Stereological assessment of extracellular polymeric substances, exo-enzymes, and specific bacterial strains in bioaggregates using fluorescence experiments

Biotechnology Advances

Volumn 28, Issue 2, 2010, Pages 255-280

  Adav, Sunil S ^a   Lin, Justin Chun Te ^a   Yang, Zhen ^b   Whiteley, Chris G ^c   Lee, Duu Jong ^a   Peng, Xiao Feng ^b   Zhang, Zhen Peng ^d  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b TSINGHUA UNIVERSITY   (China)

^c Microbiology   (South Africa)

^d BEIJING ENTERPRISES WATER GROUP LIMITED   (China)

Author keywords

CLSM; Enzyme; Extracellular polymeric substance; Fluorescence experiment; Strain

Indexed keywords

BACTERIAL STRAINS; BI-LEVEL IMAGES; BIOLOGICAL PROCESS; CALCOFLUOR WHITE; COLOR IMAGES; COLORED IMAGES; CONCANAVALIN A; CONFOCAL LASER SCANNING MICROSCOPY; DIGITAL FORMS; EXO-ENZYMES; EXTRA-CELLULAR POLYMERIC SUBSTANCES; EXTRACELLULAR POLYMERIC SUBSTANCE; FINITE ELEMENT SIMULATIONS; FLUID FLOW; FLUOROCHROMES; GRID PATTERN; HEAT AND MASS TRANSFER; HYBRIDISATION; IMAGE COLOR; IN-SITU; ISOTHIOCYANATES; MATRIX; METABOLIC ENZYMES; MICROBIAL CELLS; MICROBIAL STRAIN; MOLECULAR TAGS; NILE RED; NUMERICAL STUDIES; POLYMERIC SUBSTANCE; QUANTITATIVE DESCRIPTION; TRANSPORT PROCESS; VOLUMETRIC GRIDS;

ANTIBODIES; CALCIUM; CALCIUM ALLOYS; CATALYSTS; COLOR; COMPUTATIONAL FLUID DYNAMICS; COMPUTER SOFTWARE; CONFOCAL MICROSCOPY; ENZYMES; EXPERIMENTS; FLOW CYTOMETRY; FLOW OF FLUIDS; FLUORESCENCE; GRAFTING (CHEMICAL); LIPIDS; MASS TRANSFER; MATLAB; NUCLEIC ACIDS; POLYSACCHARIDES; SUGARS; SYNTHESIS (CHEMICAL);

TRANSPORT PROPERTIES;

ENZYME; POLYMER;

ENZYME ACTIVITY; FLOW CYTOMETRY; FLUID FLOW; FLUORESCENCE SPECTROSCOPY; HYBRIDIZATION; MASS TRANSFER; MICROORGANISM; NUCLEIC ACID; SCANNING ELECTRON MICROSCOPY; SIMULATION;

BACTERIUM; CHEMISTRY; CONFOCAL MICROSCOPY; EXTRACELLULAR SPACE; FLUORESCENCE; METABOLISM; METHODOLOGY; MICROBIOLOGY; REVIEW; SEWAGE;

BACTERIA; ENZYMES; EXTRACELLULAR SPACE; FLUORESCENCE; MICROSCOPY, CONFOCAL; POLYMERS; SEWAGE;

BACTERIA (MICROORGANISMS);

EID: 74449083629     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2009.08.006     Document Type: Review

References (172)

