Note: Front Cover -- Methods in Microbiology -- Copyright Page -- Dedication -- Contents -- Series Advisors -- List of Contributors -- 1. Taxonomy of Prokaryotes - Introduction -- References -- 2. How to Describe New Species of Prokaryotes -- I. Description of New Species of Prokaryotes - A Polyphasic Approach -- II. Components of the Description of a Novel Species -- A. Summary/Abstract -- B. Introduction -- C. Methods and Materials -- D. Results and Discussion -- E. The Species Description -- References -- 3. Phenotypic and Physiological Characterization Methods -- I. Introduction -- II. Fundamental Physiological Tests -- A. Respiratory Enzyme Tests -- 1. Oxidase test (indophenol oxidase, cytochrome c oxidase and cytochrome a3 oxidase) -- 2. Catalase test -- B. Relation to Oxygen -- 1. Semisolid agar method -- 2. Manometric method -- C. Relation to Carbon Dioxide -- 1. Manometric method (Han et al., 1991 -- Smibert and Krieg, 1994) -- 2. Methods for autotrophs -- D. Relation to Hydrogen -- 1. Manometric method for the heterotroph Campylobacter mucosalis -- 2. Manometric method for Herbaspirillum autotrophicum -- E. Temperature Range and Optima for Growth -- F. Optimum pH and pH Range for Growth -- G. NaCl or Seawater Ranges and Optima for Growth -- H. Oxidative and Fermentative Metabolism -- 1. O/F test -- I. Acid Production from Carbohydrates -- J. Gas Production from Carbohydrates -- K. Fermentation Products -- 1. Capillary GLC method -- 2. HPLC method 1 -- 3. HPLC method 2 -- L. Carbon Source Utilization -- 1. Auxanography (the use of a plate culture in which variable conditions are provided to determine the effect of these conditions on growth) -- 2. Turbidimetric method -- M. Nitrogen Source Utilization -- 1. Sole nitrogen sources -- 2. Nitrogen fixation -- N. Nitrate Reduction and Denitrification -- 1. Nitrate reduction -- 2. Nitrite reduction. , 3. Detection of N2O as evidence of denitrification -- O. Hydrolysis of Polymers -- 1. Agar hydrolysis -- 2. Azocoll™ protein hydrolysis -- 3. Cellulose hydrolysis -- 4. DNA hydrolysis -- 5. Gelatin and casein hydrolysis -- 6. Starch hydrolysis -- P. Pigmentation -- 1. Fluorescent pigments -- 2. Diffusible, non-fluorescent pigments -- 3. Water-soluble pigments from aromatic amino acids -- 4. Water-insoluble pigments -- Q. Iron Porphyrin Compounds -- III. Other Physiological Tests -- A. Acetamide Hydrolysis -- B. Ammonia from Arginine -- C. Aromatic Ring Cleavage -- D. Arylsulfatase Activity -- 1. p-Nitrophenyl sulfate method -- 2. 5-Bromo-4-chloro-3-indolyl sulfate method -- E. Bile Solubility -- 1. Colony procedure -- 2. Broth procedure -- F. Bile Tolerance -- 1. Solid medium method -- 2. Broth method for anaerobes -- G. Citrate Utilization -- H. Dye Tolerance -- I. Esculin Hydrolysis -- 1. Agar medium method -- 2. Rapid test -- J. Glycosidases -- 1. Chromogenic substrates -- 2. Fluorogenic substrates -- K. Hippurate Hydrolysis -- L. Hydrogen Sulfide Production -- 1. Thiosulfate iron H2S test -- 2. Paper strip method for amino acid desulfurase activity (Lányi, 1987) -- M. Indole Production -- 1. Kovacs′ test -- 2. Xylene extraction test -- N. Indoxyl Acetate Hydrolysis -- O. 3-Ketolactase from Lactose Oxidation -- P. Lactic Acid Optical Rotation -- Q. Lecithinase -- R. Lipase -- S. Lysine and Ornithine Decarboxylases -- T. Malonate Utilization -- U. Methyl Red Test -- V. Peptidases -- W. Phenylalanine Deaminase -- X. Phosphatases -- 1. General method for phosphatases -- 2. Broth method for acid and alkaline phosphatases -- 3. Method for alkaline phosphatase -- Y. Poly-β-Hydroxybutyrate (PHB) Formation -- 1. Visualization of PHB inclusions in cells -- 2. Chemical analysis -- Z. Triple-Sugar Iron Agar Reactions -- AA. Urease -- 1. Method 1. , 2. Method 2 -- AB. Voges-Proskauer (VP) Test -- AC. X and V Factor Requirements -- 1. Disc method -- 2. Rapid test for the ability to synthesize the X factor -- IV. Commercial Multi-Test Systems -- References -- 4. Microscopy -- I. Introduction -- II. Light Microscopy -- A. Illumination Techniques in Light Microscopy -- 1. Transmitted light microscopy -- 2. Bright field (Köhler illumination) microscopy -- 3. Dark field microscopy -- 4. Phase-contrast microscopy -- 5. Fluorescence microscopy -- 6. Confocal laser scanning microscopy -- B. Preparation Methods for Light Microscopy -- 1. Living cell suspensions -- 2. Immobilization of motile bacteria -- 3. Fixation of suspensions or smears -- 4. Negative staining of capsules and layers -- 5. Gram-staining -- 6. Flagella staining -- 7. Acid-fast staining -- 8. Endospore staining -- 9. Cytoplasmic inclusions staining -- 10. Immunofluorescence labelling of a bacterial cell surface-bound antigen -- III. Transmission Electron Microscopy (TEM) -- A. Negative-Staining Methods -- 1. Preparation of carbon film on mica -- 2. Negative staining with carbon film -- 3. Preparation of carbon-coated plastic films on grids -- 4. Negative staining with carbon-coated Formvar/Butvar films -- B. Metal-Shadowing -- C. Embedding and Ultrathin Sectioning -- 1. Conventional embedding of specimen for ultrathin sectioning -- 2. Fixation -- 3. Dehydration -- 4. Embedding with resin -- 5. Embedding for visualization of intracellular membranes -- 6. Embedding for immunocytochemistry applying the progressive lowering of temperature (PLT) method and Lowicryl resins -- 7. Embedding for immunocytochemistry using LRWhite resin -- 8. Embedding after high-pressure freezing (HPF) and freeze-substitution (FS) -- 9. Ultramicrotomy -- IV. Field Emission Scanning Electron Microscopy (FESEM) -- A Preparation Steps for FESEM -- 1. Fixation. , 2. Support for bacteria in FESEM -- 3. Dehydration -- 4. Critical-point drying -- 5. Mounting the specimen -- 6. Sputter coating of the specimen -- B. Immune FESEM -- 1. Fixation of the specimen -- 2. Incubation with antibody and protein gold-nanoparticles -- 3. Second fixation step -- 4. Mounting of the specimen -- 5. Coating of the specimen -- 6. Imaging of the specimen -- V. Suppliers of Light and Electron Microscopic Equipment and Chemicals -- VI. Concluding Remarks -- References -- 5. Peptidoglycan Structure -- I. Introduction -- II. Primary Structure of the Peptidoglycan -- III. Analytical Approaches for the Elucidation of the Peptidoglycan Structure -- A. Information from Whole-Cell Hydrolysates -- 1. Detection of Dpm isomers and of OH-Dpm -- 2. Detection of glycolic acid -- 3. Analysis of whole-cell sugars -- B. Preparation of Peptidoglycan -- 1. Gram-negative bacteria -- 2. Gram-positive acid-fast bacteria -- 3. Gram-positive non-acid-fast bacteria -- C. Analyses of Peptidoglycan Preparations -- 1. Qualitative amino acid composition -- 2. Quantitative analysis of amino acids -- 3. Enantiomeric analysis of amino acids -- 4. Arrangement of amino acids within the peptidoglycan -- IV. Concluding Remarks -- Acknowledgments -- References -- 6. Cell Wall Teichoic Acids in the Taxonomy and Characterization of Gram-positive Bacteria -- I. Introduction -- II. Cell Wall Teichoic Acids: Occurrence and Structural Diversity -- A. Poly(polyol phosphates)-Teichoic Acids of Type I -- B. Poly(glycosylpolyol phosphates)-Teichoic Acids of Type II -- C. Poly(acylglycosylpolyol phosphates)-Teichoic Acids of Type III -- D. Poly(polyol phosphate-glycosyl phosphates)-Teichoic Acids of Type IV -- E. Poly(polyol phosphate-glycosylpolyol phosphates)-Teichoic Acids of Type V -- III. Cell Wall Teichoic Acids in the Taxonomy of Gram-positive Bacteria. , A. Order Actinomycetales -- 1. Presence/absence of cell wall teichoic acids as a chemotaxonomic characteristic of members of the order Actinomycetales -- 2. Cell wall teichoic acids as a species-specific marker for members of the order Actinomycetales -- (a) Cell wall teichoic acids of Nocardiopsis species and subspecies -- (b) Cell wall teichoic acids of Brevibacterium species -- (c) Cell wall teichoic acids of Agromyces species and subspecies -- (d) Cell wall teichoic acids of Nocardioides species -- (e) Cell wall teichoic acids of Glycomyces species -- (f) Cell wall teichoic acids of Actinomadura and Nonomuraea species -- (g) Cell wall teichoic acids of Streptomyces species -- The Streptomyces cyaneus cluster (Williams et al., 1983) -- The Streptomyces fulvissimus cluster (Williams et al., 1983) -- The Streptomyces violaceusniger cluster (Williams et al., 1983) -- The Streptoverticillium species group -- B. The Genus Bacillus -- 1. Presence/absence of cell wall teichoic acids as a chemotaxonomic characteristic for species of the genus Bacillus -- 2. Cell wall teichoic acids as a species-specific marker for the representatives of the Bacillus subtilis group -- IV. Methods for the Isolation and Structural Investigation of Cell Wall Teichoic Acids -- A. Cultivation Conditions -- 1. Cultivation conditions of actinobacteria -- 2. Cultivation conditions of Bacillus species -- B. Isolation of Cell Walls -- C. Extraction of Teichoic Acids -- D. Chemical Methods of Teichoic Acids Analysis -- 1. Acid hydrolysis -- 2. Descending paper chromatography -- 3. Paper electrophoresis -- 4. Detection of compounds -- 5. Gel chromatography -- 6. Determination of the absolute configuration of the polymer components -- (a) The absolute configuration of glutamic acid -- (b) The absolute configuration of lysine -- (c) The absolute configuration of amino sugars. , (d) The absolute configuration of neutral monosaccharides.