Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms.

As a technique allowing simultaneous visualization, identification, enumeration and localization of individual microbial cells, fluorescence in situ hybridization (FISH) is useful for many applications in all fields of microbiology. FISH not only allows the detection of culturable microorganisms, but also of yet-to-be cultured (so-called unculturable) organisms, and can therefore help in understanding complex microbial communities. In this review, methodological aspects, as well as problems and pitfalls of FISH are discussed in an examination of past, present and future applications.

[1]  K. Schleifer,et al.  In situ identification of Legionellaceae using 16S rRNA-targeted oligonucleotide probes and confocal laser scanning microscopy. , 1995, Microbiology.

[2]  K. Schleifer,et al.  Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge. , 1999, Environmental microbiology.

[3]  D A Stahl,et al.  Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms , 1993, Applied and environmental microbiology.

[4]  H. Stender,et al.  Direct detection and identification of Mycobacterium tuberculosis in smear-positive sputum samples by fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes. , 1999, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[5]  J. Gerdes,et al.  Species-specific assessment of Mycobacterium leprae in skin biopsies by in situ hybridization and polymerase chain reaction. , 1992, Laboratory investigation; a journal of technical methods and pathology.

[6]  A. M. Prescott,et al.  Use of PNA oligonucleotides for the in situ detection of Escherichia coli in water. , 1999, Molecular and cellular probes.

[7]  S. E. Jorsal,et al.  Scanning Electron Microscopy and Fluorescent In Situ Hybridization of Experimental Brachyspira (Serpulina) pilosicoli Infection in Growing Pigs , 2000, Veterinary pathology.

[8]  W. D. de Vos,et al.  In Situ Detection of an Uncultured Predominant Bacillus in Dutch Grassland Soils , 1998, Applied and Environmental Microbiology.

[9]  M. Blaut,et al.  Quantification of the Flavonoid-Degrading BacteriumEubacterium ramulus in Human Fecal Samples with a Species-Specific Oligonucleotide Hybridization Probe , 1999, Applied and Environmental Microbiology.

[10]  U. Göbel.  Targeting Ribosomal RNA Sequences: A Universal Approach to the Detection and Identification of Microorganisms , 1991 .

[11]  R. Amann,et al.  Flow Cytometric Analysis of the In Situ Accessibility of Escherichia coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes , 1998, Applied and Environmental Microbiology.

[12]  A. Akkermans,et al.  Detection of Ralstonia solanacearum, Which Causes Brown Rot of Potato, by Fluorescent In Situ Hybridization with 23S rRNA-Targeted Probes , 1998, Applied and Environmental Microbiology.

[13]  K. Trebesius,et al.  Fluorescent In Situ Hybridization Allows Rapid Identification of Microorganisms in Blood Cultures , 2000, Journal of Clinical Microbiology.

[14]  M. van der Ploeg,et al.  2-Acetylaminofluorene-modified probes for the indirect hybridocytochemical detection of specific nucleic acid sequences. , 1984, Experimental cell research.

[15]  R. Sadighi,et al.  Detection of Mycoplasma pneumoniae-DNA within diseased gingiva by in situ hybridization using a biotin-labeled probe. , 1988, The Journal of Periodontology.

[16]  D. Graham,et al.  Detection of Helicobacter pylori in paraffin-embedded gastric biopsy specimens by in situ hybridization. , 1996, American journal of clinical pathology.

[17]  G. Albrecht‐Buehler.  Autofluorescence of live purple bacteria in the near infrared. , 1997, Experimental cell research.

[18]  K. Schleifer,et al.  In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes , 1993, Applied and environmental microbiology.

[19]  U. Szewzyk,et al.  Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. , 1999, International journal of systematic bacteriology.

[20]  R Amann,et al.  Flow sorting of microorganisms for molecular analysis , 1997, Applied and environmental microbiology.

[21]  R. Amann,et al.  Detection and identification of Candida species in experimentally infected tissue and human blood by rRNA-specific fluorescent in situ hybridization , 1997, Journal of clinical microbiology.

