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.

Note: Microbial Mats -- Table of Contents -- FOREWORD: -- 1. Mats and Evolution -- 2. Microbial Mats for Field Research -- 3. Archaea and Bacteria -- PREFACE -- LIST OF AUTHORS for "Microbial mats" -- WHAT ARE MICROBIAL MATS ? -- 1. Introduction -- 2. Phenotypic Variations of Microbial Mats and Related Sedimentary Structures -- 2.1. LOCAL DOMINANCE OF CERTAIN MORPHOTYPES CONTROL MAT FABRICS -- 2.2. INDUCED GROWTH PHENOMENA -- 2.2.1. Growth Induced by Sedimentation Processes -- 2.2.2. Trapping/Baffling, Binding -- 2.2.3. Competitive Overriding: Biovarvites -- 2.2.4. Mat Surface Morphologies -- 2.3. Growth Responses to Physical Mat Destruction -- 2.3.1. Healing Cracks (Case Study) -- 2.4. MICROBIAL "JOINT VENTURE" -- 3. Summary and Conclusion -- 4. References -- PAPER FROM OUTER SPACE - ON "METEORPAPIER" AND MICROBIAL MATS -- 1. Introduction -- 2. Early Reports on "Meteorpapier" and Theories on Its Origin -- 3. The Elucidation of the True Nature of the "Meteorpapier" -- 4. Final Comments -- 5. References2 -- MICROBIAL MATS ON THE EARLY EARTH: The Archean Rock Record -- 1. Introduction -- 2. Examples of Archean Microbial Mats -- 2.1. KAAPVAAL CRATON -- 2.2. PILBARA CRATON -- 3. Discussion -- 4. Conclusions -- 5. Acknowledgments -- 6. References -- GUNFLINT CHERT MICROBIOTA REVISITED - NEITHER STROMATOLITES, NOR CYANOBACTERIA -- 1. Introduction -- 2. Material and Methods -- 2.1. GUNFLINT -- 2.2. FRENCH/SWISS JURASSIC AND WARSTEIN TERTIARY -- 2.3. CULTURES -- 3. Results and Discussion -- 4. Conclusions -- 5. References -- PALEOENVIRONMENTAL CONTEXT OF MICROBIAL MAT-RELATED STRUCTURES IN SILICICLASTIC ROCKS -- 1. Introduction -- 2. Brief Overview of (Paleo)Environmental Relationships of Mat-Formed Features -- 3. The Importance of Microtopography: Influence on Mat Types, Mat Growth and Mat Features in All Settings -- 4. Case Studies. , 4.1. MAGALIESBERG FORMATION (Ca. 2.1 Ga), KAAPVAAL CRATON, SOUTH AFRICA -- 4.2. SONIA SANDSTONE (Ca. 0.6 Ga), RAJASTHAN, INDIA -- 4.3. VINDHYAN SUPERGROUP (~1.7-0.6 Ga), BHANDARA CRATON -- 5. Influence of Mat Growth on Facies Stacking Patterns and Sequence Stratigraphic Architecture -- 6. Discussion -- 7. Conclusions -- 8. References -- MICROBIALLY RELATED STRUCTURES IN SILICICLASTIC SEDIMENT RESEMBLING EDIACARAN FOSSILS: Examples from India, Ancient and Modern -- 1. Introduction -- 2. Geological Background of the Ancient Formations -- 3. Sedimentologic Frame of the Modern Setting -- 4. Microbial Mat-Related Structures Resembling Ediacaran Fossils -- 4.1. FEATURES IN THE CHORHAT SANDSTONE -- 4.2. FEATURES IN THE SIRBU SHALE -- 4.3. FEATURES IN THE SONIA SANDSTONE -- 4.4. MAT FEATURES FROM THE MODERN GULF OF CAMBAY -- 5. Discussion -- 6. Conclusions -- 7. References -- OSMOTROPHIC BIOFILMS: FROM MODERN TO ANCIENT -- 1. Introduction -- 2. Osmotrophic Biofilms in Subterranean Caves and Karsts -- 3. Osmotrophs in Other Early Terrestrial Settings -- 4. Osmotrophic Biodictyons in Ancient Tree Resins and Soils -- 5. Osmotrophic Mats in Modern Marine Settings -- 6. Osmotrophic Mats in Ediacaran Marginal Seas -- 7. Osmotrophic Mats in Deeper Ediacaran Seas -- 8. Osmotrophs and the Cambrian Explosion -- 9. Conclusion -- 10. Acknowledgments -- 11. References -- MICROBIAL MATS AS A SOURCE OF BIOSIGNATURES -- 1. What Is a Microbial Mat? -- 1.1. MICROBIAL MATS AS PRECURSORS OF STROMATOLITES -- 1.2. ACCRETION OF A MICROBIAL MAT -- 1.3. CALCIFICATION AS AN EXAMPLE OF A UBIQUITOUS MICROBIAL-MINERAL INTERACTION -- 2. Microbial Mats as a Source of Diverse Biosignatures -- 3. Chemical Biosignatures Embedded in Microbial Mats -- 4. Morphological Biosignatures -- 4.1. MACROSCOPIC -- 4.2. MICROSCOPIC BIOSIGNATURES -- 4.2.1. Microfossils -- 4.2.2. Microbial Ichnofossils. , 5. Concluding Remarks -- 6. Acknowledgments -- 7. References -- MOLECULAR INVESTIGATIONS AND EXPERIMENTAL MANIPULATIONS OF MICROBIAL MATS: A VIEW TO PALEOMICROBIAL ECOSYSTEMS -- 1. Evolution of Microbial Mats -- 2. Dominant Microorganisms in Hypersaline Microbial Mats -- 3. Community Structure of Microbial Mats as Revealed by Lipid Biomarker Analysis -- 4. Manipulation Experiments of