Skip to main content
SpringerLink
Log in

Advanced Microscopy of Microbial Cells

  • Chapter
  • First Online:
High Resolution Microbial Single Cell Analytics

Part of the book series: Advances in Biochemical Engineering / Biotechnology ((ABE,volume 124))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

AFM:

Atomic force microscope

AOBS:

Acousto-optical beam splitter

AOTF:

Acousto-optical tunable filter

CARS:

Coherent anti-Stokes Raman spectroscopy

CFP:

Cyan fluorescent protein

CLSM:

Confocal laser scanning microscope

EPS:

Extracellular polymeric substance

FRAP:

Fluorescence recovery after photobleaching

GFP:

Green fluorescent protein

MP:

Multi photon

NA:

Numerical aperture

PALM:

Photo-activated localization microscopy

PE:

Polyethylene

PI:

Propidium iodide

PMT:

Photo multiplier

PP:

Polypropylene

PVC:

Polyvinyl chloride

SIM:

Structured illumination microscopy

SERS:

Surface enhanced Raman spectroscopy

STED:

Stimulated emission depletion

TERS:

Tip enhanced Raman spectroscopy

STORM:

Stochastic optical reconstruction microscopy

YFP:

Yellow fluorescent protein

References

  1. Abbe E (1873) Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung. Arch Mikrosk Anat 9:413–468

    Google Scholar 

  2. Abràmoff MD, Magalhães PJ, Ram SJ (2004) Image processing with ImageJ. Biophotonics Int 11:36–41

    Google Scholar 

  3. Alfano RR, Shapiro SL (1970) Direct distortion of electronic clouds of rare-gas atoms in intense electric fields. Phys Rev Lett 24:1217

    CAS  Google Scholar 

  4. Alfano RR, Shapiro SL (1970) Observation of self-phase modulation and small-scale filaments in crystals and glasses. Phys Rev Lett 24:592

    CAS  Google Scholar 

  5. Amro NA, Kotra LP, Wadu-Mesthrige K et al (2000) High-resolution atomic force microscopy studies of the Escherichia coli outer membrane: structural basis for permeability. Langmuir 16:2789–2796

    CAS  Google Scholar 

  6. Baillie GS, Douglas LJ (1999) Role of dimorphism in the development of Candida albicans biofilms. J Med Microbiol 48:671–679

    CAS  Google Scholar 

  7. Balaban NQ, Merrin J, Chait R et al (2004) Bacterial persistence as a phenotypic switch. Science 305:1622–1625

    CAS  Google Scholar 

  8. Ball CS (1966) The early history of the compound microscope. Bios 37:51–60

    Google Scholar 

  9. Barken KB, Pamp SJ, Yang L et al (2008) Roles of type IV pili, flagellum-mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms. Environ Microbiol 10:2331–2343

    CAS  Google Scholar 

  10. Bates M, Huang B, Dempsey GT et al (2007) Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317:1749–1753

    CAS  Google Scholar 

  11. Begley RF, Harvey AB, Byer RL (1974) Coherent anti-Stokes Raman spectroscopy. Appl Phys Lett 25:387–390

    CAS  Google Scholar 

  12. Bertrand E, Chartrand P, Schaefer M et al (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437–445

    CAS  Google Scholar 

  13. Betzig E, Patterson GH, Sougrat R et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

    CAS  Google Scholar 

  14. Beyenal H, Donovan C, Lewandowski Z et al (2004) Three-dimensional biofilm structure quantification. J Microbiol Methods 59:395–413

    CAS  Google Scholar 

  15. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930

    Google Scholar 

  16. Birk H, Engelhardt J, Storz R et al (2002) Programmable beam-splitter for confocal laser scanning microscopy. In: Three-dimensional and multidimensional microscopy: image acquisition and processing, vol IX. SPIE, San Jose

