Abstract
Ecophysiological analysis and functions of single cells in complex microbial systems can be examined by simple combinations of Fluorescence in situ hybridization (FISH) for identification with various staining techniques targeting functional phenotypes. In this chapter, we describe methods and protocols optimized for the study of extracellular enzymes, surface hydrophobicity and specific surface structures. Although primarily applied to the study of microbes in wastewater treatment (activated sludge and biofilms), the methods may also be used with minor modifications in several other ecosystems.
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References
Nielsen, P. H., Roslev, P., Dueholm, T. E., and Nielsen, J. L. (2002) Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. Water Sci. Technol. 46, 73–80.
Kragelund, C., Remesova, Z., Nielsen, J. L., Thomsen, T. R., Eales K.l., Seviour, R. J., et al. (2007) Ecophysiology of mycolic acid containing Actinobacteria (Mycolata) in activated sludge foams. FEMS Microbiol. Ecol. 61, 174–184.
Van Ommen Kloecke, F., and Geesey, G. G. (1999) Localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs. Microb. Ecol. 38, 201–214.
Kragelund, C., Levantesi, C., Borger, A., Thelen, K., Eikelboom, D., Tandoi, V., et al. (2008) Identity, abundance and ecophysiology of filamentous bacteria belonging to the Bacteroidetes present in activated sludge plants. Microbiology 154, 886–894.
Xia, Y., Kong, Y., and Nielsen, P. H. (2007) In situ detection of protein-hydrolysing microorganisms in activated sludge. FEMS Microbiol. Ecol. 60, 156–165.
Xia, Y., Kong, Y., Thomsen, T. R., and Nielsen, P. H. (2008) Identification and ecophysiological characterization of epiphytic protein-hydrolyzing saprospiraceae ("Candidatus Epiflobacter" spp.) in activated sludge. Appl. Environ. Microbiol. 74, 2229–2238.
Zita, A., and Hermansson, M. (1997) Determination of bacterial cell surface hydrophobicity of single cells in cultures and in wastewater in situ. FEMS Microbiol. Lett.152,299–306.
Zita, A., and Hermansson, M. (1997) Effects of bacterial cell surface structures and hydrophobicity on attachment to activated sludge flocs. Appl. Environ. Microbiol. 63, 1168–1170.
Nielsen, J. L., Mikkelsen, L. H., and Nielsen, P. H. (2001) In situ detection of cell surface hydrophobicity of probe-defined bacteria in activated sludge. Water Sci. Tech. 43, 97–103.
Kragelund, C., Nielsen, J. L., Thomsen, T. R., and Nielsen, P. H. (2005) Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge. FEMS Microbiol. Ecol. 54, 111–122.
Larsen, P., Nielsen, J. L., Otzen, D., and Nielsen, P. H. (2008) Amyloid-like adhesins produced by floc-forming and filamentous bacteria in activated sludge. Appl. Environ. Microbiol. 74, 1517–1526.
Larsen, P., Nielsen, J. L., Dueholm, M. S., Wetzel, R., Otzen, D., and Nielsen, P. H. (2007) Amyloid adhesins are abundant in natural biofilms. Environ. Microbiol. 9, 3077–3090.
Chorvat, D., Jr., Kirchnerova, J., Cagalinec, M., Smolka, J., Mateasik, A., and Chorvatova, A. (2005) Spectral unmixing of flavin autofluorescence components in cardiac myocytes. Biophys. J. 89, L55–L57.
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Nielsen, J.L., Kragelund, C., Nielsen, P.H. (2010). Ecophysiological Analysis of Microorganisms in Complex Microbial Systems by Combination of Fluorescence In Situ Hybridization with Extracellular Staining Techniques. In: Cummings, S. (eds) Bioremediation. Methods in Molecular Biology, vol 599. Humana Press. https://doi.org/10.1007/978-1-60761-439-5_8
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DOI: https://doi.org/10.1007/978-1-60761-439-5_8
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