1. Adav S.S., and Lee D.J. Single-culture aerobic granules with Acinetobacter calcoaceticus. Appl Microbiol Biotechnol 78 (2008) 551-557
2. Adav S.S., Lee D.J., and Lai J.Y. Effects of aeration intensity on formation of phenol-fed aerobic granules and extracellular polymeric substances. Appl Microbiol Biotechnol 77 (2007) 175-182
3. Adav S.S., Lee D.J., and Ren N.Q. Biodegradation of pyridine using aerobic granules in the presence of phenol. Water Res 41 (2007) 2903-2910
4. Adav S.S., Lee D.J., and Tay J.H. Extracellular polymeric substances and structural stability of aerobic granule. Water Res 42 (2007) 644-650 2008
5. Adav S.S., Lee D.J., and Tay J.H. Activity and structure of stored aerobic granules. Environ Technol 28 (2007) 1227-1235
6. Adav S.S., Chang C.H., and Lee D.J. Hydraulic characteristics of aerobic granules using size exclusion chromatography. Biotechnol Bioeng 99 (2008) 791-799
7. Adav S.S., Lee D.J., and Lai J.Y. Intergeneric coaggregation of strains isolated from phenoldegrading aerobic granules. Appl Microbiol Biotechnol 79 (2008) 657-661
8. Adav S.S., Lee D.J., Show K.Y., and Tay J.H. Aerobic granular sludge: recent advances. Biotechnology Advances 26 (2008) 411-423
9. Adav S.S., Lee D.J., and Lai J.Y. Proteolytic activity in stored aerobic granular sludge and structural integrity. Bioresour Technol 100 (2009) 68-73
10. Allesen-Holm M., Barken K.B., Yang L., Klausen M., Webb J.S., Kjelleberg S., et al. A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms. Mol Microbiol 59 (2006) 1114-1128
11. Amann R.I. Fluorescently labelled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol Ecol 4 (1995) 543-554
12. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., and Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analysing mixed microbial populations. Appl Environ Microbiol 56 (1990) 1919-1925
13. Amann R., Snaidr J., Wagner M., Ludwig W., and Schleifer K.H. In situ visualization of high genetic diversity in a natural microbial community. J Bacteriol 178 (1996) 3496-3500
14. Amos W.B., and White J.G. How the confocal laser scanning microscope entered biological research. Biol Cell 95 (2003) 335-342
15. Ayol A., Filibeli A., Sir D., and Kuzyaka E. Aerobic and anaerobic bioprocessing of activated sludge: floc disintegration by enzymes. J Environ Sci Health A Tox Hazard Subst Environ Eng 43 (2008) 1528-1535
16. Ballou B., Fisher G.W., Deng J.S., Hakala T.R., Srivastava M., and Farkas D.L. Cyanine fluorochrome-labeled antibodies in vivo: assessment of tumor imaging using Cy3, Cy5, Cy5.5, and Cy7. Cancer Detect Prev 22 (1998) 251-257
17. Berod A., Hartman B.K., and Pujol J.F. Importance of fixation in immunohistochemistry. Use of formaldehyde solutions at variable pH for the localization of tyrosine hydroxylase. J Histochem Cytochem 29 (1981) 844-850
18. Blenkinsopp S.A., and Costerton J.W. Understanding bacterial biofilms. Trends Biotechnol 9 (1991) 138-143
19. Bockelmann U., Manz W., Neu T.R., and Szewzyk U. Investigation of lotic microbial aggregates by a combined technique of fluorescent in situ hybridization and lectin-binding-analysis. J Microbial Methods 49 (2002) 75-87
20. Boczar B.A., Begley W.M., and Larson R.J. Characterization of enzyme-activity in activated-sludge using rapid analyses for specific hydrolases. Water Environ Res 64 (1992) 792-797
21. Boessmann M., Staudt C., Neu T.R., Horn H., and Hempel D.C. Investigation and modeling of growth, structure, and oxygen penetration in particle supported biofilms. Chem Eng Technol 26 (2003) 219-222
22. Boessmann M., Neu T.R., Horn H., and Hempel D.C. Growth, structure and oxygen penetration in particle supported autotrophic biofilms. Water Sci Technol 49 (2004) 371-377
23. Brandtzaeg B.P. In: Bullock G.R., and Petrusz P. (Eds). Tissue preparation methods for immunohistochemistry. Techniques in immunocytochemistry vol. 1 (1982), Academic Press, London 1-75
24. Cammarota M.C., and Sant'Anna G.L. Metabolic blocking of exopolysaccharides synthesis: effects on microbial adhesion and biofilm accumulation. Biotechnol Lett 20 (1998) 1-4
25. Cerca N., Martins S., Sillankorva S., Jefferson K.K., Pier G.B., Oliveira R., et al. Effects of growth in the presence of subinhibitory concentrations of dichloroaxacillin on Staphylococcus epidermidis and Staphylococcus haemolyticus biofilms. Appl Environ Microbiol 71 (2005) 8677-8682
