Molekulare Mechanismen während der Anheftung und Biofilmbildung in Shewanella oneidensis MR-1 - Die Tücken des Besiedelns -

Grenzflächenbesiedlung durch robuste Bakteriengemeinschaften – sogenannten Biofilmen – stellt die ubiquitär verbreitete Lebensform von Mikroorganismen dar, um einer Vielzahl von Stressfaktoren zu widerstehen. Das Entwicklungsprogramm solcher Biofilme lässt sich in mehrere distinkte Schritte un...

Full description

Saved in:
Bibliographic Details
Main Author: Gödeke, Julia
Contributors: Bremer, Erhard (Prof. Dr.) (Thesis advisor)
Format: Dissertation
Language:German
Published: Philipps-Universität Marburg 2011
Biologie
Subjects:
Online Access:PDF Full Text
Tags: Add Tag
No Tags, Be the first to tag this record!

1. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-5.


2. Kirkpatrick, C. L., and P. H. Viollier. 2010. Cell dispersal in biofilms: an extracellular DNA masks nature's strongest glue. Mol Microbiol.


3. Gralnick, J. A., C. T. Brown, and D. K. Newman. 2005. Anaerobic regulation by an atypical Arc system in Shewanella oneidensis. Mol Microbiol 56:1347-1357.


4. Gralnick, J. A., H. Vali, D. P. Lies, and D. K. Newman. 2006. Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1. PNAS 103:4669-4674.


5. Chen, Y., I. Golding, S. Sawai, L. Guo, and E. C. Cox. 2005. Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biol 3:e229. 38.


6. Carrolo, M., M. J. Frias, F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2010. Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae. PLoS One 5:e15678. 35.


7. Widder, and J. F. Case. 1997. Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47:1034-9.


8. Hofle, M. G., and I. Brettar. 1996. Genotyping of heterotrophic bacteria from the central baltic sea by use of low-molecular-weight RNA profiles. Appl Environ Microbiol 62:1383-90.


9. Saffarini, D. A., and K. H. Nealson. 1993. Sequence and genetic characterization of etrA, an fnr analog that regulates anaerobic respiration in Shewanella putrefaciens MR-1. J Bacteriol 175:7938-44.


10. Kuchma, S. L., K. M. Brothers, J. H. Merritt, N. T. Liberati, F. M. Ausubel, and G. A. O'Toole. 2007. BifA, a cyclic-Di-GMP phosphodiesterase, inversely regulates biofilm formation and swarming motility by Pseudomonas aeruginosa PA14. J Bacteriol 189:8165-78.


11. Sauer, K., and A. K. Camper. 2001. Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol 183:6579-89. 220.


12. Rohwer, F., and R. Edwards. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184:4529-35.


13. Hinman, and S. M. Li. 1998. Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium. Geochimica Et Cosmochimica Acta 62:3239-3257.


14. Stanley, N. R., R. A. Britton, A. D. Grossman, and B. A. Lazazzera. 2003. Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays. Journal of Bacteriology 185:1951-7. 234.


15. McLean, J. S., P. D. Majors, C. L. Reardon, C. L. Bilskis, S. B. Reed, M. F. Romine, and J. K. Fredrickson. 2008. Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms. J Microbiol Methods 74:47-56.


16. Godeke, J., K. Paul, J. Lassak, and K. M. Thormann. 2010. Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1. Isme J. 77.


17. Yang, C., D. A. Rodionov, X. Q. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. 2006. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-29885.


18. Quellen 101. Hochberg, Y. 1988. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75:800-802.


19. Purevdorj-Gage, B., W. J. Costerton, and P. Stoodley. 2005. Phenotypic differentiation and seeding dispersal in non-mucoid and mucoid Pseudomonas aeruginosa biofilms. Microbiol 151:1569-76.


20. Hall-Stoodley, L., and P. Stoodley. 2005. Biofilm formation and dispersal and the transmission of human pathogens. Trends Microbiol 13:7-10.


21. Costerton, J. W., Z. Lewandowski, D. E. Caldwell, D. R. Korber, and H. M. Lappin- Scott. 1995. Microbial biofilms. Annu Rev Microbiol 49:711-45.


22. Holt, H. M., B. Gahrn-Hansen, and B. Bruun. 2005. Shewanella algae and Shewanella putrefaciens: clinical and microbiological characteristics. Clin Microbiol Infect 11:347-52.


23. Sauer, K. 2003. The genomics and proteomics of biofilm formation. Genome Biology 4. 219.


24. Webb, and S. Kjelleberg. 2004. Biofilm development and cell death in the marine bacterium Pseudoalteromonas tunicata. Appl Environ Microbiol 70:3232-8.


25. Gerstel, U., C. Park, and U. Romling. 2003. Complex regulation of csgD promoter activity by global regulatory proteins. Mol Microbiol 49:639-54.


26. Quellen 274. Whitchurch, C. B., T. Tolker-Nielsen, P. C. Ragas, and J. S. Mattick. 2002. Extracellular DNA required for bacterial biofilm formation. Science 295:1487. 275. Whiteley, M., M. G. Bangera, R. E. Bumgarner, M. R. Parsek, G. M. Teitzel, S.


27. Paster, E. Stackebrandt, and K. H. Nealson. 1999. Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49 Pt 4:1341-51.


28. Nealson, M. A. Cusanovich, and J. J. van Beeumen. 2004. Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. J Integrat Biol 8:57-77.


29. Kirov, S. M., M. Castrisios, and J. G. Shaw. 1939. Aeromonas flagella (polar and lateral) are enterocyte adhesins that contribute to biofilm formation on surfaces. Infection & Immunity 72:1939-45.


30. Sambrook, J., and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, third ed. Cold Spring Harbor Laboratory Press. 218.


31. Boles, B. R., and A. R. Horswill. 2008. Agr-mediated dispersal of Staphylococcus aureus biofilms. PLoS Pathog 4:e1000052. 21. Botsford, J. L., and J. G. Harman. 1992. Cyclic-Amp in Prokaryotes. Microbiol Review 56:100-122. 22. Boukhalfa, H., G. A. Icopini, S. D. Reilly, and M. P. Neu. 2007. Plutonium(IV) reduction by the metal-reducing bacteria Geobacter metallireducens GS15 and Shewanella oneidensis MR1. Appl Environ Microbiol 73:5897-5903.


