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Confocal Laser Microscopy and Digital Image Analysis in Microbial Ecology

  • Chapter
Book cover Advances in Microbial Ecology

Part of the book series: Advances in Microbial Ecology ((AMIE,volume 12))

Abstract

Microbial ecologists have extensively explored the potential applications of light microscopy for more than five decades (Henrici and Johnson, 1935; Perfil’ev and Gabe, 1969; Casida, 1969, 1972, 1975, 1976; Staley, 1971; Caldwell and Hirsch, 1973; Caldwell et al., 1973, 1975; Caldwell and Tiedje, 1975a,b; Labeda et al., 1976; Hirsch, 1977, 1980; Geesey et al., 1978; Marshall, 1986). Now traditional microscopy has given way to “microvisualization” (Friedhoff, 1991) greatly accelerating research. Microorganisms are no longer merely photographed; instead, they are digitally “imaged” using fluorescent molecular probes, confocal laser microscopy, and computer image analysis. The chemical and biological relationships between a microorganism and its microenvironment are seen directly, nondestructively, in situ, and in “real time” (Lawrence and Caldwell, 1990). Consequently, it is no longer necessary to disrupt microbial communities when studying the molecular or behavioral aspects of their ecology.

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References

  • Absolom, D. R., Lamberti, F. V., Policova, Z., Zingg, W., van Oss, C. J., and Neumann, A. W., 1983, Surface thermodynamics of bacterial adhesion, Appl. Environ. Microbiol. 46:90–97.

    PubMed  CAS  Google Scholar 

  • Agard, D. A., Hiraoka, Y., Shaw, P. J., and Sedat, J. W., 1989, Fluorescence microscopy in three dimensions, Methods Cell Biol. 30:353–377.

    PubMed  CAS  Google Scholar 

  • Anwar, H. M., Dasgupta, Lam. K., and Costerton, J. W., 1989, Tobramycin resistance of mucoid Pseudomonas aeruginosa biofilm grown under iron limitation, J. Antimicrob. Chemother. 24:647–655.

    PubMed  CAS  Google Scholar 

  • Berg, H. C., 1985, Physics of bacterial Chemotaxis, in: Sensory Perception and Transduction in Aneural Organisms (G. Colombetti, F. Linci, and P.-S. Song, eds.), Plenum Press, New York, pp. 19–30.

    Google Scholar 

  • Berg, H. C., and Brown, D. A., 1972, Chemotaxis in Escherichia coli analyzed by three-dimensional tracking, Nature 239:500–504.

    PubMed  CAS  Google Scholar 

  • Bjornsen, P. K., 1986, Automatic determination of bacterioplankton biomass by means of image analysis, Appl. Environ. Microbiol. 51:1199–1204.

    PubMed  CAS  Google Scholar 

  • Bott, T. L., and Brock, T. D., 1970, Growth and metabolism of periphytic bacteria: Methodology, Limnol. Oceanogr. 15:333–342.

    Google Scholar 

  • Boyde, A., 1990, Confocal optical microscopy, in: Modern Microscopies: Techniques and Applications (P. J. Duke and A. G. Michette, eds.), Plenum Press, New York, pp. 185–204.

    Google Scholar 

  • Bradbury, S., 1979, Microscopical image analysis: Problems and approaches, J. Microsc. 115:137–150.

    PubMed  CAS  Google Scholar 

  • Brakenhoff, G. J., van der Voort, H. T. M., Baarslag, M. W., Mans, B., Oud, J. L., Zwart, R., and van Driel, R., 1988, Visualization and analysis techniques for three dimensional information acquired by confocal microscopy, Scanning Microsc. 2:1831–1838.

    PubMed  CAS  Google Scholar 

  • Brock, T. D., 1971, Microbial growth rates in nature, Bacteriol. Rev. 35:39–58.

    PubMed  CAS  Google Scholar 

  • Buskey, E. J., and Stoecker, D. K., 1989, Behavioral responses of the marine tintinnid Favella sp. to phytoplankton: Influence of chemical, mechanical and photic stimuli, J. Exp. Mar. Biol. Ecol. 132:1–16.