26. Chen M.J., Zhang Z., and Bott T.R. Direct measurement of the adhesive strength of biofilms in pipes by micromanipulation. Biotechnol Tech 12 (1998) 875-880
27. Chen M.Y., Lee D.J., Yang Z., and Peng X.F. Fluorescent staining for study of extracellular polymeric substances in membrane biofouling layers. Environ Sci Technol 40 (2006) 6642-6646
28. Chen M.Y., Lee D.J., and Tay J.H. Distribution of extracellular polymeric substances in aerobic granules. Appl Microbiol Biotechnol 73 (2007) 1463-1469
29. Chen M.Y., Lee D.J., and Tay J.H. Staining of extracellular polymeric substances and cells in bioaggregates. Appl Microbiol Biotechnol 75 (2007) 467-474
30. Chen H., Liu S., Yang F., Xue Y., and Wang T. The development of simultaneous partial nitrification, ANAMMOX and denitrification (SNAD) process in a single reactor for nitrogen removal. Bioresour Technol 100 (2009) 1548-1554
31. Chiu Z.C., Chen M.Y., Lee D.J., Tay S.T.L., Tay J.H., and Show K.Y. Diffusivity of oxygen in aerobic granules. Biotechnol Bioeng 94 (2006) 505-513
32. Chiu Z.C., Chen M.Y., Lee D.J., Wang C.H., and Lai J.Y. Oxygen diffusion in active layer of aerobic granule with step change in surrounding oxygen levels. Water Res 41 (2007) 884-892
33. Chiu Z.C., Chen M.Y., Lee D.J., Wang C.H., and Lai J.Y. Oxygen diffusion and consumption in active aerobic granules of heterogeneous structure. Appl Microbiol Biotechnol 75 (2007) 685-691
34. Chu C.P., and Lee D.J. Multiscale structures of biological flocs. Chem Eng Sci 59 (2004) 1875-1883
35. Chu C.P., Lee D.J., and Tay J.H. Floc model and intrafloc flow. Chem Eng Sci 60 (2005) 565-575
36. Confer D.R., and Logan B.E. Location of protein and polysaccharide hydrolytic activity in suspended and biofilm wastewater cultures. Water Res 32 (1998) 31-38
37. Connil N., Dousset X., Onno B., Pilet M.F., Breuil M.F., and Montel M.C. Enumeration of Carnobacterium divergens V41, Carnobacterium piscicola V1 and Lactobacillus brevis LB62 by in situ hybridisation-flow cytometry. Lett Appl Microbiol 27 (1998) 302-306
38. Costerton J.W., Irvin R.T., and Cheng K.J. The bacterial glycocalyx in nature and disease. Annu Rev Microbiol 35 (1981) 299-324
39. Cottrell M.T., and Kirchman D.L. Natural assemblages of marine Proteobacteria and numbers of the Cytophaga-Flavobacter cluster consuming low and high-molecular weight dissolved organic matter. Appl Environ Microbiol 66 (2000) 1692-1697
40. Dalton H.M., and March P.E. Molecular genetics of bacterial attachment and biofouling. Curr Opin Biotechnol 9 (1998) 252-255
41. Dar S.A., Yao L., van Dongen U., Gijs Kuenen J., and Muyzer G. Analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16S rRNA and dsrB genes as molecular markers. Appl Environ Microbiol 73 (2007) 594-604
42. De Beer D., O'Flaharty V., Thaveesri J., Lens P., and Verstraete W. Distribution of extracellular polysaccharides and flotation of anaerobic sludge. Appl Microbiol Biotechnol 46 (1996) 197-201
43. DeLong E.F., Wickham G.S., and Pace N.R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243 (1989) 1360-1363
44. Erlandsen S.L., Kristich C.J., Dunny G.M., and Wells C.L. High-resolution visualization of the microbial glycocalyx with low-voltage scanning electron microscopy: dependence on cationic dyes. J Histochem Cytochem 52 (2004) 1427-1435
45. Farber S.A., Pack M., Ho S.Y., Johnson I.D., Wagner D.S., Dosch R., et al. Genetic analysis of digestive physiology using fluorescent phospholipid receptors. Science 292 (2001) 1385-1388
46. Fazi S., Amalfitano S., Pernthaler J., and Puddu A. Bacterial communities associated with benthic organic matter in headwater stream microhabitats. Environ Microbiol 7 (2005) 1633-1640
47. Ferrari B.C., Tujula N., Stoner K., and Kjelleberg S. Catalyzed reporter deposition-fluorescence in situ hybridization allows for enrichment-independent detection of microcolony-forming soil bacteria. Appl Environ Microbiol 72 (2006) 918-922
48. Fowler S.D., and Greenspan P. Application of Nile red, a fluorescent hydrophobic probe, for the detection of neutral lipid deposits in tissue sections: comparison with oil red O. J Histochem Cytochem 33 (1985) 833-836
49. Friedman L., and Kolter R. Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix. J Bacteriol 186 (2004) 4457-4465