Hypersaline Microcoleus Mats -- 4.1. LONG-TERM EFFECTS OF EXPERIMENTALLY LOWERED SALINITY -- 4.2. LONG-TERM EFFECTS OF LOWERED SULFATE -- 5. Acknowledgments -- 6. References -- ARCHITECTURE OF ARCHAEAL-DOMINATED MICROBIAL MATS FROM COLD SEEPS IN THE BLACK SEA (DNJEPR CANYON, LOWER CRIMEAN SHELF) -- 1. Introduction -- 2. Materials and Methods -- 3. Principal Build-up and Community Structure of the Archaeal-Dominated AOM Microbial Mats -- 4. The External Black Microbial Mat -- 5. The Internal Orange/Pink Microbial Mat -- 6. Architecture and Structure of Cold-Seep-Related Carbonate Towers -- 7. Description of the Microbial Mat Spheres: The "Sponge Model" -- 8. Carbonate and Fe-Sulfide Phases -- 9. Acknowledgments -- 10. References -- BIODYNAMICS OF MODERN MARINE STROMATOLITES -- 1. Introduction -- 2. Recent Biodynamic Studies -- 2.1. RECONSTITUTION STUDIES -- 2.2. HOW MUCH STROMATOLITE MATERIAL IS NEEDED TO STABILIZE -- 3. Discussion -- 4. Acknowledgments -- 5. References -- ENTOPHYSALIS MATS AS ENVIRONMENTAL REGULATORS -- 1. Introduction -- 2. Entophysalis in the Microbial Mats of Abu Dhabi (UAE) -- 3. Morphotypic Properties of Entophysalis -- 4. Macro- and Microscale Distribution of Entophysalis -- 5. Entophysalis and Stromatolites -- 6. Fossil Entophysalis -- 7. Concluding Remarks -- 8. References -- DIVERSITY AND ROLE OF CYANOBACTERIA AND AEROBIC HETEROTROPHIC MICROORGANISMS IN CARBON CYCLING IN ARID CYANOBACTERIAL MATS -- 1. Introduction. , 1.1. EXTREME ARID ENVIRONMENTAL CONDITIONS AND MULTIPLE STRESS -- 1.2. MICROBIAL MAT TYPES -- 2. Autotrophy and Heterotrophy: General Overview of Carbon Cycling in Microbial Mats -- 3. Carbon Flow in the Uppermost Mat Layer -- 4. Oxygenic Phototrophs: The Driving Force for Carbon Cycling -- 5. Aerobic Heterotrophic Prokaryotes: Diversity and Fundamental Role in Microbial Mats -- 5.1. DIVERSITY AND ABUNDANCE OF AEROBIC HETEROTROPHIC MICROORGANISMS -- 5.2. INTERACTION BETWEEN CYANOBACTERIA AND AEROBIC HETEROTROPHIC BACTERIA IN CARBON CYCLING -- 6. Effect of Salinity on Carbon Cycling in Microbial Mats -- 6.1. SALINITY DETERMINES THE DIVERSITY OF PHOTOTROPHS AND HETEROTROPHS -- 6.2. TIDAL POSITION AND CARBON CYCLING -- 6.3. WHY HIGH SALINITIES INHIBIT PHOTOSYNTHESIS AND AEROBIC RESPIRATION? -- 7. Temperature Regulation of Carbon Cycling -- 8. Concluding Remarks -- 9. References -- OOID ACCRETING DIATOM COMMUNITIES FROM THE MODERN MARINE STROMATOLITES AT HIGHBORNE CAY, BAHAMAS -- 1. Introduction -- 2. Stalked Diatoms -- 3. Tube-Forming Diatoms -- 4. Diatoms and Stromatolite Biogenesis -- 5. Acknowledgments -- 6. References -- EXOPOLYMERS (EXTRACELLULAR POLYMERIC SUBSTANCES) IN DIATOM-DOMINATED MARINE SEDIMENT BIOFILMS -- 1. Introduction -- 2. Measuring EPS in Natural MPB Biofilms -- 3. EPS Production in Diatom Biofilms -- 4. References -- MICROBIAL MATS FROM WIND FLATS OF THE SOUTHERN BALTIC SEA -- 1. The Baltic Sea - Special Features Enabling the Development of Microbial Mats -- 2. Microbial Mats in the "Bock" Wind Flat -- 3. Community Structure of Microbial Mats of the "Bock" Wind Flat -- 3.1. CYANOBACTERIA -- 3.2. DIATOMS -- 3.3. HETEROTROPHIC BACTERIA -- 3.4. PURPLE SULFUR BACTERIA -- 3.5. PROTOZOA AS MICROGRAZERS -- 4. Productivity of Microbial Mats in the "Bock" Wind Flat -- 5. Conclusions -- 6. References -- DIAZOTROPHIC MICROBIAL MATS. , 1. Introduction -- 2. Occurrence of Microbial Mats -- 2.1. INTERTIDAL MICROBIAL MATS -- 2.2. ANTARCTIC MICROBIAL MATS -- 2.3. HOT SPRING MICROBIAL MATS -- 2.4. HYPERSALINE MICROBIAL MATS -- 3. Factors Controlling Occurrence and Performance of Diazotrophic Microbial Mats -- 3.1. TEMPERATURE -- 3.2. SALINITY -- 4. Summary -- 5. References -- ARCHITECTURES OF BIOCOMPLEXITY: Lichen-dominated Soil Crusts and Mats -- 1. Introduction -- 2. From Lichen Crusts to Lichen Mats on Exposed Soils -- 3. Community Structure of Lichen Crusts and Mats on Soils -- 4. Interior Design of Lichen-Dominated Soil Crusts -- 5. Accessory Cyanobacteria: Cyanotrophy and Cephalodia -- 6. Selective Assemblages -- 7. Acknowledgments -- 8. References -- IRON AND BACTERIAL BIOFILM DEVELOPMENT -- 1. Introduction -- 2. Iron Acquisition and Regulation in Bacteria -- 2.1. IRON