    Google Scholar 

  • Busscher, H. J., Bellon-Fontaine, M.-N., Mozes, N., van der Mei, H. C., Sjollema, J., and Rouxhet, P. G., 1990a, Deposition of Leuconostoc mesenteroides and Streptococcus thermophilus to solid substrata in a parallel plate flow cell, Biofouling 2:55–63.

    Google Scholar 

  • Busscher, H. J., Sjollema, J., and van der Mei, H. C., 1990b, Relative importance of surface free energy as a measure of hydrophobicity in bacterial adhesion to solid surfaces, in: Microbial Cell Surface Hydrophobicty (R. J. Doyle and M. Rosenberg, eds.), ASM, Washington, D.C., pp. 335–359.

    Google Scholar 

  • Caldwell, D. E., 1985, New developments in computer-enhanced microscopy, J. Microbiol. Methods 4:117–125.

    Google Scholar 

  • Caldwell, D. E., 1987, Microbial colonization of solid-liquid interfaces, Ann. N.Y. Acad. Sci. 506:274–280.

    PubMed  CAS  Google Scholar 

  • Caldwell, D. E., and Caldwell, S. J., 1978, A Zoogloea sp. associated with blooms of Anabaena flosaquae, Can J. Microbiol. 24:922–931.

    PubMed  CAS  Google Scholar 

  • Caldwell, D. E., and Germida, J. J., 1985, Evaluation of difference imagery for visualizing and quantitating microbial growth, Can J. Microbiol. 31:35–44.

    Google Scholar 

  • Caldwell, D. E., and Hirsh, P., 1973, Growth of microorganisms in two-dimensional steady-state diffusion gradients, Can. J. Microbiol. 19:53–58.

    PubMed  CAS  Google Scholar 

  • Caldwell, D. E., and Lawrence, J. R., 1986, Growth kinetics of Pseudomonas fluorescens microcolonies within the hydrodynamic boundary layers of surface microenvironments, Microb. Ecol. 12:299–312.

    Google Scholar 

  • Caldwell, D. E., and Lawrence, J. R., 1988, Study of attached cells in continuous-flow slide culture, in: CRC Handbook of Laboratory Model Systems for Microbial Ecosystems (J. W. T. Wimpenny, ed.), CRC Press, Boca Raton, pp. 117–138.

    Google Scholar 

  • Caldwell, D. E., and Lawrence, J. R., 1989, Microbial growth and behavior within surface microenvironments, in: Proceedings of ISME-5 (T. Hattori, Y. Ishida, Y. Maruyama, R. Y. Morita, and A. Uchida, eds.), JSS Press, Tokyo, pp. 140–145.

    Google Scholar 

  • Caldwell, D. E., and Tiedje, J. M., 1975a, The structure of anaerobic bacterial communities in the hypolimnion of several Michigan lakes, Can. J. Microbiol. 21:377–385.

    PubMed  CAS  Google Scholar 

  • Caldwell, D. E., and Tiedje, J. M., 1975b, A morphological study of anaerobic bacteria from the hypolimnion of two Michigan lakes, Can. J. Microbiol. 21:362–376.

    PubMed  CAS  Google Scholar 

  • Caldwell, D. E., Lai, S. H., and Tiedje, J. M., 1973, A two-dimensional steady-state diffusion gradient for ecological studies, Bull. Ecol. Res. Commun. 17:151–158.

    Google Scholar 

  • Caldwell, D. E., Caldwell, S. J., and Tiedje, J. M., 1975, An ecological study of the sulfur-oxidizing bacteria from the littoral zone of a Michigan lake and a sulfur spring in Florida, Plant Soil 43:101–114.

    Google Scholar 

  • Caldwell, D. E., Korber, D. R., and Lawrence, J. R., 1992, Imaging of bacterial cells by fluorescence exclusion using scanning confocal laser microscopy, J. Microbiol. Methods 15:249–261.

    Google Scholar 

  • Carlsson, K., and Lileborg, A., 1989, A confocal laser microscope scanner for digital recording of optical serial sections, J. Microsc. 153:171–180.

    PubMed  CAS  Google Scholar 

  • Carlsson, K., Wallen, P., and Brodin, L., 1989, Three-dimensional imaging of neurons by confocal fluorescence microscopy, J. Microsc. 155:15–26.