    Google Scholar 

  17. Bolshakova AV, Kiselyova OI, Filonov AS et al (2001) Comparative studies of bacteria with an atomic force microscopy operating in different modes. Ultramicroscopy 86:121–128

    CAS  Google Scholar 

  18. Borlinghaus R, Gugel H, Albertano P et al (2006) Closing the spectral gap: the transition from fixed-parameter fluorescence to tunable devices in confocal microscopy. In: Three-dimensional and multidimensional microscopy: image acquisition and processing, vol XIII. SPIE, San Jose

    Google Scholar 

  19. Braga PC, Ricci D (1998) Atomic force microscopy: application to investigation of Escherichia coli morphology before and after exposure to cefodizime. Antimicrob Agents Chemother 42:18–22

    CAS  Google Scholar 

  20. Budich C, Neugebauer U, Popp J et al (2008) Cell wall investigations utilizing tip-enhanced Raman scattering. J Microsc 229:533–539

    CAS  Google Scholar 

  21. Caldwell DE, Korber DR, Lawrence JR (1992) Imaging of bacterial cells by fluorescence exclusion using scanning confocal laser microscopy. J Microbiol Methods 15:249–261

    Google Scholar 

  22. Camesano TA, Natan MJ, Logan BE (2000) Observation of changes in bacterial cell morphology using tapping mode atomic force microscopy. Langmuir 16:4563–4572

    CAS  Google Scholar 

  23. Carreira LA, Goss LP, Malloy TB Jr (1981) Applications of CARS to condensed phase systems. In: Harvey AB (ed) Chemical applications of nonlinear Raman spectroscopy. Academic Press, New York

    Google Scholar 

  24. Chai Y, Chu F, Kolter R et al (2008) Bistability and biofilm formation in Bacillus subtilis. Mol Microbiol 67:254–263

    CAS  Google Scholar 

  25. Chan JW, Winhold H, Lane SM et al (2005) Optical trapping and coherent anti-Stokes Raman scattering (CARS) spectroscopy of submicron-size particles. Sel Top Quantum Electron J IEEE 11:858–863

    CAS  Google Scholar 

  26. Chandra J, Kuhn DM, Mukherjee PK et al (2001) Biofilm formation by the fungal pathogen Candida albicans: development, architecture, and drug resistance. J Bacteriol 183: 5385–5394

    CAS  Google Scholar 

  27. Chatterjee A, Kaznessis YN, Hu WS (2008) Tweaking biological switches through a better understanding of bistability behavior. Curr Opin Biotechnol 19:475–481

    CAS  Google Scholar 

  28. Christensen BB, Sternberg C, Andersen JB et al (1999) Molecular tools for study of biofilm physiology. Methods Enzymol 310:20–42

    CAS  Google Scholar 

  29. Costerton JW, Lewandowski Z, DeBeer D et al (1994) Biofilms, the customized microniche. J Bacteriol 176:2137–2142

    CAS  Google Scholar 

  30. Costerton JW (1995) Overview of microbial biofilms. J Ind Microbiol 15:137–140

    CAS  Google Scholar 

  31. Costerton JW, Lewandowski Z, Caldwell DE et al (1995) Microbial biofilms. Annu Rev Microbiol 49:711–745

    CAS  Google Scholar 

  32. Costerton JW (1999) Introduction to biofilm. Int J Antimicrob Agents 11:217–221

    CAS  Google Scholar 

  33. Czechowska K, Johnson DR, van dM Jr (2008) Use of flow cytometric methods for single-cell analysis in environmental microbiology. Curr Opin Microbiol 11:205–212

