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  • Allegrucci, M., and Sauer, K. (2007) Characterization of colony morphology variants isolated from Streptococcus pneumoniae biofilms. J Bacteriol 189: 20302038.
  • Allegrucci, M., Hu, F.Z., Shen, K., Hayes, J., Ehrlich, G.D., Post, J.C., and Sauer, K. (2006) Phenotypic characterization of Streptococcus pneumoniae biofilm development. J Bacteriol 188: 23252335.
  • Allesen-Holm, M., Barken, K.B., Yang, L., Klausen, M., Webb, J.S., Kjelleberg, S., et al. (2006) A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms. Mol Microbiol 59: 11141128.
  • Alvarez-Ortega, C., and Harwood, C.S. (2007) Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration. Mol Microbiol 65: 153165.
  • Anderl, J.N., Franklin, M.J., and Stewart, P.S. (2000) Role of antibiotic penetration limitation in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin. Antimicrob Agents Chemother 44: 18181824.
  • Anderl, J.N., Zahller, J., Roe, F., and Stewart, P.S. (2003) Role of nutrient limitation and stationary-phase existence in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin. Antimicrob Agents Chemother 47: 12511256.
  • Banin, E., Vasil, M.L., and Greenberg, E.P. (2005) Iron and Pseudomonas aeruginosa biofilm formation. Proc Natl Acad Sci USA 102: 1107611081.
  • Barraud, N., Hassett, D.J., Hwang, S.-H., Rice, S.A., Kjelleberg, S., and Webb, J.S. (2006) Involvement of nitric oxide in biofilm dispersal of Pseudomonas aeruginosa. J Bacteriol 188: 73447353.
  • Basu Roy, A., Petrova, O.E., and Sauer, K. (2012) The phosphodiesterase DipA (PA5017) is essential for Pseudomonas aeruginosa biofilm dispersion. J Bacteriol 194: 29042915.
  • de Beer, D., Stoodley, P., and Lewandowski, Z. (1994) Liquid flow in heterogeneous biofilms. Biotechnol Bioeng 44: 636641.
  • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate – a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 57: 289300.
  • Bielecki, P., Puchałka, J., Wos-Oxley, M.L., Loessner, H., Glik, J., Kawecki, M., et al. (2011) In-vivo expression orofiling of Pseudomonas aeruginosa infections reveals niche-specific and strain-independent transcriptional programs. PLoS ONE 6: e24235.
  • Bobrov, A.G., Kirillina, O., and Perry, P.D. (2005) The phosphodiesterase activity of the HmsP EAL domain is required for negative regulation of biofilm formation in Yersinia pestis. FEMS Microbiol Lett 247: 123130.
  • Boes, N., Schreiber, K., Hartig, E., Jaensch, L., and Schobert, M. (2006) The Pseudomonas aeruginosa universal stress protein PA4352 is essential for surviving anaerobic energy stress. J Bacteriol 188: 65296538.
  • Boes, N., Schreiber, K., and Schobert, M. (2008) SpoT-triggered stringent response controls usp gene expression in Pseudomonas aeruginosa. J Bacteriol 190: 71897199.
  • Borriello, G., Werner, E., Roe, F., Kim, A.M., Ehrlich, G.D., and Stewart, P.S. (2004) Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrob Agents Chemother 48: 26592664.
  • Byrd, M.S., Sadovskaya, I., Vinogradov, E., Lu, H., Sprinkle, A.B., Richardson, S.H., et al. (2009) Genetic and biochemical analyses of the Pseudomonas aeruginosa Psl exopolysaccharide reveal overlapping roles for polysaccharide synthesis enzymes in Psl and LPS production. Mol Microbiol 73: 622638.
  • Caiazza, N.C., and O'Toole, G.A. (2004) SadB is required for the transition from reversible to irreversible attachment during biofilm formation by Pseudomonas aeruginosa PA14. J Bacteriol 186: 44764485.
  • Carlson, C.A., and Ingraham, J.L. (1983) Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans. Appl Environ Microbiol 45: 12471253.
  • Carlson, C.A., Ferguson, L.P., and Ingraham, J.L. (1982) Properties of dissimilatory nitrate reductase purified from the denitrifier Pseudomonas aeruginosa. J Bacteriol 151: 162171.
  • Chen, W., Honma, K., Sharma, A., and Kuramitsu, H.K. (2006) A universal stress protein of Porphyromonas gingivalis is involved in stress responses and biofilm formation. FEMS Microbiol Lett 264: 1521.
  • Comolli, J.C., and Donohue, T.J. (2004) Differences in two Pseudomonas aeruginosa cbb3 cytochrome oxidases. Mol Microbiol 51: 11931203.