32. Caccavo, F., R. P. Blakemore, and D. R. Lovley. 1992. A hydrogen-oxidizing, Fe(III)- reducing microorganism from the Great Bay Estuary, New-Hampshire. Appl Environ Microbiol 58:3211-3216.


33. Branda, S. S., F. Chu, D. B. Kearns, R. Losick, and R. Kolter. 2006. A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol 59:1229-38.


34. Hoffman, L. R., D. A. D'Argenio, M. J. MacCoss, Z. Zhang, R. A. Jones, and S. I. Miller. 2005. Aminogycoside antibiotics induce bacterial biofilm formation. Nature 436:1171-1175.


35. Jagadeesan, S., P. Mann, C. W. Schink, and P. I. Higgs. 2009. A novel "four- component" two-component signal transduction mechanism regulates developmental progression in Myxococcus xanthus. J Biol Chem 284:21435-45.


36. Stewart, P. S., and J. W. Costerton. 2001. Antibiotic resistance of bacteria in biofilms. Lancet 358:135-8.


37. Drenkard, E. 2003. Antimicrobial resistance of Pseudomonas aeruginosa biofilms. Microbes & Infection 5:1213-9.


38. Choi, K. H., J. B. Gaynor, K. G. White, C. Lopez, C. M. Bosio, R. R. Karkhoff- Schweizer, and H. P. Schweizer. 2005. A Tn7-based broad-range bacterial cloning and expression system. Nature Methods 2:443-8.


39. Palmer, J., S. Flint, and J. Brooks. 2007. Bacterial cell attachment, the beginning of a biofilm. J Ind Microbiol Biotechnol 34:577-88.


40. Waldor. 2002. Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol Microbiol 44:957-70.


41. Hung, D. T., J. Zhu, D. Sturtevant, and J. J. Mekalanos. 2006. Bile acids stimulate biofilm formation in Vibrio cholerae. Mol Microbiol 59:193-201.


42. O'Toole, G., H. B. Kaplan, and R. Kolter. 2000. Biofilm formation as microbial development. Annu Rev Microbiol 54:49-79.


43. Haeussler, S. 2004. Biofilm formation by the small colony variant phenotype of Pseudomonas aeruginosa. Environ Microbiol 6:546-51.


44. Branda, S. S., A. Vik, L. Friedman, and R. Kolter. 2005. Biofilms: the matrix revisited. Trends in Microbiology 13:20-26.


45. Nealson, K. H., A. Belz, and B. McKee. 2002. Breathing metals as a way of life: geobiology in action. Antonie van Leeuwenhoek 81:215-22.


46. Reid, G. A., C. S. Miles, R. K. Moysey, K. L. Pankhurst, and S. K. Chapman. 2000. Catalysis in fumarate reductase. Biochim Biophys Acta 1459:310-5.


47. Neal, A. L., T. L. Bank, M. F. Hochella, Jr., K. M. Rosso, and M. B. Djamgoz. 2005. Cell adhesion of Shewanella oniedensis MR-1 to iron oxide minerals: Effect of different single crystal faces. Geochemical Transactions 6:77-84.


48. Southey-Pillig, C. J., D. G. Davies, and K. Sauer. 2005. Characterization of temporal protein production in Pseudomonas aeruginosa biofilms. J Bacteriol 187:8114-8126. 232. Spormann, A. M. 2008. Physiology of microbes in biofilms. Curr Top Microbiol Immunol 322:17-36.


49. Heun, M. 2010. Charakterisierung von zwei putativen extrazellulären Endonukleasen in Shewanella oneidensis MR-1 (lvorläufiger Titel). Master-Arbeit.


50. Long, H. F., and B. W. Hammer. 1941. Classification of organisms important in diary products. III. Pseudomonas putrefaciens. IOWA Agricultural Experiment Station Research Bulletin 285:176-95.


51. Thormann, K. M., S. Duttler, R. M. Saville, M. Hyodo, S. Shukla, Y. Hayakawa, and A. M. Spormann. 2006. Control of formation and cellular detachment from Shewanella oneidensis MR-1 biofilms by cyclic di-GMP. J Bacteriol 188:2681-91.


52. Kaplan, J. B., C. Ragunath, N. Ramasubbu, and D. H. Fine. 2003. Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity. J Bacteriol 185:4693-8.


53. Prigent-Combaret, C., G. Prensier, T. T. Le Thi, O. Vidal, P. Lejeune, and C. Dorel. 2000. Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid. Environ Microbiol 2:450-64. 195.


54. Paul, K. 2009. Die Rolle der putativen extrazellulären Endonukleasen SO_1066 und SO_1844 in der Biofilmbildung von Shewanella oneidensis MR-1. Bachelor-Arbeit.


55. Gescher, J. S., C. D. Cordova, and A. M. Spormann. 2008. Dissimilatory iron reduction in Escherichia coli: identification of CymA of Shewanella oneidensis and NapC of E. coli as ferric reductases. Mol Microbiol 68:706-719.


56. Renelli, M., V. Matias, R. Y. Lo, and T. J. Beveridge. 2004. DNA-containing membrane vesicles of Pseudomonas aeruginosa PAO1 and their genetic transformation potential. Microbiol 150:2161-9. 206. Resch, A., B. Fehrenbacher, K. Eisele, M. Schaller, and F. Gotz. 2005. Phage release from biofilm and planktonic Staphylococcus aureus cells. FEMS Microbiol Lett 252:89-96. 207.


57. Klausen, M., M. Gjermansen, J. U. Kreft, and T. Tolker-Nielsen. 2006. Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms. FEMS Microbiol Lett 261:1-11. 125. Klausen, M., A. Heydorn, P. Ragas, L. Lambertsen, A. Aaes-Jorgensen, S. Molin, and T. Tolker-Nielsen. 2003. Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. Mol Microbiol 48:1511-24.


58. Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127-81. 273.


59. Wildung, R. E., Y. A. Gorby, K. M. Krupka, N. J. Hess, S. W. Li, A. E. Plymale, J. P. McKinley, and J. K. Fredrickson. 2000. Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens. Appl Environ Microbiol 66:2451-2460. 278. Wimpenny, J., W. Manz, and U. Szewzyk. 2000. Heterogeneity in biofilms. FEMS Microbiology Reviews 24:661-71.


60. Obuekwe, C. O., and D. W. Westlake. 1982. Effects of medium composition on cell pigmentation, cytochrome content, and ferric iron reduction in a Pseudomonas sp. isolated from crude oil. Can J Microbiol 28:989-92.


61. Goller, C. C., and T. Romeo. 2008. Environmental influences on biofilm development. Curr Top Microbiol Immunol 322:37-66.


62. Stanley, N. R., and B. A. Lazazzera. 2004. Environmental signals and regulatory pathways that influence biofilm formation. Mol Microbiol 52:917-24.


63. Simon, J. 2002. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26:285-309. 229. Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular subsequences. J Mol Biol 147:195-7. 230. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-17.


64. Heilmann, C., M. Hussain, G. Peters, and F. Gotz. 1997. Evidence for autolysin- mediated primary attachment of Staphylococcus epidermidis to a polystyrene surface. Mol Microbiol 24:1013-24.


65. Lassak, J. 2010. Evolution von Zwei-Komponenten-Systemen in Shewanella oneidensis MR- 1 Dissertation.


66. Sutherland, I. W. 2001. Exopolysaccharides in biofilms, flocs and related structures. Water Science & Technology 43:77-86.


67. Miller, J. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY. 158. Miller, V. L., and M. J. J. 1988. A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J Bacteriol 170:2575 -2583.


68. Monds, R. D., M. W. Silby, and H. K. Mahanty. 2001. Expression of the Pho regulon negatively regulates biofilm formation by Pseudomonas aureofaciens PA147-2. Mol Microbiol 42:415-26.


69. Catlin, B. W. 1956. Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor. Science 124:441-2.


70. Mulcahy, H., L. Charron-Mazenod, and S. Lewenza. 2008. Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms. PLoS Pathog 4:e1000213. 167. Mulcahy, H., L. Charron-Mazenod, and S. Lewenza. 2010. Pseudomonas aeruginosa produces an extracellular deoxyribonuclease that is required for utilization of DNA as a nutrient source. Environ Microbiol 12:1621-9.


71. Grande, R., M. Di Giulio, L. J. Bessa, E. Di Campli, M. Baffoni, S. Guarnieri, and L. Cellini. 2011. Extracellular DNA in Helicobacter pylori biofilm: a backstairs rumour. J Appl Microbiol 110:490-8.


72. Steinberger, R. E., and P. A. Holden. 2005. Extracellular DNA in single-and multiple- species unsaturated biofilms. Appl Environ Microbiol 71:5404-10.


73. Vlassov, V. V., P. P. Laktionov, and E. Y. Rykova. 2007. Extracellular nucleic acids. Bioessays 29:654-67.


74. Cao, B., L. Shi, R. N. Brown, Y. Xiong, J. K. Fredrickson, M. F. Romine, M. J. Marshall, M. S. Lipton, and H. Beyenal. 2011. Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics. Environ Microbiol.


75. Myers, C. R., and J. M. Myers. 1994. Ferric iron reduction-linked growth yields of Shewanella putrefaciens MR-1. J App Bacteriol 76:253-8.


76. Wen, Z. T., and R. A. Burne. 2002. Functional genomics approach to identifying genes required for biofilm development by Streptococcus mutans.[erratum appears in Appl Environ Microbiol. 2003 Jan;69(1):722.]. Appl Environ Microbiol 68:1196-203.


77. Van Dellen, K. L., L. Houot, and P. I. Watnick. 2008. Genetic analysis of Vibrio cholerae monolayer formation reveals a key role for DeltaPsi in the transition to permanent attachment. J Bacteriol 190:8185-96. 254. van Schaik, E. J., C. L. Giltner, G. F. Audette, D. W. Keizer, D. L. Bautista, C. M. Slupsky, B. D. Sykes, and R. T. Irvin. 2005. DNA binding: a novel function of Pseudomonas aeruginosa type IV pili. J Bacteriol 187:1455-64.


78. Puyet, A., B. Greenberg, and S. A. Lacks. 1990. Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae. J Mol Biol 213:727-38.


79. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 20:1118-23.


80. Simm, R., M. Morr, A. Kader, M. Nimtz, and U. Romling. 2004. GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 53:1123-34.


81. Inoue, H., H. Nojima, and H. Okayama. 1990. High efficiency transformation of Escherichia coli with plasmids. Gene 96:23-8.


82. Wang, I. N., D. L. Smith, and R. Young. 2000. Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54:799-825.


83. McFall-Ngai, M. 2008. Host-microbe symbiosis: the squid-Vibrio association-a naturally occurring, experimental model of animal/bacterial partnerships. Adv Exp Med Biol 635:102-12.


84. O'Toole, G. 2008. How Pseudomonas aeruginosa regulates surface behaviors. Microbe 3:65- 71.


85. Driscoll, M. E., M. F. Romine, F. S. Juhn, M. H. Serres, L. A. McCue, A. S. Beliaev, J. K. Fredrickson, and T. S. Gardner. 2007. Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling. Genome Inform 18:287-98.


86. Thormann, K. M., R. M. Saville, S. Shukla, and A. M. Spormann. 2005. Induction of rapid detachment in Shewanella oneidensis MR-1 biofilms. J Bacteriol 187:1014-21. 252. Tischler, A. D., and A. Camilli. 2004. Cyclic diguanylate (c-di-GMP) regulates Vibrio cholerae biofilm formation. Mol Microbiol 53:857-69.


87. Thormann, K. M., R. M. Saville, S. Shukla, D. A. Pelletier, and A. M. Spormann. 2004. Initial Phases of biofilm formation in Shewanella oneidensis MR-1. J Bacteriol 186:8096- 104.