    Google Scholar 

  34. Daims H, Lucker S, Wagner M (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8:200–213

    CAS  Google Scholar 

  35. Davidson CJ, Surette MG (2008) Individuality in bacteria. Annu Rev Genet 42:253–268

    CAS  Google Scholar 

  36. Denk W, Strickler JH, Webb WW (1990) Two-photon laser scanning fluorescence microscopy. Science 248:73–76

    CAS  Google Scholar 

  37. Dubnau D (1991) The regulation of genetic competence in Bacillus subtilis. Mol Microbiol 5:11–18

    CAS  Google Scholar 

  38. Dubnau D (1991) Genetic competence in Bacillus subtilis. Microbiol Rev 55:395–424

    CAS  Google Scholar 

  39. Dubnau D, Losick R (2006) Bistability in bacteria. Mol Microbiol 61:564–572

    CAS  Google Scholar 

  40. Dyba M, Keller J, Hell SW (2005) Phase filter enhanced STED-4pi fluorescence microscopy: theory and experiment. New J Phys 134:1–21

    Google Scholar 

  41. Egner A, Jakobs S, Hell SW (2002) Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast. Proc Natl Acad Sci USA 99:3370–3375

    CAS  Google Scholar 

  42. Eklund H, Roos A, Eng ST (1975) Rotation of laser beam polarization in acousto-optic devices. Opt Quant Electron 7:73–79

    Google Scholar 

  43. Fichtner L, Schulze F, Braus GH (2007) Differential Flo8p-dependent regulation of FLO1 and FLO11 for cell-cell and cell-substrate adherence of S. cerevisiae S288c. Mol Microbiol 66:1276–1289

    CAS  Google Scholar 

  44. Gad M, Ikai A (1995) Method for immobilizing microbial cells on gel surface for dynamic AFM studies. Biophys J 69:2226–2233

    CAS  Google Scholar 

  45. Giaever G, Chu AM, Ni L et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391

    CAS  Google Scholar 

  46. Gimeno CJ, Ljungdahl PO, Styles CA et al (1992) Unipolar cell divisions in the yeast Saccharomyces-Cerevisiae lead to filamentous growth—regulation by starvation and Ras. Cell 68:1077–1090

    CAS  Google Scholar 

  47. Gonzalez-Pastor JE, Hobbs EC, Losick R (2003) Cannibalism by sporulating bacteria. Science 301:510–513

    CAS  Google Scholar 

  48. Gustafsson MGL (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198:82–87

    CAS  Google Scholar 

  49. Gustafsson MGL (2005) Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci USA 102:13081–13086

    CAS  Google Scholar 

  50. Guthold M, Bezanilla M, Erie DA et al (1994) Following the assembly of RNA polymerase–DNA complexes in aqueous solutions with the scanning force microscope. Proc Natl Acad Sci USA 91:12927–12931

    CAS  Google Scholar 

  51. Göppert-Mayer M (1931) Über Elementarakte mit zwei Quantensprüngen. Ann Phys 401:273–294

    Google Scholar 

  52. Hahn J, Kong L, Dubnau D (1994) The regulation of competence transcription factor synthesis constitutes a critical control point in the regulation of competence in Bacillus subtilis. J Bacteriol 176:5753–5761

    CAS  Google Scholar 

  53. Haim L, Zipor G, Aronov S et al (2007) A genomic integration method to visualize localization of endogenous mRNAs in living yeast. Nat Methods 4:409–412

    CAS  Google Scholar 

  54. Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2:95–108

    CAS  Google Scholar 

  55. Hallett P, Offer G, Miles MJ (1995) Atomic-force microscopy of the myosin molecule. Biophys J 68:1604–1606

    CAS  Google Scholar 

  56. Hansma HG, Vesenka J, Siegerist C et al (1992) Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope. Science 256:1180–1184

    CAS  Google Scholar 

  57. Harke B, Keller J, Ullal CK et al (2008) Resolution scaling in STED microscopy. Opt Express 16:4154–4162

    Google Scholar 

  58. Harz M, Rösch P, Peschke KD et al (2005) Micro-Raman spectroscopic identification of bacterial cells of the genus Staphylococcus and dependence on their cultivation conditions. Analyst 130:1543–1550