    PubMed  CAS  Google Scholar 

  • Casida, L. E., 1969, Observation of microorganisms in soil and other natural habitats, Appl. Microbiol. 18:1065–1071.

    PubMed  Google Scholar 

  • Casida, L. E., 1972, Interval scanning photomicrography of microbial cell populations, Appl. Microbiol. 23:190–192.

    PubMed  Google Scholar 

  • Casida, L. E., 1975, Infrared color photomicrography of soil microorganisms, Can. J. Microbiol. 21:1892–1893.

    PubMed  Google Scholar 

  • Casida, L. E., 1976, Continuously variable amplitude contrast microscopy for the detection and study of microorganisms in soil, Appl. Environ. Microbiol. 31:605–608.

    PubMed  Google Scholar 

  • Cheng, K.-J., Ingram, J. M., and Costerton, J. W., 1970, Alkaline phosphatase localization and spheroplast formation of Pseudomonas aeruginosa, Can J. Microbiol. 16:1319–1324.

    PubMed  CAS  Google Scholar 

  • Cooksey, B., and Cooksey, K. E., 1988, Chemical signal-response in diatoms of the genus Amphora, J. Cell Sci. 91:523–529.

    CAS  Google Scholar 

  • Costello, P. J., and Monk, P. R., 1985, Image analysis method for the rapid counting of Saccharomyces cerevisiae cells, Appl. Environ. Microbiol. 49:863–866.

    PubMed  CAS  Google Scholar 

  • Costerton, J. W., 1988, Structure and plasticity at various organization levels in the bacterial cell, Can. J. Microbiol. 34:513–521.

    PubMed  CAS  Google Scholar 

  • Costerton, J. W., Ingram, J. M., and Cheng, K.-J., 1974, Structure and function of the cell envelope of gram-negative bacteria, Bacteriol. Rev. 38:87–110.

    PubMed  CAS  Google Scholar 

  • Costerton, J. W., Cheng, K.J., Geesey, G. G., Ladd, T., Nickel, J. C., Dasgupta, M., and Marrie, T. J., 1987, Bacterial biofilms in nature and disease, Annu. Rev. Microbiol. 41:435–464.

    PubMed  CAS  Google Scholar 

  • Davenport, D., 1973, Studies of the behavior of microorganisms by computerized television, in: Behavior of Micro-organisms (A. Perez-Miravete, ed.), Proceedings of the 10th International Congress, Plenum Press, New York.

    Google Scholar 

  • DeYoung, H. G., 1988, Microscopy and image analysis, Bio/Technology 6:78–79.

    Google Scholar 

  • Donovan, R. M., Goldstein, E., Kim, Y., Lippert, W., Kailath, E., Aoki, K. T., Cheung, A. T. W., Miller, M. E., and Chang, D. P., 1987, A computer-assisted image-analysis system for analyzing polymorphonuclear leukocyte chemotaxis in patients with Diabetes mellitus, J. Infect. Dis. 155:737–741.

    PubMed  CAS  Google Scholar 

  • Drake, B., Prater, C. B., Weisenhorn, A. L., Gould, S. A. C., Albrecht, T. R., Quate, C. F., Cannell, D. S., Hansma, H. G., and Hansma, P. K., 1989, Imaging crystals, polymers, and processes in water with the atomic force microscope, Science 241:1586–1589.

    Google Scholar 

  • Edgar, L. A., 1979, Diatom locomotion: Computer-assisted analysis of cine film, Br. Phycol. J. 14:83–101.

    Google Scholar 

  • Eighmy, T. T., Maratea, D., and Bishop, P. L., 1983, Electron microscopic examination of wastewater biofilm formation and structural components, Appl. Environ. Microbiol. 45:1921–1931.

    PubMed  CAS  Google Scholar 

  • Ellwood, D. C., Keevil, C. W., Marsh, P. D., Brown, C. M., and Wardell, J. N., 1982, Surface-associated growth, Philos. Trans. R. Soc. London Ser. B 297:517–532.

