Advances in Applied Microbiology (eBook)

Front Cover 1
Applied Microbiology 4
Copyright Page 5
Content 6
Contributors 12
Chapter 1: Phage Evolution and Ecology 14
I. Introduction 15
II. Bacteriophage Types 17
III. Phage Ecology 19
A. Phage organismal and population ecology 21
B. Phage community ecology 21
C. Phage ecosystem ecology 21
IV. Phage Evolutionary Biology 22
A. Microevolution versus macroevolution 22
B. Fitness and natural selection 24
C. Mutation 26
D. Genetic drift 31
E. Migration (Introgression) 31
F. Recombination 32
V. Phage Evolutionary Ecology 34
A. Life history evolution 34
B. Adsorption 35
C. Infection, prereproductive period 37
D. Infection, reproductive period 38
E. Burst 39
VI. Phage Genome Evolution 40
A. Horizontal gene transfer 40
B. Genomics and mosaicism 42
C. "All the world's a phage" 47
VII. Concluding Remarks 48
References 48
Chapter 2: Nucleoid-Associated Proteins and Bacterial Physiology 60
I. Introduction 61
II. The Multifunctional Fis Protein 63
III. The Fis Protein and Bacterial Physiology 64
IV. The Characteristic Expression Pattern of Fis 65
V. Fis and the Global Transcription Pattern 68
VI. The H-NS Protein, a Universal Repressor 69
VII. Proteins HU and IHF 70
VIII. RpoS as a Regulatory Target of NAPs 71
IX. Perspective 72
Acknowledgments 72
References 72
Chapter 3: Biodegradation of Pharmaceutical and Personal Care Products 78
I. Introduction 79
II. What Are PPCPs? 80
III. Human Interactions With PPCPs 81
IV. Biological Transformation of PPCPs During Wastewater Treatment 85
V. Biological Transformation of PPCPs in The Environment 98
VI. Growth on PPCPs 101
VII. Pathways for the Degradation of Selected PPCPs 104
A. Octylphenol degradation by Sphingomonas sp. strain PWE1 104
B. Ibuprofen degradation by Sphingomonas sp. strain Ibu-2 107
C. Deet degradation by P. putida DTB 109
VIII. Conclusions 111
References 112
Chapter 4: Bioremediation of Cyanotoxins 122
I. Introduction 123
II. Hepatoxic Peptides-Microcystins and Nodularins 124
A. Persistence and biodegradation 125
B. Biodegrading bacteria 128
C. Characterization of MC-LR degradation pathway 130
D. Exploitation of microcystin-degrading bacteria 133
III. Other Toxins 135
A. Saxitoxins 135
B. Cylindrospermopsin 136
C. Anatoxin-a 138
IV. Conclusions 138
References 139
Chapter 5: Virulence in Cryptococcus Species 144
I. Cryptococcus and Cryptococcosis 145
A. C. neoformans 148
B. C. gattii 149
C. Other species 151
D. Cryptococcosis 151
E. Genome sequencing project 155
II. Virulence Factors 156
A. Capsule 156
B. Melanin 159
C. Ability to grow at physiological temperature 159
D. Degradative enzymes 160
E. Mating type 161
F. Phenotypic switching 162
G. The origin and maintenance of virulence factors 163
III. Signaling Pathways Regulating Pathogenicity 165
A. cAMP-PKA 165
B. MAP kinase pathway 166
C. Ras pathway and the Ca2+-calcineurin pathway 167
IV. Cryptococcus and the Host Response 168
A. Immunocompromised host 168
B. Immunocompetent host 174
C. Conclusion 178
V. Current Understanding on How Cryptococcus Crosses the Blood-Brain Barrier 178
VI. Animal Models 180
VII. Perspectives 182
References 183
Chapter 6: Molecular Networks in the Fungal Pathogen Candida albicans 204
I. Introduction 205
II. Ras1 Interrelated Networks 206
A. Mitogen-activated protein kinase signaling 206
B. Cyclic AMP-dependent PKA pathway 209
III. Carbon Dioxide Sensing 212
A. Adenylyl cyclase (Cyr1) senses environmental CO2 212
B. CO2 sensing: A role for carbonic anhydrase 213
IV. Quorum Sensing and its Effects on C. albicans Morphology 213
A. Farnesol exerts its effects through cAMP signaling cascades 214
B. Tup1p is involved in quorum sensing in C. albicans 216
C. Transcriptional analysis of quorum sensing in C. albicans 216
V. pH Regulation of Cell Morphology 217
VI. Other Pathways Affecting Morphology 218
VII. Conclusions 219
Acknowledgments 220
References 220
Chapter 7: Temperature Sensors of Eubacteria 226
I. Introduction 227
II. Thermosensors 228
A. Nucleoid modulators 228
B. RNA 229
C. Proteins 230
III. Responses to Sudden Changes in the Growth Temperature 231
A. The high temperature response 234
B. The heat shock response 234
C. The low temperature response 235
D. The cold shock response 236
IV. Sensors of the HTR 236
A. Nucleoid modulators as thermosensor 237
B. RNA as thermosensor 241
C. Proteins as thermosensor 244
V. Sensors of the HSR 246
A. Molecular chaperones as thermosensors 246
B. Proteases as thermosensors 249
VI. Sensors of the LTR 250
A. RNA as thermosensor 250
B. Proteins as thermosensors 252
VII. Sensors of the CSR 254
A. RNA as sensor 255
B. Proteins as sensor 256
VIII. The Thermotactic Response 256
Acknowledgment 258
References 258
Chapter 8: Deciphering Bacterial Flagellar Gene Regulatory Networks in the Genomic Era 270
I. Introduction 271
II. Master Regulators 274
A. FlhDC 275
B. CtrA 277
C. VisNR 279
D. sigma54-dependent master regulators 280
E. Other master regulators 284
III. RpoN (sigma54) Regulators 287
A. FlbD 287
B. FleR/FlrC 291
C. FlgR 292
D. FleT 293
IV. FliA (sigma28) and FlgM 293
A. SigD and other systems 295
V. Conclusions 297
References 297
Chapter 9: Genetic Tools to Study Gene Expression During Bacterial Pathogen Infection 310
I. Introduction 311
II. In Vivo Expression Technology 312
A. Selection by selection for complementation of auxotrophy in Salmonella 313
B. Antibiotic-based IVET selection for ivi genes 314
C. Recombinase-mediated IVET and analysis of Vibrio cholerae gene regulation 315
III. DFI: S. Typhimurium Genes Induced by Low-ph and Intracellular Growth Conditions In Vitro and In Vivo 319
IV. Repression of an Anti-Colonization Factor in V. Cholerae 321
V. Conclusion and Future Prospects 324
Acknowledgment 325
References 325
Index 328
Contents of Previous Volumes 336
Color Plate Section 348