    CAS  Google Scholar 

  59. Harz M, Rösch P, Popp J (2009) Vibrational spectroscopy—a powerful tool for the rapid identification of microbial cells at the single-cell level. Cytometry Part A 75A:104–113

    CAS  Google Scholar 

  60. Heimstädt O (1911) Das Fluoreszenzmikroskop. Z Wiss Mikrosk 28:330–337

    Google Scholar 

  61. Hein B, Willig KI, Hell SW (2008) Stimulated emission depletion (STED) nanoscopy of a fluorescent protein-labeled organelle inside a living cell. Proc Natl Acad Sci USA 105:14271–14276

    CAS  Google Scholar 

  62. Heintzmann R, Jovin TM, Cremer C (2002) Saturated patterned excitation microscopy? A concept for optical resolution improvement. J Opt Soc Am A 19:1599–1609

    Google Scholar 

  63. Hell SW (2003) Toward fluorescence nanoscopy. Nat Biotechnol 21:1347–1355

    CAS  Google Scholar 

  64. Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258–4272

    CAS  Google Scholar 

  65. Heydorn A, Nielsen AT, Hentzer M et al (2000) Quantification of biofilm structures by the novel computer program COMSTAT. Microbiol 146(10):2395–2407

    CAS  Google Scholar 

  66. Hirvonen L, Wicker K, Mandula O et al (2009) Structured illumination microscopy of a living cell. Eur Biophys J 38:807–812

    Google Scholar 

  67. Hopt A, Neher E (2001) Highly nonlinear photodamage in two-photon fluorescence microscopy. Biophys J 80:2029–2036

    CAS  Google Scholar 

  68. Huang B, Wang W, Bates M et al (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–813

    CAS  Google Scholar 

  69. Huang G, Wang H, Chou S et al (2006) Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc Natl Acad Sci USA 103:12813–12818

    CAS  Google Scholar 

  70. Huang W, Ude S, Spiers A (2007) Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles. Microb Ecol 53:471–474

    CAS  Google Scholar 

  71. Huh WK, Falvo JV, Gerke LC et al (2003) Global analysis of protein localization in budding yeast. Nature 425:686–691

    CAS  Google Scholar 

  72. Haagensen JA, Klausen M, Ernst RK et al (2007) Differentiation and distribution of colistin- and sodium dodecyl sulfate-tolerant cells in Pseudomonas aeruginosa biofilms. J Bacteriol 189:28–37

    CAS  Google Scholar 

  73. Jarvis RM, Brooker A, Goodacre R (2006) Surface-enhanced Raman scattering for the rapid discrimination of bacteria. Faraday Discuss 132:281–292

    CAS  Google Scholar 

  74. Jarvis RM, Goodacre R (2008) Characterisation and identification of bacteria using SERS. Chemi Soc Rev 37:931–936

    CAS  Google Scholar 

  75. Jeanmaire DL, Van Duyne RP (1977) Surface Raman spectroelectrochemistry: Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode. J Electroanal Chem 84:1–20

    CAS  Google Scholar 

  76. Juette MF, Gould TJ, Lessard MD et al (2008) Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat Methods 5:527–529

    CAS  Google Scholar 

  77. Kasas S, Ikai A (1995) A method for anchoring round shaped cells for atomic force microscope imaging. Biophys J 68:1678–1680

    CAS  Google Scholar 

  78. Kearns DB, Losick R (2005) Cell population heterogeneity during growth of Bacillus subtilis. Genes Dev 19:3083–3094

    CAS  Google Scholar 

  79. Klar TA, Jakobs S, Dyba M et al (2000) Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc Natl Acad Sci USA 97:8206–8210

    CAS  Google Scholar 

  80. Klausen M, Aaes-Jorgensen A, Molin S et al (2003) Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms. Mol Microbiol 50:61–68

    CAS  Google Scholar 

  81. Knight JC, Birks TA, Russell PSJ et al (1996) All-silica single-mode optical fiber with photonic crystal cladding. Opt Lett 21:1547–1549

