Advances in Applied Microbiology (eBook)

Cover 1
Contents 6
Contributors 12
Chapter 1: Anaerobic Biodegradation of Methyl tert-Butyl Ether (MTBE) and Related Fuel Oxygenates 14
I. Introduction 14
II. Fuel Oxygenates as Contaminants of Water Sources 16
III. Environmental Fate 17
IV. MTBE Biodegradation 18
V. Monitoring Natural Attenuation 24
VI. Summary 28
References 29
Chapter 2: Controlled Biomineralization by and Applications of Magnetotactic Bacteria 34
I. Introduction 35
II. Features of the Magnetotactic Bacteria 35
A. General features 35
B. Distribution and ecology 36
C. Phylogeny and taxonomy 37
D. Physiology 39
III. The Magnetosome 43
A. Composition of magnetosome crystals 43
B. Size of magnetosome crystals 44
C. Magnetosome crystal morphologies 44
D. Arrangement of magnetosomes within cells 46
E. Biological advantage of magnetotaxis 47
IV. Chemical and Molecular Basis of Magnetosome Synthesis 48
A. Genomics of magnetotactic bacteria 49
B. Genetic systems and manipulations in magnetotactic bacteria 50
C. The magnetosome membrane 51
D. Physiological conditions under which magnetite magnetosomes are synthesized 59
E. Regulation of the expression of magnetosome genes 60
V. Applications of Magnetotactic Bacteria, Magnetosomes, and Magnetosome Crystals 61
A. Mass cultivation of magnetotactic bacteria 61
B. Applications of cells of magnetotactic bacteria 62
C. Applications of magnetosomes and magnetosome crystals 63
VI. Conclusions and Future Research Directions 65
Acknowledgments 65
References 65
Chapter 3: The Distribution and Diversity of Euryarchaeota in Termite Guts 76
I. Introduction 76
II. Euryarchaeota in Termite Guts 77
A. Termite gut structure and metabolism 77
III. Detection of Euryarchaeota in Termite Guts 80
A. Isolated Euryarchaeota from termite guts 80
B. Uncultured Euryarchaeota in lower termite guts 85
C. Uncultured Euryarchaeota in higher termite guts 86
IV. Why Are There Different Euryarchaeota in Different Termites? 89
V. Conclusion 90
References 90
Chapter 4: Understanding Microbially Active Biogeochemical Environments 94
I. Introduction 95
II. An Introduction to the Molecular Microbial World 96
A. 16S approaches 97
B. rRNA and mRNA 98
C. Recent technological advances 99
III. Microorganisms in the Environment 100
A. Microbes and minerals 100
B. Silicate minerals 103
C. Metals 104
IV. Extreme Environments 105
A. Microbes in iron- and sulfur-rich environments 106
B. Cave systems 108
C. The deep subsurface 109
D. Radioactive environments 109
V. The Origin of Life on Earth, and Beyond 110
VI. Conclusions 111
References 111
Chapter 5: The Scale-Up of Microbial Batch and Fed-Batch Fermentation Processes 118
I. Introduction 119
II. Engineering Considerations Involved in Scale-Up 120
A. Agitator tasks in the bioreactor 120
B. Unaerated power draw P (or mean specific energy dissipation rate epsivhorbarT W/kg) 123
C. Aerated power draw Pg (or aerated (epsivhorbarT)g W/kg) 124
D. Flow close to the agitator-single phase and air–liquid 125
E. Variation in local specific energy dissipation rates, epsivTW/kg 125
F. Air dispersion capability 125
G. Bulk fluid- and air-phase mixing 126
H. Main differences across the scales 127
III. Process Engineering Considerations for Scale-Up 128
A. Fluid mechanical stress or so-called "shear damage" 128
B. Operational constraints at the large scale 132
C. The physiological response of cells to the large-scale environment 135
D. Small-scale experimental simulation models of the large scale 137
E. Results from small-scale experimental trials of large-scale E. coli fed-batch processes 139
IV. Conclusions and Future Perspective 145
References 188
Chapter 6: Production of Recombinant Proteins in Bacillus subtilis 150
I. Introduction 151
II. Vector Systems 152
A. Rolling circle-type replication vectors 152
B. Theta-type replication vectors 154
C. Integrative vectors 159
D. Bacteriophage vectors 161
III. Expression Systems 162
A. Promoter systems 162
B. Secretion systems 167
