Environmental Molecular Microbiology: Protocols and Applications
Publisher: Horizon Scientific Press
Editor: Paul A. Rochelle Metropolitan Water District of Southern California, Water Quality Laboratory, La Verne, California 91750, U.S.A.
Publication date: August, 2001
ISBN-10: 1-898486-29-8 (hbk)
ISBN-13: 978-1-898486-29-9 (hbk)
Pages: x + 264
Molecular based techniques have revolutionized our understanding of environmental microbiology. Over the last decade, the application of these techniques has improved our understanding of the composition, phylogeny, and physiology of microbial communities in the environment. However a thorough understanding of the limitations of these methods is essential to prevent researchers being led astray by their results. This book helps the reader to be aware of these limitations, and will therefore be invaluable for both the novice and the experienced molecular biologist.
This volume contains a collection of protocols and descriptive narratives written by researchers working in diverse fields. Chapters contain valuable background information on the techniques, laboratory protocols, published examples and applications, and cautionary notes to help the readers avoid some of the common problems, either with the mechanics of the techniques themselves or in interpreting the results. In addition, chapters describing fundamental principles, advanced applications of selected techniques, and speculation on future methodological advances are also included. Many of the chapters focus on nucleic acid based methodologies and the poylmerase chain reaction (PCR). Methods based on the analysis of protein, and lipid, and the interaction of DNA analogues are also included.
Written by internationally renown authors, this book is aimed at all scientists working in the field of environmental microbiology, including those involved in the analysis of microbial diversity, the changes in microbial community structure, bioremediation, and the detection of specific microorganisms (eg pathogens) in the environment. An essential volume for anyone who has an interest in environmental microbes.
Key Topics
• Methods for the extraction of DNA and RNA from environmental samples
• Phylogenetic analysis of 16S rRNA gene sequences
• PCR using environmental samples (including discussion of potential pitfalls)
• Proteome analysis
• Phospholipid analysis
• DGGE, SSCP and TGGE analysis
• In situ based detection (eg. PNA,hybridization, PCR)
• Future directions
Chapter List
1. Environmental Molecular Microbiology: Introduction
Paul A. Rochelle
2. Extraction of Nucleic Acids from Environmental Samples
Yu-Li Tsai and Paul A. Rochelle
3. The Polymerase Chain Reaction as a Tool to Investigate Microbial Diversity in Environmental Samples
Philip Hugenholtz and Brett M. Goebel
4. Primer Design for PCR Amplification of Environmental DNA Targets
Julian R. Marchesi
5. Direct Detection of Mycobacteria in the Environment with Sequence Capture PCR
Timothy P. Stinear, Paul D. R. Johnson, and John K. Davies
6. Protocols for Nucleic Acid-based Detection and Quantitation of Microorganisms in Water
Knut Rudi and Kjetill S. Jakobsen
7. Genomic Polymorphisms and the Diversity of Oxygenic Phototrophs
Brett A. Neilan
8. Detection of Protozoa in Environmental Water Samples
Paul A. Rochelle
9. Quantitative Polymerase Chain Reaction Assay
Clifford F. Brunk and Jinliang Li
10. Microbial Community Proteomics
Oladele A. Ogunseitan, James LeBlanc, and Enrique A. Dalmasso
11. A Combined Phospholipid and 16S rDNA PCR-DGGE Analysis to Study Bioremediative Microbial Communities In-Situ
Sarah J. Macnaughton and John R. Stephen
12. Single-Strand Conformation Polymorphism (SSCP) for Microbial Community Analysis
Christoph C. Tebbe, Achim Schmalenberger, Sabine Peters, and Frank Schwieger
13. Bacterial Community Profiling Using DGGE or TGGE Analysis
Holger Heuer, Gabriele Weiland, Jens Schönfeld, Annett Schönwälder, Newton C. M. Gomes, and Kornelia Smalla
14. Differential Display of Prokaryotic Messenger RNA and Application to Soil Microbial Communities
James T. Fleming, Aaron Nagel, James Rice, and Gary S. Sayler
15. Fluorescent PNA Probes for In-Situ Bacterial Identification
Heather Perry-O'Keefe and Jens J. Hyldig-Nielsen
16. Nucleic Acid-Based In-Situ Analyses of Microbial Diversity and Physiology
Bronwyn R. Robertson and Brett A. Neilan
17. Technological Innovations in Biodetection Systems for Environmental Molecular Microbiology
Darrell P. Chandler
(EAN: 9781898486299)