UPTAKE BY SIDEROPHORES -- 2.2. NON-SIDEROPHORE IRON UPTAKE -- 2.3. IRON sTARVATION SIGMA FACTOR -- 2.4. FUR AND sRNA REGULATION -- 3. Biofilms and Corrosion -- 4. Biofilm Formation and Iron Regulation -- 4.1. STAPHYLOCOCCUS AUREUS -- 4.2. STAPHYLOCOCCUS EPIDERMIDIS -- 4.3. PSEUDOMONAS AERUGINOSA -- 4.4. ESCHERICHIA COLI -- 4.5. VIBRIO CHOLERAE -- 4.6. ORAL PATHOGENS -- 4.7. MYCOBACTERIUM SMEGMATIS -- 4.8. IRON AND THE BIOFILM MATRIX -- 5. Concluding Remarks -- 6. References -- MATS OF FILAMENTOUS AND UNICELLULAR CYANOBACTERIA IN HYPERSALINE ENVIRONMENTS -- 1. Introduction -- 2. Microcoleus chthonoplastes as a Mat-Forming Microorganism -- 3. Mats of Unicellular and Filamentous Cyanobacteria Embedded in Gypusm Crusts -- 4. Final Comments -- 5. Acknowledgments -- 6. References -- MARINE HYPERSALINE MICROCOLEUS-DOMINATED CYANOBACTERIAL MATS IN THE SALTERN AT GUERRERO NEGRO, BAJA CALIFORNIA SUR, MEXICO: -- 1. Introduction. , 2. Seawater Evaporation Ponds and Photosynthetic Biota along the Salinity Gradient in the Exportadora de Sal, S. A. (ESSA), G.

Note: Intro -- Contents -- Contributors -- Preface -- 1: Ecology and Evolution of Haloquadratum walsbyi Through the Lens of Genomics and Metagenomics -- Introduction -- The ecology of solar saltern crystallizer -- Haloquadratum walsbyi: the uncultivable species -- Unveiling the extent of intragenomic diversity in Haloquadratum walsbyi -- Metagenomic islands -- Interactions between Haloquadratum walsbyi and other species in the crystallizer pond -- The metagenomic insight into predator-prey interplay in aquatic environments -- The 'Constant diversity' dynamics model -- Conclusion -- 2: Salinibacter ruber: The Never Ending Microdiversity? -- Introduction -- Abundance and distribution revisited -- Microdiversity and recombination -- Inter-domain (Archaea-Bacteria) lateral gene transfer: archaeal genes in Salinibacter ruber genomes -- The power of metabolomics to explore phenotypic microdiversity -- Future trends -- 3: Horizontal Gene Transfer in Halobacteria -- Introduction -- Mechanisms of horizontal gene transfer -- Mechanisms of horizontal gene transfer in Halobacteria -- Evidence for horizontal gene transfer in Halobacteria from single gene studies -- The origins of the Halobacteria may be rooted in horizontal gene transfer -- Homologous recombination within and between Halobacterial lineages -- Geographic isolation and barriers to recombination -- 4: Comparative Genomics of Haloarchaeal Viruses -- Introduction -- Haloarchaeal versus prokaryotic viruses -- Infection cycle -- Related or not related, that's the problem -- The influence of viral genes on their hosts -- Haloarchaeal viruses -- Conclusions and future prospects -- 5: Microbial Adaptation to Saline Environments: Lessons from the Genomes of Natranaerobius thermophilus and Halobacillus halophilus -- Introduction -- The anaerobic polyextremophile Natranaerobius thermophilus. , The aerobic moderately halophilic Halobacillus halophilus -- Synopsis -- 6: Staying in Shape: The Haloarchaeal Cell Wall -- Introduction -- Structure of haloarchaeal surface (S)-layers -- Haloarchaeal S-layer glycoproteins -- Glycosylation of haloarchaeal S-layer glycoproteins -- Modulation of haloarchaeal S-layer glycoprotein N-glycosylation as an adaptive response -- Lipid-modification of haloarchaeal S-layer glycoproteins -- The cell envelope of the square haloarchaeon, Haloquadratum walsbyi -- Does the haloarchaeal cell envelope include a periplasmic space? -- The heteropolysaccharide cell walls of Halococcus morrhuae and Natronococcus occultus -- Future trends -- 7: Cell Cycle and Polyploidy in Haloarchaea -- Introduction -- The cell cycle of Halobacterium salinarum -- Regulated polyploidy in haloarchaea -- Evolutionary advantages of haloarchaeal polyploidy -- Gene conversion and escape from 'Muller's ratchet' -- Conclusions and outlook -- 8: Cell Regulation by Proteolytic Systems and Protein Conjugation -- Introduction -- Intramembrane proteolysis -- Energy-dependent proteases -- Targeting proteins for proteolysis -- Conclusions -- Index.