[22]  R. Amann,et al.  Development and use of fluorescent in situ hybridization probes for the detection and identification of 'Microthrix parvicella' in activated sludge , 1997 .

[23]  Rudolf Amann,et al.  Morphological and Compositional Changes in a Planktonic Bacterial Community in Response to Enhanced Protozoan Grazing , 1999, Applied and Environmental Microbiology.

[24]  G J Olsen,et al.  Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells , 1988, Journal of bacteriology.

[25]  U. Göbel,et al.  Molecular Epidemiology of Oral Treponemes Associated with Periodontal Disease , 1998, Journal of Clinical Microbiology.

[26]  K. Schleifer,et al.  Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilms , 1996, Applied and environmental microbiology.

[27]  S. Macnaughton,et al.  Permeabilization of mycolic-acid-containing actinomycetes for in situ hybridization with fluorescently labelled oligonucleotide probes. , 1994, Microbiology.

[28]  M Wagner,et al.  In situ identification of nocardioform actinomycetes in activated sludge using fluorescent rRNA-targeted oligonucleotide probes. , 1998, Microbiology.

[29]  J. C. van den Heuvel,et al.  Microscale Distribution of Populations and Activities ofNitrosospira and Nitrospira spp. along a Macroscale Gradient in a Nitrifying Bioreactor: Quantification by In Situ Hybridization and the Use of Microsensors , 1999, Applied and Environmental Microbiology.

[30]  S. Fujita,et al.  A NOVEL FLUORESCENT METHOD FOR IN SITU HYBRIDIZATION , 1993 .

[31]  E. N. Buckley,et al.  Response of marine bacterioplankton to differential filtration and confinement , 1984, Applied and environmental microbiology.

[32]  E. Lowbury,et al.  Use of an improved cetrimide agar medium and other culture methods for Pseudomonas aeruginosa , 1965, Journal of clinical pathology.

[33]  Yves Van de Peer,et al.  The European Small Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[34]  R. Amann,et al.  In Situ Identification of Cyanobacteria with Horseradish Peroxidase-Labeled, rRNA-Targeted Oligonucleotide Probes , 1999, Applied and Environmental Microbiology.

[35]  R. Spear,et al.  Quantitative fluorescence in situ hybridization of Aureobasidium pullulans on microscope slides and leaf surfaces , 1997, Applied and environmental microbiology.

[36]  Michael H. F. Wilkinson,et al.  Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry, and Motility Techniques and Applications , 1998 .

[37]  M. Birnstiel,et al.  RNA-DNA Hybrids at the Cytological Level , 1969, Nature.

[38]  S. McOrist,et al.  Specific in situ Hybridization of the Intracellular Organism of Porcine Proliferative Enteropathy , 1994, Veterinary pathology.

[39]  C. S. Kristensen,et al.  Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization , 1994, Infection and immunity.

[40]  P. Kemp,et al.  Use of multiple 16S rRNA-targeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria , 1993 .

[41]  T. R. Licht,et al.  Role of lipopolysaccharide in colonization of the mouse intestine by Salmonella typhimurium studied by in situ hybridization , 1996, Infection and immunity.

[42]  R. Amann,et al.  In situ analysis of microbial consortia in activated sludge using fluorescently labelled, rRNA‐targeted oligonucleotide probes and confocal scanning laser microscopy , 1994, Journal of microscopy.

[43]  K. Schleifer,et al.  Specific Detection of Legionella pneumophila: Construction of a New 16S rRNA-Targeted Oligonucleotide Probe , 1998, Applied and Environmental Microbiology.

[44]  D A Stahl,et al.  Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology , 1990, Journal of bacteriology.

[45]  G. Bottiroli,et al.  Natural fluorescence of white blood cells: spectroscopic and imaging study. , 1995, Journal of photochemistry and photobiology. B, Biology.

[46]  J. Gall,et al.  Molecular hybridization of radioactive DNA to the DNA of cytological preparations. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Amann,et al.  Microbial Community Composition of Wadden Sea Sediments as Revealed by Fluorescence In Situ Hybridization , 1998, Applied and Environmental Microbiology.