88. O'Toole, G. A., and R. Kolter. 1998. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis.


89. Wielinga, B., M. M. Mizuba, C. M. Hansel, and S. Fendorf. 2001. Iron promoted reduction of chromate by dissimilatory iron-deducing bacteria. Environmental Science & Technology 35:522-527.


90. Visca, P., L. Leoni, M. J. Wilson, and I. L. Lamont. 2002. Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas. Mol Microbiol 45:1177-90.


91. Maier, T. M., and C. R. Myers. 2001. Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: reassessment of the role of EtrA. J Bacteriol 183:4918-26.


92. Nealson, K. H., C. R. Myers, and B. B. Wimpee. 1991. Isolation and identification of manganese-reducing bacteria and estimates of microbial Mn(IV)-reducing potential in the Black-Sea. Deep-Sea Research Part a-Oceanographic Research Papers 38:S907-S920. 178. Niemeyer, J., and F. Gessler. 2002. Determination of free DNA in soils. J. Plant Nutr. Soil Sci. 165:121-124.


93. Wang, F., P. Wang, M. Chen, and X. Xiao. 2004. Isolation of extremophiles with the detection and retrieval of Shewanella strains in deep-sea sediments from the west Pacific. Extremophiles 8:165-8.


94. Hendrix, R. W. 1983. Lambda II. Cold Spring Harb Lab Press:694 pp. 95.


95. Little, J. W. 2005. Lysogeny, prophage induction, and lysogenic conversion. In M.K. Waldor, D.I. Friedman, and S. Adhya (ed.), Phage. ASM press, Washington, DC:37-54. 137.


96. Brown, R. N., M. F. Romine, A. A. Schepmoes, R. D. Smith, and M. S. Lipton. 2010. Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification. J Proteome Res 9:4454-63. 28. Brunskill, E. W., and K. W. Bayles. 1996. Identification of LytSR-regulated genes from Staphylococcus aureus. J Bacteriol 178:5810-2. 29. Bubendorfer, S. 2010. Die Funktion von Flagelle und Chemotaxis in der Biofilmbildung. Master-Arbeit.


97. Klipper-Aurbach, Y., M. Wasserman, N. Braunspiegel-Weintrob, D. Borstein, S. Peleg, S. Assa, M. Karp, Y. Benjamini, Y. Hochberg, and Z. Laron. 1995. Mathematical formulae for the prediction of the residual beta cell function during the first two years of disease in children and adolescents with insulin-dependent diabetes mellitus. Med Hypotheses 45:486-90.


98. Mah, T. F., and G. A. O'Toole. 2001. Mechanisms of biofilm resistance to antimicrobial agents. Trends in Microbiology. 9:34-9.


99. Green, D. R., and J. C. Reed. 1998. Mitochondria and apoptosis. Science 281:1309-12. 84.


100. Mann, E. E., K. C. Rice, B. R. Boles, J. L. Endres, D. Ranjit, L. Chandramohan, L. H. Tsang, M. S. Smeltzer, A. R. Horswill, and K. W. Bayles. 2009. Modulation of eDNA release and degradation affects Staphylococcus aureus biofilm maturation. PLoS One 4:e5822. 150. Marsh, P. D., and D. J. Bradshaw. 1995. Dental plaque as a biofilm. J Ind Microbiol 15:169-75.


101. Costerton, J. W. 1995. Overview of microbial biofilms. J Ind Microbiol 15:137-40. 41. Costerton, J. W., G. G. Geesey, and K. J. Cheng. 1978. How bacteria stick. Sci Am 238:86-95.


102. McLean, J. S., G. E. Pinchuk, O. V. Geydebrekht, C. L. Bilskis, B. A. Zakrajsek, E. A. Hill, D. A. Saffarini, M. F. Romine, Y. A. Gorby, J. K. Fredrickson, and A. S. Beliaev. 2008. Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1. Environ Microbiol 10:1861-76.


103. Kiley, P. J., and H. Beinert. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. Fems Microbiol Reviews 22:341-352.


104. Gerstel, U., and U. Romling. 2001. Oxygen tension and nutrient starvation are major signals that regulate agfD promoter and expression of the multicellular morphotype in Salmonella typhimurium. Environ Microbiol 3:638-648.


105. Stewart, V., Y. Lu, and A. J. Darwin. 2002. Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J Bacteriol 184:1314-23. 239. Sutherland, I. W. 2001. The biofilm matrix--an immobilized but dynamic microbial environment. Trends in Microbiology 9:222-7.


106. Monds, R. D., P. D. Newell, R. H. Gross, and G. A. O'Toole. 2007. Phosphate- dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol Microbiol 63:656-79.


107. Brettar, I., E. R. Moore, and M. G. Hofle. 2001. Phylogeny and abundance of novel denitrifying bacteria isolated from the water column of the Central Baltic Sea. Microb Ecol 42:295-305.


108. Izano, E. A., I. Sadovskaya, H. Wang, E. Vinogradov, C. Ragunath, N. Ramasubbu, S. Jabbouri, M. B. Perry, and J. B. Kaplan. 2008. Poly-N- acetylglucosamine mediates biofilm formation and detergent resistance in Aggregatibacter actinomycetemcomitans. Microb Pathog 44:52-60.


109. Venkateswaran, K., D. P. Moser, M. E. Dollhopf, D. P. Lies, D. A. Saffarini, B. J. MacGregor, D. B. Ringelberg, D. C. White, M. Nishijima, H. Sano, J. Burghardt, E. Stackebrandt, and K. H. Nealson. 1999. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49 Pt 2:705-24. 258.


110. Canchaya, C., C. Proux, G. Fournous, A. Bruttin, and H. Brussow. 2003. Prophage genomics. Microbiol Mol Biol Rev 67:238-76, table of contents.


111. Zhu, J., and J. J. Mekalanos. 2003. Quorum sensing-dependent biofilms enhance colonization in Vibrio cholerae. Dev Cell 5:647-56.


