Reporter systems for microscopic analysis of microbial biofilms

Methods in Enzymology

Volumn 310, Issue , 1999, Pages 3-20

  Korber, Darren R ^a   Wolfaardt, Gideon M ^a   Brözel, Volker ^a   Macdonald, Raynard ^a   Niepel, Tanja ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; FLUOROCHROME; GREEN FLUORESCENT PROTEIN; RIBOSOME RNA;

ARTICLE; BACTERIAL METABOLISM; BACTERIUM DETECTION; BIOFILM; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; FLUORESCENT ANTIBODY TECHNIQUE; IN SITU HYBRIDIZATION; METHODOLOGY; MICROBIAL GROWTH; MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; REPORTER GENE; RESEARCH; RIBOSOME;

EID: 0032698335     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(99)10003-X     Document Type: Article

References (79)

1. G. M. Wolfaardt, J. R. Lawrence, R. D. Robarts, and D. E. Caldwell, Appl. Environ. Microbiol. 60, 434 (1994).
2. D. R. Korber, A. Choi, G. M. Wolfaardt, and D. E. Caldwell, Appl. Environ. Microbiol. 62, 3939 (1996).
3. D. R. Korber, A. Choi, G. M. Wolfaardt, S. C. Ingham, and D. E. Caldwell, Appl. Environ. Microbiol. 63, 3352 (1997).
4. S. Møller, D. R. Korber, G. M. Wolfaardt, S. Molin, and D. E. Caldwell, Appl. Environ. Microbiol. 63, 2432 (1997).
5. D. R. Korber, G. A. James, and J. W. Costerton, Appl. Environ. Microbiol. 60, 1663 (1994).
6. G. M. Wolfaardt, J. R. Lawrence, R. D. Robarts, and D. E. Caldwell, Microb. Ecol. 35, 213 (1998).
7. D. E. Caldwell and J. R. Lawrence, Microb. Ecol. 12, 299 (1986).
8. D. R. Korber, J. R. Lawrence, B. Sutton, and D. E. Caldwell, Microb. Ecol. 18, 1 (1989).
9. D. R. Korber, J. R. Lawrence, L. Zhang, and D. E. Caldwell, Biofouling 2, 335 (1990).
10. G. M. Wolfaardt, J. R. Lawrence, J. V. Headley, R. D. Robarts, and D. E. Caldwell, Microb. Ecol. 27, 279 (1994).
11. D. E. Caldwell and J. R. Lawrence, in "CRC Handbook of Laboratory Model Systems for Microbial Ecology Research" (J. Wimpenny, ed.), p. 117. CRC Press, Boca Raton, FL, 1988.
12. J. R. Lawrence, D. R. Korber, and D. E. Caldwell, J. Microbiol. Methods 10, 123 (1989).
13. R. I. Amann, W. Ludwig, and K. H. Schleifer, Microbiol. Rev. 59, 143 (1995).
14. R. I. Amann, J. Stromley, R. Devereux, R. Key, and D. A. Stahl, Appl. Environ. Microbiol. 58, 614 (1992).
15. C. R. Woese, Microbiol. Rev. 51, 221 (1987).
16. K. H. Schleifer, W. Ludwig, and R. I. Amann, Fresenius J. Anal. Chem. 343, 47 (1992).
17. G. J. Olsen and C. R. Woese, FASEB J. 7, 113 (1993).
18. R. I. Amann, in "Molecular Microbial Ecology Manual" (A. D. L. Akkermans, J. D. van Elsas, and F. D. de Bruijn, eds.), p. 1. Kluwer, Dortrecht, 1995.
19. T. J. DiChristina and E. F. DeLong, Appl. Environ. Microbiol. 59, 4152 (1993).
20. W. Manz, U. Szewzyk, P. Ericsson, R. Amann, K. H. Schleifer, and T. A. Stenström, Appl. Environ. Microbiol. 59, 2293 (1993).
21. J. B. Risatti, W. C. Capman, and D. A. Stahl, Proc. Natl. Acad. Sci. U.S.A. 91, 10173 (1994).
22. J. B. Andersen, C. Sternberg, L. K. Poulsen, S. P. Bjørn, M. Givskov, and S. Molin, Appl. Environ. Microbiol. 64, 2240 (1998).
23. S. Møller, C. Sternberg, J. B. Andersen, B. B. Christensen, J. L. Ramos, M. Givskov, and S. Molin, Appl. Environ. Microbiol. 64, 721 (1998).
24. S. Stretton, S. Techkarnjanaruk, A. M. McLennan, and A. E. Goodman, Appl. Environ. Microbiol. 64, 2554 (1998).