  • Conibear, T.C.R., Collins, S.L., and Webb, J.S. (2009) Role of mutation in Pseudomonas aeruginosa biofilm development. PLoS ONE 4: e6289.
  • Davey, M.E., Caiazza, N.C., and O'Toole, G.A. (2003) Rhamnolipid surfactant production affects biofilm architecture in Pseudomonas aeruginosa PAO1. J Bacteriol 185: 10271036.
  • Davies, K.J.P., Lloyd, D., and Boddy, L. (1989) The effect of oxygen on denitrification in Paracoccus denitrificans and Pseudomonas aeruginosa. J Gen Microbiol 135: 24452451.
  • Dietrich, L.E.P., Price-Whelan, A., Petersen, A., Whiteley, M., and Newman, D.K. (2006) The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol Microbiol 61: 13081321.
  • Dietrich, L.E.P., Teal, T.K., Price-Whelan, A., and Newman, D.K. (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321: 12031206.
  • Drumm, J.E., Mi, K., Bilder, P., Sun, M., Lim, J., Bielefeldt-Ohmann, H., et al. (2009) Mycobacterium tuberculosis universal stress protein Rv2623 regulates bacillary growth by ATP-binding: requirement for establishing chronic persistent infection. PLoS Pathog 5: e1000460.
  • Eschbach, M., Schreiber, K., Trunk, K., Buer, J., Jahn, D., and Schobert, M. (2004) Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol 186: 45964604.
  • Filiatrault, M.J., Picardo, K.F., Ngai, H., Passador, L., and Iglewski, B.H. (2006) Identification of Pseudomonas aeruginosa genes involved in virulence and anaerobic growth. Infect Immun 74: 42374245.
  • Garcia-Medina, R., Dunne, W.M., Singh, P.K., and Brody, S.L. (2005) Pseudomonas aeruginosa acquires biofilm-like properties within airway epithelial cells. Infect Immun 73: 82988305.
  • Hassett, D.J., Cuppoletti, J., Trapnell, B., Lymar, S.V., Rowe, J.J., Yoon, S.S., et al. (2002) Anaerobic metabolism and quorum sensing by Pseudomonas aeruginosa biofilms in chronically infected cystic fibrosis airways: rethinking antibiotic treatment strategies and drug targets. Adv Drug Deliv Rev 54: 14251443.
  • Hassett, D.J., Sutton, M.D., Schurr, M.J., Herr, A.B., Caldwell, C.C., and Matu, J.O. (2009) Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 17: 130138.
  • Heydorn, A., Nielsen, A.T., Hentzer, M., Sternberg, C., Givskov, M., Ersboll, B.K., and Molin, S. (2000) Quantification of biofilm structures by the novel computer program COMSTAT. Microbiology 146: 23952407.
  • Høiby, N., Krogh Johansen, H., Moser, C., Song, Z., Ciofu, O., and Kharazmi, A. (2001) Pseudomonas aeruginosa and the in vitro and in vivo biofilm mode of growth. Microbes Infect 3: 2335.
  • Irie, Y., Starkey, M., Edwards, A.N., Wozniak, D.J., Romeo, T., and Parsek, M.R. (2010) Pseudomonas aeruginosa biofilm matrix polysaccharide Psl is regulated transcriptionally by RpoS and post-transcriptionally by RsmA. Mol Microbiol 78: 158172.
  • Kaneko, Y., Thoendel, M., Olakanmi, O., Britigan, B.E., and Singh, P.K. (2007) The transition metal gallium disrupts Pseudomonas aeruginosa iron metabolism and has antimicrobial and antibiofilm activity. J Clin Invest 117: 877888.
  • Kuchma, S.L., Brothers, K.M., Merritt, J.H., Liberati, N.T., Ausubel, F.M., and O'Toole, G.A. (2007) BifA, a c-di-GMP phosphodiesterase, inversely regulates biofilm formation and swarming motility by Pseudomonas aeruginosa PA14. J Bacteriol 189: 81658178.
  • Kuramitsu, H.K., Chen, W., and Ikegami, A. (2005) Biofilm formation by the periodontopathic bacteria Treponema denticola and Porphyromonas gingivalis. J Periodontol 76: 20472051.
  • Lam, J., Chan, R., Lam, K., and Costerton, J.W. (1980) Production of mucoid microcolonies by Pseudomonas aeruginosa within infected lungs in cystic fibrosis. Infect Immun 28: 546556.