50. Frolund B., Palmgren R., Keiding K., and Nielsen P. Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Res 30 (1996) 1749-1758
51. Gerhardt P., Murray R.G.E., Wood W.A., and Krieg N.R. Methods for general and molecular bacteriology (1994), American Society for Microbiology, Washington, D.C
52. Goel R., Mino T., Satoh H., and Matsuo T. Comparison of hydrolytic enzyme systems in pure culture and activated sludge under different electron acceptor conditions. Water Sci Technol 37 (1998) 335-343
53. Goldberg J. Biofilms and antibiotic resistance: a genetic linkage. Trends Microbiol 10 (2002) 264
54. Gonzalez J.E., and Maher M.P. Ellular fluorescent indicators and voltage/ion probe reader (VIPR™): tools for ion channel and receptor drug discovery. Recept Channels 8 (2002) 283-295
55. Gonzalez J.E., and Tsien R.Y. Voltage sensing by fluorescence resonance energy transfer in single cells. Biophys J 69 (1995) 1272-1280
56. Gonzalez J.E., and Tsien R.Y. Improved indicators of cell membrane potential that use fluorescence resonance energy transfer. Chem Biol 4 (1997) 269-277
57. Griffiths G. Fine structure immunocytochemistry (1993), Springer-Verlag, New York
58. Heydorn A., Nielsen A.T., Hentzer M., Sternberg C., Givskov M., Ersboll B.K., et al. Quantification of biofilm structures by the novel computer program COMSTAT. Microbiol 146 (2000) 2395-2407
59. Heydorn A., Ersboll B.K., Hentzer M., Parsek M.R., Givskov M., and Molin S. Experimental reproducibility in flowchamber grown biofilms. Microbiology 146 (2000) 2409-2415
60. Heydorn A., Ersboll B.J., Kato J., Hentzer M., Parsek M.R., Tolker-Nielsen T., et al. Statistical analysis of Pseudomonas aeruginosa biofilm development: impact of mutations in genes involved in twitching motility, cell-to-cell signalling, and stationary-phase sigma factor expression. Appl Environ Microbiol 68 (2002) 2008-2017
61. Hogardt M., Trebesius K., Geiger A.M., Hornef M., Rosenecker J., and Heesemann J. Specific and rapid detection by fluorescent in situ hybridization of bacteria in clinical samples obtained from cystic fibrosis patients. J Clin Microbiol 38 (2000) 818-825
62. Jackson K.D., Starkey M., Kremer S., Parsek M.R., and Wozniak D.J. Identification of psl, a locus encoding a potential exopolysaccharide that is essential for Pseudomonas aeruginosa PAO1 biofilm formation. J Bacteriol 186 (2004) 4466-4475
63. Jang A., Yoon Y.H., Kim I.S., Kim K.S., and Bishop P.L. Character and evaluation of aerobic granules in sequencing batch reactor. J Biotechnol 105 (2003) 71-82
64. Jang A., Okabe S., Watanabe Y., Kim I., and Bishop P. Measurement of growth rate of ammonia oxidizing bacteria in partially submerged rotating biological contactor by fluorescent in situ hybridization (FISH). J Environ Sci Eng 4 (2005) 413-420
65. Jiang H.L., Tay J.H., Maszenan A.M., and Tay S.T.L. Bacterial diversity and function of aerobic granules engineered in a sequencing batch reactor for phenol degradation. Appl Environ Microbiol 70 (2004) 6767-6775
66. Jiang H.L., Tay J.H., and Tay S.T. Changes in structure, activity and metabolism of aerobic granules as a microbial response to high phenol loading. Appl Microbiol Biotechnol. 63 (2004) 602-608
67. Kang H.C., Fisher P.J., Prendergast F.G., and Haugland R.P. Bodipy: a novel fluorescein and NBD substitute. J Cell Biol 107 (1988) 34a
68. Kaufmann P., Pfefferkorn A., Teuber M., and Meile L. Identification and quantification of Bifidobacterium species isolated from food with genusspecific 16S rRNA-targeted probes by colony hybridization and PCR. Appl Environ Microbiol 63 (1997) 1268-1273
69. Kim H.Y., Yeon K.M., Lee C.H., Lee S., and Swaminathan T. Biofilm structure and extracellular polymeric substances in low and high dissolved oxygen membrane bioreactors. Sep Sci Technol 41 (2006) 1213-1230
70. Kjelleberg S., and Molin S. Is there a role for quorum sensing signals in bacterial biofilms?. Curr Opin Microbiol 5 (2002) 254-258
71. Kloeke F.V., and Geesey G.G. Localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs. Microb Ecol 38 (1999) 201-214
72. s-dependent gene expression in Pseudomonas fluorescens in soil. Appl Environ Microbiol 67 (2001) 3363-3370
73. Kolloffel B., Meile L., and Teuber M. Analysis of brevibacteria on the surface of gruyere cheese detected by in situ hybridisation and by colony hybridisation. Lett Appl Microbiol 29 (1999) 317-322
