Benzerara K, Menguy N, Guyot F, Skouri F, De Luca G, Barakat M,
Heulin T (2004) Biologically controlled precipitation of calcium
phosphate by Ramlibacter tataouinensis. Earth Planet Sci Lett
228:439–449
Benzerara K et al (2006) Nanoscale detection of organic signatures in
carbonate microbialites. Proc Natl Acad Sci U S A 103:9440–9445
Beyhan S, Tischler AD, Camilli A, Yildiz FH (2006) Transcriptome
and phenotypic responses of Vibrio cholerae to increased cyclic diGMP level. J Bacteriol 188:3600–3613
Bjarnsholt T, Givskov M (2007) Quorum-sensing blockade as a strategy for enhancing host defences against bacterial pathogens. Philos
Trans R Soc Lond B Biol Sci 362:1213–1222
Bolwell GP (1996) The origin of the oxidative burst in plants. Biochem
Soc Trans 24:438–442
Breukink E, de Kruijff B (2006) Lipid II as a target for antibiotics. Nat
Rev Drug Discov 5:321–332
Brock T (1997) The value of basic research: discovery of Thermus
aquaticus and other extreme thermophiles. Genetics 146:1207–1210
Brumbley SM, Carney BF, Denny TP (1993) Phenotype conversion in
Pseudomonas solanacearum due to spontaneous inactivation of
PhcA, a putative LysR transcriptional regulator. J Bacteriol
175:5477–5487
Cervantes C, Ji G, Ramirez JL, Silver S (1994) Resistance to arsenic
compounds in microorganisms. FEMS Microbiol Rev 15:355–367
Challis GL, Hopwood DA (2003) Synergy and contingency as driving
forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Natl Acad Sci U S A 100(Suppl
2):14555–14561
Chanal A et al (2006) The desert of Tataouine: an extreme environment
hosts a wide diversity that of microorganisms and bacteria
radiotolerant. About Microbiol 8:514–525
Christen B (2007) Principles of C-di-GMP signaling. PhD thesis, Faculty of Sciences, University of Basel, Basel
Chugani SA, Whiteley M, Lee KM, D’Argenio D, Manoil C, Greenberg
EP (2001) QscR, a modulator of quorum-sensing signal synthesis
and virulence in Pseudomonas aeruginosa. Proc Natl Acad Sci U S
A 98:2752–2757
Chung J, Goo E, Yu S, Choi O, Lee J, Kim J, Kim H, Igarashi J, Suga H,
Moon JS, Hwang I, Rhee S (2011) Small-molecule inhibitor binding
to an N-acyl-homoserine lactone synthase. Proc Natl Acad Sci U S
A 108:12089–12094
Cirou A, Mondy S, An S, Charrier A, Sarrazin A, Thoison O, DuBow
M, Faure D (2011) Efficient biostimulation of native and introduced
quorum-quenching Rhodococcus erythropolis populations is
revealed by a combination of analytical chemistry, microbiology,
and pyrosequencing. Appl Environ Microbiol 78:481–492
Cirz RT, Chin JK, Andes DR, de Crecy-Lagard V, Craig WA,
Romesberg FE (2005) Inhibition of mutation and combating the
evolution of antibiotic resistance. PLoS Biol 3:e176
Condemine G, Ghazi A (2007) Differential regulation of two
oligogalacturonate outer membrane channels, KdgN and KdgM, of
Dickeya dadantii (Erwinia chrysanthemi). J Bacteriol 189:5955–5962
Cox MM (1998) A broadening view of recombinational DNA repair in
bacteria. Genes Cells 3:65–78
Cui L, Neoh HM, Iwamoto A, Hiramatsu K (2012) Coordinated phenotype switching with large-scale chromosome flip-flop inversion
observed in bacteria. Proc Natl Acad Sci U S A 109:E1647–E1656
D’Costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling
the antibiotic resistome. Science 311:374–377
Dantas G, Sommer MO, Oluwasegun RD, Church GM (2008) Bacteria
subsisting on antibiotics. Science 320:100–103
Davison J (1999) Genetic exchange between bacteria in the environment. Plasmid 42:73–91
de Groot A, Chapon V, Servant P, Christen R, Saux F, Sommer S,
Heulin T (2005) Deinococcus deserti sp. November, a gammaradiation-tolerant bacterium isolated from the Sahara Desert. Int J
Syst Evol Microbiol 55:2441–2446
de Groot A et al (2009) Genomics and proteomics of Alliance to
unravel the specificities of Sahara bacterium Deinococcus deserti.