[48]  M. Wilkinson,et al.  Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples , 1995, Applied and environmental microbiology.

[49]  H. Harmsen,et al.  Rapid Identification of Bacteria in Blood Cultures by Using Fluorescently Labeled Oligonucleotide Probes , 2000, Journal of Clinical Microbiology.

[50]  N. Ashbolt,et al.  Evaluation of fluorochromes for flow cytometric detection of Cryptosporidium parvum oocysts labelled by fluorescent in situ hybridization , 1998, Letters in applied microbiology.

[51]  G. Fox,et al.  Rapid in situ hybridization technique using 16S rRNA segments for detecting and differentiating the closely related gram-positive organisms Bacillus polymyxa and Bacillus macerans , 1992, Applied and environmental microbiology.

[52]  F E Dewhirst,et al.  Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis , 1994, Infection and immunity.

[53]  R. Amann,et al.  On the Occurrence of Anoxic Microniches, Denitrification, and Sulfate Reduction in Aerated Activated Sludge , 1999, Applied and Environmental Microbiology.

[54]  Poonpilas Hongmanee,et al.  Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes for Differentiation between Tuberculous and Nontuberculous Mycobacterium Species in Smears of Mycobacterium Cultures , 1999, Journal of Clinical Microbiology.

[55]  Christina M. Preston,et al.  Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization , 1999, Applied and Environmental Microbiology.

[56]  F. Dewhirst,et al.  Molecular phylogeny and in situ detection of the etiologic agent of necrotizing hepatopancreatitis in shrimp , 1996, Applied and environmental microbiology.

[57]  N. Yamaguchi,et al.  Detection of specific bacterial cells with 2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate and fast red TR in situ hybridization , 1996, Applied and environmental microbiology.

[58]  A. Bruns,et al.  In situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rRNA-directed oligonucleotide probes. , 1998, Microbiology.

[59]  A. Graham.  Fungal autofluorescence with ultraviolet illumination. , 1983, American journal of clinical pathology.

[60]  K Kogure,et al.  A tentative direct microscopic method for counting living marine bacteria. , 1979, Canadian journal of microbiology.

[61]  U. Göbel,et al.  Identification of Bacteroides forsythus in subgingival plaque from patients with advanced periodontitis , 1993, Journal of clinical microbiology.

[62]  P Capodieci,et al.  Automated In Situ Hybridization: Diagnostic and Research Applications , 1998, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[63]  B. Christensson,et al.  Persistence of nontypeable Haemophilus influenzae in adenoid macrophages: a putative colonization mechanism. , 1996, Acta oto-laryngologica.

[64]  James R. Cole,et al.  The RDP (Ribosomal Database Project) continues , 2000, Nucleic Acids Res..

[65]  Mark Hernandez,et al.  Quantification of Gordona amarae Strains in Foaming Activated Sludge and Anaerobic Digester Systems with Oligonucleotide Hybridization Probes , 1998, Applied and Environmental Microbiology.

[66]  R Amann,et al.  Resuscitation of viable but nonculturable Legionella pneumophila Philadelphia JR32 by Acanthamoeba castellanii , 1997, Applied and environmental microbiology.

[67]  G. Welling,et al.  Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. , 1999, Journal of microbiological methods.

[68]  K. Schleifer,et al.  Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira-Like Bacteria as Dominant Populations , 1998, Applied and Environmental Microbiology.

[69]  M. Wagner,et al.  Fluorescence in situ hybridization shows spatial distribution of as yet uncultured treponemes in biopsies from digital dermatitis lesions. , 1998, Microbiology.

[70]  K. Schleifer,et al.  The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. , 1999, Systematic and applied microbiology.

[71]  T. Ferdelman,et al.  Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms , 1998, Applied and Environmental Microbiology.

[72]  K. Schleifer,et al.  Occurrence of fragmented 16S rRNA in an obligate bacterial endosymbiont of Paramecium caudatum. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[73]  K. Schleifer,et al.  In situ detection of a virulence factor mRNA and 16S rRNA in Listeria monocytogenes. , 1998, FEMS microbiology letters.

[74]  R Amann,et al.  In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides. , 1994, Microbiology.