    CAS  Google Scholar 

  • Emmett, A., 1991, In search of the miracle hologram: Spatial image researchers strive to achieve stereoscopic reality, Comput. Graphics World 14:44–52.

    Google Scholar 

  • Escher, A. R., and Characklis, W. G., 1988, Microbial colonization of a smooth substratum: A kinetic analysis using image analysis, Water Sci. Technol. 20:45–51.

    Google Scholar 

  • Fernandes, M. A., Jackman, P. J., Clark, S. A., and Gunard, S. R., 1988, Detection and quantification of microorganisms in a heterogenous foodstuff by image analysis, Comput. Appl. Biosci. 4:291–295.

    PubMed  CAS  Google Scholar 

  • Friedhoff, R. M., 1991, Microvisualization, Comput. Graphics World 14:38–44.

    Google Scholar 

  • Fry, J. C., 1988, Determination of biomass, in: Methods in Aquatic Bacteriology (B. Austin, ed.), Wiley, New York, pp. 27–72.

    Google Scholar 

  • Fry, J. C., and Davies, A. R., 1985, An assessment of methods for measuring volumes of planktonic bacteria, with particular reference to television image analysis, J. Appl. Bacteriol. 58:105–112.

    Google Scholar 

  • Gaju, N., Guerrero, R., and Pedros-Alio, C., 1989, Measurement of cell volume of phototrophic bacteria in pure cultures and natural samples: Phase contrast, epifluorescence and particle sizing, FEMS Microbiol. Ecol. 62:295–302.

    Google Scholar 

  • Geesey, G. C., Mutch, R., and Costerton, J. W., 1978, Sessile bacteria: An important component of the microbial population in small mountain streams, Limnol. Oceanogr. 23:1214–1223.

    CAS  Google Scholar 

  • Getliff, J. M., and Fry, J. C., 1989, Using the solitaire plus image analyser for direct estimates of bacterial volume, Binary 1:93–100.

    Google Scholar 

  • Gonzalez, R. C., and Wintz, P., 1977, Digital Image Processing. Addison-Wesley, Reading, Mass.

    Google Scholar 

  • Gratton, E., and van deVen, M. J., 1990, Laser sources for confocal microscopy, in Handbook of Biological Confocal Microscopy (J. B. Pawley, ed.), Plenum Press, New York, pp. 53–67.

    Google Scholar 

  • Gualtieri, P., Colombetti, G., and Lend, F. 1985, Automatic analysis of the motion of microorganisms, J. Microsc. 139:57–62.

    Google Scholar 

  • Gualtieri, P., Francesco, G., Passarelli, V., and Barsanti, L., 1988, Microorganism track reconstruction: An image processing approach, Comput. Biol. Med. 18:57–63.

    PubMed  CAS  Google Scholar 

  • Hansma, P. K., Drake, B., Mari, O., Gould, S. A. C., and Prater, C. B., 1989a, The scanning ionconductance microscope, Science 243:641–643.

    PubMed  CAS  Google Scholar 

  • Hansma, P. K., Elings, V. B., Mari, O., and Bracker, C. E., 1989b, Scanning tunneling microscopy and atomic force microscopy: Application to biology and technology, Science 241:209–216.

    Google Scholar 

  • Harris, R., 1991, Confocal microscopy, Microsc. Soc. Can. Bull. 19:33–35.

    Google Scholar 

  • Haugland, R. P., 1989, Handbook of Fluorescent Probes and Research Chemicals, Molecular Probes Inc., Eugene, Oreg.

    Google Scholar 

  • Henrici, A. T., and Johnson, D. E., 1935, Studies of freshwater bacteria. II. Stalked bacteria, a new order of Schizomycetes, J. Bacteriol. 30:61–93.

    PubMed  CAS  Google Scholar 

  • Hirsch, P., 1974, Budding bacteria, Annu. Rev. Microbiol. 28:391–433.

    PubMed  CAS  Google Scholar 

  • Hirsch, P., 1977, Distribution and pure culture studies of morphologically distinct solar lake microorganisms, in: Hypersaline Brines and Evaporinc Environments (A. Nissenbaum, ed.), Elsevier, Amsterdam, pp. 41–60.

