Info

20. DeLong, E.F., Wickham, G.S., and Pace, N.R., Phylogenetic stains: ribosomal RNA based probes for the identification of single cells, Science, 243, 1360, 1989.

21. Ludwig, W. etal., ARB: a software environment for sequence data, Nucleic Acids Res., 32, 1363, 2004.

22. Cole, J.R. et al., The Ribosomal Database Project (RDP-II): previewing a new auto-aligner that allows regular updates and the new prokaryotic taxonomy, Nucleic Acids Res., 31, 442, 2003.

23. Loy, A., Horn, M., and Wagner, M., probeBase: an online resource for rRNA-targeted oligonucleotide probes, Nucleic Acids Res. ,31,514, 2003.

24. Amann, R. et al., In situ visualization of high genetic diversity in a natural microbial community, J. Bacteriol., 178, 3496, 1996.

25. Wagner, M. et al., Probing activated sludge with oligonucleotides specific for Proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure, Appl. Environ. Microbiol., 59, 1520, 1993.

26. Manz, W. et al., In situ characterization of the microbial consortia active in two wastewater treatment plants, Water Res., 28, 1715, 1994.

27. Snaidr, J. et al., Phylogenetic analysis and in situ identification of bacteria in activated sludge, Appl. Environ. Microbiol., 63, 2884, 1997.

28. Juretschko, S. et al., The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach, Sys. Appl. Microbiol., 25, 84, 2002.

29. Wagner, M. et al., In situ identification of ammonia-oxidizing bacteria, Syst. Appl. Microbiol., 18, 251, 1995.

30. Mobarry, B.K. et al., Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria, Appl. Environ. Microbiol., 62, 2156, 1996.

31. Daims, H. et al., In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants, Appl. Environ. Microbiol., 67, 5273, 2001.

Schramm, A. et al., Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor, Appl. Environ. Microbiol., 64, 3480, 1998.

Wagner, M. et al., Identification and in situ detection of gram-negative filamentous bacteria in activated sludge, Syst. Appl. Microbiol., 17, 405, 1994. Rossello-Mora, R.A. et al., The abundance of Zoogloea ramigera in sewage treatment plants, Appl. Environ. Microbiol., 61, 702, 1995.

Erhart, R. et al., Development and use of fluorescent in situ hybridization probes for the detection and identification of "Microthrix parvicella" in activated sludge, Syst. Appl. Microbiol., 20, 310, 1997.

Kanagawa, T. et al., Phylogenetic analysis of and oligonucleotide probe development for eikelboom type 021N filamentous bacteria isolated from bulking activated sludge, Appl. Environ. Microbiol., 66, 5043, 2000.

van der Waarde, J. et al., Molecular monitoring of bulking sludge in industrial wastewater treatment plants, Water Sci. Technol., 46, 551, 2002.

Thomsen, T.R. et al., In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth, Environ. Microbiol., 4, 383, 2002.

Schmid, M. et al., Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis, Water Res., 37, 2043, 2003.

Hesselmann, R.P.X. et al., Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge, Syst. Appl. Microbiol., 22, 454, 1999.

Crocetti, G.R. et al., Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation, Appl. Environ. Microbiol., 66, 1175, 2000.

Levantesi, C. et al., Analysis of the microbial community structure and function of a laboratory scale enhanced biological phosphorus removal reactor, Environ. Microbiol., 4, 559, 2002.

Lee, N. et al., Population dynamics and in situ physiology of phosphorus-accumulating bacteria in wastewater treatment plants with enhanced biological phosphorus removal operated with and without nitrogen removal, in 3rd IWA International Specialized Conference on Microorganisms in Activated Sludge and Biofilm Processes, Rome, p. 114, 2001.

Liu, W.T. et al., In situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process, Environ. Microbiol., 3, 110, 2001.

Wagner, M., Horn, M., and Daims, H., Fluorescence in situ hybridization for the identification of prokaryotes, Curr. Opin. Microbiol., 6, 302, 2003.

Wallner, G., Erhart, R., and Amann, R., Flow cytometric analysis of activated sludge with rRNA-targeted probes, Appl. Environ. Microbiol., 61, 1859, 1995.

Wallner, G. et al., Flow sorting of microorganisms for molecular analysis, Appl.

Environ. Microbiol., 63, 4223, 1997.

Bloem, J., Veninga, M., and Shepherd, J., Fully automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser scanning microscopy and image analysis, Appl. Environ. Microbiol., 61, 926, 1995. Ramsing, N.B. et al., Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column, Appl. Environ. Microbiol., 62, 1391, 1996. Pernthaler, J., Pernthaler, A., and Amann, R., Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization, Appl. Environ. Microbiol., 69, 2631, 2003.

51. Shopov, A., Williams, S.C., and Verity, P.G., Improvements in image analysis and fluorescence microscopy to discriminate and enumerate bacteria and viruses in aquatic samples, Aquat. Microb. Ecol., 22, 103, 2000.

52. Thompson, E., Quantitative microscopic analysis, J. Geol., 38, 193, 1930.

53. Amann, R.I. et al., Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations, Appl. Environ. Microbiol., 56, 1919, 1990.

54. Daims, H. et al., The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set, Syst. Appl. Microbiol., 22, 434, 1999.

55. Hicks, R.E., Amann, R.I., and Stahl, D.A., Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences, Appl. Environ. Microbiol., 58, 2158, 1992.

