• [1]
    Pernthaler, J., Glöckner, F.O., Unterholzner, S., Alfreider, A., Psenner, R., Amann, R. (1998) Seasonal community and population dynamics of pelagic Bacteria and Archaea in a high mountain lake. Appl. Environ. Microbiol. 64, 42994306.
  • [2]
    Glöckner, F.O., Fuchs, B.M., Amann, R. (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65, 37213726.
  • [3]
    Cottrell, M.T., Kirchman, D.L. (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66, 16921697.
  • [4]
    Pernthaler, A., Preston, C.M., Pernthaler, J., Delong, E.F., Amann, R. (2002) Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl. Environ. Microbiol. 68, 661667.
  • [5]
    Karner, M., Fuhrman, J.A. (1997) Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl. Environ. Microbiol. 63, 12081213.
  • [6]
    Delong, E.F., Wickham, G.S., Pace, N.R. (1989) Phylogenetic stains: Ribosomal RNA-based probes for the identification of single cells. Science 243, 13601363.
  • [7]
    Oda, Y., Slagman, S.-J., Meijer, W.G., Forney, L.J., Gottschal, J.C. (2000) Influence of growth rate and starvation on fluorescent in situ hybridization of Rhodopseudomonas palustris. FEMS Microbiol. Ecol. 32, 205213.
  • [8]
    Kerkhof, L., Ward, B.B. (1993) Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl. Environ. Microbiol. 59, 13031309.
  • [9]
    Christensen, H., Hansen, M., Sørensen, J. (1999) Counting and size classification of active soil bacteria by fluorescence In Situ hybridization with an rRNA oligonucleotide probe. Appl. Environ. Microbiol. 65, 17531761.
  • [10]
    Preston, C.M., Yiong Wu, K., Molinski, T.F., Delong, E.F. (1996) A psychrophylic Crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., spec. nov. Proc. Natl. Acad. Sci. USA 93, 62416246.
  • [11]
    Battin, T.J., Wille, A., Sattler, B., Psenner, R. (2001) Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl. Environ. Microbiol. 67, 799807.
  • [12]
    Ouverney, C.C., Fuhrman, J.A. (2000) Marine planktonic archaea take up amino acids. Appl. Environ. Microbiol. 66, 48294833.
  • [13]
    Vetriani, C., Jannasch, H.W., Mcgregor, B.J., Stahl, D.A., Reysenbach, A.L. (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediment. Appl. Environ. Microbiol. 65, 43754385.
  • [14]
    Massana, R., Murray, A.E., Preston, C.M., Delong, E.F. (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63, 5056.
  • [15]
    Fuchs, B.M., Wallner, G., Beisker, W., Schwippl, I., Ludwig, W., Amann, R. (1998) Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64, 49734982.
  • [16]
    Amann, R.I., Ludwig, W., Schleifer, K.-H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143169.
  • [17]
    Moter, A., Göbel, U.B. (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J. Microbiol. Methods 42, 85112.
  • [18]
    Eilers, H., Pernthaler, J., Glöckner, F.O., Amann, R.I. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66, 30443051.
  • [19]
    Šimek, K., Pernthaler, J., Weinbauer, M.G., Hornák, K., Dolan, J.R., Nedoma, J., Mašin, M., Amann, R.I. (2001) Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl. Environ. Microbiol. 67, 27232733.
  • [20]
    Gasol, J.M., Comerma, M., García, J.C., Armengol, J., Casamayor, E.O., Kojecká, P., Šimek, K. (2002) A transplant experiment to identify the factors controlling bacterial abundance, activity, production, and community composition in a eutrophic canyon-shaped reservoir. Limnol. Oceanogr. 47, 6277.
  • [21]
    Alfreider, A., Pernthaler, J., Amann, R., Sattler, B., Glöckner, F.O., Wille, A., Psenner, R. (1996) Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high montain lake by in situ hybridization. Appl. Environ. Microbiol. 62, 21382144.
  • [22]
    Lebaron, P., Servais, S., Troussellier, M., Courties, C., Muyzer, G., Bernard, L., Schäfer, H., Pukall, R., Stackebrandt, E., Guindulain, T., Vives-Rego, J. (2001) Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition. FEMS Microbiol. Ecol. 34, 255266.