    Google Scholar 

  • Hirsch, P., 1980, Some thoughts on and examples of microbial interactions in the natural environment, in: Aquatic Microbial Ecology (R. R. Colwell and A. J. Foster, eds.), University of Maryland, pp. 36–54.

    Google Scholar 

  • Inoué, S., 1986, Video Microscopy, Plenum Press, New York, pp. 263–307.

    Google Scholar 

  • Inoué, S., 1990, Foundations of confocal scanned imaging in light microscopy, in: Handbook of Confocal Laser Microscopy (J. B. Pawley, ed.), Plenum Press, New York, pp. 1–14.

    Google Scholar 

  • Jenkinson, D. S., Powlson, D. S., and Wedderburn, R. M. W., 1976, The effects of biocidal treatments on metabolism in soil. III. The relationship between soil biovolume, measured by optical microscopy and the flush of decomposition cause by fumigation, Soil Biol. Biochem. 8:189–202.

    CAS  Google Scholar 

  • Kesterson, J., and Richardson, M., 1991, Confocal microscope capability with desktop affordability, Advanced Imaging 6:23–25.

    Google Scholar 

  • Kinner, N. E., Balkwill, D. L., and Bishop, P. L., 1983, Light and electron microscopic studies of microorganisms growing in rotating biological contactor biofilms, Appl. Environ. Microbiol. 45:1659–1669.

    PubMed  CAS  Google Scholar 

  • Kjelleberg, S., Humphrey, B., and Marshall, K. C., 1982, The effect of interfaces on small starved marine bacteria, Appl. Environ. Microbiol. 43:1166–1172.

    PubMed  CAS  Google Scholar 

  • Kohen, E., and Hirschberg, J. G., 1989, Cell Structure and Function by Microspectrofluorometry, Academic Press, New York.

    Google Scholar 

  • Korber, D. R., Lawrence, J. R., Sutton, B., and Caldwell, D. E., 1989a, Effect of laminar flow velocity on the kinetics of surface recolonization by mot+ and mot- Pseudomonas fluorescens, Microb. Ecol. 18:1–19.

    Google Scholar 

  • Korber, D. R., Lawrence, J. R., Cooksey, K. E., Cooksey, B., and Caldwell, D. E., 1989b, Computer image analysis of diatom Chemotaxis, Binary 2:335–350.

    Google Scholar 

  • Korber, D. R., Lawrence, J. R., Zhang, L., and Caldwell, D. E., 1990, Effect of gravity on bacterial deposition and orientation in laminar flow environments, Biofouling 2:335–350.

    Google Scholar 

  • Krambeck, C., Krambeck, H. J., Schroder, D., and Newell, S. Y., 1990, Sizing bacterioplankton: A juxtaposition of bias due to shrinkage, halos, subjectivity in image interpretation and asymmetric distributions, Binary 2:5–14.

    Google Scholar 

  • Kuhn, D. A., and Starr, M. P., 1970, Effects of microscope illumination on bacterial development, Arch. Mikrobiol. 74:292–300.

    Google Scholar 

  • Labeda, D. P., Liu, K., and Casida, L. E., 1976, Colonization of soil by Arthrobacter and Pseudomonas under varying conditions of water and nutrient availability as studied by plate counts and transmission electron microscopy, Appl. Environ. Microbiol. 31:551–561.

    PubMed  CAS  Google Scholar 

  • Lappin-Scott, H. M., and Costerton, J. W., 1990, Bacterial biofilms and surface fouling, Biofouling 1:323–342.

    Google Scholar 

  • Lawrence, J. R., and Caldwell, D. E., 1987, Behavior of bacterial stream populations within the hydrodynamic boundary layers of surface microenvironments, Microb. Ecol. 14:15–27.

    Google Scholar 

  • Lawrence, J. R., and Caldwell, D. E., 1990, Scanning confocal laser microscopy of biofilms, Can. Lab. 2:12.

    Google Scholar 

  • Lawrence, J. R., Delaquis, P. J., Korber, D. R., and Caldwell, D. E., 1987, Behavior of Pseudomonas fluorescens within the hydrodynamic boundary layers of surface microenvironments, Microb. Ecol. 14:1–14.

