Quantifying biofilm structure using image analysis

Journal of Microbiological Methods

Volumn 39, Issue 2, 2000, Pages 109-119

  Yang, Xinmin ^a   Beyenal, Haluk ^a   Harkin, Gary ^b   Lewandowski, Zbigniew ^a,b  

^a MONTANA STATE UNIVERSITY   (United States)

^b Idaho National Laboratory   (United States)

Author keywords

Biofilm; Heterogeneity quantification; Image analysis; Structure

Indexed keywords

ALGORITHM; BACTERIAL FLORA; BIOFILM; CALCULATION; DIFFUSION; DYNAMICS; IMAGE ANALYSIS; MORPHOLOGY; NONHUMAN; POROSITY; PRIORITY JOURNAL; REVIEW; SPECIES;

EID: 0033991082     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(99)00097-4     Document Type: Article

References (44)

1. Beyenal H., Tanyolaç A., Lewandowski Z. Measurement of local effective diffusivity in heterogeneous biofilms. Water Sci. Technol. 38:1998;171-178.
2. Bishop P.L. Biofilm structure and kinetics. Water Sci. Technol. 36:1997;287-294.
3. Brakenhoff G., van der Hoort H., Baarslag M., Oud J., Zwart R., var Driel R. Visualization and analysis techniques for three-dimensional information acquired by confocal microscopy. Scan. Microsc. 2:1988;1831-1838.
4. Bremer P., Geesey G., Drake B. Atomic force microscopy examination of the topography of a hydrated bacterial biofilm on a copper surface. Curr. Microbiol. 24:1992;223-230.
5. Caldwell D., Korer D., Lawrence J. Confocal laser microscopy and digital image analysis in microbial ecology. Adv. Microbiol. Ecol. 12:1992;1-67.
6. Cao Y.S., Alaerts G.J. Influence of reactor type and shear stress on aerobic biofilm morphology, population and kinetics. Water Res. 29:1995;107-118.
7. Christensen F.R., Kristensen G.H., la Cour Jansen J. Biofilm structure: An important and neglected parameter in wastewater treatment. Water Sci. Technol. 21:1989;805-814.
8. Dalton H.M., Poulsen L.K., Halasz P., Angles M.L., Goodman A.E., Marshall K.C. Substratum-induced morphological changes in a marine bacterium and their relevance to biofilm structure. J. Bacteriol. 11:1994;6090-6096.
9. Danielsson P. Euclidean distance mapping. Comput. Graphics Imag. Proc. 14:1980;227-248.
10. De Beer D., Stoodley P., Roe F., Lewandowski Z. Effects of biofilm structures on oxygen distribution and mass transport. Biotechnol. Bioeng. 43:1994;1131-1138.
11. De Beer D., Stoodley P., Lewandowski Z. Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy. Biotechnol. Bioeng. 53:1997;151-158.
12. De Beer D., Schramm A., Santegoeds C.M., Kuhl M. A nitrite microsensor for profiling environmental biofilms. Appl. Environ. Microbiol. 63:1997;973-977.
13. Gibbs J.T., Bishop P.L. A method for describing biofilm surface roughness using geostatistical techniques. Water Sci. Technol. 32:1995;91-98.
14. Gjaltema A., Arts P.A.M., van Loosdrecht M.C.M., Kuenen J.G., Heijnen J.J. Heterogeneity of biofilms in rotating annular reactors: Occurrence, structure, and consequences. Biotechnol. Bioeng. 44:1994;194-204.
15. Gjaltema A., Vinke J. L, van Loosdrecht M.C.M., Heijnen J.J. Abrasion of suspended biofilm pellets in airlift reactors: Importance of shape, structure, and particle concentrations. Biotechnol. Bioeng. 53:1997;88-99.
16. Haralick R.M., Shanmugam K., Dinstein I. Texture features for image classification. IEEE Trans. Syst. Man, Cybernet. SMC-3:1973;610-621.
17. Haralick R., Shapiro L. Computer and Robot Vision. 1992;453-493 Addison-Wesley, Reading, MA.
18. Hermanowics S.W., Schindler U., Wilderer P. Fractal structure of biofilm: New tools for investigation of morphology. Water Sci. Technol. 32:1995;99-105.
19. Holden P.A., Hunt J.R., Firestone M.K. Toluene diffusion and reaction in unstructured Pseudomonas putida biofilms. Biotechnol. Bioeng. 56:1997;656-670.
20. Jain A. Algorithms For Clustering Data. 1988;Prentice Hall, New York.
21. Kaandorp J. Fractal Modeling Growth and Form in Biology. 1994;Springer, Berlin.