112. Gorby, Y., J. McLean, A. Korenevsky, K. Rosso, M. Y. El-Naggar, and T. J. Beveridge. 2008. Redox-reactive membrane vesicles produced by Shewanella. Geobiol 6:232-41.


113. Fredrickson, J. M. Tiedje, and J. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. Isme J 3:966-76.


114. Lorenz, M. G., D. Gerjets, and W. Wackernagel. 1991. Release of transforming plasmid and chromosomal DNA from two cultured soil bacteria. Arch Microbiol 156:319-26.


115. Myers, C. R., and J. M. Myers. 1997. Replication of plasmids with the p15A origin in Shewanella putrefaciens MR-1. L Appl Microbiol 24:221-5.


116. McClaine, J. W., and R. M. Ford. 2002. Reversal of flagellar rotation is important in initial attachment of Escherichia coli to glass in a dynamic system with high-and low-ionic- strength buffers. Appl Environ Microbiol 68:1280-9.


117. Venkateswaran, K., M. E. Dollhopf, R. Aller, E. Stackebrandt, and K. H. Nealson. 1998. Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 48 Pt 3:965-72.


118. Zhao, J. S., D. Manno, C. Beaulieu, L. Paquet, and J. Hawari. 2005. Shewanella sediminis sp nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-trinitro-degrading bacterium from marine sediment. International Journal of Systematic and Evolutionary Microbiology 55:1511-1520.


119. Hengge-Aronis, R. 2002. Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373-95, table of contents.


120. Kumar, C. G., and S. K. Anand. 1998. Significance of microbial biofilms in food industry: a review. Int J of Food Microbiol 42:9-27.


121. Saito, T., M. R. Wormald, and R. J. Williams. 1991. Some structural features of the iron-uptake regulation protein. Eur J Biochem 197:29-38.


122. Teal, T. K., D. P. Lies, B. J. Wold, and D. K. Newman. 2006. Spatiometabolic stratification of Shewanella oneidensis biofilms. Appl Environ Microbiol 72:7324-30. 247. Theunissen, S., B. Vergauwen, L. De Smet, J. Van Beeumen, P. Van Gelder, and S. N. Savvides. 2009. The agglutination protein AggA from Shewanella oneidensis MR-1 is a TolC-like protein and forms active channels in vitro. Biochem Biophys Res Commun 386:380-5.


123. Saville, R. M., N. Dieckmann, and A. M. Spormann. 2010. Spatiotemporal activity of the mshA gene system in Shewanella oneidensis MR-1 biofilms. FEMS Microbiol Lett 308:76- 83. 222. Schooling, S. R., A. Hubley, and T. J. Beveridge. 2009. Interactions of DNA with biofilm-derived membrane vesicles. J Bacteriol 191:4097-102.


124. Shockman, G. D., and J. F. Barrett. 1983. Structure, function, and assembly of cell walls of gram-positive bacteria. Annu Rev Microbiol 37:501-27.


125. Nogi, Y., C. Kato, and K. Horikoshi. 1998. Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170:331-8.


126. Hughes, K. T., and K. Mathee. 1998. The anti-sigma factors. Annu Rev Microbiol 52:231-86.


127. Iuchi, S., Z. Matsuda, T. Fujiwara, and E. C. Lin. 1990. The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon. Mol Microbiol 4:715-27.


128. Saltikov, C. W., A. Cifuentes, K. Venkateswaran, and D. K. Newman. 2003. The ars detoxification system is advantageous but not required for As(V) respiration by the genetically tractable Shewanella species strain ANA-3. Appl Environ Microbiol 69:2800-9.


129. Gerstel, U., and U. Romling. 2003. The csgD promoter, a control unit for biofilm formation in Salmonella typhimurium. Res Microbiol 154:659-667.


130. Monds, R. D., and G. A. O'Toole. 2009. The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol 17:73-87.


131. Flemming, H. C., T. R. Neu, and D. J. Wozniak. 2007. The EPS matrix: the "house of biofilm cells". J Bacteriol 189:7945-7.


132. Sutherland, I. W., K. A. Hughes, L. C. Skillman, and K. Tait. 2004. The interaction of phage and biofilms. FEMS Microbiol Lett 232:1-6.


133. Holtje, J. V., and E. I. Tuomanen. 1991. The murein hydrolases of Escherichia coli: properties, functions and impact on the course of infections in vivo. J Gen Microbiol 137:441-54.


134. Ptashne, M., and N. Hopkins. 1968. The operators controlled by the lambda phage repressor. Proc Natl Acad Sci U S A 60:1282-7.


135. Vasseur, P., I. Vallet-Gely, C. Soscia, S. Genin, and A. Filloux. 2005. The pel genes of the Pseudomonas aeruginosa PAK strain are involved at early and late stages of biofilm formation. Microbiol 151:985-97.


136. Zhulin, and J. M. Tiedje. 2008. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 6:592-603.


137. Muto, Y., and S. Goto. 1986. Transformation by extracellular DNA produced by Pseudomonas aeruginosa. Microbiol Immunol 30:621-8.


138. Hinsa, S. M., M. Espinosa-Urgel, J. L. Ramos, and G. A. O'Toole. 2003. Transition from reversible to irreversible attachment during biofilm formation by Pseudomonas fluorescens WCS365 requires an ABC transporter and a large secreted protein. Mol Microbiol 49:905-18.


139. Pinchuk, G. E., C. Ammons, D. E. Culley, S. M. Li, J. S. McLean, M. F. Romine, K. H. Nealson, J. K. Fredrickson, and A. S. Beliaev. 2008. Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl Environ Microbiol 74:1198-208. 192. Pospiech, A., and B. Neumann. 1995. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 11:217-8.


140. Palmgren, J., and P. Kirkinen. 1996. Venous circulation in the maternal lower limb: a Doppler study with the Valsalva maneuver. Ultrasound Obstet Gynecol 8:93-7.


141. Wolfe, A. J., D. S. Millikan, J. M. Campbell, and K. L. Visick. 2004. Vibrio fischeri sigma54 controls motility, biofilm formation, luminescence, and colonization. Appl Environ Microbiol 70:2520-4.