    CAS  Google Scholar 

  • Lawrence, J. R., Korber, D. R., and Caldwell, D. E., 1989a, Computer-enhanced darkfield microscopy for the quantitative analysis of bacterial growth and behavior on surfaces, J. Microbiol. Methods 10:123–138.

    Google Scholar 

  • Lawrence, J. R., Malone, J. A., Korber, D. R., and Caldwell, D. E., 1989b, Computer image enhancement to increase depth of field in phase contrast microscopy, Binary 1:181–185.

    Google Scholar 

  • Lawrence, J. R., Delaquis, P. J., Zanyk, B. N., Korber, D. R., and Caldwell, D. E., 1990, Computer-enhanced microscopy study of Pseudomonas fragi biofilm development, Abstracts of the ASM Conference on Multicellular Behavior of Bacteria in Nature, Industry, and the Laboratory, Woods Hole Marine Biological Laboratory.

    Google Scholar 

  • Lawrence, J. R., Korber, D. R., Hoyle, B. D., Costerton, J. W., and Caldwell, D. E., 1991, Optical sectioning of microbial biofilms, J. Bacteriol. 173:6558–6567.

    PubMed  CAS  Google Scholar 

  • Linfoot, E. H., and Wolfe, E., 1953, Diffraction images in systems with an annular aperture, Proc. Phys. Soc. B 66:145–149.

    Google Scholar 

  • Luby-Phelps, K., Lanni, F., and Taylor, D. L., 1988, The submicroscopic properties of cytoplasm as a determinant of cellular function, Annu. Rev. Biophys. Chem. 17:369–396.

    CAS  Google Scholar 

  • McLean, R. J. C., Lawrence, J. R., Korber, D. R., and Caldwell, D. E., 1991, Proteus mirabilis biofilm protection against struvite crystal dissolution and its implications in struvite urolithiasis, J. Urol. 146:1130–1142.

    Google Scholar 

  • Malone, J. A., 1988, Colonization of surface microenvironments by Rhizobium spp., M.Sc. thesis, University of Sask.

    Google Scholar 

  • Marshall, K. C., 1986, Microscopic methods for the study of bacterial behavior at inert surfaces, J. Microbiol. Methods 4:217–227.

    Google Scholar 

  • Marshall, K. C., 1988, Adhesion and growth of bacteria at surfaces in oligotrophic habitats, Can J. Microbiol. 34:503–506.

    Google Scholar 

  • Marshall, K. C., and Cruickshank, R. H., 1973, Cell surface hydrophobicity and the orientation of certain bacteria at interfaces, Arch. Mikrobiol. 91:29–40.

    PubMed  CAS  Google Scholar 

  • Marshall, K. C., Stout, R., and Mitchell, R., 1971, Mechanisms of the initial events in the sorption of marine bacteria to solid surfaces, J. Gen. Microbiol. 68:337–348.

    CAS  Google Scholar 

  • Marshall, K. C., Cruikshank, R. H., and Bushby, H. V. A., 1975, The orientation of certain root-nodule bacteria at interfaces, including legume root-hair surfaces, J. Gen. Microbiol. 91:198–200.

    PubMed  CAS  Google Scholar 

  • Martin, Y., Williams, C. C., and Wickramasinghe, H. K., 1988, Tip techniques for microcharacterization of materials, Scanning Microsc. 2:3–8.

    Google Scholar 

  • Meadows, P. S., 1971, The attachment of bacteria to solid surfaces, Arch. Mikrobiol. 75:374–381.

    PubMed  CAS  Google Scholar 

  • Meijer, B.C., Kootstra, G. J., and Wilkinson, M. H. F., 1990, A theoretical and practical investigation into the characterization of bacterial species by image analysis, Binary 2:21–31.

    Google Scholar 

  • Pawley, J. B. (ed.), 1990, Handbook of Biological Confocal Microscopy, Plenum Press, New York.

    Google Scholar 

  • Perfil’ev, B. V., and Gabe, D. R., 1969, Capillary Methods of Investigating Microorganisms (J. M. Shewan, trans.), University of Toronto Press, Toronto.

    Google Scholar 

  • Peters, A. C., 1990, Using image analysis to map bacterial growth on solid media. Binary 2:73–75.

    Google Scholar 

  • Peters, A.C., Wimpenny, J. W. T., Thomas, L. V., and Griffiths, J., 1991, Mapping bacterial growth on gradient plates using image analysis, Binary 3:147–154.

    Google Scholar 

  • Pettipher, G. L., and Rodrigues, U. M., 1982, Semi-automated counting of bacteria and somatic cells in milk using epifluorescence microscopy and television image analysis, J. Appl. Bacteriol. 53:323–329.

    PubMed  CAS  Google Scholar 

  • Power, K., and Marshall, K. C., 1988, Cellular growth and reproduction of marine bacteria on surface-bound substrate, Biofouling 1:163–174.

    Google Scholar 

  • Read, N. D., Knight, H., and Trewas, A. J., 1992, Fluorescence ratio imaging and confocal microscopy in filamentous fungi, Binary 4:50–52.

    Google Scholar 

  • Robinson, R. W., Akin, D. E., Nordstedt, R. A., Thomas, M. V., and Aldrich, H. C., 1984, Light and electron microscopic examinations of methane-producing biofilms from anaerobic fixed-bed reactors, Appl. Environ. Microbiol. 48:127–136.

    PubMed  CAS  Google Scholar 

  • Russ, J. C., 1990, Computer-Assisted Microscopy: The Measurement and Analysis of Images, Plenum Press, New York.

    Google Scholar 

  • Shaw, P. J., and Rawlins, P. J., 1991, The point-spread function of a confocal microscope: Its measurement and use in deconvolution of 3-D data, J. Micros. 163:151–165.

    Google Scholar 

  • Shotton, D. M., 1989, Confocal scanning optical microscopy and its applications for biological specimens, J. Cell Sci. 94:175–206.

    Google Scholar 

  • Shotton, D., and White, N., 1989, Confocal scanning microscopy: Three dimensional biological imaging, Trends Biochem. Sci. 14:435–438.

    PubMed  CAS  Google Scholar 

  • Sieracki, M. E., and Webb, K. L., 1986, A color video image analysis system for studying pico-and nanoplanktonic bacteria, EOS Trans. Am. Geophys. Union 66:1298.

    Google Scholar 

  • Sieracki, M. E., Johnson, P. W., and Sieburth, J. M., 1985, Detection, enumeration, and sizing of planktonic bacteria by image-analzyed epifluorescence microscopy, Appl. Environ. Microbiol. 49:799–810.

    PubMed  CAS  Google Scholar 

  • Sieracki, M. E., Reichenback, S. E., and Webb, K. L., 1989, Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis, Appl. Environ. Microbiol. 55:2762–2772.

    PubMed  CAS  Google Scholar 

  • Silverman, M., and Simon, M., 1974, Flagellar rotation and the mechanism of bacterial motility, Nature 249:73–74.

    PubMed  CAS  Google Scholar 

  • Singh, A., Yu, F.-P., and McFeters, G. A., 1990, Rapid detection of chlorine-induced bacterial injury by the direct viable count method using image analysis, Appl. Environ. Microbiol. 56:389–394.

    PubMed  CAS  Google Scholar 

  • Sjollema, J., Busscher, H. J., and Weerkamp, A. H., 1988, Deposition of oral streptococci and polystyrene lattices onto glass in a parallel plate flow cell, Biofouling 1:101–112.

    Google Scholar 

  • Sjollema, J., Busscher, H. J., and Weerkamp, A. H., 1989, Real-time enumeration of adhering microorganisms in a parallel plate flow cell using automated image analysis, J. Microbiol. Methods 9:73–78.

    Google Scholar 

  • Sjollema, J., van der Mei, H. M., and Busscher, H. J., 1990a, Direct observations of cooperative effects in oral streptococcal adhesion to glass by analysis of the spatial arrangement of adhering bacteria, FEMS Microbiol. Ecol. Lett. 69:263–270.

    Google Scholar 

  • Sjollema, J., van der Mei, H. M., and Busscher, H. J., 1990b, The influence of collector and bacterial cell surface properties on the deposition of oral streptococci in a parallel plate flow cell. J. Adhesion Sci. Technol. 4:765–777.