  • [23]
    Šimek, K., Kojecká, P., Nedoma, J., Hartman, P., Vrba, J., Dolan, J.R. (1999) Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnol. Oceanogr. 44, 16341644.
  • [24]
    Kirchman, D.L., Meon, B., Cottrell, M.T., Hutchins, D.A., Weeks, D., Bruland, K.W. (2000) Carbon versus iron limitation of bacterial growth in the California upwelling regime. Limnol. Oceanogr. 45, 16811688.
  • [25]
    Bouvier, T.C., Del Giorgio, P.A. (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol. Oceanogr. 47, 453470.
  • [26]
    Kenzaka, T., Yamaguchi, N., Tani, K., Nasu, M. (1998) rRNA-targeted fluorescent in situ hybridization analysis of bacterial community structure in river water. Microbiology 144, 20852093.
  • [27]
    Wessendorf, M.W., Brelje, T.C. (1992) Which fluorophore is brightest? A comparison of the staining obtained using fluorescein, tetramethylrhodamine, lissamine rhodamine, Texas Red, and cyanine 3.18. Histochemistry 98, 8185.
  • [28]
    Manz, W., Eisenbrecher, M., Neu, T.R., Szewzyk, U. (1998) Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol. Ecol. 25, 4361.
  • [29]
    Manz, W., Szewzyk, U., Ericsson, P., Amann, R., Schleifer, K.-H., Stenström, T.-A. (1993) In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl. Environ. Microbiol. 59, 22932298.
  • [30]
    Wagner, M., Amann, R., Lemmer, H., Schleifer, K.-H. (1993) Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59, 15201525.
  • [31]
    Kämpfer, P., Erhart, R., Beimfohr, C., Böhringer, J., Wagner, M. (1996) Characterization of bacterial communities from activated sludge: culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNA-targeted oligonucleotide probes. Mar. Ecol. 32, 101121.
  • [32]
    Snaidr, J., Amann, R., Huber, I., Ludwig, W., Schleifer, K.-H. (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63, 28842896.
  • [33]
    Neef, A., Zaglauer, A., Heier, H., Amann, R., Lemmer, H., Schleifer, K.-H. (1996) Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilm. Appl. Environ. Microbiol. 62, 43294339.
  • [34]
    Weiss, P., Schweitzed, B., Amann, R., Simon, M. (1996) Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl. Environ. Microbiol. 62, 19982005.
  • [35]
    Grossart, H.-P., Simon, M. (1998) Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquat. Microb. Ecol. 15, 127140.
  • [36]
    Schweitzed, B., Huber, I., Amann, R., Ludwig, W., Simon, M. (2001) α- and β-Proteobacteria control the consumption and release of amino acids on lake snow aggregates. Appl. Environ. Microbiol. 67, 632645.
  • [37]
    Stahl, D.A. and Amann, R. (1991) Development and Application of Nucleic Acid Probes. In: Nucleic Acid Techniques in Bacterial Systematic (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 205–248. John Wiley and Sons Ltd, Chichester.
  • [38]
    Lathe, R. (1985) Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations. J. Mol. Biol. 183, 1112.
  • [39]
    Manz, W., Amann, R., Ludwig, W., Wagner, M., Schleifer, K.-H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15, 593600.
  • [40]
    Bond, P.L., Banfield, J.F. (2001) Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. Microb. Ecol. 41, 149161.
  • [41]
    Roller, C., Wagner, M., Amann, R., Ludwig, W., Schleifer, K.-H. (1994) In situ probing of Gram-positive bacteria with high DNA G1C content using 23S rRNA-targeted oligonucleotides. Microbiology 140, 28492858.
  • [42]
    Manz, W., Wagner, M., Amann, R., Schleifer, K.-H. (1994) In situ characterization of the microbial consortia active in two wastewater treatment plants. Wat. Res. 28, 17151723.
  • [43]
    Hicks, R., Amann, R., Stahl, D.A. (1992) Dual staining of natural bacterioplankton with 4′,6-diamidina-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl. Environ. Microbiol. 58, 21582163.