Note: Intro -- CONTENTS -- Foreword -- Joseph Seckbach -- Introduction -- Nina Gunde-Cimerman, Aharon Oren and Ana Plemenitaš -- Section I. The environments and their diversity -- Microbial diversity of Great Salt Lake -- Bonnie K. Baxter, Carol D. Litchfield, Kevin Sowers, Jack D. Griffith, Priya Arora DasSarma and Shiladitya DasSarma -- Microbial communities in the Dead Sea - past, present and future -- Aharon Oren, Ittai Gavrieli, Jonah Gavrieli, Marco Kohen, Joseph Lati and Mordehay Aharoni -- Microscopic examination of microbial communities along a salinity gradient in saltern evaporation ponds: a 'halophilic safari -- Aharon Oren -- The microbial diversity of a solar saltern on San Francisco Bay -- Carol D. Litchfield, Masoumeh Sikaroodi and Patrick M. Gillivet -- Diversity of microbial communities: the case of solar salterns -- Carlos Pedrós-Alió -- Isolation of viable haloarchaea from ancient salt deposits and application of fluorescent stains for in situ detection of halophiles in hypersaline environmental samples and model fluid inclusions -- Stefan Leuko, Andrea Legat, Sergiu Fendrihan, Heidi Wieland, Christian Radax, Claudia Gruber, Marion Pfaffenhuemer, Gerhard Weidler and Helga Stan-Lotter -- Hydrocarbon degradation under hypersaline conditions. Some facts, some experiments and many open questions -- Heiko Patzelt -- The relevance of halophiles and other extremophiles to Martian and extraterrestrial environments -- Joseph Seckbach -- Halophiles: a terrestrial analog for life in brines on Mars - Halophiles on Mars -- Rocco L. Mancinelli -- Section II. Archaea -- Comparative genomic survey of information transfer systems in two diverse extremely halophilic Archaea, Halobacterium sp. strain NRC-1 and Haloarcula Marismortui -- Brian R. Berquist, Jeetendra Soneja and Shiladitya DasSarma -- Walsby's square archaeon. , it's hip to be square but even more hip to be culturable Henk Bolhuis -- Henk Bolhuis -- Gene regulation and the initiation of translation in halophilic Archaea -- Felicitas Pfeifer, Peter Zimmermann, Sandra Scheuch and Simone Sartorius-Neef -- Protein Translation, Targeting and Translocation in Haloferax Volcanii -- Jerry Eichler, Gabriela Ring, Vered Irihimovitch, Tovit Lichi, Irit Tozik and Zvia Konrad -- Enzymes of halophilic Archaea. Recent findings on ureases and nucleoside diphosphate kinases -- Toru Mizuki, Ron Usami, Masayuki Kamo, Masaru Tanokura and Masahiro Kamekura -- Osmoadaptation in methanogenic Archaea: recent insights from a genomic perspective -- Katharina Pflüger, Heidi Wieland and Volker Müller -- Section III. Bacteria -- Salinibacter ruber: genomics and biogeography -- Josefa Antón, Arantxa Peña, Maria Valens, Fernando Santos, Frank-Oliver Glöckner, Margarete Bauer, Joaquín Dopazo, Javier Herrero, Ramon Rosselló-Mora and Rudolf Amann -- What we can deduce about metabolism in the moderate Halophile Chromohalobacter salexigens from its genomic sequence -- Laszlo N. Csonka, Kathleen O'Connor, Frank Larimer, Paul Richardson, Alla Lapidus, Adam D. Ewing, Bradley W. Goodner and Aharon Oren -- K+ Transport and its role for osmoregulation in an Halophilic member of the Bacteria Domain: Characterization of the K+ uptake systems from Halomonas Elongata -- Hans-Jörg Kunte -- The chloride regulon of Halobacillus halophilus: a novel regulatory network for salt perception and signal transduction in bacteria -- Volker Müller and Stephan H. Saum -- Biosynthesis of the compatible solute mannosylglycerate from hyperthermophiles to mesophiles. Genes, enzymes and evolutionary perspectives -- Milton S. da Costa and Nuno Empadinhas. , Genes and enzymes of ectoine biosynthesis in the haloalkaliphilic obligate methanotroph "Methylomicrobium alcaliphilum 20Z" -- Alexander S. Reshetnikov, Valentina N. Khmelenina, Ildar I. Mustakhimov, Yana V. Ryzhmanova and Yuri A. Trotsenko -- Halophilic Archaea and Bacteria as a source of extracellular hydrolytic enzymes -- Antonio Ventosa, Cristina Sánchez-Porro, Sara Martín and Encarnación Mellado -- Biopolyester production: halophilic microorganisms as an attractive source -- Jorge Quillaguamán, Bo Mattiasson and Rajni Hatti-Kaul -- Section IV. Fungi -- Relation of halotolerance to human pathogenicity in the fungal tree of life: an overview of ecology