PLoS Genet DOI: 10. 1371/
De Koning-Ward TF, Robins-Browne RM (1995) Contribution of
urease to acid tolerance in Yersinia enterocolitica. Infect Immun
63:3790–3795
De Luca G, Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Py B,
Fichant G, Coutinho PM, Voulhoux R, Bastien O, Mare ´chal E,
Henrissat B, Quentin Y, Noirot P, Filloux A, Me ´jean V, DuBow
M, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Verme ´glio A,
Achouak W, Heulin T (2011) The cyst-dividing bacterium
Ramlibacter tataouinensis genome reveals a well-stocked toolbox
for adaptation to a desert environment. PLoS One 6(9):e23784
Degrassi G, Aguilar C, Bosco M, Zahariev S, Pongor S, Venturi V
(2002) Plant growth-promoting Pseudomonas putida WCS358
produces and secretes four cyclic dipeptides: cross-talk with quorum sensing bacterial sensors. Curr Microbiol 45:250–254
DiMango E, Zar HJ, Bryan R, Prince A (1995) Diverse Pseudomonas
aeruginosa gene products stimulate respiratory epithelial cells to
produce interleukin-8. J Clin Invest 96:2204–2210
Donadio S, Monciardini P, Sosio M (2007) Polyketide synthases and
nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat Prod Rep 24:1073–1109
Dong YH, Zhang XF, Soo HM, Greenberg EP, Zhang LH (2005) The
two-component response regulator PprB modulates quorumsensing signal production and global gene expression in Pseudomonas aeruginosa. Mol Microbiol 56:1287–1301
Drlica K, Malik M (2003) Fluoroquinolones: action and resistance.
Curr Top Med Chem 3:249–282
Duncan L, Losick R (1993) SpoIIAB is an anti-sigma factor that binds
to and inhibits transcription by regulatory protein sigma F from
Bacillus subtilis. Proc Natl Acad Sci U S A 90:2325–2329
Dworkin J, Blaser MJ (1997) Nested DNA inversion as a paradigm of
programmed gene rearrangement. Proc Natl Acad Sci U S A
94:985–990
Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH,
Oppenheimer NJ (1981) Structural identification of autoinducer of
Photobacterium fischeri luciferase. Biochemistry 20:2444–2449
Fetherston JD, Schuetze P, Perry RD (1992) Loss of the pigmentation
phenotype in Yersinia pestis is due to the spontaneous deletion of
102 kb of chromosomal DNA which is flanked by a repetitive
element. Mol Microbiol 6:2693–2704
Fredrickson JK et al (2008) Protein oxidation: key to bacterial desiccation
resistance? ISME J 2:393–403
Freitag CS, Abraham JM, Clements JR, Eisenstein BI (1985) Genetic
analysis of the phase variation control of expression of type 1
fimbriae in Escherichia coli. J Bacteriol 162:668–675
Funa N, Ohnishi Y, Fujii I, Shibuya M, Ebizuka Y, Horinouchi S (1999)
A new pathway for polyketide synthesis in microorganisms. Nature
400:897–899
Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing
in bacteria: the LuxR-LuxI family of cell density – responsive
transcriptional regulators. J Bacteriol 176:269–275
Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene
expression by cell-to-cell communication: acylhomoserine lactone
quorum sensing. Annu Rev Genet 35:439–468
Galinski EA, Tru ¨per HG (1982) Betaine, a compatible solute in the
extremely halophilic phototrophic bacterium, Ectothiorhodospira
halochloris. FEMS Microbiol Lett 13:357–361
Galperin MY (2005) A census of membrane-bound and intracellular
signal transduction proteins in bacteria: bacterial IQ, extroverts and
introverts. BMC Microbiol 5:35
Galperin MY (2006) Structural classification of bacterial response
regulators: diversity of output domains and domain combinations.