  • Leistikow, R.L., Morton, R.A., Bartek, I.L., Frimpong, I., Wagner, K., and Voskuil, M.I. (2010) The Mycobacterium tuberculosis DosR regulon assists in metabolic homeostasis and enables rapid recovery from nonrespiring dormancy. J Bacteriol 192: 16621670.
  • Lenz, A.P., Williamson, K.S., Pitts, B., Stewart, P.S., and Franklin, M.J. (2008) Localized gene expression in Pseudomonas aeruginosa biofilms. Appl Environ Microbiol 74: 44634471.
  • Mashburn, L.M., Jett, A.M., Akins, D.R., and Whiteley, M. (2005) Staphylococcus aureus serves as an iron source for Pseudomonas aeruginosa during in vivo coculture. J Bacteriol 187: 554566.
  • Mikkelsen, H., Bond, N.J., Skindersoe, M.E., Givskov, M., Lilley, K.S., and Welch, M. (2009) Biofilms and type III secretion are not mutually exclusive in Pseudomonas aeruginosa. Microbiology 155: 687698.
  • Morici, L.A., Carterson, A.J., Wagner, V.E., Frisk, A., Schurr, J.R., zu Bentrup, K.H., et al. (2007) Pseudomonas aeruginosa AlgR represses the Rhl quorum-sensing system in a biofilm-specific manner. J Bacteriol 189: 77527764.
  • Nachin, L., Nannmark, U., and Nyström, T. (2005) Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol 187: 62656272.
  • Newman, J.R., and Fuqua, C. (1999) Broad-host-range expression vectors that carry the arabinose-inducible Escherichia coli araBAD promoter and the araC regulator. Gene 227: 197203.
  • O'Toole, G.A., and Kolter, R. (1998) Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol Microbiol 28: 449461.
  • O'Toole, G.A., Gibbs, K.A., Hager, P.W., Phibbs, P.V., Jr, and Kolter, R. (2000) The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J Bacteriol 182: 425431.
  • Pérez-Osorio, A.C., Williamson, K.S., and Franklin, M.J. (2010) Heterogeneous rpoS and rhlR mRNA levels and 16S rRNA/rDNA (rRNA gene) ratios within Pseudomonas aeruginosa biofilms, sampled by laser capture microdissection. J Bacteriol 192: 29913000.
  • Petrova, O.E., and Sauer, K. (2009) A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development. PLoS Pathog 5: e1000668.
  • Petrova, O.E., and Sauer, K. (2011) SagS contributes to the motile-sessile switch and acts in concert with BfiSR to enable Pseudomonas aeruginosa biofilm formation. J Bacteriol 193: 66146628.
  • Petrova, O.E., and Sauer, K. (2012) Sticky situations: key components that control bacterial surface attachment. J Bacteriol 194: 24132425.
  • Petrova, O.E., Schurr, J.R., Schurr, M.J., and Sauer, K. (2011) The novel Pseudomonas aeruginosa two-component regulator BfmR controls bacteriophage-mediated lysis and DNA release during biofilm development through PhdA. Mol Microbiol 81: 767783.
  • Platt, M.D., Schurr, M.J., Sauer, K., Vazquez, G., Kukavica-Ibrulj, I., Potvin, E., et al. (2008) Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions. J Bacteriol 190: 27392758.
  • Price-Whelan, A., Dietrich, L.E.P., and Newman, D.K. (2007) Pyocyanin alters redox homeostasis and carbon flux through central metabolic pathways in Pseudomonas aeruginosa PA14. J Bacteriol 189: 63726381.
  • Ramos, I., Dietrich, L.E.P., Price-Whelan, A., and Newman, D.K. (2010) Phenazines affect biofilm formation by Pseudomonas aeruginosa in similar ways at various scales. Res Microbiol 161: 187191.
  • Rani, S.A., Pitts, B., Beyenal, H., Veluchamy, R.A., Lewandowski, Z., Davison, W.M., et al. (2007) Spatial patterns of DNA replication, protein synthesis, and oxygen concentration within bacterial biofilms reveal diverse physiological states. J Bacteriol 189: 42234233.
  • Rasmussen, K., and Lewandowski, Z. (1998) Microelectrode measurements of local mass transport rates in heterogeneous biofilms. Biotechnol Bioeng 59: 302309.
  • San, K.-Y., Bennett, G.N., Berríos-Rivera, S.J., Vadali, R.V., Yang, Y.-T., Horton, E., et al. (2002) Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metab Eng 4: 182192.
  • Sauer, K., and Camper, A.K. (2001) Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol 183: 65796589.
  • Sauer, K., Camper, A.K., Ehrlich, G.D., Costerton, J.W., and Davies, D.G. (2002) Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J Bacteriol 184: 11401154.
