Advances in Applied Microbiology
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Table of contents
- Contentsv
- Contributorsxi
- Chapter 1: Anaerobic Biodegradation of Methyl tert-Butyl Ether (MTBE) and Related Fuel Oxygenates1
- I. Introduction1
- II. Fuel Oxygenates as Contaminants of Water Sources3
- III. Environmental Fate4
- IV. MTBE Biodegradation5
- V. Monitoring Natural Attenuation11
- VI. Summary15
- References16
- Chapter 2: Controlled Biomineralization by and Applications of Magnetotactic Bacteria21
- I. Introduction22
- II. Features of the Magnetotactic Bacteria22
- A. General features22
- B. Distribution and ecology23
- C. Phylogeny and taxonomy24
- D. Physiology26
- III. The Magnetosome30
- A. Composition of magnetosome crystals30
- B. Size of magnetosome crystals31
- C. Magnetosome crystal morphologies31
- D. Arrangement of magnetosomes within cells33
- E. Biological advantage of magnetotaxis34
- IV. Chemical and Molecular Basis of Magnetosome Synthesis35
- A. Genomics of magnetotactic bacteria36
- B. Genetic systems and manipulations in magnetotactic bacteria37
- C. The magnetosome membrane38
- D. Physiological conditions under which magnetite magnetosomes are synthesized46
- E. Regulation of the expression of magnetosome genes47
- V. Applications of Magnetotactic Bacteria, Magnetosomes, and Magnetosome Crystals48
- A. Mass cultivation of magnetotactic bacteria48
- B. Applications of cells of magnetotactic bacteria49
- C. Applications of magnetosomes and magnetosome crystals50
- VI. Conclusions and Future Research Directions52
- Acknowledgments52
- References52
- Chapter 3: The Distribution and Diversity of Euryarchaeota in Termite Guts63
- I. Introduction63
- II. Euryarchaeota in Termite Guts64
- A. Termite gut structure and metabolism64
- III. Detection of Euryarchaeota in Termite Guts67
- A. Isolated Euryarchaeota from termite guts67
- B. Uncultured Euryarchaeota in lower termite guts72
- C. Uncultured Euryarchaeota in higher termite guts73
- IV. Why Are There Different Euryarchaeota in Different Termites?76
- V. Conclusion77
- References77
- Chapter 4: Understanding Microbially Active Biogeochemical Environments81
- I. Introduction82
- II. An Introduction to the Molecular Microbial World83
- A. 16S approaches84
- B. rRNA and mRNA85
- C. Recent technological advances86
- III. Microorganisms in the Environment87
- A. Microbes and minerals87
- B. Silicate minerals90
- C. Metals91
- IV. Extreme Environments92
- A. Microbes in iron- and sulfur-rich environments93
- B. Cave systems95
- C. The deep subsurface96
- D. Radioactive environments96
- V. The Origin of Life on Earth, and Beyond97
- VI. Conclusions98
- References98
- Chapter 5: The Scale-Up of Microbial Batch and Fed-Batch Fermentation Processes105
- I. Introduction106
- II. Engineering Considerations Involved in Scale-Up107
- A. Agitator tasks in the bioreactor107
- B. Unaerated power draw P (or mean specific energy dissipation rate epsivhorbarT W/kg)110
- C. Aerated power draw Pg (or aerated (epsivhorbarT)g W/kg)111
- D. Flow close to the agitator-single phase and air–liquid112
- E. Variation in local specific energy dissipation rates, epsivTW/kg112
- F. Air dispersion capability112
- G. Bulk fluid- and air-phase mixing113
- H. Main differences across the scales114
- III. Process Engineering Considerations for Scale-Up115
- A. Fluid mechanical stress or so-called "shear damage"115
- B. Operational constraints at the large scale119
- C. The physiological response of cells to the large-scale environment122
- D. Small-scale experimental simulation models of the large scale124
- E. Results from small-scale experimental trials of large-scale E. coli fed-batch processes126
- IV. Conclusions and Future Perspective132
- References175
- Chapter 6: Production of Recombinant Proteins in Bacillus subtilis137
- I. Introduction138
- II. Vector Systems139
- A. Rolling circle-type replication vectors139
- B. Theta-type replication vectors141
- C. Integrative vectors146
- D. Bacteriophage vectors148
- III. Expression Systems149
- A. Promoter systems149
- B. Secretion systems154
- C. Vectors allowing the addition of tags to recombinant proteins157
