme iron oxygenases., Journal of Bacteriology, vol.179, issue.11, pp.3549-3554, 1997.
DOI : 10.1128/jb.179.11.3549-3554.1997

S. Fetzner, Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions, Applied Microbiology and Biotechnology, vol.49, issue.3, 1998.
DOI : 10.1007/s002530051164

I. Sa-nogueira and L. J. Mota, Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene., Journal of Bacteriology, vol.179, issue.5, pp.1598-1608, 1997.
DOI : 10.1128/jb.179.5.1598-1608.1997

R. Saari and J. C. Torma, Microwave-assisted synthesis of quinoline, isoquinoline, quinoxaline and quinazoline derivatives as CB2 receptor agonists, Bioorganic & Medicinal Chemistry, vol.19, issue.2, pp.939-950, 2011.
DOI : 10.1016/j.bmc.2010.11.059

K. Sasaki and M. Morita, Syntrophic degradation of proteinaceous materials by the thermophilic strains Coprothermobacter proteolyticus and Methanothermobacter thermautotrophicus, Journal of Bioscience and Bioengineering, vol.112, issue.5, pp.469-472, 2011.
DOI : 10.1016/j.jbiosc.2011.07.003

J. A. Sawitzke and L. C. Thomason, Recombineering: In Vivo Genetic Engineering in E. coli, S. enterica, and Beyond, Methods Enzymol, vol.421, pp.171-199, 2007.
DOI : 10.1016/S0076-6879(06)21015-2

G. Schwarz and R. Bauder, B1, Biological Chemistry Hoppe-Seyler, vol.370, issue.2, pp.1183-1189, 1989.
DOI : 10.1515/bchm3.1989.370.2.1183
URL : https://hal.archives-ouvertes.fr/in2p3-00196617

B. Sen and J. Hamelin, Structural divergence of bacterial communities from functionally similar laboratory-scale vermicomposts assessed by PCR-CE-SSCP, Journal of Applied Microbiology, vol.2, issue.6, pp.2123-2132, 2008.
DOI : 10.1111/j.1365-2672.2008.03911.x

K. Sergueev and D. Yu, Cell toxicity caused by products of the pL operon of bacteriophage lambda, Gene, vol.272, issue.1-2, pp.227-235, 2001.
DOI : 10.1016/S0378-1119(01)00535-2

S. K. Sharan and L. C. Thomason, Recombineering: a homologous recombination-based method of genetic engineering, Nature Protocols, vol.24, issue.2, pp.206-223, 2009.
DOI : 10.1128/JB.01695-07

Y. Shinoda and J. Akagi, Strains: Isolation and Degradation Genes, Bioscience, Biotechnology, and Biochemistry, vol.69, issue.8, pp.1483-1491, 2005.
DOI : 10.1271/bbb.69.1483

O. P. Shukla, Microbial transformation of quinoline by a Pseudomonas sp, Appl Environ Microbiol, vol.51, issue.6, pp.1332-1342, 1986.

P. Shukla, Microbiological transformation and biodegradation of quinoline isolation and characterization of quinoline-degrading bacteria and identification of early intermediates, Biology and Medicine, vol.13, 1987.

Z. Silberstein, M. S. Berger, I. Cohen, and A. , Lambda red-mediated synthesis of plasmid linear multimers in Escherichia coli K12, MGG Molecular & General Genetics, vol.223, issue.3, p.12, 1990.
DOI : 10.1007/BF00264459

M. R. Singleton and M. S. Dillingham, Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks, Nature, vol.54, issue.7014, pp.187-193, 2004.
DOI : 10.1016/S0076-6879(97)77028-9

C. Smith, The strange case of David Acer: myth and reality, CDS Rev, vol.89, issue.2, pp.10-20, 1996.

H. O. Smith and K. W. Wilcox, A Restriction enzyme from Hemophilus influenzae, Journal of Molecular Biology, vol.51, issue.2, pp.379-391, 1970.
DOI : 10.1016/0022-2836(70)90149-X

H. O. Smith and K. W. Wilcox, A restriction enzyme from Hemophilus influenzae. I. Purification and general properties, Biotechnology, vol.24, pp.38-50, 1970.

V. R. Solomon and H. Lee, Quinoline as a Privileged Scaffold in Cancer Drug Discovery, Current Medicinal Chemistry, vol.18, issue.10, pp.1488-1508, 2011.
DOI : 10.2174/092986711795328382

B. Song and B. B. Ward, Genetic Diversity of Benzoyl Coenzyme A Reductase Genes Detected in Denitrifying Isolates and Estuarine Sediment Communities, Applied and Environmental Microbiology, vol.71, issue.4, pp.2036-2045, 2005.
DOI : 10.1128/AEM.71.4.2036-2045.2005

J. Song and H. Dong, Construction and functional characterization of an integrative form lambda Red recombineering Escherichia coli strain, FEMS Microbiol Lett, vol.309, issue.2, pp.178-183, 2010.

A. M. Spormann and F. Widdel, Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria, Biodegradation, vol.11, issue.2/3, pp.85-105, 2000.
DOI : 10.1023/A:1011122631799

K. Sugaya, Biodegradation of quinoline in crude oil, Journal of Chemical Technology and Biotechnology, vol.76, issue.6, 2001.