142. Zhao, J. S., D. Manno, C. Leggiadro, D. O'Neil, and J. Hawari. 2006. Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile. Int J Syst Evol Microbiol 56:205-12.


143. Pratt, L. A., and R. Kolter. 1998. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 30:285-93. 194.


144. O'Toole, G. A., and R. Kolter. 1998. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30:295-304.


145. Gilbert, P., D. J. Evans, E. Evans, I. G. Duguid, and M. R. Brown. 1991. Surface characteristics and adhesion of Escherichia coli and Staphylococcus epidermidis. J Appl Bacteriol 71:72-7.


146. Domka, J., J. Lee, T. Bansal, and T. K. Wood. 2007. Temporal gene-expression in Escherichia coli K-12 biofilms. Environ Microbiol 9:332-46.


147. Lappann, M., H. Claus, T. van Alen, M. Harmsen, J. Elias, S. Molin, and U. Vogel. 2010. A dual role of extracellular DNA during biofilm formation of Neisseria meningitidis. Mol Microbiol 75:1355-71.


148. Gjermansen, M., P. Ragas, C. Sternberg, S. Molin, and T. Tolker-Nielsen. 2005. Characterization of starvation-induced dispersion in Pseudomonas putida biofilms. Environ Microbiol 7:894-906.


149. Reisner, A., J. A. Haagensen, M. A. Schembri, E. L. Zechner, and S. Molin. 2003. Development and maturation of Escherichia coli K-12 biofilms. Mol Microbiol 48:933-46.


150. Yang, L., K. B. Barken, M. E. Skindersoe, A. B. Christensen, M. Givskov, and T. Tolker-Nielsen. 2007. Effects of iron on DNA release and biofilm development by Pseudomonas aeruginosa. Microbiol 153:1318-28.


151. Molin, S., and T. Tolker-Nielsen. 2003. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr Opin Biol 14:255-61.


152. Lambertsen, L., C. Sternberg, and S. Molin. 2004. Mini-Tn7 transposons for site- specific tagging of bacteria with fluorescent proteins. Enviro Microbiol 6:726-32.


153. Qin, Z., Y. Ou, L. Yang, Y. Zhu, T. Tolker-Nielsen, S. Molin, and D. Qu. 2007. Role of autolysin-mediated DNA release in biofilm formation of Staphylococcus epidermidis. Microbiol 153:2083-92.


154. Lory, and E. P. Greenberg. 2001. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860-4.


155. Myers, C. R., and K. H. Nealson. 1988. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319-21.


156. Heeb, S., Y. Itoh, T. Nishijyo, U. Schnider, C. Keel, J. Wade, U. Walsh, F. O'Gara, and D. Haas. 2000. Small, stable shuttle vectors based on the minimal pVS1 replicon for use in Gram-negative, plant-associated bacteria. Mol Plant-Microbe Interactions 13:232- 237.


157. Lovley, D. R. 2003. Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1:35-44.


158. Jenal, U., and J. Malone. 2006. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40:385-407.


159. Hau, H. H., and J. A. Gralnick. 2007. Ecology and biotechnology of the genus Shewanella. Annu Rev Microbiol 61:237-58.


160. Gao, H., X. Wang, Z. K. Yang, T. Palzkill, and J. Zhou. 2008. Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses. BMC Genomics 9:42. 67.


161. Folsom, J. P., L. Richards, B. Pitts, F. Roe, G. D. Ehrlich, A. Parker, A. Mazurie, and P. S. Stewart. 2010. Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. BMC Microbiol 10:294. 63. Fredrickson, J. K., M. F. Romine, A. S. Beliaev, J. M. Auchtung, M. E. Driscoll, T. S. Gardner, K. H. Nealson, A. L. Osterman, G. Pinchuk, J. L. Reed, D. A. Rodionov, J. L. Rodrigues, D. A. Saffarini, M. H. Serres, A. M. Spormann, I. B.


162. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin, and J. Zhou. 2009. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics 10:131. 284.


163. Flemming, H. C., and J. Wingender. 2010. The biofilm matrix. Nat Rev Microbiol 8:623-33.


164. Finkel, S. E., and R. Kolter. 2001. DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol 183:6288-93.


165. Liu, X., C. Ng, and T. Ferenci. 2000. Global adaptations resulting from high population densities in Escherichia coli cultures. J Bacteriol 182:4158-64.


166. Watnick, P., and R. Kolter. 2000. Biofilm, city of microbes. J Bacteriol 182:2675-9. 270.


167. Qiu, X., G. W. Sundin, L. Wu, J. Zhou, and J. M. Tiedje. 2005. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. Journal of Bacteriology 187:3556-64.


168. Newman. 2005. Shewanella oneidensis MR-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for biofilms. Appl Environ Microbiol 71:4414-26.


169. Hickman, J. W., D. F. Tifrea, and C. S. Harwood. 2005. A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. PNAS 102:14422-14427.


170. Hentzer, M., L. Eberl, and M. Givskov. 2005. Transcriptome analysis of Pseudomonas aeruginosa biofilm development: anaerobic respiration and iron limitation. Biofilms 2:37-61.


171. Purevdorj, B., J. W. Costerton, and P. Stoodley. 2002. Influence of hydrodynamics and cell signaling on the structure and behavior of Pseudomonas aeruginosa biofilms. Appl Environ Microbiol 68:4457-64.


172. Steinmoen, H., E. Knutsen, and L. S. Havarstein. 2002. Induction of natural competence in Streptococcus pneumoniae triggers lysis and DNA release from a subfraction of the cell population. Proc Natl Acad Sci U S A 99:7681-6.


173. Wagner, P. L., and M. K. Waldor. 2002. Bacteriophage control of bacterial virulence. Infect Immun 70:3985-93.


174. Qiu, X., M. J. Daly, A. Vasilenko, M. V. Omelchenko, E. K. Gaidamakova, L. Wu, J. Zhou, G. W. Sundin, and J. M. Tiedje. 2006. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J Bacteriol 188:1199-1204.


175. Morris, C. E., J. Monier, and M. Jacques. 1997. Methods for observing microbial biofilms directly on leaf surfaces and recovering them for isolation of culturable microorganisms. Appl Environ Microbiol 63:1570-6.