    Google Scholar 

  • Soderstrom, B., 1977, Vital staining of fungi in pure cultures and in soil with fluorescein diacetate, Soil Biol. Biochem. 9:59–63.

    Google Scholar 

  • Soderstrom, B. E., 1979, Some problems in assessing the fluorescein diacetate-active fungal biomass in the soil, Soil Biol. Biochem. 11:147–148.

    Google Scholar 

  • Staley, J. T., 1971, Growth rates of algae determined in situ using an immersed microscope, J. Phytol. 7:13–17.

    Google Scholar 

  • Tsien, R. Y., 1989, Fluorescent indicators of ion concentrations, Methods Cell Biol. 30:127–156.

    PubMed  CAS  Google Scholar 

  • Tsien, R. Y., and Waggoner, A., 1990, Fluorophores for confocal microscopy: Photophysics and photochemistry, in: Handbook of Confocal Microscopy (J. B. Pawley, ed.), Plenum Press, New York, pp. 169–178.

    Google Scholar 

  • Vaitzus, Z., and Doetsch, R. N., 1969, Motility tracks: Technique for quantitative study of bacterial movement, Appl. Environ. Microbiol. 17:584–588.

    Google Scholar 

  • van Loosdrecht, M. C. W., Lyklema, J., Norde, W., and Zehnder, A. J. B., 1990, Influence of interfaces on microbial activity, Microbiol. Rev. 54:75–87.

    PubMed  Google Scholar 

  • van Veen, J., and Paul, E. A., 1979, Conversion of biovolume measurements of soil organisms, grown under various moisture tensions, to biomass and their nutrient content, Appl. Environ. Microbiol. 37:686–692.

    PubMed  Google Scholar 

  • Verran, J., and Rocliffe, M. D., 1986, Feasibility of using automatic image analysis for measuring dental plaque in situ, J. Dent., 14:11–13.

    PubMed  CAS  Google Scholar 

  • Wells, K. S., Sandison, D. R., Strickler, J., and Webb, W. W., 1990, Imaging with laser scanning confocal microscopy, in: Handbook of Biological Confocal Microscopy (J. B. Pawley, ed.), Plenum Press, New York, pp. 27–39.

    Google Scholar 

  • White, J. G., Amos, W. B., and Fordham, M., 1987, An evaluation of confocal versus conventional imaging of biological structure by fluorescence light microscopy, J. Cell Biol. 105:41–48.

    PubMed  CAS  Google Scholar 

  • Wimpenny, J. W. T., Waters, P., and Peters, A. C., 1988, Gel-plate methods in microbiology, in: Handbook of Laboratory Model Systems for Microbial Ecosystems, Vol. 1 (J. W. T. Wimpenny, ed.), CRC Press, Boca Raton, pp. 229–251.

    Google Scholar 

  • Wolfaardt, G. M., Lawrence, J. R., Hendry, M. J., Roberts, R. D., and Caldwell, D. E., 1992, The use of model diffusion gradients for the isolation of degradative microbial consortia, Abstracts of the Annual Meeting of the Canadian Society of Microbiologists.

    Google Scholar 

  • Wynn-Williams, D. D., 1988a, Television image analysis of microbial communities in Antarctic fellfields, Polarforschung 58:239–249.

    Google Scholar 

  • Wynn-Williams, D. D., 1988b, Microbial colonization processes in Antarctic fellfield soils—An experimental overview, in: Proceedings of the NIPR Symposium on Polar Biology, National Institute of Polar Research, Tokyo, Vol. 3, pp. 164–178.

    Google Scholar 

  • Zanyk, B. N., Korber, D. R., Lawrence, J. R., and Caldwell, D. E., 1991, 4-D visualization of biofilm development by Pseudomonas fragi, Binary 3:24–29.

    Google Scholar 

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© 1992 Plenum Press, New York

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Caldwell, D.E., Korber, D.R., Lawrence, J.R. (1992). Confocal Laser Microscopy and Digital Image Analysis in Microbial Ecology. In: Marshall, K.C. (eds) Advances in Microbial Ecology. Advances in Microbial Ecology, vol 12. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-7609-5_1

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