Genetic Interactions Among Microorganisms in the Natural Environment (eBook)

J.D. van Elsas, E.M.H. Wellington (Herausgeber)

eBook Download: PDF

2013 | 1. Auflage
314 Seiten
Elsevier Science (Verlag)
978-1-4832-8777-5 (ISBN)

Infos

This book gives an overview of gene transfer and stability in those aquatic and terrestrial environments where bacteria and fungi can survive and interact genetically. It examines the role played by sex between microbes in the evolution of populations and their survival. Special emphasis is placed on methodology, including the analysis by novel techniques of genetic material extracted directly from soils, rivers and lakes. The natural spread of antibiotic resistance and the safe use of genetically manipulated microbes are matters of considerable scientific, medical and public concern upon which the investigations presented here have direct bearing. This unique collection will be of value to specialist researchers in applied microbiology, ecology and biotechnology as well as biomedical scientists interested in the environmental risks of genetic engineering.

Inhalt

Front Cover 1
Genetic Interactions among Microorganisms in the Natural Environment 4
Copyright Page 5
Table of Contents 6
Contributors 8
Preface 10
Part I: General introduction 12
Chapter 1. The role of gene transfer in bacterial evolution 14
1.1. The scope of this chapter 14
1.2. The mechanisms of bacterial gene transfer 14
1.3. The consequences of bacterial gene transfer 16
1.4. What can we conclude? 21
References 22
Part II: Evidence for gene transfer between bacteria in nature 26
Chapter 2. Antibiotic resistance gene transfer in the environment: an overview 28
2.1. Introduction 28
2.2. Antibiotic resistance mechanisms and genes 31
2.3. Indirect (retrospective) evidence of natural antibiotic resistance gene transfer 32
2.4. Scope of natural genes transfer mechanisms 36
2.5. Environments favouring antibiotic resistance gene transfer 40
2.6. Concluding remarks 44
Acknowledgements 44
References 44
Part III: Methods for studying genetic interactions in terrestrial environments 52
Chapter 3. Horizontal gene transfer in bacterial soil communities and its significance for risk assessment 54
3.1. Introduction 54
3.2. Evidence for distribution of microbial genes in natural environments 54
3.3. Widespread class II transposons contain systems for gene integration and dispersal among bacteria 55
3.4. In situ horizontal mobility and intra-species expression of rDNA 60
3.5. Is a pool of free DNA available for soil microorganisms in situ! 63
3.6. Is genetic communication assisted by soil animals? 65
3.7. Problems of evaluating gene mobility for risk assessment analysis 65
3.8. Conclusions 66
Acknowledgements 66
References 66
Chapter 4. Detection of genetic exchange in the terrestrial environment 70
4.1. Introduction 70
4.2. Sterile soil systems 75
4.3. Gene transfer in non-sterile soil 80
4.4. The direct extraction of DNA and RNA from soil for analysis of inoculant and excipient populations 85
4.5. General considerations about sex in the soil bacterium Streptomyces 86
4.6. General conclusions 88
Acknowledgments 89
References 89
Chapter 5. Detection systems for streptomycetes 94
5.1. Introduction 94
5.2. Immunological detection 95
5.3. Development and detection of a genetic marker system 97
5.4. Summary and conclusions 99
Acknowledgements 100
References 100
Chapter 6. Extraction of Streptomyces spores from soil and detection of rare gene transfer events 102
6.1. Introduction 102
6.2. Method development and experimental results 104
Acknowledgements 112
References 112
Chapter 7. Methods for extracting bacterial cells from soil 115
7.1. Introduction 115
7.2. Methodological development 116
7.3. Discussion of results 118
7.4. Conclusions 121
References 122
Chapter 8. Methods for studying conjugative plasmid transfer in soil 124
8.1. Introduction 124
8.2. Plating methodology 125
8.3. Transconjugant isolation and enumeration 125
8.4. Selectable markers 126