56. Bouchez, T. et al., Ecological study of a bioaugmentation failure, Environ. Microbiol., 2, 179, 2000.

57. Schmid, M. et al., Molecular evidence for a genus-level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation, Syst. Appl. Microbiol., 23, 93, 2000.

58. Daims, H. et al., Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization, Appl. Environ. Microbiol., 67, 5810, 2001.

59. Nedoma, J. et al., Quantification of pelagic filamentous microorganisms in aquatic environments using the line-intercept method, FEMS Microbiol. Ecol., 38, 81, 2001.

60. Pernthaler, J. et al., In situ classification and image cytometry of pelagic bacteria from a high mountain lake (Gossenköllesee, Austria), Appl. Environ. Microbiol., 63, 4778, 1997.

61. Blackburn, N. et al., Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis, Appl. Environ. Microbiol., 64, 3246, 1998.

62. Manz, W. et al., Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions, Syst. Appl. Microbiol., 15, 593, 1992.

63. Morgenroth, E. etal., Effect of long-term idle periods on the performance of sequencing batch reactors, Water Sci. Tech., 41, 105, 2000.

64. Heydorn, A. et al., Quantification of biofilm structures by the novel computer program COMSTAT, Microbiology, 146, 2395, 2000.

65. Xavier, J.B. et al., Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images, J. Microbiol. Methods, 47, 169, 2001.

66. Kuehn, M. et al., Automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms, Appl. Environ. Microbiol., 64, 4115, 1998.

67. Gueziec, A. and Hummel, R., Exploiting triangulated surface extraction using tetrahedral decomposition, IEEE Trans. Vis. Comput. Graph., 1, 328, 1995.

68. Brock, T.D. and Brock, M.L., Autoradiography as a tool in microbial ecology, Nature, 209, 734, 1968.

69. Ouverney, C.C. andFuhrman, J.A., Combinedmicroautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ, Appl. Environ. Microbiol., 65, 1746, 1999.

70. Lee, N. et al., Combination of fluorescent in situ hybridization and microautoradiography — a new tool for structure-function analyses in microbial ecology, Appl. Environ. Microbiol., 65, 1289, 1999.

Nielsen, P.H., de Muro, M.A., and Nielsen, J.L., Studies on the in situ physiology of Thiothrix spp. presentin activated sludge, Environ. Microbiol., 2, 389, 2000. Nielsen, P.H. et al., Microthrixparvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants, Water Sci. Technol., 46, 73, 2002. Ouverney, C.C. and Fuhrman, J.A., Marine planktonic archaea take up amino acids, Appl. Environ. Microbiol., 66, 4829, 2000.

Nielsen, J.L. et al., Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization, Environ. Microbiol., 5, 202, 2003.

Radajewski, S. et al., Stable-isotope probing as a tool in microbial ecology, Nature, 403, 646, 2000.

Whitby, C.B. et al., (13)C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations, Lett. Appl. Microbiol., 32, 398, 2001.

Manefield, M. et al., RNA stable isotope probing, a novel means of linking microbial community function to phylogeny, Appl. Environ. Microbiol., 68, 5367, 2002.

Ginige, M.P. et al., Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community, Appl. Environ. Microbiol., 70, 588, 2004. Adamczyk, J. et al., The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function, Appl. Environ. Microbiol., 69, 6875, 2003.

Wu, L. et al., Development and evaluation of functional gene arrays for detection of selected genes in the environment, Appl. Environ. Microbiol., 67, 5780, 2001. Dennis, P. et al., Monitoring gene expression in mixed microbial communities by using DNA microarrays, Appl. Environ. Microbiol., 69, 769, 2003.

Rodriguez, G.G. et al., Use of a fluorescent redox probe for direct visualization of actively respiring bacteria, Appl. Environ. Microbiol., 58, 1801, 1992. Karner, M. and Fuhrman, J.A., Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining, Appl. Environ. Microbiol., 63, 1208, 1997.

Nielsen, J.L., Aquino de Muro, M., and Nielsen, P.H., Evaluation of the redox dye 5-cyano-2,3-tolyl-tetrazolium chloride for activity studies by simultaneous use of microautoradiography and fluorescence in situ hybridization, Appl. Environ. Microbiol., 69, 641, 2003.

Bremer, H. and Dennis, P.P., Modulation of chemical composition and other parameters of the cell by growth rate, in Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., Neidhardt, F.C. et al., Eds., ASM Press, Washington, DC, p. 1553, 1996.

Binder, B.J. and Liu, Y.C., Growth rate regulation of rRNA content of a marine Synechococcus (Cyanobacterium) strain, Appl. Environ. Microbiol., 64, 3346, 1998. Cangelosi, G.A. and Brabant, W.H., Depletion of pre-16S rRNA in starved Escherichia coli cells, J. Bacteriol., 179, 4457, 1997.

Schmid, M. et al., 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection, Environ. Microbiol., 3, 450, 2001.

Oerther, D.B. et al., Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems, Appl. Environ. Microbiol., 66, 2154, 2000.

90. Bever, J., Stein, A., and Teichmann, H., Weitergehende Abwasserreinigung, R. Oldenbourg Verlag, München, 1995.

91. Henze, M. et al., Wastewater Treatment, 2nd ed., Springer-Verlag, Berlin, 1997.

92. Hovanec, T.A. and DeLong, E.F., Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria, Appl. Environ. Microbiol., 62, 2888,

0 0

Post a comment