176. Serres, M. H., and M. Riley. 2006. Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments. Journal of Bacteriology 188:4601-4609.


177. Romine, D. A. Saffarini, E. A. Hill, L. Shi, D. A. Elias, D. W. Kennedy, G. Pinchuk, K. Watanabe, S. Ishii, B. Logan, K. H. Nealson, and J. K. Fredrickson. 2006. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc Natl Acad Sci U S A 103:11358-63.


178. Saffarini, D. A., R. Schultz, and A. Beliaev. 2003. Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis. J Bacteriol 185:3668-71.


179. Wozniak, D. J., T. J. Wyckoff, M. Starkey, R. Keyser, P. Azadi, G. A. O'Toole, and M. R. Parsek. 2003. Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms. Proc Natl Acad Sci U S A 100:7907-12.


180. Webb, J. S., L. S. Thompson, S. James, T. Charlton, T. Tolker-Nielsen, B. Koch, M. Givskov, and S. Kjelleberg. 2003. Cell death in Pseudomonas aeruginosa biofilm development. J Bacteriol 185:4585-92.


181. Myers, C. R., and J. M. Myers. 1997. Cloning and sequence of cymA, a gene encoding a tetraheme cytochrome c required for reduction of iron(III), fumarate, and nitrate by Shewanella putrefaciens MR-1. J Bacteriol 179:1143-52.


182. Parise, G., M. Mishra, Y. Itoh, T. Romeo, and R. Deora. 2007. Role of a putative polysaccharide locus in Bordetella biofilm development. J Bacteriol 189:750-60. 188. Park, T., D. K. Struck, J. F. Deaton, and R. Young. 2006. Topological dynamics of holins in programmed bacterial lysis. Proc Natl Acad Sci U S A 103:19713-8.


183. Rice, K. C., E. E. Mann, J. L. Endres, E. C. Weiss, J. E. Cassat, M. S. Smeltzer, and K. W. Bayles. 2007. The cidA murein hydrolase regulator contributes to DNA release and biofilm development in Staphylococcus aureus. Proc Natl Acad Sci U S A 104:8113-8. 209.


184. Jurcisek, J. A., and L. O. Bakaletz. 2007. Biofilms formed by nontypeable Haemophilus influenzae in vivo contain both double-stranded DNA and type IV pilin protein. J Bacteriol 189:3868-75.


185. Lower, B. H., L. Shi, R. Yongsunthon, T. C. Droubay, D. E. McCready, and S. K. Lower. 2007. Specific bonds between an iron oxide surface and outer membrane cytochromes MtrC and OmcA from Shewanella oneidensis MR-1. J Bacteriol 189:4944-52.


186. Kierek, K., and P. I. Watnick. 2003. Environmental determinants of Vibrio cholerae biofilm development. Appl Environ Microbiol 69:5079-88.


187. Dow, J. M., L. Crossman, K. Findlay, Y. Q. He, J. X. Feng, and J. L. Tang. 2003. Biofilm dispersal in Xanthomonas campestris is controlled by cell-cell signaling and is required for full virulence to plants. Proceedings of the National Academy of Sciences of the United States of America 100:10995-1000.


188. Shi, L., T. C. Squier, J. M. Zachara, and J. K. Fredrickson. 2007. Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Mol Microbiol 65:12-20.


189. Boyd, A., and A. M. Chakrabarty. 1994. Role of alginate lyase in cell detachment of Pseudomonas aeruginosa. Appl Environ Microbiol 60:2355-9.


190. Scott, J. H., and K. H. Nealson. 1994. A biochemical study of the intermediary carbon metabolism of Shewanella putrefaciens. J Bacteriol 176:3408-11.


191. Ruby, E. G., and M. J. McFall-Ngai. 1992. A squid that glows in the night: development of an animal-bacterial mutualism. J Bacteriol 174:4865-70.


192. Ryder, C., M. Byrd, and D. J. Wozniak. 2007. Role of polysaccharides in Pseudomonas aeruginosa biofilm development. Curr Opin Microbiol 10:644-8.


193. Izano, E. A., M. A. Amarante, W. B. Kher, and J. B. Kaplan. 2008. Differential roles of poly-N-acetylglucosamine surface polysaccharide and extracellular DNA in Staphylococcus aureus and Staphylococcus epidermidis biofilms. Appl Environ Microbiol 74:470-6.


194. Houot, L., and P. I. Watnick. 2008. A novel role for enzyme I of the Vibrio cholerae phosphoenolpyruvate phosphotransferase system in regulation of growth in a biofilm. J Bacteriol 190:311-20.


195. Yildiz, F. H., and G. K. Schoolnik. 1999. Vibrio cholerae O1 El Tor: identification of a gene cluster required for the rugose colony type, exopolysaccharide production, chlorine resistance, and biofilm formation. Proc Natl Acad Sci U S A 96:4028-33.


196. Rice, K. C., and K. W. Bayles. 2008. Molecular control of bacterial death and lysis. Microbiol Mol Biol Rev 72:85-109.


197. Garcia-Contreras, R., X. S. Zhang, Y. Kim, and T. K. Wood. 2008. Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes. PLoS One 3:e2394.


198. Moorthy, S., and P. I. Watnick. 2004. Genetic evidence that the Vibrio cholerae monolayer is a distinct stage in biofilm development. Mol Microbiol 52:573-87. 164.


199. Thomas, V. C., L. R. Thurlow, D. Boyle, and L. E. Hancock. 2008. Regulation of autolysis-dependent extracellular DNA release by Enterococcus faecalis extracellular proteases influences biofilm development. J Bacteriol 190:5690-8.


200. Tang, X., W. Yi, G. R. Munske, D. P. Adhikari, N. L. Zakharova, and J. E. Bruce. 2007. Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes. J Proteome Res 6:724-34.


201. Moorthy, S., and P. I. Watnick. 2005. Identification of novel stage-specific genetic requirements through whole genome transcription profiling of Vibrio cholerae biofilm development. Mol Microbiol 57:1623-35.