74. 1-acid glycoprotein for characterization of the progesterone binding site. Biochim Biophys Acta 420 (1976) 195-213
75. Lahtinen S.J., Gueimonde M., Ouwehand A.C., Reinikainen J.P., and Salminen S.J. Probiotic bacteria may become dormant during storage. Appl Environ Microbiol 71 (2005) 1662-1663
76. Larsson L.I. Immunocytochemistry: theory and practice (1988), CRC Press, Boca Raton
77. Larsson L.I. Tissue preparation methods for light microscopic immunohistochemistry. Appl Immunohistochem 1 (1993) 2-16
78. Laue H., Schenk A., Li H., Lambertsen L., Neu T.R., Molin S., et al. Contribution of alginate and levan production to biofilm formation by Pseudomonas syringae. Microbiology 152 (2006) 2909-2918
79. Lawrence T.R., Neu T.R., and Swerhone G.D.W. Application of multiple parameter imaging for the quantification of algae, bacterial, and exopolymer components of microbial biofilms. J Microbial Methods 32 (1998) 253-261
80. Lawrence J.R., Swerhone G.D.W., Leppard G.G., Araki T., Zhang X., West M.M., et al. Scanning transmission X-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofilms. Appl Environ Microbiol 69 (2003) 5543-5554
81. Lawrence J.R., Chenier M.R., Roy R., Beaumier D., Fortin N., Swerhone G.D.W., et al. Microscale and molecular assessment of impacts of nickel, nutrients, and oxygen level on structure and function of river biofilm communities. Appl Environ Microbiol 70 (2004) 4326-4339
82. Lawrence J.R., Swerhone G.D.W., Wassenaar L.I., and Neu T.R. Effects of selected pharmaceuticals on riverine biofilm communities. Can J Microbiol 51 (2005) 655-669
83. Lawrence J.R., Swerhone G.D., Kuhlicke U., and Neu T.R. In situ evidence for microdomains in the polymer matrix of bacterial microcolonies. Can J Microbiol 53 (2007) 450-458
84. Lee N., Nielsen P.H., Adersen K.H., Juretschko S., Nielsen J.L., Schleifer K.H., et al. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65 (1999) 1289-1297
85. Lee S.K., Lee J.Y., Lee M.Y., Chung S.M., and Chung J.H. Advantages of calcium green-1 over other fluorescent dyes in measuring cytosolic calcium in platelets. Anal Biochem 273 (1999) 186-191
86. Lee C.C., Lee D.J., and Lai J.Y. Amylase activity in substrate deficiency aerobic granules. Appl Microbiol Biotechnol 81 (2009) 961-967
87. Lee C.C., Lee D.J., and Lai J.Y. Labeling enzymes and extracellular polymeric substances in aerobic granules. J Taiwan Inst Chem Eng 40 (2009) 505-510
88. Lehtola M.J., Torvinen E., Miettinen I.T., and Keevil C.W. Fluorescence in situ hybridization using peptide nucleic acid probes for rapid detection of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis in potable-water biofilms. Appl Environ Microbiol 72 (2006) 848-853
89. Lemaire R., Webb R.I., and Yuan Z.G. Micro-scale observations of the structure of aerobic granules used for the treatment of nutrient-rich industrial wastewater. ISME J 2 (2008) 528-541
90. Li Y., and Liu Y. Diffusion of substrate and oxygen in aerobic granule. Biochem Eng J 27 (2005) 45-52
91. Lippincott-Schwartz J., and Patterson G. Development and use of fluorescent protein markers in living cells. Science 300 (2003) 87-91
92. Losekann T., Knittel K., Nadalig T., Fuchs B., Niemann H., Boetius A., et al. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 73 (2007) 3348-3362
93. Ma Y., Peng X.F., and Lee D.J. Stereological estimation of structural change in floc matrix following weak ultrasonication. J Chin Inst Chem Engrs 38 (2007) 275-280
94. Magnuson T.S., Neal A.L., and Geesey G.G. Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities. Microb Ecol 48 (2004) 578-588
95. Mao S.Y. Conjugation of fluorochromes to antibodies. methods in molecular biology. In: Vaces L.C. (Ed). Immunocytochemical Methods and Protocols (2008) 43-47 34
96. Massol-Deya A.A., Whallon J., Hickey R.F., and Tiedje J.M. Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl Environ Microbiol 61 (1995) 769-777
97. McSwain B.S., Irvine R.L., Hausner M., and Wilderer P.A. Composition and distribution of extracellular polymeric substances in aerobic flocs and granular sludge. Appl Environ Microbiol 71 (2005) 1051-1057
98. Michael T., and Smith C.M. Lectins probe molecular film in biofouling: characterization of early films on non-living and living surfaces. Mar Ecol Prog Ser 119 (1995) 229-236