[75]  Christiane Cantin,et al.  Differentiation of Methanosaeta concilii andMethanosarcina barkeri in Anaerobic Mesophilic Granular Sludge by Fluorescent In Situ Hybridization and Confocal Scanning Laser Microscopy , 1999, Applied and Environmental Microbiology.

[76]  S. E. Jorsal,et al.  Specific detection of the genusSerpulina, S. hyodysenteriaeandS. pilosicoliin porcine intestines by fluorescent rRNAin situhybridization , 1998 .

[77]  E. Nordheim,et al.  Quantitative imaging and statistical analysis of fluorescence in situ hybridization (FISH) of Aureobasidium pullulans. , 1999, Journal of microbiological methods.

[78]  S. Houston,et al.  Combined fluorescent in situ hybridisation and immunolabelling of Bacteroides fragilis. , 1998, Journal of immunological methods.

[79]  A. Lindberg,et al.  Haemophilus influenzae resides and multiplies intracellularly in human adenoid tissue as demonstrated by in situ hybridization and bacterial viability assay , 1994, Infection and immunity.

[80]  J. LaRoche,et al.  Estimating the Growth Rate of Slowly Growing Marine Bacteria from RNA Content , 1993, Applied and environmental microbiology.

[81]  R Amann,et al.  Phylogenetic analysis and in situ identification of bacteria in activated sludge , 1997, Applied and environmental microbiology.

[82]  L. Raskin,et al.  Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems , 1997, Applied and environmental microbiology.

[83]  K. Schleifer,et al.  Identification in situ and phylogeny of uncultured bacterial endosymbionts , 1991, Nature.

[84]  M. Wagner,et al.  Identification of Some of the Major Groups of Bacteria in Efficient and Nonefficient Biological Phosphorus Removal Activated Sludge Systems , 1999, Applied and Environmental Microbiology.

[85]  G. Murphy,et al.  Detection of Anaplasma Marginale DNA in Bovine Erythrocytes by Slot-Blot and in Situ Hybridization with a PCR-Mediated Digoxigenin-Labeled DNA Probe , 1995, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[86]  R. Amann,et al.  Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification , 1997, Applied and environmental microbiology.

[87]  J. Fuhrman,et al.  Combined Microautoradiography–16S rRNA Probe Technique for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ , 1999, Applied and Environmental Microbiology.

[88]  T. Oshima,et al.  Phylogenetic Diversity of Symbiotic Methanogens Living in the Hindgut of the Lower Termite Reticulitermes speratus Analyzed by PCR and In Situ Hybridization , 1999, Applied and Environmental Microbiology.

[89]  B K Ahring,et al.  Whole-cell hybridization of Methanosarcina cells with two new oligonucleotide probes , 1997, Applied and environmental microbiology.

[90]  D. Corey,et al.  Peptide nucleic acids: expanding the scope of nucleic acid recognition. , 1997, Trends in biotechnology.

[91]  K. Schleifer,et al.  Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides. , 1991, Journal of General Microbiology.

[92]  K. Schleifer,et al.  Detection and in situ identification of representatives of a widely distributed new bacterial phylum. , 1997, FEMS microbiology letters.

[93]  K. Schleifer,et al.  Combination of Fluorescent In Situ Hybridization and Microautoradiography—a New Tool for Structure-Function Analyses in Microbial Ecology , 1999, Applied and Environmental Microbiology.

[94]  Gerwin C. Raangs,et al.  Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes , 1998, Applied and Environmental Microbiology.

[95]  K. Schleifer,et al.  Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure , 1993, Applied and environmental microbiology.

[96]  F. Drobniewski,et al.  Differentiation of Mycobacterium tuberculosis Complex and Nontuberculous Mycobacterial Liquid Cultures by Using Peptide Nucleic Acid-Fluorescence In Situ Hybridization Probes , 2000, Journal of Clinical Microbiology.

[97]  R. Lathe.  Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations. , 1985, Journal of molecular biology.

[98]  Bjarke Bak Christensen,et al.  In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members , 1998, Applied and Environmental Microbiology.