    CAS  Google Scholar 

  82. Kolter R, Greenberg EP (2006) Microbial sciences: the superficial life of microbes. Nature 441:300–302

    CAS  Google Scholar 

  83. König K (2000) Multiphoton microscopy in life sciences. J Microsc 200:83–104

    Google Scholar 

  84. Lal P, Sharma D, Pruthi P et al (2009) Exopolysaccharide analysis of biofilm-forming Candida albicans. J Appl Microbiol 109:128–136

    Google Scholar 

  85. Lawrence JR, Korber DR, Hoyle BD et al (1991) Optical sectioning of microbial biofilms. J Bacteriol 173:6558–6567

    CAS  Google Scholar 

  86. Le CE, Frechon D, Barray M et al (1994) Observation of binding and polymerization of Fur repressor onto operator-containing DNA with electron and atomic force microscopes. Proc Natl Acad Sci USA 91:11816–11820

    Google Scholar 

  87. Lewandowski Z, Beyenal H (2007) Fundamentals of biofilm research. CRC Press, Boca Raton

    Google Scholar 

  88. Liu H (2001) Transcriptional control of dimorphism in Candida albicans. Curr Opin Microbiol 4:728–735

    CAS  Google Scholar 

  89. Minsky M (1988) Memoir on inventing the confocal scanning microscope. Scanning 10:128–138

    Google Scholar 

  90. Müller M, Zumbusch A (2007) Coherent anti-Stokes Raman scattering microscopy. Chem Phys Chem 8:2156–2170

    Google Scholar 

  91. Müller S, Nebe-von-Caron G (2010) Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol Rev 34:554–587

    Google Scholar 

  92. Maamar H, Dubnau D (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 56:615–624

    CAS  Google Scholar 

  93. Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317:526–529

    CAS  Google Scholar 

  94. Naumann D, Keller S, Helm D et al (1995) FT-IR spectroscopy and FT-Raman spectroscopy are powerful analytical tools for the non-invasive characterization of intact microbial cells. J Mol Struct 347:399–405

    CAS  Google Scholar 

  95. Neu TR, Walczysko P, Lawrence JR (2004) Two-photon imaging for studying the microbial ecology of biofilm systems. Microbes Environ 19:1–6

    Google Scholar 

  96. Neu TR, Lawrence JR (2005) One-photon versus two-photon laser scanning microscopy and digital image analysis of microbial biofilms. Methods Microbiol 34:89–136

    Google Scholar 

  97. Neu TR, Manz B, Volke F et al (2010) Advanced imaging techniques for assessment of structure, composition and function in biofilm systems. FEMS Microbiol Ecol 72:1–21

    CAS  Google Scholar 

  98. Neugebauer U, Rösch P, Schmitt M et al (2006) On the way to nanometer-sized information of the bacterial surface by tip-enhanced Raman spectroscopy. Chem Phys Chem 7:1428–1430

    CAS  Google Scholar 

  99. Neugebauer U, Schmid U, Baumann K et al (2006) Characterization of bacterial growth and the influence of antibiotics by means of UV resonance Raman spectroscopy. Biopolymers 82:306–311

    CAS  Google Scholar 

  100. Neugebauer U, Schmid U, Baumann K et al (2007) Towards a detailed understanding of bacterial metabolism—spectroscopic characterization of Staphylococcus epidermidis. Chem Phys Chem 8:124–137

    CAS  Google Scholar 

  101. Newman JR, Ghaemmaghami S, Ihmels J et al (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441:840–846

    CAS  Google Scholar 

  102. Pamp SJ, Gjermansen M, Johansen HK et al (2008) Tolerance to the antimicrobial peptide colistin in Pseudomonas aeruginosa biofilms is linked to metabolically active cells, and depends on the pmr and mexAB-oprM genes. Mol Microbiol 68:223–240