  • [44]
    Amann, R.I., Lin, C., Key, R., Montgomery, L., Stahl, D.A. (1992) Diversity among Fibrobacter isolates: towards a phylogenetic and habitat based classification. Syst. Appl. Microbiol. 15, 2331.
  • [45]
    Frischer, M.E., Danforth, J.M., Newton Healy, M.A., Saunders, F.M. (2000) Whole-cell versus total RNA extraction for analysis of microbial community structure with 16S rRNA-targeted oligonucleotide probes in salt marsh sediments. Appl. Environ. Microbiol. 66, 30373043.
  • [46]
    Rappé, D.M., Vergin, K., Giovannoni, S.I. (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol. Ecol. 33, 219232.
  • [47]
    Fegatella, F., Lim, J., Kjelleberg, S., Cavicchioli, R. (1998) Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 64, 44334438.
  • [48]
    Yun, N.R., Shin, Y.K., Hwang, S.Y., Kuraishi, H., Sugiyama, J., Kawahara, K. (2000) Chemotaxonomic and phylogenetic analyses of Sphingomonas strains isolated from ears of plants in the family Gramineae and a proposal of Sphingomonas roseoflava sp. nov. J. Gen. Microbiol. 46, 918.
  • [49]
    Ouverney, C.C., Fuhrman, J.A. (1999) Combined microautoradiography-16rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65, 17461752.
  • [50]
    Del Giorgio, P.A., Bouvier, T.C. (2002) Linking the physiologic and phylogenetic successions in free- living bacterial communities along an estuarine salinity gradient. Limnol. Oceanogr. 47, 471486.
  • [51]
    Ruimy, R., Breittmayer, V., Boivin, V., Christen, R. (1994) Assessment of the state of activity of individual bacterial cells by hybridization with a ribosomal RNA-targeted fluorescently-labelled oligonucleotidic probe. FEMS Microbiol. Ecol. 15, 207214.
  • [52]
    Kemp, P.F., Laroche, J. (1993) Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59, 25942601.
  • [53]
    Llobet-Brossa, E., Rosselló-Mora, R., Amann, R. (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64, 26912696.
  • [54]
    Murray, A.E., Preston, C.M., Massana, R., Taylor, L.T., Blakis, A., Wu, K., Delong, E.F. (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64, 25852595.
  • [55]
    Pernthaler, A., Alfreider, A., Posch, T., Andreatta, S., Psenner, R. (1997) In situ classification and image cytometry of pelagic bacteria from a high mountain lake (Gossenköllesee, Austria). Appl. Environ. Microbiol. 62, 47784783.
  • [56]
    Zarda, B., Mattison, G., Hess, A., Hahn, D., Höhener, P., Zeyer, J. (1998) Analysis of bacterial and protozoan communities in an aquifer contaminated with monoaromatic hydrocarbons. FEMS Microbiol. Ecol. 27, 141152.
  • [57]
    Zarda, B., Hahn, D., Chatzinotas, A., Schönhuber, W., Neef, A., Amann, R., Zeyer, J. (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch. Microbiol. 168, 185192.
  • [58]
    Kerkhof, L., Kemp, P.F. (1999) Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth. FEMS Microbiol. Ecol. 30, 253260.
  • [59]
    Fukui, M., Suwa, Y., Urushigawa, Y. (1996) High survival efficiency and ribosomal RNA decaying pattern of Desulfobacter latus, a highly specific acetate-utilizing organism, during starvation. FEMS Microbiol. Ecol. 19, 1725.
  • [60]
    Kramer, J.G., Singleton, F.L. (1992) Variation in rRNA content of marine vibrio spp. during starvation-survival and recovery. Appl. Environ. Microbiol. 58, 201207.
  • [61]
    Whiteley, A.S., Bailey, M.J. (2000) Bacterial community structure and physiological state within an industrial phenol bioremediation system. Appl. Environ. Microbiol. 66, 24002407.
  • [62]
    Williams, S.C., Hong, Y., Danavall, D.C.A., Howard-Jones, M.H., Gibson, D., Frischer, M.E., Verity, P.G. (1998) Distinguishing between living and nonliving bacteria: evaluation of the vital stain propidium iodide and the combined use with molecular probes in aquatic samples. J. Microbiol. Methods 32, 225236.