Q. Sun and Y. Bai, Aerobic biodegradation characteristics and metabolic products of quinoline by a Pseudomonas strain, Bioresource Technology, vol.100, issue.21, pp.5030-5036, 2009.
DOI : 10.1016/j.biortech.2009.05.044

S. Swaminathan, E. H. Waters, L. Yu, D. Lee, E. Court et al., Rapid engineering of bacterial artificial chromosomes using oligonucleotides, genesis, vol.37, issue.1, p.8, 2001.
DOI : 10.1002/1526-968X(200101)29:1<14::AID-GENE1001>3.0.CO;2-X

B. Swingle, Recombineering Using RecTE from Pseudomonas syringae, Applied and Environmental Microbiology, vol.76, issue.15, 2010.
DOI : 10.1128/AEM.00911-10
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916495

B. Tanti and S. K. Ray, Differentiation of petroleum hydrocarbon-degrading Pseudomonas spp. based on PCR-RFLP of the 16S-23S rDNA intergenic spacer region, Folia Microbiologica, vol.51, issue.1, pp.47-52, 2011.
DOI : 10.1007/s12223-011-0088-z

K. Terpe, Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems, Applied Microbiology and Biotechnology, vol.62, issue.2, pp.211-222, 2006.
DOI : 10.1007/s00253-006-0465-8

L. C. Thomason and N. Costantino, Multicopy plasmid modification with phage ?? Red recombineering, Plasmid, vol.58, issue.2, pp.148-158, 2007.
DOI : 10.1016/j.plasmid.2007.03.001

S. Tian and C. Qian, Biodegradation of Biomass Gasification Wastewater by Two Species of <I>Pseudomonas</I> Using Immobilized Cell Reactor, Applied Biochemistry and Biotechnology, vol.128, issue.2, pp.141-148, 2006.
DOI : 10.1385/ABAB:128:2:141

B. K. Tischer and G. A. Smith, En Passant Mutagenesis: A Two Step Markerless Red Recombination System, Methods Mol Biol, vol.634, pp.421-430, 2010.
DOI : 10.1007/978-1-60761-652-8_30

V. Torsvik and J. Goksoyr, High diversity in DNA of soil bacteria, Appl Environ Microbiol, vol.56, issue.3, pp.782-787, 1990.

J. T. Trevors and J. D. Van-elsas, Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm, Appl Environ Microbiol, vol.56, issue.2, pp.401-408, 1990.

H. N. Tuntufye, Use of lambda Red-mediated recombineering and Cre/lox for generation of markerless chromosomal deletions in avian pathogenic Escherichia coli, FEMS Microbiology Letters, vol.325, issue.2, 2011.
DOI : 10.1111/j.1574-6968.2011.02421.x

B. H. Tuo and J. B. Yan, Biodegradation characteristics and bioaugmentation potential of a novel quinoline-degrading strain of Bacillus sp. isolated from petroleum-contaminated soil, Bioresource Technology, vol.107, pp.55-60, 2012.
DOI : 10.1016/j.biortech.2011.12.114

T. Uchiyama and K. Miyazaki, Functional metagenomics for enzyme discovery: challenges to efficient screening, Current Opinion in Biotechnology, vol.20, issue.6, pp.616-622, 2009.
DOI : 10.1016/j.copbio.2009.09.010

A. Ulonska, Degradation of quinoline by immobilized Comamonas acidovorans in a three-phase airlift reactor, Biotechnol Bioeng, vol.46, 1995.

S. Uroz and C. Calvaruso, Mineral weathering by bacteria: ecology, actors and mechanisms, Trends in Microbiology, vol.17, issue.8, pp.378-387, 2009.
DOI : 10.1016/j.tim.2009.05.004

P. Valentin-hansen, DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor, EMBO J, vol.5, 1986.

L. Villa-komaroff and A. Efstratiadis, A bacterial clone synthesizing proinsulin., Proceedings of the National Academy of Sciences, vol.75, issue.8, pp.3727-3731, 1978.
DOI : 10.1073/pnas.75.8.3727

L. Villa-komaroff and A. Efstratiadis, A bacterial clone synthesizing proinsulin., Proceedings of the National Academy of Sciences, vol.75, issue.8, pp.316-320, 1978.
DOI : 10.1073/pnas.75.8.3727

J. Wang and M. Sarov, An Improved Recombineering Approach by Adding RecA to ?? Red Recombination, Molecular Biotechnology, vol.32, issue.1, pp.43-53, 2006.
DOI : 10.1385/MB:32:1:043

J. L. Wang and W. Z. Wu, Microbial degradation of quinoline: kinetics study with Burkholderia picekttii, Biomed Environ Sci, vol.17, issue.1, pp.21-26, 2004.

Y. Wang, Anaerobic activated carbon filter for the degradation of polycyclic N-aromatic compounds Water Pollution Control Federation 56, 1984.

Y. T. Wang and M. T. Suidan, Anaerobic biodegradation of indole to methane, Appl Environ Microbiol, vol.48, issue.5, pp.1058-1060, 1984.