  • Schobert, M., and Jahn, D. (2010) Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung. Int J Med Microbiol 300: 549556.
  • Schreiber, K., Boes, N., Eschbach, M., Jaensch, L., Wehland, J., Bjarnsholt, T., et al. (2006) Anaerobic survival of Pseudomonas aeruginosa by pyruvate fermentation requires an Usp-type stress protein. J Bacteriol 188: 659668.
  • Schweizer, H.P. (1991) The agmR gene, an environmentally responsive gene, complements defective glpR, which encodes the putative activator for glycerol metabolism in Pseudomonas aeruginosa. J Bacteriol 173: 67986806.
  • Shirtliff, M.E., Mader, J.T., and Camper, A.K. (2002) Molecular interactions in biofilms. Chem Biol 9: 859871.
  • Somerville, G., Mikoryak, C.A., and Reitzer, L. (1999) Physiological characterization of Pseudomonas aeruginosa during exotoxin A synthesis: glutamate, iron limitation, and aconitase activity. J Bacteriol 181: 10721078.
  • Southey-Pillig, C.J., Davies, D.G., and Sauer, K. (2005) Characterization of temporal protein production in Pseudomonas aeruginosa biofilms. J Bacteriol 187: 81148126.
  • Sriramulu, D.D., Lünsdorf, H., Lam, J.S., and Römling, U. (2005) Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J Med Microbiol 54: 667676.
  • Stewart, P.S. (1996) Theoretical aspects of antibiotic diffusion into microbial biofilms. Antimicrob Agents Chemother 40: 25172522.
  • Stoodley, P., deBeer, D., and Lewandowski, Z. (1994) Liquid flow in biofilm systems. Appl Environ Microbiol 60: 27112716.
  • Stoodley, P., Yang, S., Lappin-Scott, H., and Lewandowski, Z. (1997) Relationship between mass transfer coefficient and liquid flow velocity in heterogenous biofilms using microelectrodes and confocal microscopy. Biotechnol Bioeng 56: 681688.
  • Sumitani, M., Takagi, S., Tanamura, Y., and Inoue, H. (2004) Oxygen indicator composed of an organic/inorganic hybrid compound of methylene blue, reductant, surfactant and saponite. Anal Sci 20: 11531157.
  • Toyofuku, M., Nomura, N., Fujii, T., Takaya, N., Maseda, H., Sawada, I., et al. (2007) Quorum sensing regulates denitrification in Pseudomonas aeruginosa PAO1. J Bacteriol 189: 49694972.
  • Van Alst, N.E., Picardo, K.F., Iglewski, B.H., and Haidaris, C.G. (2007) Nitrate sensing and metabolism modulate motility, biofilm formation, and virulence in Pseudomonas aeruginosa. Infect Immun 75: 37803790.
  • Waite, R., Paccanaro, A., Papakonstantinopoulou, A., Hurst, J., Saqi, M., Littler, E., and Curtis, M. (2006) Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles. BMC Genomics 7: 162.
  • Walters, M.C. III, Roe, F., Bugnicourt, A., Franklin, M.J., and Stewart, P.S. (2003) Contributions of antibiotic penetration, oxygen limitation, and low metabolic activity to tolerance of Pseudomonas aeruginosa biofilms to ciprofloxacin and tobramycin. Antimicrob Agents Chemother 47: 317323.
  • Winsor, G.L., Van Rossum, T., Lo, R., Khaira, B., Whiteside, M.D., Hancock, R.E.W., and Brinkman, F.S.L. (2009) Pseudomonas genome database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 37: D483D488.
  • Wu, M., Guina, T., Brittnacher, M., Nguyen, H., Eng, J., and Miller, S.I. (2005) The Pseudomonas aeruginosa proteome during anaerobic growth. J Bacteriol 187: 81858190.
  • Wu, Z., and Irizarry, R.A. (2004) Preprocessing of oligonucleotide array data. Nat Biotechnol 22: 656658.
  • Yang, L., Barken, K.B., Skindersoe, M.E., Christensen, A.B., Givskov, M., and Tolker-Nielsen, T. (2007) Effects of iron on DNA release and biofilm development by Pseudomonas aeruginosa. Microbiology 153: 13181328.
  • Yoon, S.S., Hennigan, R.F., Hilliard, G.M., Ochsner, U.A., Parvatiyar, K., Kamani, M.C., et al. (2002) Pseudomonas aeruginosa anaerobic respiration in biofilms: relationships to cystic fibrosis pathogenesis. Dev Cell 3: 593603.