    CAS  Google Scholar 

  103. Pamp SJ, Sternberg C, Tolker-Nielsen T (2009) Insight into the microbial multicellular lifestyle via flow-cell technology and confocal microscopy. Cytometry Part A 75A: 90–103

    Google Scholar 

  104. Patterson GH, Betzig E, Lippincott-Schwartz J et al (2007) Devloping Photoactivated Localization Microscopy (PALM). In: 4th IEEE international symposium on biomedical imaging: from nano to macro, ISBI 2007

    Google Scholar 

  105. Pavani SRP, Thompson MA, Biteen JS et al (2009) Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc Natl Acad Sci USA 106:2995–2999

    CAS  Google Scholar 

  106. Pätzold R, Keuntje M, Anders-von Ahlften A (2006) A new approach to non-destructive analysis of biofilms by confocal Raman microscopy. Anal Bioanal Chem 386:286–292

    Google Scholar 

  107. Radmacher M, Fritz M, Hansma HG et al (1994) Direct observation of enzyme-activity with the atomic-force microscope. Science 265:1577–1579

    CAS  Google Scholar 

  108. Ramage G, Mowat E, Jones B et al (2009) Our current understanding of fungal biofilms. Crit Rev Microbiol 35:340–355

    CAS  Google Scholar 

  109. Reynolds TB, Fink GR (2001) Bakers’ yeast, a model for fungal biofilm formation. Science 291:878–881

    CAS  Google Scholar 

  110. Rikkerink EH, Magee BB, Magee PT (1988) Opaque-white phenotype transition: a programmed morphological transition in Candida albicans. J Bacteriol 170:895–899

    CAS  Google Scholar 

  111. Rittweger E, Han KY, Irvine SE et al (2009) STED microscopy reveals crystal colour centres with nanometric resolution. Nat Photon 3:144–147

    CAS  Google Scholar 

  112. Robichon D, Girard J-C, Cenatiempo Y et al (1999) Atomic force microscopy imaging of dried or living bacteria. Comptes Rendus de l’Académie des Sciences - Series III - Sciences de la Vie 322:687–693

    CAS  Google Scholar 

  113. Rosch P, Harz M, Schmitt M et al (2005) Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations. Appl Environ Microbiol 71:1626–1637

    Google Scholar 

  114. Ruska E (1987) The development of the electron microscope and of electron microscopy. Rev Mod Phys 59:627

    CAS  Google Scholar 

  115. Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–796

    CAS  Google Scholar 

  116. Sandt C, Smith Palmer T, Pink J et al (2008) Quantification of local water and biomass in wild type PA01 biofilms by confocal Raman microspectroscopy. J Microbiol Methods 75:148–152

    CAS  Google Scholar 

  117. Schabert FA, Engel A (1994) Reproducible acquisition of Escherichia coli porin surface topographs by atomic force microscopy. Biophys J 67:2394–2403

    CAS  Google Scholar 

  118. Schermelleh L, Carlton PM, Haase S et al (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320:1332–1336

    CAS  Google Scholar 

  119. Schuster KC, Urlaub E, Gapes JR (2000) Single-cell analysis of bacteria by Raman microscopy: spectral information on the chemical composition of cells and on the heterogeneity in a culture. J Microbiol Methods 42:29–38

    CAS  Google Scholar 

  120. Seneviratne CJ, Silva WJ, Jin LJ et al (2009) Architectural analysis, viability assessment and growth kinetics of Candida albicans and Candida glabrata biofilms. Arch Oral Biol 54:1052–1060

    CAS  Google Scholar 

  121. Shi L, Günther S, Hübschmann T et al (2007) Limits of propidium iodide as a cell viability indicator for environmental bacteria. Cytometry Part A 71A: 592–598

    Google Scholar 

  122. Shroff H, Galbraith CG, Galbraith JA et al (2007) Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci USA 104:20308–20313

    CAS  Google Scholar 

  123. Shtengel G, Galbraith JA, Galbraith CG et al (2009) Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci USA 106:3125–3130