J Bacteriol 188:4169–4182
Galperin MY, Gomelsky M (2005) Bacterial signal transduction
modules: from genomics to biology. ASM News 71:326–333
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
347
Heulin T (2004) Biologically controlled precipitation of calcium
phosphate by Ramlibacter tataouinensis. Earth Planet Sci Lett
228:439–449
Benzerara K et al (2006) Nanoscale detection of organic signatures in
carbonate microbialites. Proc Natl Acad Sci U S A 103:9440–9445
Beyhan S, Tischler AD, Camilli A, Yildiz FH (2006) Transcriptome
and phenotypic responses of Vibrio cholerae to increased cyclic diGMP level. J Bacteriol 188:3600–3613
Bjarnsholt T, Givskov M (2007) Quorum-sensing blockade as a strategy for enhancing host defences against bacterial pathogens. Philos
Trans R Soc Lond B Biol Sci 362:1213–1222
Bolwell GP (1996) The origin of the oxidative burst in plants. Biochem
Soc Trans 24:438–442
Breukink E, de Kruijff B (2006) Lipid II as a target for antibiotics. Nat
Rev Drug Discov 5:321–332
Brock T (1997) The value of basic research: discovery of Thermus
aquaticus and other extreme thermophiles. Genetics 146:1207–1210
Brumbley SM, Carney BF, Denny TP (1993) Phenotype conversion in
Pseudomonas solanacearum due to spontaneous inactivation of
PhcA, a putative LysR transcriptional regulator. J Bacteriol
175:5477–5487
Cervantes C, Ji G, Ramirez JL, Silver S (1994) Resistance to arsenic
compounds in microorganisms. FEMS Microbiol Rev 15:355–367
Challis GL, Hopwood DA (2003) Synergy and contingency as driving
forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Natl Acad Sci U S A 100(Suppl
2):14555–14561
Chanal A et al (2006) The desert of Tataouine: an extreme environment
hosts a wide diversity that of microorganisms and bacteria
radiotolerant. About Microbiol 8:514–525
Christen B (2007) Principles of C-di-GMP signaling. PhD thesis, Faculty of Sciences, University of Basel, Basel
Chugani SA, Whiteley M, Lee KM, D’Argenio D, Manoil C, Greenberg
EP (2001) QscR, a modulator of quorum-sensing signal synthesis
and virulence in Pseudomonas aeruginosa. Proc Natl Acad Sci U S
A 98:2752–2757
Chung J, Goo E, Yu S, Choi O, Lee J, Kim J, Kim H, Igarashi J, Suga H,
Moon JS, Hwang I, Rhee S (2011) Small-molecule inhibitor binding
to an N-acyl-homoserine lactone synthase. Proc Natl Acad Sci U S
A 108:12089–12094
Cirou A, Mondy S, An S, Charrier A, Sarrazin A, Thoison O, DuBow
M, Faure D (2011) Efficient biostimulation of native and introduced
quorum-quenching Rhodococcus erythropolis populations is
revealed by a combination of analytical chemistry, microbiology,
and pyrosequencing. Appl Environ Microbiol 78:481–492
Cirz RT, Chin JK, Andes DR, de Crecy-Lagard V, Craig WA,
Romesberg FE (2005) Inhibition of mutation and combating the
evolution of antibiotic resistance. PLoS Biol 3:e176
Condemine G, Ghazi A (2007) Differential regulation of two
oligogalacturonate outer membrane channels, KdgN and KdgM, of
Dickeya dadantii (Erwinia chrysanthemi). J Bacteriol 189:5955–5962
Cox MM (1998) A broadening view of recombinational DNA repair in
bacteria. Genes Cells 3:65–78
Cui L, Neoh HM, Iwamoto A, Hiramatsu K (2012) Coordinated phenotype switching with large-scale chromosome flip-flop inversion
observed in bacteria. Proc Natl Acad Sci U S A 109:E1647–E1656
D’Costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling
the antibiotic resistome. Science 311:374–377
Dantas G, Sommer MO, Oluwasegun RD, Church GM (2008) Bacteria
subsisting on antibiotics. Science 320:100–103
Davison J (1999) Genetic exchange between bacteria in the environment. Plasmid 42:73–91
de Groot A, Chapon V, Servant P, Christen R, Saux F, Sommer S,
Heulin T (2005) Deinococcus deserti sp. November, a gammaradiation-tolerant bacterium isolated from the Sahara Desert. Int J
Syst Evol Microbiol 55:2441–2446
de Groot A et al (2009) Genomics and proteomics of Alliance to
unravel the specificities of Sahara bacterium Deinococcus deserti.