S. Warming, C. N. Court, D. Jenkins, N. Copeland, and N. , Simple and highly efficient BAC recombineering using galK selection, Nucleic Acids Research, vol.33, issue.4, p.12, 2005.
DOI : 10.1093/nar/gni035
URL : http://doi.org/10.1093/nar/gni035

F. Warnecke and P. Hugenholtz, Building on basic metagenomics with complementary technologies, Genome Biology, vol.8, issue.12, p.231, 2007.
DOI : 10.1186/gb-2007-8-12-231

J. Wei and P. Liang, Recent progress in electrodes for microbial fuel cells, Bioresource Technology, vol.102, issue.20, pp.9335-9344, 2011.
DOI : 10.1016/j.biortech.2011.07.019

S. Wischgoll and D. Heintz, Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens, Molecular Microbiology, vol.149, issue.5, pp.1238-1252, 2005.
DOI : 10.1111/j.1365-2958.2005.04909.x

C. Wittmann, Fluxome analysis using GC-MS, Microb Cell Fact, vol.6, 2007.

J. C. Wooley and A. Godzik, A Primer on Metagenomics, PLoS Computational Biology, vol.14, issue.2, p.1000667, 2010.
DOI : 10.1371/journal.pcbi.1000667.t002

J. Xu, Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances, Molecular Ecology, vol.6, issue.7, pp.1713-1731, 2006.
DOI : 10.1111/j.1365-294X.2006.02882.x

S. Yajima and Y. Muto, The three-dimensional structure of the colicin E3 immunity protein by distance geometry calculation, FEBS Letters, vol.11, issue.3, pp.257-260, 1993.
DOI : 10.1016/0014-5793(93)80665-H

M. Yamabhai and B. Buranabanyat, Efficient E. coli expression systems for the production of recombinant ??-mannanases and other bacterial extracellular enzymes, Bioengineered Bugs, vol.2, issue.1, pp.45-49, 2011.
DOI : 10.4161/bbug.2.1.13419

S. Yamamoto and H. Izumiya, Application of ?? Red recombination system to Vibrio cholerae genetics: Simple methods for inactivation and modification of chromosomal genes, Gene, vol.438, issue.1-2, pp.57-64, 2009.
DOI : 10.1016/j.gene.2009.02.015

Y. Yang and S. K. Sharan, A simple two-step, 'hit and fix' method to generate subtle mutations in BACs using short denatured PCR fragments, Nucleic Acids Research, vol.31, issue.15, pp.31-80, 2003.
DOI : 10.1093/nar/gng080

Z. Yang and J. R. Horton, Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI, Nucleic Acids Research, vol.33, issue.6, pp.1892-1901, 2005.
DOI : 10.1093/nar/gki337

I. Yosef and N. Bloushtain, Restoration of Gene Function by Homologous Recombination: from PCR to Gene Expression in One Step, Applied and Environmental Microbiology, vol.70, issue.12, pp.7156-7160, 2004.
DOI : 10.1128/AEM.70.12.7156-7160.2004

C. Y. Yu, Hydrodenitrogenation of quinoline with Y-type zeolite, Industrial & Engineering Chemistry Research, vol.28, issue.1, 1989.
DOI : 10.1021/ie00085a004

D. Yu and H. M. Ellis, An efficient recombination system for chromosome engineering in Escherichia coli, Proceedings of the National Academy of Sciences, vol.97, issue.11, pp.5978-5983, 2000.
DOI : 10.1073/pnas.100127597

R. Zarivach and E. Ben-zeev, On the interaction of colicin E3 with the ribosome, Biochimie, vol.84, issue.5-6, pp.5-6, 2002.
DOI : 10.1016/S0300-9084(02)01449-9

K. Zengler, Central Role of the Cell in Microbial Ecology, Microbiology and Molecular Biology Reviews, vol.73, issue.4, pp.712-729, 2009.
DOI : 10.1128/MMBR.00027-09

X. M. Zhang and J. D. Huang, Combination of overlapping bacterial artificial chromosomes by a two-step recombinogenic engineering method, Nucleic Acids Research, vol.31, issue.15, pp.31-81, 2003.
DOI : 10.1093/nar/gng081

X. Y. Zhang, Studies on quinoline biodegradation by a white rot fungus (Pleurotus ostreatus BP) in liquid and solid state substrates, Fresenius Environmental Bulletin, vol.16, issue.8, 2007.

Y. Zhang and F. Buchholz, A new logic for DNA engineering using recombination in Escherichia coli, Nature Genetics, vol.20, issue.2, pp.123-128, 1998.
DOI : 10.1038/2417

S. N. Zhu and D. Q. Liu, Degradation of quinoline by Rhodococcus sp. QL2 isolated from activated sludge, Journal of Hazardous Materials, vol.160, issue.2-3, pp.289-294, 2008.
DOI : 10.1016/j.jhazmat.2008.02.112

W. G. Zumft, Cell biology and molecular basis of denitrification, Microbiol Mol Biol Rev, vol.61, issue.4, pp.533-616, 1997.