    CAS  Google Scholar 

  124. Sil A, Herskowitz I (1996) Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene. Cell 84:711–722

    CAS  Google Scholar 

  125. Slutsky B, Staebell M, Anderson J et al (1987) “White-opaque transition”: a second high-frequency switching system in Candida albicans. J Bacteriol 169:189–197

    CAS  Google Scholar 

  126. Smith E, Dent G (2005) Modern Raman spectroscopy: a practical approach. Wiley, New York

    Google Scholar 

  127. Smits WK, Eschevins CC, Susanna KA et al (2005) Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development. Mol Microbiol 56:604–614

    CAS  Google Scholar 

  128. Smits WK, Kuipers OP, Veening J-W (2006) Phenotypic variation in bacteria: the role of feedback regulation. Nat Rev Microbiol 4:259–271

    CAS  Google Scholar 

  129. Sprague GF Jr, Blair LC, Thorner J (1983) Cell interactions and regulation of cell type in the yeast Saccharomyces cerevisiae. Annu Rev Microbiol 37:623–660

    CAS  Google Scholar 

  130. Sternberg C, Christensen BB, Johansen T et al (1999) Distribution of bacterial growth activity in flow-chamber biofilms. Appl Environ Microbiol 65:4108–4117

    CAS  Google Scholar 

  131. Sternberg C, Tolker-Nielsen T (2006) Growing and analyzing biofilms in flow cells. Curr Protoc Microbiol Chapter 1:Unit 1B.2

    Google Scholar 

  132. Stoodley P, Sauer K, Davies DG et al (2002) Biofilms as complex differentiated communities. Annu Rev Microbiol 56:187–209

    CAS  Google Scholar 

  133. Thundat T, Allison DP, Warmack RJ et al (1992) Atomic force microscopy of DNA on mica and chemically modified mica. Scanning Microsc 6:911–918

    CAS  Google Scholar 

  134. Thundat T, Allison DP, Warmack RJ et al (1992) Imaging isolated strands of dna-molecules by atomic force microscopy. Ultramicroscopy 42:1101–1106

    Google Scholar 

  135. Tolker-Nielsen T, Molin S (2000) Spatial organization of microbial biofilm communities. Microb Ecol 40:75–84

    Google Scholar 

  136. van Sinderen D, Luttinger A, Kong L et al (1995) comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol Microbiol 15:455–462

    Google Scholar 

  137. Vaziri A, Tang J, Shroff H et al (2008) Multilayer three-dimensional super resolution imaging of thick biological samples. Proc Natl Acad Sci USA 105:20221–20226

    CAS  Google Scholar 

  138. Veening J-W, Smits WK, Hamoen LW et al (2006) Single cell analysis of gene expression patterns of competence development and initiation of sporulation in Bacillus subtilis grown on chemically defined media. J Appl Microbiol 101:531–541

    CAS  Google Scholar 

  139. Veening J-W, Stewart EJ, Berngruber TW et al (2008) Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci USA 105:4393–4398

    CAS  Google Scholar 

  140. Veening JW, Smits WK, Hamoen LW et al (2004) Visualization of differential gene expression by improved cyan fluorescent protein and yellow fluorescent protein production in Bacillus subtilis. Appl Environ Microbiol 70:6809–6815

    CAS  Google Scholar 

  141. Veening JW, Stewart EJ, Berngruber TW et al (2008) Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Nat lAcad Sci USA 105:4393–4398

    CAS  Google Scholar 

  142. Vizeacoumar FJ, van Dyk N, Vizeacoumar S et al (2010) Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol 188:69–81

    CAS  Google Scholar 

  143. Vlamakis H, Aguilar C, Losick R et al (2008) Control of cell fate by the formation of an architecturally complex bacterial community. Genes Dev 22:945–953