99. Miyawaki A., Sawano A., and Kogure T. Lighting up cells: labeling proteins with fluorophores. Nat Cell Biol 5 (2003) S1-S7
100. Moller S., Pedersen A.R., Poulsen L.K., Arvin E., and Molin S. Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl Environ Microbiol 62 (1996) 4632-4640
101. Mook O.R., Van Overbeek C., Ackema E.G., Van Maldegem F., and Frederiks W.M. In situ localization of gelatinolytic activity in the extracellular matrix of metastages of colon cancer in rat liver using quenched fluorogenic DQ-gelatin. J Histochem Cytochem 51 (2003) 821-829
102. Moreno Y., Botella S., Alonso J.L., Ferrus M.A., Hernandez M., and Hernandez J. Specific detection of Arcobacter and Campylobacter strains in water and sewage by PCR and fluorescent in situ hybridization. Appl Environ Microbiol 69 (2003) 1181-1186
103. Mujumdar R.B., Ernst L.A., Mujumdar S.R., Lewis C.J., and Waggoner A.S. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjug Chem 4 (1993) 105-111
104. Murray J., Marusich M.F., Capaldi R.A., and Aggeler R. Focused proteomics: monoclonal antibody-based isolation of the oxidative phosphorylation machinery and detection of phosphoproteins using a fluorescent phosphoprotein gel stain. Electrophoresis 25 (2004) 2520-2525
105. Neu T.R. Significance of bacterial surface-active compounds in interaction of bacteria with interfaces. Microbiol Rev 60 (1996) 151-166
106. Neu T.R. In situ cell and glycoconjugate distribution in river snow studied by confocal laser scanning microscopy. Aquat Microb Ecol 21 (2000) 85-95
107. Neu T.R., and Lawrence J.R. Development and structure of microbial biofilms in river water studied by confocal laser scanning microscopy. FEMS Microbiol Immunol 24 (1997) 11-25
108. Neu T., Swerhone G.D., and Lawrence J.R. Assessment of lectin-binding analysis for in situ detection of glycoconjugates in biofilm systems. Microbiology 147 (2001) 299-313
109. Neu T.R., Kuhlicke U., and Lawrence J.R. Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms. Appl Environ Microbiol 68 (2002) 901-909
110. Neu T.R., Woelfl S., and Lawrence J.R. Three-dimensional differentiation of photo-autotrophic biofilm constituents by multi-channel laser scanning microscopy (single-photon and two-photon excitation). J Microbiol Methods 56 (2004) 161-172
111. Nielsen P.H., and Jahn A. Extraction of EPS, p. 50-72. In: Wingender J., Neu T.R., and Flemming H.-C. (Eds). Microbial extracellular polymeric substances: characterization, structure, and function (1999), Springer-Verlag, Berlin, Germany 21-47
112. Nielsen P.H., Raunkjaer K., Norsker N.H., Jensen N.A., and Hvitved-Jacobsen T. Transformation of wastewater in sewer systems - a review. Water Sci Technol 25 (1992) 17-31
113. Nielsen P.H., Frolund B., and Keiding K. Changes in the composition of extracellular polymeric substances in activated sludge during anaerobic storage. Appl Microbiol Biotechnol 44 (1996) 823-830
114. Nielsen P.H., Roslev P., Dueholm T.E., and Nielsen J.L. Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. Water Sci Technol 46 (2002) 73-80
115. Nivens D.E., Ohman D.E., Williams J., and Franklin M.J. Role of alginate and its O acetylation in formation of Pseudomonas aeruginosa microcolonies and biofilms. J Bacteriol 183 (2001) 1047-1057
116. Nosyk O., Haseborg E.T., Metzger U., and Frimmel F.H. A standardized pre-treatment method of biofilm flocs for fluorescence microscopic characterization. J Microbiol Methods 75 (2008) 449-456
117. Nybroe O., Jorgensen P.E., and Henze M. Enzyme-activities in waste-water and activated-sludge. Water Res 26 (1992) 579-584
118. Okabe S., Satoh H., and Watanabe Y. In situ analysis of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes. Appl Environ Microbiol 65 (1999) 3182-3191
119. Ouverney C.C., and Fuhrman J.A. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65 (1999) 1746-1752
120. Panchuk-Voloshina N., Haugland R.P., Bishop-Stewart J., Bhalgat M.K., Millard P.J., Mao F., et al. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J Histochem Cytochem 47 (1999) 1179-1188
121. Peng J.S., Tsai W.C., and Chou C.C. Inactivation and removal of Bacillus cereus by sanitizer and detergent. Int J Food Microbiol 77 (2002) 11-18
122. Pernthaler A., Pernthaler J., and Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68 (2002) 3094-3101