8.5. Genetic elements 128
8.6. Colony hybridisation 129
8.7. Donor counterselection 131
8.8. Plasmid transfer to indigenous soil bacteria 133
Acknowledgement 134
References 134
Chapter 9. Detection systems for phylloplane pseudomonads 138
9.1. Introduction 138
9.2. Selection 140
9.3. Determination of community composition 140
9.5. Conclusions 149
Acknowledgements 150
References 151
Part IV: Methods for studying genetic interactions in aquatic environments 154
Chapter 10. Detection of gene transfer in aquatic environments 156
10.1. Introduction 156
10.2. Mechanisms for gene transfer in the aquatic environment 156
10.3. Studying gene transfer in the aquatic environment 159
10.4. Molecular methods for assessing gene transfer in the aquatic environment 167
10.5. Conclusions 170
Acknowledgements 170
References 170
Chapter 11. The development of detection systems for pseudomonads released into lake water 176
11.1. Introduction 176
11.2. Marker plasmids 177
11.3. Regulation of xylE expression in marker systems 179
11.4. Detection methods 180
11.5. Discussion 183
References 185
Chapter 12. Bacteriophage-host interactions in aquatic systems 187
12.1. Introduction 187
12.2. Concentrations of bacteria and bacteriophages in aquatic environments 187
12.3. Bacteriophages as regulators of natural microbial population densities 190
12.4. Productive phage-host interaction under environmental conditions 194
12.5. Potential for bacteriophage-mediated genetic transmission in aquatic environments 195
Acknowledgements 199
References 199
Chapter 13. Survival of genetically engineered microorganisms in activated sludge 205
13.1. Introduction 205
13.2. Microbiology of activated sludge 206
13.3. Bioaugmentation in activated sludge sewage treatment 207
13.4. Survival and function of G E M s 210
13.5. Mechanisms for bacterial mortality 216
13.6. Persistence of DNA 217
13.7. Monitoring the survival of GEMs and DNA persistence 218
13.8. The future of catabolic GEMs in sewage treatment 220
Acknowledgements 222
References 222
Chapter 14. Transformation in natural environments 227
14.1. Introduction 227
14.2. Overview of the natural transformation process 227
14.3. Evidence for transformation in the environment 233
14.4. Directions for future research 236
14.5. Conclusions 239
References 240
Part V: Evaluation of some methods for detecting genes and gene transfer in nature 246
Chapter 15. Nucleic acid extraction and analysis: detecting genes and their activity in the environment 248
15.1. Introduction 248
15.2. Approach in nucleic acid analysis 256
15.3. Recovery and analysis of nucleic acids 260
15.4. Summary and conclusions 264
1.1. References 266
Chapter 16. The estimation of gene transfer in natural environments 269
References 273
Part VI: Gene transfer between fungi 276
Chapter 17. Monitoring genetic interactions between fungi in terrestrial habitats 278
17.1. Introduction 278
17.2. The structure of natural fungal populations and its relation to ecological and breeding strategies 279
17.3. Methods for monitoring genetic interactions in natural populations 283
17.4. Destabilising and stabilising mechanisms: routine and episodic selection processes 285
Acknowledgements 292
References 292
Part VII: Regulatory aspects 298
Chapter 18. USDA requirements for safe field testing in the environment 300
18.1. Introduction 300
18.2. U.S. biotechnology regulation in general 301
18.3. USDA regulation 302
18.4. Environmental reviews for releases under 7 CFR Part 340 303
18.5. Field testing principles 305
18.6. USDA permit process 305
18.7. Other scientific issues 307
References 308
Epilogue 309
Index 311

Produkt-Details

• Erscheint lt. Verlag: 22.10.2013
• Sprache: englisch
• Themenwelt: Medizin / Pharmazie
• Themenwelt: Naturwissenschaften ► Biologie ► Evolution
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Biologie ► Ökologie / Naturschutz
• Themenwelt: Technik
• ISBN-10: 1-4832-8777-7 / 1483287777
• ISBN-13: 978-1-4832-8777-5 / 9781483287775