C. Vectors allowing the addition of tags to recombinant proteins 170
D. DNA elements improving the production of recombinant proteins 171
IV. Transformation Systems 173
A. Natural competence 173
B. Protoplasts 174
C. Electrotransformation 175
D. Mobilization from E. coli to B. subtilis 175
V. Chromosomal Mutations Enhancing Production of Native Intra- and Extracellular Proteins 176
A. Molecular chaperones 176
B. Cellular factors affecting extracytoplasmic protein folding and degradation 177
C. Chromosomal mutations enhancing the production of recombinant proteins 180
VI. Production of Recombinant Proteins in B. subtilis and Other Bacilli 181
A. B. subtilis 181
B. B. brevis 181
C. B. megaterium 182
VII. Conclusions 184
Acknowledgments 188
References 188
Chapter 7: Quorum Sensing: Fact, Fiction, and Everything in Between 204
I. Preface 205
II. Introduction 206
III. The Basics of Microbial Linguistics 206
A. Autoinducers: The language of prokaryotic communication 206
B. Autoinducers with antimicrobial activity 208
C. Multiple quorum-sensing systems: Integrating the sensory information 211
D. The "Environment Sensing" theory: So much for social engagements of bacteria! 213
IV. Lost in Translation 215
A. AI-2: The most talked about molecule in the field 215
B. The early years of research: AI-2 goes interspecies 216
C. The pivotal case of EHEC 217
D. The role of luxS in cell physiology: Activated methyl cycle 222
E. lsr operon: The missing link... is still missing 225
F. Multilingual bacteria: Another look at the role of interspecies communication in V. harveyi 228
G. The recent years: Research involving synthetic AI-2 229
H. AI-2 in foods: A few words about the currently accepted AI-2 detection assay 233
V. Quorum Quenching: All Quiet on the Microbial Front 236
A. Halogenated furanones: The defense system of algae 236
B. AHL lactonases and acylases: Too early to judge 236
C. Quorum quenching: Practical applications 238
D. The available screening procedures for quorum-sensing inhibitors 239
VI. The Update 240
VII. Concluding Remarks 241
Acknowledgments 188
References 188
Chapter 8: Rhizobacteria and Plant Sulfur Supply 248
I. Introduction 249
II. Assimilation of Sulfur by Plants 250
A. Uptake and assimilation of inorganic sulfate 250
B. Amino acids/peptides as a source of plant sulfur 253
C. Plant assimilation of oxidized organosulfur 254
III. Microbial Transformations of Sulfur in Soil and Rhizosphere 255
A. Mineralization and immobilization of soil sulfur 255
B. Transformations of sulfate esters 258
C. Microbial sulfur transformations in nonaerobic soils 259
D. Sulfur transformations by fungi 260
IV. Functional Specificity of Bacteria in Soil Sulfur Transformations 261
A. Sulfonate desulfurization by rhizosphere bacteria 262
B. Diversity of desulfonation genes in rhizosphere 263
C. Changes in microbial community with sulfur supply 268
D. Sulfatase genes in rhizosphere 270
E. Influence of mycorrhizal interactions on sulfur supply 271
V. Plant Growth Promotion and the Sulfur Cycle 272
VI. Conclusions 274
Acknowledgments 188
References 188
Chapter 9: Antibiotics and Resistance Genes: Influencing the Microbial Ecosystem in the Gut 282
I. Introduction 283
II. Antibiotic Use and the Emergence of Resistant Bacteria 283
III. Transfer of Antibiotic Resistance Genes Between Bacteria 286
A. Mechanisms of transfer 286
B. Why is the gut a good site for gene transfer 288
C. In vivo demonstrations of resistance gene transfer 289
IV. Consequences of Antibiotic Use 290
A. Increased carriage of resistant bacteria and resistance genes and the emergence of bacterial strains carrying multiple resistance genes 290
B. Evolution of novel forms of resistance genes 291
C. Impact of antibiotics on the commensal gut microbiota 293
D. Combination therapy: Antibiotics and pro/prebiotics 294
E. Antibiotics and the early development of the gut microbiota 295
V. Conclusions 296
Acknowledgments 188
References 297
Index 306
Contents of Previous Volumes 318
Color Plate Section 331