123. Picioreanu C., van Loosdrecht M.C.M., and Heijnen J.J. Mathematical modeling of biofilm structure with a hybrid differential-discreet cellular automata approach. Biotechnol Bioeng 58 (1998) 101-116
124. Poppert S., Essig A., Stoehr B., Steingruber A., Wirths B., Juretschko S., et al. Rapid diagnosis of bacterial meningitis by real-time PCR and fluorescence in situ hybridization. J Clin Microbiol 43 (2005) 3390-3397
125. Puchtler H., and Meloan S.N. On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. Histochemistry 82 (1985) 201-204
126. Recktenwald M., Wawrzynczyk J., Dey E.S., and Norrlow O. Enhanced efficiency of industrial-scale anaerobic digestion by the addition of glycosidic enzymes. J Environ Sci Health 43 (2008) 1536-1540
127. Ren T.T., Liu L., Sheng G.P., Liu X.W., Yu H.Q., Zhang M.C., et al. Calcium spatial distribution in aerobic granules and its effects on granule structure, strength and bioactivity. Water Res 42 (2008) 3343-3352
128. Ross W.R. The phenomenon of sludge pelletizationin in the anaerobic treatment of a maize processing waste. Water SA 10 (1984) 197-204
129. Sarkisova S., Patrauchan M.A., Berglund D., Nivens D.E., and Franklin M.J. Calcium-induced virulence factors associated with the extracellular matrix of mucoid Pseudomonas aeruginosa biofilms. J Bacteriol 187 (2005) 4327-4337
130. Sato K., and Anzai J. Fluorometric determination of sugars using fluorescein-labeled concanavalin A-glycogen conjugates. Anal Bioanal Chem 384 (2006) 1297-1301
131. Schmid M., Twachtmann U., Klein M., Strous M., Juretschko S., Jetten M., et al. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst Appl Microbiol 23 (2000) 93-106
132. Schmid M., Thill A., Purkhold U., Walcher M., Bottero J.Y., Ginestet P., et al. Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis. Water Res 37 (2003) 2043-2052
133. Schmidt J.E., and Ahring B.K. Extracellular polymers in granular sludge from different upflow anaerobic sludge blanket (UASB) reactors. Appl Microbiol Biotechnol 42 (1994) 457-462
134. Schramm A., Larsen L.H., Revsbech N.P., Amann R.I., and Schleifer K.H. Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Appl Environ Microbiol 62 (1996) 641-647
135. Schramm A., de Beer D., Wagner M., and Amann R.I. Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl Environ Microbiol 64 (1998) 3480-3485
136. Sekar R., Griebe T., and Flemming H.C. Influence of image acquisition parameters on quantitative measurement of biofilms using confocal laser scanning microscopy. Biofouling 18 (2002) 47-56
137. Seveus L., Vaisala M., Hammlia I., Kojola H., Roomans G.M., and Soini E. Use of fluorescent Europium chelates as labels in microscopy allows glutaraldehyde fixation and permanent mounting and leads to reduced autofluorescence and good long-term stability. Microsc Res Techn 28 (1994) 149-154
138. Shen C.F., Kosaric N., and Blaszczyk R. The effect of selected heavy metals (Ni, Co and Fe) on anaerobic granules and their extracellular polymeric substance (EPS). Water Res 27 (1993) 25-33
139. Sohier D., and Lonvaud-Funel A. Rapid and sensitive in situ hybridization method for detecting and identifying lactic acid bacteria in wine. Food Microbiol 15 (1998) 391-397
140. Staudt C., Horn H., Hempel D.C., and Neu T.R. Volumeric measurements of bacterial cells and extracellular polymeric substance glycoconjugates in biofilms. Biotechnol Bioeng 88 (2004) 585-592
141. Strathmann M., Wingender J., and Flemming H.C. Application of fluorescently labelled lectins for the visualization and biochemical characterization of polysaccharides in biofilms of Pseudomonas aeruginosa. J. Microbiol. Methods 50 (2002) 237-248
142. Strathmann M., Wingender J., and Flemming H.C. Application of fluorescently labeled lectins for the visualization and biochemical characteristics of polysaccharides in biofilm of Pseudomonas aeruginosa. J Microbiol Methods 50 (2003) 237-248
143. Takeda M., Nakano F., Nagase T., Iohara K., and Koizumi J.I. Isolation and chemical composition of the sheath of Sphaerotilus natans. Biosci Biotechnol Biochem 62 (1998) 1138-1143
144. Tay J.H., Yang S.F., and Liu Y. Hydraulic selection pressure-induced nitrifying granulation in sequencing batch reactors. Appl Microbiol Biotechnol 59 (2002) 332-337
145. Teuber M., and Brodisch K.E.U. Enzymatic-activities of activated-sludge. Eur J Appl Microbiol 4 (1977) 185-194