and evolution under stress -- Sybren de Hoog, Polona Zalar, Bert Gerrits van den Ende and Nina Gunde-Cimerman -- Halotolerant and halophilic fungi from coastal environments in the Arctics -- Nina Gunde-Cimerman, Lorena Butinar, Silva Sonjak, Martina Turk, Viktor Uršic, Polona Zalar and Ana Plemenitaš -- Halotolerant and halophilic fungi and their extrolite production -- Jens C. Frisvad -- Introducing Debaryomyces hansenii, a salt-loving yeast -- José Ramos -- Cellular responses in the halophilic black yeast Hortaea werneckii to high environmental salinity -- Ana Plemenitaš and Nina Gunde-Cimerman -- Halotolerance and lichen symbioses -- Martin Grube and Juliane Blaha -- Section V. Algae -- A century of Dunaliella research: 1905-2005 -- Aharon Oren -- Molecular determinants of protein Halotolerance: Structural and functional studies of the extremely salt tolerant carbonic anhydrases from Dunaliella Salina -- Lakshmane Premkumar, Michal Volkovitsky, Irena Gokhman, Joel L. Sussman and Ada Zamir -- Section VI. Protozoa -- Heterotrophic protozoa from hypersaline environments -- Gwen Hauer and Andrew Rogerson -- Heterotrophic flagellates in hypersaline waters -- Byung C. Cho -- Section VII. Viruses. , Haloviruses and their hosts. Recent progress in the cultivation of haloarchaea, includung square haloarchaea of Walsby and the isolation of novel haloarchaeal viruses -- Mike L. Dyall-Smith, David G. Burns, Helen M. Camakaris, Peter H. Janssen, Brandan E. Russ and Kate Porter -- Subject Index -- Organisms Index -- Author Index.

Note: Intro -- Methods in Microbiology -- Methods in Microbiology Volume 35 Extremophiles -- Contents -- Series Advisors -- Contributors -- Colour Plate Section -- 1 Extremophile Microorganisms and the Methods to Handle Them -- Thermophiles -- 2 In Situ Activity Studies in Thermal Environments -- 3 The Isolation of Thermophiles from Deep-sea Hydrothermal Environments -- 4 Growth of Hyperthermophilic Microorganisms for Physiological and Nutritional Studies -- 5 Toward the Large Scale Cultivation of Hyperthermophiles at High-Temperature and High-Pressure -- 6 Analysis of Lipids from Extremophilic Bacteria -- 7 Membranes of Thermophiles and Other Extremophiles -- 8 Characterization and Quantification of Compatible Solutes in (Hyper)thermophilic Microorganisms -- 9 Functional Genomics of the Thermo-Acidophilic Archaeon Sulfolobus solfataricus -- 10 Heat Shock Proteins in Hyperthermophiles -- 11 Deep-sea Thermococcales and their Genetic Elements: Plasmids and Viruses -- 12 Genetic Systems for Thermus Beate Averhoff -- 13 Gene Transfer Systems for Obligately Anaerobic Thermophilic Bacteria -- 14 Hyperthermophilic Virus-Host Systems: Detection and Isolation -- 15 Preservation of Thermophilic Microorganisms -- Psychrophiles -- 16 Handling of Psychrophilic Microorganisms -- 17 Proteins from Psychrophiles -- Alkaliphiles -- 18 Cultivation of Aerobic Alkaliphiles -- 19 Isolation, Cultivation and Characterization of Alkalithermophiles -- Acidophiles -- 20 The Isolation and Study of Acidophilic Microorganisms Acidophilic microorganisms -- Halophiles -- 21 Characterization of Natural Communities of Halophilic Microorganisms -- 22 Cultivation of Haloarchaea -- 23 Extraction of Halophiles from Ancient Crystals -- 24 The Assessment of the Viability of Halophilic Microorganisms in Natural Communities -- 25 Characterization of Lipids of Halophilic Archaea. , 26 Characterization of Organic Compatible Solutes of Halotolerant and Halophilic Microorganisms -- 27 Genetic Systems for Halophilic Archaea -- 28 The Isolation and Study of Viruses of Halophilic Microorganisms -- 29 Detection, Quantification and Purification of Halocins: Peptide Antibiotics from Haloarchaeal Extremophiles -- 30 Storage of Halophilic Bacteria -- Barophiles -- 31 Handling of Piezophilic Microorganisms -- Radiation- Resistant Microorganisms -- 32 Measuring Survival in Microbial Populations Following Exposure to Ionizing Radiation -- Strict Anaerobes -- 33 The Study of Strictly Anaerobic Microorganisms -- Applications of Extremophiles -- 34 Applications of Extremophiles: The Industrial Screening of Extremophiles for Valuable Biomolecules -- Index.