  • [63]
    Ouverney, C.C., Fuhrman, J.A. (1997) Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol. Appl. Environ. Microbiol. 63, 27352740.
  • [64]
    Tani, K., Kurokawa, K., Nasu, M. (1998) Development of a direct in situ PCR method for detection of specific bacteria in natural environments. Appl. Environ. Microbiol. 64, 15361540.
  • [65]
    Bruns, A., Berthe-Corti, L. (1998) In situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rRNA-directed oligonucleotide probes. Microbiology 144, 27832790.
  • [66]
    Kalmbach, S., Manz, W., Szewzyk, U. (1997) Dynamics of biofilm formation in drinking water: phylogenetic affiliation and metabolic potential of single cells assessed by formazan reduction and in situ hybridization. FEMS Microbiol. Ecol. 22, 265279.
  • [67]
    Wagner, M., Erhart, R., Manz, W., Amann, R., Lemmer, H., Wedi, D., Schleifer, K.-H. (1994) Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60, 792800.
  • [68]
    Ravenschlag, K., Sahm, K., Amann, R. (2001) Quantitative molecular analysis of the microbial community in marine artic sediments (Svalbard). Appl. Environ. Microbiol. 67, 387395.
  • [69]
    Hahn, D., Amann, R., Ludwig, W., Akkermans, A.D.L., Schleifer, K.-H. (1992) Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides. J. Gen. Microbiol. 138, 879887.
  • [70]
    Böckelmann, U., Manz, W., Thomas, R.N., Szewzyk, U. (2000) Characterization of the microbial community of lotic organic aggregates (‘river snow’) in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33, 157170.
  • [71]
    Pernthaler, A., Posch, T., Šimek, K., Vrba, J., Amann, R., Psenner, R. (1997) Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl. Environ. Microbiol. 63, 596601.
  • [72]
    Glöckner, F.O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A., Amann, R. (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl. Environ. Microbiol. 66, 50535065.
  • [73]
    Glöckner, F.O., Amann, R., Alfreider, A., Pernthaler, J., Psenner, R., Trebesius, K., Schleifer, K.-H. (1996) An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst. Appl. Microbiol. 19, 403406.
  • [74]
    Bosshard, P.P., Santini, Y., Grüter, D., Stettler, R., Bachofen, R. (2000) Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS Microbiol. Ecol. 31, 173182.
  • [75]
    Jürgens, K., Pernthaler, J., Schalla, S., Amann, R. (1999) Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl. Environ. Microbiol. 65, 12411250.
  • [76]
    Langenheder, S., Jürgens, K. (2001) Regulation of bacterial biomass and community structure by metezoan and protozoan predation. Limnol. Oceanogr. 46, 121134.
  • [77]
    Schrenk, M.O., Edwards, K.J., Goodman, R.M., Hamers, R.J., Banfield, J.F. (1998) Distribution of Thiobacillus ferroxidans and Leptospirillum ferrooxidans: Implications for generation of acid mine drainage. Science 279, 15191522.
  • [78]
    Manz, W., Wendt-Potthoff, K., Neu, T.R., Szewzyk, U., Lawrence, J.R. (1999) Phylogenetic composition, spatial structure and dynamics of lotic bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. Microb. Ecol. 37, 225237.
  • [79]
    Cottrell, M.T., Kirchman, D.L. (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl. Environ. Microbiol. 66, 51165122.
  • [80]
    Fuchs, B.M., Zubkov, M.V., Sahm, K., Burkill, P.H., Amann, R. (2000) Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Environ. Microbiol. 2, 191201.
  • [81]
    Ramsing, N.B., Fossing, H., Ferdelman, T.G., Andersen, F., Thamdrup, B. (1996) 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, 13911404.
  • [82]
    Eilers, H., Pernthaler, J., Amann, R. (2000) Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl. Environ. Microbiol. 66, 46344640.
  • [83]
    Simon, M., Glöckner, F.O., Amann, R. (1999) Different community structure and temperate optima of heterotrophic picoplankton in various regions of the southern ocean. Aquat. Microb. Ecol. 18, 275284.