146. Thurnheer T., Gmur R., and Guggenheim B. Multiplex FISH analysis of a six-species bacterial biofilm. J Microbiol Methods 56 (2004) 37-47
147. Tsai M.W., Lee D.J., and Lai J.Y. Mass transfer limit of fluorescent dyes during multicolor staining of aerobic granules. Appl Microbiol Biotechnol 78 (2008) 907-913
148. Tsien R.Y. Fluorescent indicators of ion concentrations. Methods Cell Biol 30 (1989) 127-156
149. Tsien R.Y. Building and breeding molecules to spy on cells and tumors. FEBS Letts 579 (2005) 927-932
150. Vereb G., Jares-Erijman E., Selvin P.R., and Jovin T.M. Temporally and spectrally resolved imaging microscopy of lanthanide chelates. Biophys J 74 (1998) 2210-2222
151. Vesey G., Ashbolt N., Fricker E.J., Deere D., Williams K.L., Veal D.A., et al. The use of ribosomal rRNA targeted oligonucleotide probes for fluorescent labeling viable Cryptosporidium oocysts. J Appl Microbiol 85 (1999) 429-440
152. Wallner G., Amann R.I., and Beisker W. Optimising fluorescent in-situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14 (1993) 136-143
153. Wallner G., Erhart R., and Amann R. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl Environ Microbiol 61 (1995) 1859-1866
154. Wang Z.W., Liu Y., and Tay J.H. Distribution of EPS and cell surface hydrophobicity in aerobic granules. Appl Microbiol Biotechnol 69 (2005) 469-473
155. Wanner O., and Gujer P. A multispecies biofilm model. Biotechnol Bioeng 47 (1985) 172-184
156. Wessendorf M.W., and Brelje T.C. Which fluorophore is brightest? A comparison of staining obtained using fluorescein, tetramethylrhodamine,lissmine rhodamine. Texas red and cynine 3.18. Histchemistry 98 (1992) 81-85
157. Whitchurch C.B., Tolker-Nielsen T., Ragas P.C., and Mattick J.S. Extracellular DNA required for bacterial biofilm formation. Science 295 (2002) 1487
158. Whiteley CG, Lee DJ. Enzymology of sludge-floc degradation using confocal laser scanning microscopy: an enzyme-floc model. Focus on Biotechnology Research, Chap. 7, pp. 213-133. EC HEarns Ed. Nova Pub, USA. ISBN: 1-59454-863-3. (2006).
159. Wories H.J., Koek J.H., Lodder G., Lugtenburg J., Fokkens R., Driessen O., et al. A novel water soluble fluorescent probe: synthesis, luminescence and biological properties of the sodium salt of the 4-sulfonato-3, 3′5, 5′-tetramethyl-2, 2′-pyrromethene-1, 1′-BF2 complex. Recl Trav Chim Pays-Bas. 104 (1985) 280-291
160. Wu X., Liu H., Liu J., Haley K.N., Treadway J.A., Larson J.P., et al. Immonofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots. Nat Biotechnol 21 (2003) 41-46
161. Xia Y., Kong Y., and Nielsen P.H. In situ detection of protein-hydrolysing microorganisms in activated sludge. FEMS Microbiol Ecol 60 (2007) 156-165
162. Xia Y., Kong Y., and Nielsen P.H. In situ detection of starch-hydrolyzing microorganisms in activated sludge. FEMS Microbiol Ecol 66 (2008) 462-471
163. Xu K.D., McFeters G.A., and Stewart P.S. Biofilm resistance to antimicrobial agents. Microbiology 146 (2000) 547-549
164. Yang Z., Peng X.F., Lee D.J., and Su A. Advective flow in spherical floc. J Colloid Interf Sci 308 (2007) 451-459
165. Yang Z., Peng X.F., Chen M.Y., Lee D.J., and Lai J.Y. Intra-layer flow in fouling layer on membranes. J Membr Sci 297 (2007) 280-286
166. Yang Z., Peng X.F., Lee D.J., and Su A. Reynolds-number-dependent permeability of wastewater sludge flocs. J Chin Inst Chem Engrs 38 (2007) 135-141
167. Yang Z., Lee D.J., Mujumdar A.S., Peng X.F., Su A., and Hsu C. Probing heterogeneous structure of aggregates. Drying Technol 26 (2008) 1018-1023
168. Yip K.P., and Kurtz I. Confocal fluorescence microscopy measurements of pH and calcium in living cells. Methods Cell Biol 70 (2002) 417-427
169. Yoshioka T., Hikita I., Matsutani T., Yoshida R., Asakawa M., Toyosaki-Maeda T., et al. DS-Nh as an experimental model of atopic dermatitis induced by Staphylococcus aureus producing staphylococcal enterotoxin C. Immunology 108 (2003) 562-569
170. Zhang J., Campbell R.E., Ting A.Y., and Tsien R.Y. Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3 (2002) 906-918
171. Zhang Z.P., Adav S.S., Show K.Y., Tay J.H., Liang D.T., Lee D.J., et al. Characteristics of rapidly formed hydrogen-producing granules and biofilms. Biotechnol Bioeng 101 (2008) 926-936
172. Zimmer M. Green fluorescent protein: applications, structure, and related photophysical behavior. Chem Rev 102 (2002) 759-781