25. M. Wagner, P. Hutzler, and R. Amann, in "Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications" (M. H. F. Wilkinson and F. Schut, eds.), p. 467. Wiley, New York, 1998.
26. M. Wagner, B. Assmus, A. Hartmann, P. Hutzler, and R. Amann, J. Microsc. 176, 181 (1994).
27. M. Wagner, B. Assmus, A. Hartmann, P. Hutzler, N. Springer, and K.-H. Schleifer, J. Microsc. 176, 251 (1994).
28. M. Wagner, G. Rath, H.-P. Koops, J. Flood, and R. Amann, Wat. Sci. Technol. 34, 237 (1996).
29. W. Hönerlage, D. Hahn, and J. Zeyer, Arch. Microbiol. 163, 235 (1995).
30. A. Neef, A. Zaglauer, H. Meier, R. Amann, H. Lemmer, and K.-H. Schleifer, Appl. Environ. Microbiol. 62, 4329 (1996).
31. J. Snaidr, R. Amann, I. Huber, L. Ludwig, and K.-H. Schleifer, Appl. Environ. Microbiol. 63, 2884 (1997).
32. B. Zarda, D. Hahn, A. Chatzinotas, W. Schoenhuber, A. Neef, R. Amann, and J. Zeyer, Arch. Microbiol. 185, (1997).
33. R. I. Amann, F. O. Glöckner, and A. Neef, FEMS Microbiol. Rev. 20, 191 (1997).
34. G. E. Fox, K. R. Pechman, and C. R. Woese, Int. J. Syst. Bacteriol. 27, 44 (1977).
35. R. I. Amann, W. Ludwig, and K. H. Schleifer, ASM News 60, 360 (1994).
36. W. Manz, R. Amann, W. Ludwig, M. Wagner, and K. H. Schleifer, Syst. Appl. Microbiol. 15, 593 (1992).
37. G. Muyzer and N. B. Ramsing, Wat. Sci. Tech. 32, 1 (1995).
38. R. I. Amann, W. Ludwig, R. Schulze, S. Spring, E. Moore, and K. H. Schleifer, Syst. Appl. Microbiol. 19, 501 (1996).
39. O. Strunk and W. Ludwig, ARB software program package; htpp://www.biol.chemie. tu-muenchen.de/pub/ARB/ (1997).
40. S. Møller, C. S. Kristensen, L. K. Poulsen, J. M. Carstensen, and S. Molin, Appl. Environ. Microbiol. 61, 741 (1995).
41. R. P. Haugland, in "Handbook of Fluorescent Probes and Research Chemicals." Molecular Probes, Eugene, OR 1996.
42. B. Zarda, R. I. Amann, G. Wallner, and K.-H. Schleifer, J. Gen. Mlcrobiol 137, 2823 (1991).
43. R. I. Amann, B. Zarda, D. A. Stahl, and K. Schleifer, Appl. Environ. Microbiol. 58, 3007 (1992).
44. 29 Bacteria should be washed with PBS solution, described in step 2, to halt enzymatic activity.
45. M. Schuppler, M. Wagner, G. Schoen, and U. B. Goebel, Microbiology 144, 249 (1998).
46. S. J. MacNaughton, A. G. O'Donnel, and T. M. Embley, Appl. Environ. Microbiol. 62, 4632 (1994).
47. 13 requires empirical confirmation using a range of FA concentrations (e.g., 0, 10, 20, 30, 40, 50), testing with appropriate nontarget controls, and so on.
48. The stringency of the washing step is also probe dependent. It is generally adjusted by changing the NaCl concentration in the washing buffer. In general, the higher the formamide concentration, the lower the concentration of NaCl (e.g., at 5% FA, 636 mM NaCl is used; at 30% FA, 112 mM NaCl is used).
49. 23 or other materials. Our work has shown that this is not necessary in all cases. Biofilms imaged before and after FISH showed that the architecture and thickness of biofilms at reference positions (determined using SCLM and a computer-controlled microscope stage) remained unchanged during and after fixation and hydridization without the need for gel stabilization.