PLoS Genet DOI: 10. 1371/
De Koning-Ward TF, Robins-Browne RM (1995) Contribution of
urease to acid tolerance in Yersinia enterocolitica. Infect Immun
63:3790–3795
De Luca G, Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Py B,
Fichant G, Coutinho PM, Voulhoux R, Bastien O, Mare ´chal E,
Henrissat B, Quentin Y, Noirot P, Filloux A, Me ´jean V, DuBow
M, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Verme ´glio A,
Achouak W, Heulin T (2011) The cyst-dividing bacterium
Ramlibacter tataouinensis genome reveals a well-stocked toolbox
for adaptation to a desert environment. PLoS One 6(9):e23784
Degrassi G, Aguilar C, Bosco M, Zahariev S, Pongor S, Venturi V
(2002) Plant growth-promoting Pseudomonas putida WCS358
produces and secretes four cyclic dipeptides: cross-talk with quorum sensing bacterial sensors. Curr Microbiol 45:250–254
DiMango E, Zar HJ, Bryan R, Prince A (1995) Diverse Pseudomonas
aeruginosa gene products stimulate respiratory epithelial cells to
produce interleukin-8. J Clin Invest 96:2204–2210
Donadio S, Monciardini P, Sosio M (2007) Polyketide synthases and
nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat Prod Rep 24:1073–1109
Dong YH, Zhang XF, Soo HM, Greenberg EP, Zhang LH (2005) The
two-component response regulator PprB modulates quorumsensing signal production and global gene expression in Pseudomonas aeruginosa. Mol Microbiol 56:1287–1301
Drlica K, Malik M (2003) Fluoroquinolones: action and resistance.
Curr Top Med Chem 3:249–282
Duncan L, Losick R (1993) SpoIIAB is an anti-sigma factor that binds
to and inhibits transcription by regulatory protein sigma F from
Bacillus subtilis. Proc Natl Acad Sci U S A 90:2325–2329
Dworkin J, Blaser MJ (1997) Nested DNA inversion as a paradigm of
programmed gene rearrangement. Proc Natl Acad Sci U S A
94:985–990
Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH,
Oppenheimer NJ (1981) Structural identification of autoinducer of
Photobacterium fischeri luciferase. Biochemistry 20:2444–2449
Fetherston JD, Schuetze P, Perry RD (1992) Loss of the pigmentation
phenotype in Yersinia pestis is due to the spontaneous deletion of
102 kb of chromosomal DNA which is flanked by a repetitive
element. Mol Microbiol 6:2693–2704
Fredrickson JK et al (2008) Protein oxidation: key to bacterial desiccation
resistance? ISME J 2:393–403
Freitag CS, Abraham JM, Clements JR, Eisenstein BI (1985) Genetic
analysis of the phase variation control of expression of type 1
fimbriae in Escherichia coli. J Bacteriol 162:668–675
Funa N, Ohnishi Y, Fujii I, Shibuya M, Ebizuka Y, Horinouchi S (1999)
A new pathway for polyketide synthesis in microorganisms. Nature
400:897–899
Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing
in bacteria: the LuxR-LuxI family of cell density – responsive
transcriptional regulators. J Bacteriol 176:269–275
Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene
expression by cell-to-cell communication: acylhomoserine lactone
quorum sensing. Annu Rev Genet 35:439–468
Galinski EA, Tru ¨per HG (1982) Betaine, a compatible solute in the
extremely halophilic phototrophic bacterium, Ectothiorhodospira
halochloris. FEMS Microbiol Lett 13:357–361
Galperin MY (2005) A census of membrane-bound and intracellular
signal transduction proteins in bacteria: bacterial IQ, extroverts and
introverts. BMC Microbiol 5:35
Galperin MY (2006) Structural classification of bacterial response
regulators: diversity of output domains and domain combinations.
J Bacteriol 188:4169–4182
Galperin MY, Gomelsky M (2005) Bacterial signal transduction
modules: from genomics to biology. ASM News 71:326–333
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
347