Table of Contents
Contributors ix
Diversity of Microbial Toluene Degradation Pathways R. E. Parales J. V. Parales D. A. Pelletier J. L. Ditty
Introduction 2
Dioxygenase Mediated Pathway: Pseudomonas putida F1 4
Pathway details and enzymology 4
Genetics and regulation 8
Toluene 2-Monooxygenase Pathway: Burkholderia vietnamiensis G4 12
Pathway details and enzymology 12
Genetics and pathway regulation 14
Toluene-3-monooxygenase Pathway: Ralstonia pickettii PKO1 15
Toluene-4-monooxygenase Pathway: Pseudomonas mendocina KR1 20
A Strain with Multiple Toluene Degradation Pathways: Burkholderia sp. Strain JS150 25
A Nonspecific Toluene Monooxygenase Pathway: Pseudomonas stutzeri OX1 28
Pathway details and enzymology 28
Pathway regulation 32
TOL Pathway: Pseudomonas putida mt-2 33
Pathway and enzymology 34
Genetics and regulation 40
A Fungal Toluene Degradation Pathway 43
Anaerobic Toluene Pathway: Thauera aromatica K172 47
Pathway details and enzymology 47
Genetics and regulation 52
Conclusions 52
Acknowledgments 55
References 55
Microbial Endocrinology: Experimental Design Issues in the Study of Interkingdom Signalling in Infectious Disease Primrose P. E. Freestone Mark Lyte
Microbial Endocrinology as a New Scientific Discipline 76
Overview and goal of review 76
The stress response and its influence on the immune system and the infectious agent 77
Mechanisms by which stress-related neuroendocrine hormones can enhance bacterial growth and virulence 79
The spectrum of catecholamine responsive bacteria 84
Catecholamine specificity in enteric bacteria 85
Molecular analyses of bacterial catecholamine responsiveness 88
Experimental Design Issues in the Study of Microbial Endocrinology 89
Medium comparability 90
Bacterial inoculum size and its influence on stress neurohormone responsiveness 92
The importance of neuroendocrine hormone concentration 94
Neuroendocrine stress neurohormone assay methodologies 97
Conclusions and Future Directions 101
References 102
Molecular Genetics of Selenate Reduction by Enterobacter cloacae SLD1a-1 Nathan Yee Donald Y. Kobayashi
Introduction 108
Physiology and Biochemistry of E. cloacae SLD1a-1 108
Basic Systems of Molecular Genetics in Facultative Se-reducing Bacteria 110
Growth of E. cloacae SLD1a-1 on selenate-containing agar plates 110
Direct cloning experiments 110
Gene specific mutagenesis 112
Random mutagenesis using transposons 113
Genetic Analysis of Selenate Reduction in E. cloacae SLD1a-1 115
A Molecular Model for Selenate Reduction in E. cloacae SLD1a-1 118
Conclusions and Future Prospects 120
Acknowledgments 120
References 120
Metagenomics of Dental Biofilms Peter Mullany Stephanie Hunter Elaine Allan
Introduction 126
Isolation of Metagenomic DNA 126
Sample Collection and Processing 126
DNA Extraction 128
Preparation of the Insert DNA for Cloning 128
Partial restriction digestion 129
Mechanical shearing of the DNA 129
Removal of Human DNA 129
Metagenomic Library Construction 130
Construction of large insert metagenomic libraries 130
Construction of small insert libraries 132
Phage display 132
Limitations of Metagenomics 133
Conclusions and Future Perspectives 134
References 134
Biosensors for Ligand Detection Alison K. East Tim H. Mauchline Philip S. Poole
Introduction 137
Induction Biosensors 139
General considerations for use of induction biosensors 139
Reporter genes 140
Molecular Biosensors 150
Optical biosensors 150
Electrical biosensors 159
Conclusions and Future Prospects 160
Acknowledgments 160
References 160
Islands Shaping Thought in Microbial Ecology Christopher J. van der Gast
Introduction 167
The Importance of Islands 169
Biogeographic islands for studies of bacterial diversity 169
Island biogeography 170
Species-Area Relationships 170
Microbial biogeography 171
Island size and bacterial diversity 172
Beta Diversity 174
Smaller islands are less stable than larger ones 175
Species-time relationships 175
Distance-decay relationships 177
Opposing Perspectives on Community Assembly 177
Conclusions 179
Acknowledgments 180
References 180
Human Pathogens and the Phyllosphere John M. Whipps Paul Hand David A. C. Pink Gary D. Bending
Introduction 183
Food Poisoning Outbreaks Associated with Consumption of Fresh and Minimally Processed Fresh Vegetables, Salads, and Fruit 185
Sources of Human Pathogens on Plants 186
Ecology of Human Pathogens in Relation to Phyllosphere Contamination 189
Ecology and survival in sewage, manure, soil, and water 189
Ecology and survival in association with plants 190
Ecology and survival during processing 203
Conclusions and Future 208
Acknowledgments 209
References 209
Microbial Retention on Open Food Contact Surfaces and Implications for Food Contamination Joanna Verran Paul Airey Adele Packer Kathryn A. Whitehead
Introduction 224
Microbial Attachment, Biofilm Formation, and Cell Retention 225
Surfaces (substrata) Encountered 226
Factors Affecting Retention 227
Surface topography 227
Surface chemistry 230
Presence of organic material 231
Characterization of Surfaces 232
Topography 232
Chemistry 234
Measuring Retention and Assessing Cleaning and Disinfection 234
Substratum preparation 234
Amount of retention 235
Strength of retention 238
Quantifying organic material 240
Conclusions 241
References 241
Index 247
Contents of Previous Volumes 255