50. Readers should also note that current studies failed to demonstrate a difference in the brightness of probe signal (using GPHGC, Eub 388, γ subclass of the class proteobacteria, and species-specific probes for Aureobacterium sp., Terrabacter sp., and Cellulomonas sp.) of native PCB-degrading biofilms fixed with 4% paraformaldehyde and then ethanol versus those simply stained with ethanol. Furthermore, little or no difference was noted between biofilms stained with the standard 50, 80, and 96% ethanol series and those simply stained with 96% ethanol for 3 min. It is suggested that readers evaluate the efficacy and necessity of excessive fixation, especially during analysis of biofilms where native structure is of importance.
51. T. Boehnisch, in "Handbook of Immunochemical Staining Methods" (S. J. Naish, ed.), p. 2. Dako, Carpinteria, CA, 1989.
52. D. B. Roszak and R. R. Colwell, Microbiol. Rev. 51, 365 (1987).
53. W. Schönhuber, B. Fuchs, S. Juretschko, and R. Amann, Appl. Environ. Microbiol. 63, 3268 (1997).
54. E. Bidnenko, C. Mercierm, J. Tremblay, P. Tailliez, and S. Kulakauskas, Appl. Environ. Microbiol. 64, 3059 (1998).
55. I. M. Head, J. R. Saunders, and R. W. Pickup, Microb. Ecol. 35, 1 (1998).
56. L. K. Poulsen, G. Ballard, and D. A. Stahl, Appl. Environ. Microbiol. 59, 1354 (1993).
57. C. C. Ouverney and J. A. Fuhrman, Appl. Environ. Microbiol. 63, 2735 (1997).
58. S. Lee, C. Malone, and P. F. Kemp, Mar. Ecol. Prog. Ser. 101, 193 (1993).
59. R. Amann, R. Snaidr, M. Wagner, W. Ludwig, and K. H. Schleifer, J. Bacteriol. 178, 3496 (1996).
60. P. Lebaron, P. Catala, C. Fajon, F. Joux, J. Baudart, and L. Bernard, Appl. Environ. Microbiol. 63, 3274 (1997).
61. D. R. Corey, Trends Biotechnol. 15, 226 (1997).
62. D. G. Davies and G. G. Geesey, Appl. Environ. Microbiol. 61, 860 (1995).
63. G. A. O'Toole and R. Kolter, Mol. Microbiol. 28, 449 (1998).
64. A. Cebolla, C. Guzmán, and V. de Lorenzo, Appl. Environ. Microbiol 62, 214 (1996).
65. G. Wolfaardt, A. Matin, and D. Caldwell, unpublished data (1996).
66. A. Suarez, A. Güttler, M. Strätz, L. H. Staendner, K. N. Timmis, and C. A. Guzmán, Gene 196, 69 (1997).
67. V. S. Brözel, G. M. Strydom, and T. E. Cloete, Biofouling 8, 195 (1995).
68. M. Chalfie, Y. Tu, G. Euskirchen, W. W. Ward, and D.C. Prasher, Science 263, 802 (1994).
69. B. B. Christensen, C. Sternberg, and S. Molin, Gene 173, 59 (1996).
70. B. B. Christensen, C. Sternberg, J. B. Andersen, L. Eberl, S. Møller, M. Givskov, and S. Molin, Appl. Environ. Microbiol. 64, 2247 (1998).
71. C. Dahlberg, M. Bergström, and M. Hermansson, Appl. Environ. Microbiol. 64, 2670 (1998).
72. B. Normander, B. B. Christensen, S. Molin, and N. Kroer, Appl. Environ. Microbiol. 64, 1902 (1998).
73. S. Karthikeyan, G. Wolfaardt, D. Korber, and D. Caldwell, unpublished data (1998).
74. "Current Protocols in Molecular Biology." Wiley, New York.
75. V. de Lorenzo, M. Herrero, U. Jakubzik, and K. N. Timmis, J. Bacteriol. 172, 6568 (1990).
76. -1) need to be obtained. Cells from step 2 should thus be plated spotwise on LB plates supplemented with 50 μg/ml kanamycin as well as 100 μg/ml rifampicin.
77. 76 J. Winkler, K. N. Timmis, and R. A. Snyder, Appl. Environ. Microbiol. 61, 448 (1995).
78. J. R. Lawrence, D. R. Korber, G. M. Wolfaardt, and D. E. Caldwell, in "Manual of Environmental Microbiology" (C. J. Hurst, G. R. Knudsen, M. J. McInerney, L. D. Stetzenback, and M. V. Walter, eds.), p. 79. ASM Press, Washington, DC, 1997.
79. J. J. Smith, J. P. Howington, and G. A. McFeters, Appl. Environ. Microbiol. 60, 2977 (1994).