[99]  U. Göbel,et al.  Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. , 1997, FEMS microbiology reviews.

[100]  R. Amann,et al.  Use of green fluorescent protein as a marker for ecological studies of activated sludge communities , 1997 .

[101]  C. V. D. van de Lest,et al.  Elimination of autofluorescence in immunofluorescence microscopy with digital image processing. , 1995, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[102]  J. Lanser,et al.  Problems associated with identification of Legionella species from the environment and isolation of six possible new species , 1990, Applied and environmental microbiology.

[103]  J. Heesemann,et al.  Specific and Rapid Detection by Fluorescent In Situ Hybridization of Bacteria in Clinical Samples Obtained from Cystic Fibrosis Patients , 2000, Journal of Clinical Microbiology.

[104]  C. Margo,et al.  The diagnostic value of fungal autofluorescence. , 1985, Survey of ophthalmology.

[105]  F. Waldman,et al.  Autofluorescence correction for fluorescence in situ hybridization. , 1995, Cytometry.

[106]  C Zimmer,et al.  Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. , 1986, Progress in biophysics and molecular biology.

[107]  J. Hacker,et al.  Detection of Staphylococcus aureus andStaphylococcus epidermidis in Clinical Samples by 16S rRNA-Directed In Situ Hybridization , 1999, Journal of Clinical Microbiology.

[108]  R. Amann,et al.  Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. , 1993, Cytometry.

[109]  R. Amann,et al.  Seasonal Community and Population Dynamics of Pelagic Bacteria and Archaea in a High Mountain Lake , 1998, Applied and Environmental Microbiology.

[110]  A. Pospischil,et al.  Detection of Chlamydia in formalin-fixed and paraffin-embedded avian tissue by in situ hybridization. A comparison between in situ hybridization and peroxidase-antiperoxidase labelling. , 1996, Zentralblatt fur Veterinarmedizin. Reihe B. Journal of veterinary medicine. Series B.

[111]  H. Niki,et al.  Dynamic organization of chromosomal DNA in Escherichia coli. , 2000, Genes & development.

[112]  R. Amann,et al.  Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow) , 1996, Applied and environmental microbiology.

[113]  J. Heesemann,et al.  Development of rRNA-Targeted PCR and In Situ Hybridization with Fluorescently Labelled Oligonucleotides for Detection of Yersinia Species , 1998, Journal of Clinical Microbiology.

[114]  M. Frischer,et al.  Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure. , 1996, Canadian journal of microbiology.

[115]  L. Leff,et al.  Comparison of Methods for the Concentration of Bacterioplankton for in Situ Hybridization , 1997 .

[116]  D. Relman,et al.  Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates , 1996, Clinical microbiology reviews.

[117]  W. Gilbert,et al.  Dealing with database explosion: a cautionary note. , 1997, Science.

[118]  K. Schleifer,et al.  In situ visualization of high genetic diversity in a natural microbial community , 1996, Journal of bacteriology.

[119]  R. Amann,et al.  Combination of rRNA-Targeted Hybridization Probes and Immuno-Probes for the Identification of Bacter , 1996 .

[120]  N. Yamaguchi,et al.  rRNA-targeted fluorescent in situ hybridization analysis of bacterial community structure in river water. , 1998, Microbiology.

[121]  T. R. Licht,et al.  Klebsiella pneumoniae Capsule Expression Is Necessary for Colonization of Large Intestines of Streptomycin-Treated Mice , 1999, Infection and Immunity.

[122]  U. Göbel,et al.  Qualitative und quantitative Untersuchungen zur Autofluoreszenz bei Pilzen , 1998 .

[123]  Frank Oliver Glöckner,et al.  An in situ hybridization protocol for detection and identification of planktonic bacteria , 1996 .

[124]  W. Ghiorse,et al.  Applications of laser scanning microscopy for analysis of aquatic microhabitats , 1996, Microscopy research and technique.

[125]  R. Amann,et al.  Specific detection of Candida albicans and Candida tropicalis by fluorescent in situ hybridization with an 18S rRNA-targeted oligonucleotide probe. , 1996, Microbiology.