Note: Intro -- Contents -- 1 -- 2 -- 3 -- 4 -- 5 -- 6 -- 7 -- 8 -- 9 -- 10 -- Index.

Note: Intro -- Table of Contents -- Introduction -- Foreword -- Preface -- Pioneering Studies of Extremophiles -- Thermophiles -- Alkaliphiles -- Extreme Environments -- Definition of Extremophiles -- Distribution of Polyextremophiles -- References -- Editors' Biographies -- List of Authors and their Addresses -- Part I: GENERAL ASPECTS -- Polyextremophiles and the Constraints for Terrestrial Habitability -- 1. Introduction -- 2. Adaptations for Life at Individual Extremes -- 2.1. Temperature: Thermophiles and Psychrophiles -- 2.2. pH: Acidophiles and Alkaliphiles -- 2.3. Salinity: Halophiles -- 2.4. Pressure: Piezophiles -- 2.5. Radiation: Radioresistance -- 2.6. Desiccation: Xerophiles -- 2.7. Oxygen: Aerobes, Anaerobes, and Microaerophiles -- 3. Polyextremophiles: Life at the Interface of Extremes -- 3.1. Temperature and pH -- 3.2. Temperature and Salinity -- 3.3. Temperature and Pressure -- 3.4. Temperature and Radiation -- 3.5. pH and Salinity -- 3.6. pH and Pressure -- 3.7. pH and Radiation -- 3.8. Salinity and Pressure -- 3.9. Desiccation, Temperature, and Pressure -- 3.10. Desiccation, pH, and Salinity -- 3.11. Desiccation and Radiation -- 4. Synthetic Polyextremophiles and Space Exploration -- 5. References -- Life on the Edge and Astrobiology: Who Is Who in the Polyextremophiles World? -- 1. Introduction -- 2. The Extremophiles -- 2.1. Categories of the Extremophiles -- 2.2. Habitats and Living Conditions of Extremophiles -- 2.3. Publication and Distribution of Extremophiles -- 3. The Polyextremophiles and Early Earth -- 3.1. Biodistribution of Extremophiles -- 3.2. Long-Lived Bacteria -- 3.3. Eukaryotic Lower and Higher Extremophilic Organisms -- 3.3.1. Shrimp Beneath Ice and Pompeii Worm -- 3.3.2. Subsurface Nematodes -- 3.3.3. Tardigrades -- 3.3.4. Ticks Inside the Electrons Stream -- 4. Astrobiology. , 4.1. The Possibility for Extremophiles to Live in Extraterrestrial Places -- 4.1.1. Mars: Our Sister Planet -- 4.1.2. Europa: The Ocean Moon of Jupiter -- 4.1.3. "JUICE" Mission to the Jovian Moons Next Decade -- 4.1.4. Penetrator with a Drill Designed to Enter into Europa's Ice -- 4.1.5. Titan -- 4.1.6. Enceladus: The Satellite of Saturn (The King of the Rings) -- 4.1.7. Venus: Out of the Habitability Question -- 4.2. The Extremophiles as Analogues for Extraterrestrial Bodies: Mars and Europa -- 4.3. Blood Falls, Antarctica as a Model for Extraterrestrial Life -- 4.4. Conclusion for Possibility of Extraterrestrial Life -- 5. General Summary and Conclusions -- 6. Acknowledgements -- 7. References -- The Dynamic Genomes of Acidophiles -- 1. Introduction -- 2. Genomic Variation in Natural Populations -- 3. Virus and CRISPR Loci -- 4. Genomic Islands and Plasmids -- 5. Insertion Sequences and Transposase Activity -- 6. Conclusions -- 7. Acknowledgments -- 8. References -- Part II: HALOPHILES -- Two Centuries of Microbiological Research in the Wadi Natrun, Egypt: A Model System for the Study of the Ecology, Physiology, and Taxonomy of Haloalkaliphilic Microorganisms -- 1. Introduction -- 2. Studies of the Microbiology of the Wadi Natrun Lakes in the Nineteenth and Early Twentieth Centuries -- 3. The Anoxygenic Phototrophic Sulfur Bacteria and the Chemoautotrophic Sulfur Oxidizers of the Wadi Natrun Lakes -- 4. Haloalkaliphilic Archaea in the Wadi Natrun Lakes and Their Contribution to the Color of the Brines -- 5. Alkaliphilic Aerobic and Anaerobic Endospore-Forming Bacteria from the Wadi Natrun Lakes -- 6. The Wadi Natrun Lakes Revisited: Discovery of the Anaerobic Haloalkalithermophiles -- 7. Final Comments -- 8. Acknowledgments -- 9. References -- Adaptation in haloalkaliphiles and Natronophilic Bacteria -- 1. Introduction. , 