    CAS  Google Scholar 

  144. Wagner M, Ivleva NP, Haisch C et al (2009) Combined use of confocal laser scanning microscopy (CLSM) and Raman microscopy (RM): investigations on EPS-matrix. Water Res 43:63–76

    CAS  Google Scholar 

  145. Wildanger D, Rittweger E, Kastrup L et al (2008) STED microscopy with a supercontinuum laser source. Opt Express 16:9614–9621

    Google Scholar 

  146. Willig KI, Kellner RR, Medda R et al (2006) Nanoscale resolution in GFP-based microscopy. Nat Methods 3:721–723

    CAS  Google Scholar 

  147. Willig KI, Harke B, Medda R et al (2007) STED microscopy with continuous wave beams. Nat Methods 4:915–918

    CAS  Google Scholar 

  148. Yang L, Liu Y, Sternberg C et al (2010) Evaluation of enoyl-acyl carrier protein reductase inhibitors as Pseudomonas aeruginosa quorum-quenching reagents. Molecules 15:780–792

    CAS  Google Scholar 

  149. Yang X, Beyenal H, Harkin G et al (2000) Quantifying biofilm structure using image analysis. J Microbiol Methods 39:109–119

    CAS  Google Scholar 

  150. Zernike F (1935) Das Phasenkontrastverfahren bei der mikroskopischen Beobachtung. Z Tech Phys 16:454–457

    Google Scholar 

  151. Zipor G, Haim-Vilmovsky L, Gelin-Licht R et al (2009) Localization of mRNAs coding for peroxisomal proteins in the yeast, Saccharomyces cerevisiae. Proc Natl Acad Sci USA 106:19848–19853

    CAS  Google Scholar 

  152. Zordan RE, Galgoczy DJ, Johnson AD (2006) Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc Natl Acad Sci USA 103:12807–12812

    CAS  Google Scholar 

  153. Zumbusch A, Holtom GR, Xie XS (1999) Three-dimensional vibrational imaging by coherent anti-Stokes Raman scattering. Phys Rev Lett 82:4142

    CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the Carlsberg Foundation and the Lundbeck Foundation to Janus A. J. Haagensen. Birgitte Regenberg was supported by The Danish Council for Independent Research | Natural Sciences (FNU). Claus Sternberg was supported by a grant from the Danish National Advanced Technology Foundation. The authors wish to thank Dr. Ninell P. Mortensen for information about atomic force microscopy, Dr. Rolf W. Berg for information about coherent anti-Stokes Raman spectroscopy and Rune L. Jensen for Fig. 14.

Author information

Authors and Affiliations

  1. Stanford University, The Bio-X Program, Clark Center, 318 Campus Drive, Stanford, CA, 94305, USA

    Janus A. J. Haagensen

  2. Department of Systems Biology, Technical University of Denmark, Building 301, 2800, Kongens, Lyngby, Denmark

    Birgitte Regenberg & Claus Sternberg

  3. Department of Biology, Molecular Integrative Physiology, Universitetsparken 13, 2100, Copenhagen, Denmark

    Birgitte Regenberg

Authors
  1. Janus A. J. Haagensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Birgitte Regenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Claus Sternberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Claus Sternberg .

Editor information

Editors and Affiliations

  1. GmbH (UFZ), Dept. Umweltmikrobiologie, Helmholtz-Zentrum für Umweltforschung, Permoserstr. 15, Leipzig, 04318, Germany

    Susann Müller

  2. Fak. Maschinenwesen, Inst. Lebensmittel- und, TU Dresden, Bergstr. 120, Dresden, 01069, Sachsen, Germany

    Thomas Bley

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Haagensen, J.A.J., Regenberg, B., Sternberg, C. (2010). Advanced Microscopy of Microbial Cells. In: Müller, S., Bley, T. (eds) High Resolution Microbial Single Cell Analytics. Advances in Biochemical Engineering / Biotechnology, vol 124. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10_2010_83

Download citation

Publish with us

Policies and ethics

Search

Navigation