202. Rice, S. A., C. H. Tan, P. J. Mikkelsen, V. Kung, J. Woo, M. Tay, A. Hauser, D. McDougald, J. S. Webb, and S. Kjelleberg. 2009. The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage. Isme J 3:271-82.


203. Ma, L., M. Conover, H. Lu, M. R. Parsek, K. Bayles, and D. J. Wozniak. 2009. Assembly and development of the Pseudomonas aeruginosa biofilm matrix. PLoS Pathog 5:e1000354. 144. MacDonell, M. T., and R. R. Colwell. 1985. Phylogeny of the Vibrionaceae, and Recommendation for 2 New Genera, Listonella and Shewanella. Syst Appl Microbiol 6:171- 182.


204. Vilain, S., J. M. Pretorius, J. Theron, and V. S. Brozel. 2009. DNA as an adhesin: Bacillus cereus requires extracellular DNA to form biofilms. Appl Environ Microbiol 75:2861-8.


205. Karatan, E., and P. Watnick. 2009. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol Mol Biol Rev 73:310-47.


206. Guiton, P. S., C. S. Hung, K. A. Kline, R. Roth, A. L. Kau, E. Hayes, J. Heuser, K. W. Dodson, M. G. Caparon, and S. J. Hultgren. 2009. Contribution of autolysin and Sortase a during Enterococcus faecalis DNA-dependent biofilm development. Infect Immun 77:3626-38.


207. Wang, X., Y. Kim, and T. K. Wood. 2009. Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms. ISME J 3:1164-79.


208. Tamayo, R., J. T. Pratt, and A. Camilli. 2007. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu Rev Microbiol 61:131-48.


209. Ghosh, D., K. Roy, K. E. Williamson, S. Srinivasiah, K. E. Wommack, and M. Radosevich. 2009. Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl Environ Microbiol 75:7142- 52.


210. Harmsen, M., M. Lappann, S. Knochel, and S. Molin. 2010. Role of extracellular DNA during biofilm formation by Listeria monocytogenes. Appl Environ Microbiol 76:2271-9.


211. Lassak, J., A. L. Henche, L. Binnenkade, and K. M. Thormann. 2010. ArcS, the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. Appl Environ Microbiol 76:3263-74.


212. Burton, B., and D. Dubnau. 2010. Membrane-associated DNA transport machines. Cold Spring Harb Perspect Biol 2:a000406.


213. El-Naggar, M. Y., G. Wanger, K. M. Leung, T. D. Yuzvinsky, G. Southam, J. Yang, W. M. Lau, K. H. Nealson, and Y. A. Gorby. 2010. Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1. Proc Natl Acad Sci U S A 107:18127-31. 59.


214. Rakshe, S., M. Leff, and A. M. Spormann. 2011. Indirect Modulation of the Intracellular c-Di-GMP Level in Shewanella oneidensis MR-1 by MxdA. Appl Environ Microbiol 77:2196-8.


215. Wang, X., Y. Kim, Q. Ma, S. H. Hong, K. Pokusaeva, J. M. Sturino, and T. K. Wood. 2010. Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1:147.


216. Hong, S. H., X. Wang, and T. K. Wood. 2010. Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli. Microbial Biotech 3:344-356.


217. Quellen 19. Bodenmiller, D., E. Toh, and Y. V. Brun. 2004. Development of surface adhesion in Caulobacter crescentus. J Bacteriol 186:1438-47.


218. Lovley, D. R., D. E. Holmes, and K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219-86.


219. Wang, X., J. F. Preston, 3rd, and T. Romeo. 2004. The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. J Bacteriol 186:2724-34.


220. Chen, I., P. J. Christie, and D. Dubnau. 2005. The ins and outs of DNA transfer in bacteria. Science 310:1456-1460.


221. Friedman, L., and R. Kolter. 2004. Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix. J Bacteriol 186:4457-65.


222. Sauer, K., M. C. Cullen, A. H. Rickard, L. A. Zeef, D. G. Davies, and P. Gilbert. 2004. Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm. J Bacteriol 186:7312-26.


223. Choy, W.-K., L. Zhou, C. K.-C. Syn, L.-H. Zhang, and S. Swarup. 2004. MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. J Bacteriol 186:7221-7228.


224. Webb, J. S., M. Lau, and S. Kjelleberg. 2004. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J Bacteriol 186:8066-73.


225. Myers, J. M., and C. R. Myers. 2001. Role for outer membrane cytochromes OmcA and OmcB of Shewanella putrefaciens MR-1 in reduction of manganese dioxide. Appl Environ Microbiol 67:260-269.


226. Janakiraman, R. S., and Y. V. Brun. 1999. Cell cycle control of a holdfast attachment gene in Caulobacter crescentus. J Bacteriol 181:1118-25.


227. Myers, J. M., and C. R. Myers. 2000. Role of the tetraheme cytochrome CymA in anaerobic electron transport in cells of Shewanella putrefaciens MR-1 with normal levels of menaquinone. J Bacteriol 182:67-75.


228. Taylor, B. L., and I. B. Zhulin. 1999. PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiology and Molecular Biology Reviews 63:479-+.


229. Hamilton, H. L., K. J. Schwartz, and J. P. Dillard. 2001. Insertion-duplication mutagenesis of Neisseria: use in characterization of DNA transfer genes in the gonococcal genetic island. J Bacteriol 183:4718-26.


230. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. Journal of Molecular Biology 166:557-580.


231. Thormann. 2009. Two different stator systems drive a single polar flagellum in Shewanella oneidensis MR-1. Mol Microbiol 71:836-50.


232. Mikkelsen, H., N. J. Bond, M. E. Skindersoe, M. Givskov, K. S. Lilley, and M. Welch. 2009. Biofilms and type III secretion are not mutually exclusive in Pseudomonas aeruginosa. Microbiol 155:687-98.


233. Hindre, T., H. Bruggemann, C. Buchrieser, and Y. Hechard. 2008. Transcriptional profiling of Legionella pneumophila biofilm cells and the influence of iron on biofilm formation. Microbiol 154:30-41.