Three-dimensional quantification of soil biofilms using image analysis

Environmental Engineering Science

Volumn 24, Issue 1, 2007, Pages 96-103

  Rodríguez, Sylian J ^a   Bishop, Paul L ^b  

^a Department of Civil and Environmental Engineering   (Colombia)

^b 705 Engineering Research Center   (United States)

Author keywords

Biofilm; Confocal laser scanning microscopy; Image analysis; Quantification; Structure

Indexed keywords

CELLS; FILM GROWTH; IMAGE ANALYSIS; MICROORGANISMS; POROUS MATERIALS; SOILS;

CONFOCAL LASER SCANNING MICROSCOPY (CLSM); QUANTIFICATION; SOIL BIOFILMS; STANDARD DEVIATION;

BIOFILMS;

ARTICLE; BIOFILM; CELL AGGREGATION; CELL DENSITY; CONFOCAL LASER MICROSCOPY; IMAGE ANALYSIS; STRUCTURE ANALYSIS;

EID: 33845920374     PISSN: 10928758     EISSN: None     Source Type: Journal    
DOI: 10.1089/ees.2007.24.96     Document Type: Article

References (28)

1. BATTIN, T.J., KAPLAN, L.A., NEWBOLD, J., CHENG, X., and HANSEN, C. (2003). Effects of current velocity on the nascent architecture of stream microbial biofilms. Appl. Environ. Microb. 69, 5443.
2. BEYENAL, H., and LEWANDOWSKI, Z. (2000). Combined effect of substrate concentration and flow velocity on effective diffusivity in biofilms. Water Res. 34(2), 528.
3. BEYENAL, H., and LEWANDOWSKI, Z. (2004). Quantifying biofilm structure: Facts and fiction. Biofouling 20, 1.
4. BEYENAL, H., TANYOLAC, A., and LEWANDOWSKI, Z. (1998). Measurement of local effective diffusivity in heterogeneous biofilms. Water Sci. Technol., 38, 171.
5. BEYENAL, H., DONOVAN, C., LEWANDOSKI, Z., and HARKIN, G. (2004). Three-dimensional biofilm structure quantification. J. Microb. Methods, 59, 395.
6. BISHOP, P.L. (1997). Biofilm structure and kinetics. Water Sci. Technol. 36, 287.
7. CORTIZO, M., and FERNÁNDEZ LORENZO DE MELE, M. (2003). Microstructurul characteristics of thin biofilms through optical and scanning electron microscopy. World J. Microb. Biotechnol., 19(8), 805.
8. DE BEER, D., STOODLEY, P., ROE, F., und LEWANDOWSKI, F. (1994). Effects of biofilms structures on oxygen distribution and mass transport. Biotechnol. Bioeng. 43, 1131.
9. EBIHARA, T., and BISHOP, P.L. (1999). Biofilm structural forms in porous media utilized in organic compounds degradation. Water Sci. Technol. 39(7), 203.
10. GIBBS, J.T., and BISHOP. P.L. (1995). A method for describing biofilm surface roughness using geostatistical techniques. Water Sci. Technol. 32, 91.
11. HEYDORN, A., NIELSEN, A., HENTZER, M., STENBERG, C., GIVSKOV, M., ERSBOLL, B.K., and MOLIN, S. (2000). Quantification of biofilm structures by the novel computer program COMSTAT. Microbiol. UK 146, 2395.
12. HORN, H., and HEMPEL, D.C. (1995). Muss transfer coefficients for an uutotrophic und a heterotrophic biofilm system. Water Sci. Technol. 32, 199.
13. JACKSON, G., BEYENAL, H., REES, W., and LEWANDOWSKI, Z. (2001). Growing reproducible biofilms with respect to structure und viable cell counts. J. Microb. Methods 47, 1.
14. LEWANDOWSKI, Z. (2000). Notes on biofilm porosity. Water Res. 34(9), 2620.
15. LEWANDOWSKI, Z., WEBB, D., HAMILTON, M., and HARKIN G. (1999). Quantifying biofilm structure. Water Sci. Technol. 39, 71.
16. MASSART, D., VANDEGINSTE, B., BUYDENS, L., DE JONG, S., and SMEYERS-VERBEKE, J. (1997). Handbook of Chemometrics and Qualimetrics: Part A. Data Handling in Science and Technology. Elsevier Science, Amsterdam, Vol. 20a.
17. NEU, T., and LAWRENCE, J. (2002). Laser scanning microscopy in combination with fluorescence techniques for biofilm study. In: Bitton G. Ed., The Encyclopedia of Environmental Microbiology. New York: John Wiley & Sons, p. 1772, vol. 4.
18. OKABE, S., HIRATA, K., OZAWA, Y., and WATANABE, Y. (1996). Spatiul microbial distribution of nitrifiers and heterotrophs in mixed-population biofilms. Biotechnol. Bioeng. 50, 24.
19. OKABE, S., KINDAICHI, T., ITO, T., and SATOH, H. (2004). Analysis of size distribution and areal density of ammonia-oxidizing bacterial microcolonies in relation to substrate microprofiles in biofilms. Biotechnol. Bioeng., 85(1), 86.
20. PAULSEN, J., OPPEN, E., and BAKKE, R. (1997). Biofilm morphology in porous media: A study with microscopic and imaging techniques. Water Sci. Technol. 36(1), 1.
21. PICIOREANU, C., M.C. VAN LOOSDRECHT, et al. (1998). A new combined differential-discrete cellular automaton approach for biofilm modeling: application for growth in gel beads. Biotechnol. Bioengineer. 57(6), 718-731.
22. PICIOREANU, C., M.C. VAN LOOSDRECHT, et al. (1998). Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach. Biotechnol. Bioengineer 58(1), 101-116.
23. WASCHE, S., HORN, H., and HEMPEL, D. (2002). Influence of growth conditions on biofilm development and mass transfer at the bulk/biofilm interface. Water Res. 36, 4775.
24. WIJEYEKOON, S., MINO, T., HIROYASU, S., and TOMONORI, M. (2004). Effects of substrate loading rate on biofilm structure. Water Res. 38(10), 2479.
25. XAVIER, J.B., WHITE, D.C., and ALMEIDA J.S. (2003). Automated biofilm morphology quantification from confocal laser scanning microscopy imaging. Water Sci. Technol. 47, 31.
26. YANG, X., BEYENAL, H., HARKIN, G., and LEWANDOWSKI, Z. (2000). Quantifying biofilm structure using image analysis. J. Microb. Methods 39, 109.
27. ZACARIAS, G.D., FERREIRA, C.P., and VELASCO-HERNÁNDEZ, J.X. (2005). Porosity and tortuosity relations as revealed by a mathematical model of biofilm structure. J. Theor. Biol. 233(2), 245.
28. ZHANG, T., and BISHOP, P.L. (1994). Density, porosity and pore structure of biofilms. Water Res. 28, 2267.