2. Habitats and Diversity of Haloalkaliphilic and Natronophilic Bacteria -- 2.1. Saline-Alkaline Habitats -- 2.2. Biodiversity of Soda Environments -- 3. Mechanisms of High-Salt and Alkaline Adaptation in Bacteria -- 3.1. Adaptation of the Bacterial Cell Envelope to Haloalkaline Conditions -- 3.1.1. Phospholipid and Fatty Acid Composition of Halophilic, Alkaliphilic, and Haloalkaliphilic Membranes -- 3.1.2. The Acidic Cell Wall of Halo- and Alkaliphiles -- 3.2. Osmoadaptation in Haloalkaliphilic and Natronophilic Bacteria -- 3.2.1. The Universal Compatible Solute, Glycine Betaine -- 3.2.2. Ectoine Is a Multivalent Compatible Solute -- 3.2.3. Glutamate as an Additional Anionic Osmolyte -- 3.2.4. Sucrose and Trehalose: Minor Osmolytes with Stabilizing Roles -- 3.2.5. K + Is the Main Osmolyte in Anaerobic Extreme Haloalkaliphiles -- 3.3. Adaptation of the Oxidative Phosphorylation (OXPHOS) Machinery to Overcome Low PMF -- 3.3.1. Features of Alkaliphilic F-Type ATP Synthase -- 3.3.2. Adaptation of Respiratory Chain Components at Alkaline pH -- 3.4. NA + -Dependent Flagellar Movement -- 3.5. pH and Ion Homeostasis in the Cytoplasm of Haloalkaliphiles -- 3.5.1. Na + /H + Antiporters -- 3.5.2. Mrp and Mrp-Like Antiporters -- 3.5.3. K + Transport and Intracellular Homeostasis -- 3.5.4. Sodium Import Closes the Sodium Cycle in Salt- and Alkaline-Adapted Cells -- 3.5.5. Bicarbonate Transport in Lithotrophic Haloalkaliphiles and Natronophiles -- 3.6. Adaptation to High-Light and Oxidative Stress by Specific Membrane Pigments -- 4. Conclusions -- 5. Acknowledgements -- 6. References -- A Random Biogeochemical Walk into Three Soda Lakes of the Western USA: With an Introduction to a Few of Their Microbial Denizens -- 1. Introduction -- 2. Big Soda Lake, Nevada -- 3. Mono Lake, California -- 4. Searles Lake, California -- 5. References. , Halophilic, Acidophilic, and Haloacidophilic Prokaryotes -- 1. Introduction -- 2. Halophilic Prokaryotes -- 3. Acidophilic Prokaryotes -- 4. Microbial Communities of the Acid-Saline Environment -- 5. Acidophilic Haloarchaea -- 5.1. Searching for Acidophilic Haloarchaea -- 5.2. Phylogeny Analysis of Acidophilic Haloarchaea -- 5.3. Physiology of Acido-haloarchaea -- 6. References -- Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions -- 1. Introduction -- 2. Divalent Cation Concentrations and Halophily: The Hofmeister Series -- 3. Intracellular Concentrations of Divalent Cations in Halophilic Microorganisms -- 4. Case Studies -- 4.1. Solar Salterns -- 4.2. The Dead Sea -- 4.3. The Limits of Life at High Magnesium Chloride: Studies on Discovery Brine -- 4.4. The Magnesium Sulfate Brines of Hot Lake, Washington -- 4.5. The Concentrated Calcium Chloride Brines of Don Juan Pond, Antarctica: The Supreme Challenge to Life -- 5. Do "Chaophilic" Microorganisms Exist? -- 6. References -- Survival Strategies of Halophilic Oligotrophic and Desiccation Resistant Prokaryotes -- 1. Introduction -- 2. General Strategies -- 2.1. Response to High Concentrations of Salt: Osmoadaptation -- 2.2. Oligotrophy and Starvation -- 2.3. Desiccation and Low Water Activity -- 3. Specific Strategies of Halophilic Prokaryotes -- 3.1. A Unique Protein of Hqt . walsbyi Protects Against Desiccation -- 3.2. Surviving Oligotrophic Conditions and Starvation -- 3.3. Sphere Formation in Fluid Inclusions -- 3.4. Further Aspects and Future Research -- 4. Extraterrestrial Halite -- 5. Conclusions and Considerations for Astrobiology -- 6. Summary -- 7. Acknowledgements -- 8. References -- Radiation Resistance in Extremophiles: Fending Off Multiple Attacks -- 1. Extremophiles and Radiation Resistance -- 2. Cellular Effects of Ionizing Radiation. , 3. Radioprotection and Damage Repair -- 4. Enzymatic Defense and IR -- 5. Manganese (Mn) Antioxidants -- 6. What Is the Basis for the Radiation Resistance of the Polyextremophile H. salinarum ? -- 7. What About Thermophiles? -- 8. Relevance to Astrobiology -- 9. Conclusion -- 10. Acknowledgment -- 11. References -- Part III: THERMOPHILES -- Thermoalkaliphilic Microbes -- 1. Introduction -- 2. Life in Hot and Alkaline Conditions: General Considerations -- 3. Definitions and Taxonomical Importance -- 3.1. Alkaliphiles -- 3.2. Thermophiles -- 3.3. Thermoalkaliphilic Microbes -- 4. Habitats: Environmental Conditions Where They Thrive Well -- 5. Physiological Properties: Adaptation or Natural Selection? -- 5.1. Adaptive Mechanisms for Alkaline Conditions -- 6. Use of Thermoalkaliphiles in Biotechnology -- 6.1. Proteases -- 6.2. Amylases -- 6.3. Cellulases -- 6.4. Xylanases -- 7. Conclusions and Future Prospects -- 8. References -- Acido- and Thermophilic Microorganisms: Their Features, and the Identification of Novel Enzymes or Pathways -- 1. Introduction to Acido- and Thermophilic Microorganisms -- 2. Characteristics of Microorganisms in the Genus Sulfolobus -- 3. Features Detected from the Genomic Information of Microorganisms in Sulfolobus -- 4. Resources Identified from Sulfolobus Species -- 4.1. Hexose Kinase -- 4.2. ST0452 Protein as a Sugar-1-Phosphate Nucleotidylyl-Transferase and an Amino-Sugar-1-Phosphate Acetyltransferase -- 5. Acknowledgements -- 6. References -- Microbial Diversity in Acidic High-Temperature Steam Vents -- 1. Introduction -- 2. Steam Cave and Vent Sites -- 3. Fumarole Characteristics and Sample Collection -- 3.1. Steam Sample Collection -- 3.2. Steam Deposit Collection -- 4. Steam Deposit DNA Extraction -- 5. Clones Obtained and Phylogenetic Analysis -- 6. Steam Deposit Cultures -- 7. Final Considerations. , 8. Acknowledgments.

Note: Intro -- Halophiles and Hypersaline Environments -- Preface -- Contents -- Contributors -- Chapter 1: Helge Larsen (1922-2005) and His Contributions to the Study of Halophilic Microorganisms -- Chapter 2: The Halophilic World of Lourens Baas Becking -- Chapter 3: Taxonomy, Phylogeny, and Biotechnological Interest of the Family Halomonadaceae -- Chapter 4: The Hypersaline Lakes of Inner Mongolia: The MGAtech Project -- Chapter 5: From Genomics to Microevolution and Ecology: The Case of Salinibacter ruber -- Chapter 6: Impact of Lipidomics on the Microbial World of Hypersaline Environments -- Chapter 7: Molecular Mechanisms of Adaptations to High Salt Concentration in the Extremely Halotolerant Black Yeast Hortaea wer -- Chapter 8: Viruses from the Hypersaline Environment -- Chapter 9: Haloviruses of Great Salt Lake: A Model for Understanding Viral Diversity -- Chapter 10: Initiation and Regulation of Translation in Halophilic Archaea -- Chapter 11: Protein Transport Into and Across Haloarchaeal Cytoplasmic Membranes -- Chapter 12: Salty and Sweet: Protein Glycosylation in Haloferax volcanii -- Chapter 13: Effect of Anoxic Conditions and Temperature on Gas Vesicle Formation in Halobacterium salinarum -- Chapter 14: Halophiles Exposed Concomitantly to Multiple Stressors: Adaptive Mechanisms of Halophilic Alkalithermophiles -- Chapter 15: Cellular Adjustments of Bacillus subtilis and Other Bacilli to Fluctuating Salinities -- Chapter 16: The Nature and Function of Carotenoids in the Moderately Halophilic Bacterium Halobacillus halophilus -- Chapter 17: Xanthorhodopsin -- Chapter 18: Potential Enhancement of Biofuel Production Through Enzymatic Biomass Degradation Activity and Biodiesel Production by Halophilic Microorganisms -- Chapter 19: Enzymes from Halophilic Archaea: Open Questions. , Chapter 20: A Short History of the Symposia on Halophilic Microorganisms: From Rehovot 1978 to Beijing 2010 -- Index.

Note: Includes bibliographical references and index