[126]  H. Christensen,et al.  Evaluation of a fluorescence-labelled oligonucleotide probe targeting 23S rRNA for in situ detection of Salmonella serovars in paraffin-embedded tissue sections and their rapid identification in bacterial smears , 1997, Journal of clinical microbiology.

[127]  H. Harmsen,et al.  Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. , 2000, Journal of pediatric gastroenterology and nutrition.

[128]  K. Schleifer,et al.  In situ Identification of Lactococci, Enterococci and Streptococci , 1993 .

[129]  J. Whittum-Hudson,et al.  In Situ Hybridization for Detection of Inapparent Infection With Chlamydia trachomatis in Synovial Tissue of a Patient With Reiter’s Syndrome , 1995 .

[130]  R. Amann,et al.  Identification and Activities In Situ of Nitrosospiraand Nitrospira spp. as Dominant Populations in a Nitrifying Fluidized Bed Reactor , 1998, Applied and Environmental Microbiology.

[131]  A. Balows,et al.  Rapid Methods and Automation in Microbiology and Immunology , 1991, Springer Berlin Heidelberg.

[132]  S. Macnaughton,et al.  Physical stabilization and confocal microscopy of bacteria on roots using 16S rRNA targeted, fluorescent-labeled oligonucleotide probes , 1996 .

[133]  S. D. De Boer,et al.  Improved microscopic identification of Clavibacter michiganensis subsp. sepedonicus cells by combining in situ hybridization with immunofluorescence , 1997, Letters in applied microbiology.

[134]  U. Szewzyk,et al.  Widefield deconvolution epifluorescence microscopy combined with fluorescence in situ hybridization reveals the spatial arrangement of bacteria in sponge tissue. , 2000, Journal of microbiological methods.

[135]  H. Harmsen,et al.  Comparison of viable cell counts and fluorescence in situ hybridization using specific rRNA-based probes for the quantification of human fecal bacteria. , 2000, FEMS microbiology letters.

[136]  D. Veal,et al.  Evaluation of fluorochromes and excitation sources for immunofluorescence in water samples. , 1997, Cytometry.

[137]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[138]  K. Schleifer,et al.  In Situ Detection of Novel Bacterial Endosymbionts of Acanthamoeba spp. Phylogenetically Related to Members of the Order Rickettsiales , 1999, Applied and Environmental Microbiology.

[139]  C. Cullander.  Fluorescent probes for confocal microscopy. , 1999, Methods in molecular biology.

[140]  D. Sá,et al.  Development of a rapid method for detecting bacterial cells in situ using 16S rRNA-targeted probes. , 1992 .

[141]  T. Ferdelman,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 , 1996, Applied and environmental microbiology.

[142]  J. Waite,et al.  Use of Methacrylate De-embedding Protocols for In Situ Hybridization on Semithin Plastic Sections with Multiple Detection Strategies , 1998, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[143]  J. T. Staley,et al.  Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. , 1985, Annual review of microbiology.

[144]  R. Amann,et al.  Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations , 1990, Applied and environmental microbiology.

[145]  Ellen Jo Baron,et al.  Manual of clinical microbiology , 1975 .

[146]  K. Schleifer,et al.  The phylogenetic status of Sarcobium lyticum, an obligate intracellular bacterial parasite of small amoebae. , 1992, FEMS microbiology letters.

[147]  S. Kulakauskas,et al.  Estimation of the State of the Bacterial Cell Wall by Fluorescent In Situ Hybridization , 1998, Applied and Environmental Microbiology.

[148]  B. Christensen,et al.  Establishment of New Genetic Traits in a Microbial Biofilm Community , 1998, Applied and Environmental Microbiology.

[149]  Edward Ardern,et al.  Experiments on the oxidation of sewage without the aid of filters , 1914 .

[150]  S. Goodison,et al.  16S ribosomal DNA amplification for phylogenetic study , 1991, Journal of bacteriology.

[151]  D. Pinkel,et al.  Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[152]  E. Delong,et al.  Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. , 1989, Science.

[153]  R. Amann,et al.  Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization , 1996, Applied and environmental microbiology.