22. Keevil C.W., Dowsett A.B., Rogers J. Legionella biofilms and their control. Society for Applied Bacteriology. 1993;201-215. Technical series: microbial biofilms.
23. Lawrence J.R., Korber D.R., Hoyle B.D., Costerton J.W., Caldwell D.E. Optical sectioning of microbial biofilms. J. Bacteriol. 10:1991;6558-6567.
24. Lewandowski Z., Altobelli S.A., Majors P.D., Fukushima E. NMR imaging of hydrodynamics near microbially colonized surfaces. Water Sci. Technol. 26:1992;577-584.
25. Lewandowski Z., Stoodley P., Altobelli S., Fukushima E. Hydrodynamics and kinetics in biofilm systems: recent advances and new problems. Proc. of the 2nd IAWQ International Specialized Conference on Biofilm Reactors, September 29-October 1, 1993, Paris, France :1993;313-319.
26. Obert M., Pfeifer P., Sernetz M. Microbial growth patterns described by fractal geometry. J. Bacteriol. 1:1990;1180-1185.
27. Palmer R.J., Caldwell D.E. A flowcell for study of plaque removal and regrowth. J. Microbiol. Methods. 24:1995;171-182.
28. Paulsen J.E., Oppen E., Bakke R. Biofilm morphology in porous media. A study with microscopic and image techniques. Water Sci. Technol. 36:1997;1-9.
29. Picioreanu C., van Loosdrecht M.C.M., Heijnen J.J. A new combined differential-discrete cellular automaton approach for biofilm modeling: Application for growth in gel beads. Biotechnol. Bioeng. 57:1998;718-731.
30. Picioreanu C., van Loosdrecht M.C.M., Heijnen J.J. Mathematical modeling of biofilms structure with a hybrid differential-discrete cellular automaton approach. Biotechnol. Bioeng. 58:1998;101-116.
31. Robinson R.W., Akin D.E., Nordstedt R.A., Thomas M.V., Aldrich H.C. Light and electron microscopic examinations of methane producing biofilms from anaerobic fixed bed reactors. Appl. Environ. Microbiol. 48:1984;127-136.
32. Russ J. Fractal Surfaces. 1994;Plenum Press, New York.
33. Stewart P.S., Murga R., Srinivasan R., de Beer D. Biofilm structural heterogeneity visualized by three microscopic methods. Water Res. 29:1995;2006-2009.
34. Suci P.A., Siedlecki K.J., Palmer R.J., White D.C., Geesey G.G. Combined light microscopy and attenuated total reflection Fourier transform infrared spectroscopy for integration of biofilm structure, distribution, and chemistry at solid-liquid interfaces. Appl. Environ. Microbiol. 63:1997;4600-4603.
35. Swope K.L., Flickinger M.C. The use of confocal scanning laser microscopy and other tools to characterize Escherichia coli in a high cell density synthetic biofilm. Biotechnol. Bioeng. 52:1996;340-356.
36. Tijhuis L., Rekswinkel E., van Loosdrecht M.C.M., Heijnen J.J. Dynamics of population and biofilm structure in the biofilm airlift suspension reactor for carbon and nitrogen removal. Water Sci. Technol. 29:1994;377-384.
37. van Loosdrecht M.C.M., Eikelboom D., Gjaltema A., Mulder A., Tijhuis L., Heijnen J.J. Biofilm structures. Water Sci. Technol. 32:1995;35-43.
38. Walker J.T., Mackerness C.W., Rogers J., Keevil C.W. Heterogeneous mosaic: a haven for waterborne pathogens. Lappin-Scott H.M., Costerton) J.W. Microbial Biofilms. 1995;196-204 Cambridge University Press, Cambridge, UK.
39. White D.C., Arrage A.A., Nivens D.E., Palmer R.J., Rice J.F., Sayler G.S. Biofilm ecology: on-line methods bring new insights into MIC and microbial biofouling. Biofouling. 10:1996;1-3.
40. Wimpenny J.W., Colasanti R. A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models. FEMS Microbiol. Ecol. 22:1997;1-16.
41. Xia F., Beyenal H., Lewandowski Z. An electrochemical technique to measure local flow velocity in biofilms. Water Res. 32:1998;3631-3636.
42. Yang S., Lewandowski Z. Measurement of local mass transfer coefficient in biofilms. Biotechnol. Bioeng. 48:1995;737-744.
43. Zahid W.M., Ganczarczyk J.J. Fractal properties of the RBC biofilm structure. Water Sci. Technol. 29:1994;271-279.
44. Zhang T.C., Bishop P.L. Density, porosity, and pore structure of biofilms. Water Res. 28:1994;2267-2277.