- D. DNA elements improving the production of recombinant proteins158
- IV. Transformation Systems160
- A. Natural competence160
- B. Protoplasts161
- C. Electrotransformation162
- D. Mobilization from E. coli to B. subtilis162
- V. Chromosomal Mutations Enhancing Production of Native Intra- and Extracellular Proteins163
- A. Molecular chaperones163
- B. Cellular factors affecting extracytoplasmic protein folding and degradation164
- C. Chromosomal mutations enhancing the production of recombinant proteins167
- VI. Production of Recombinant Proteins in B. subtilis and Other Bacilli168
- A. B. subtilis168
- B. B. brevis168
- C. B. megaterium169
- VII. Conclusions171
- Acknowledgments175
- References175
- Chapter 7: Quorum Sensing: Fact, Fiction, and Everything in Between191
- I. Preface192
- II. Introduction193
- III. The Basics of Microbial Linguistics193
- A. Autoinducers: The language of prokaryotic communication193
- B. Autoinducers with antimicrobial activity195
- C. Multiple quorum-sensing systems: Integrating the sensory information198
- D. The "Environment Sensing" theory: So much for social engagements of bacteria!200
- IV. Lost in Translation202
- A. AI-2: The most talked about molecule in the field202
- B. The early years of research: AI-2 goes interspecies203
- C. The pivotal case of EHEC204
- D. The role of luxS in cell physiology: Activated methyl cycle209
- E. lsr operon: The missing link... is still missing212
- F. Multilingual bacteria: Another look at the role of interspecies communication in V. harveyi215
- G. The recent years: Research involving synthetic AI-2216
- H. AI-2 in foods: A few words about the currently accepted AI-2 detection assay220
- V. Quorum Quenching: All Quiet on the Microbial Front223
- A. Halogenated furanones: The defense system of algae223
- B. AHL lactonases and acylases: Too early to judge223
- C. Quorum quenching: Practical applications225
- D. The available screening procedures for quorum-sensing inhibitors226
- VI. The Update227
- VII. Concluding Remarks228
- Acknowledgments
- References
- Chapter 8: Rhizobacteria and Plant Sulfur Supply235
- I. Introduction236
- II. Assimilation of Sulfur by Plants237
- A. Uptake and assimilation of inorganic sulfate237
- B. Amino acids/peptides as a source of plant sulfur240
- C. Plant assimilation of oxidized organosulfur241
- III. Microbial Transformations of Sulfur in Soil and Rhizosphere242
- A. Mineralization and immobilization of soil sulfur242
- B. Transformations of sulfate esters245
- C. Microbial sulfur transformations in nonaerobic soils246
- D. Sulfur transformations by fungi247
- IV. Functional Specificity of Bacteria in Soil Sulfur Transformations248
- A. Sulfonate desulfurization by rhizosphere bacteria249
- B. Diversity of desulfonation genes in rhizosphere250
- C. Changes in microbial community with sulfur supply255
- D. Sulfatase genes in rhizosphere257
- E. Influence of mycorrhizal interactions on sulfur supply258
- V. Plant Growth Promotion and the Sulfur Cycle259
- VI. Conclusions261
- Acknowledgments
- References
- Chapter 9: Antibiotics and Resistance Genes: Influencing the Microbial Ecosystem in the Gut269
- I. Introduction270
- II. Antibiotic Use and the Emergence of Resistant Bacteria270
- III. Transfer of Antibiotic Resistance Genes Between Bacteria273
- A. Mechanisms of transfer273
- B. Why is the gut a good site for gene transfer275
- C. In vivo demonstrations of resistance gene transfer276
- IV. Consequences of Antibiotic Use277
- A. Increased carriage of resistant bacteria and resistance genes and the emergence of bacterial stra277
- B. Evolution of novel forms of resistance genes278
- C. Impact of antibiotics on the commensal gut microbiota280
- D. Combination therapy: Antibiotics and pro/prebiotics281
- E. Antibiotics and the early development of the gut microbiota282
- V. Conclusions283
- Acknowledgments
- References284
- Index293
- Contents of Previous Volumes305
- Color Plate Section318
Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in Microbiology.
The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays.
The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays.