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Environmental Microbiology: Methods and Protocols

Handbook / Manual
Provides up-to-date molecular techniques for investigating microbial communities and their biological activities
Includes step-by-step, readily reproducible protocols
Features key tips and expert implementation advice to ensure quality results

Series: Methods in Molecular Biology Volume: 1096

By: Ian T Paulsen (Editor), Andrew J Holmes (Editor)

252 pages, 19 colour & 16 b/w illustrations, 23 tables

Humana Press

Hardback | Feb 2014 | Edition: 2 | #217858 | ISBN-13: 9781627037112
Availability: Usually dispatched within 1-2 weeks Details
NHBS Price: £78.50 $96/€88 approx

About this book

An up-to-date view of molecular mechanisms for investigating microbial communities and their biological activities, this new volume of Environmental Microbiology: Methods and Protocols looks at recent advances that are having a big impact on the field such as metagenomics and other "omics" technologies, NanoSIMS, as well as stable isotope probing and more. Conveniently divided into four parts, the first section looks at methods involved in sampling environmental microorganisms, the second profiles different methods for investigating the diversity and composition of microbial communities, the third focuses on techniques for analyzing biological activities in situ, and the final section examines high throughput "omics" approaches for the characterization of environmental microbial communities.

Environmental Microbiology: Methods and Protocols was written as part of the highly successful Methods in Molecular Biology series, and, as such, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Fully updated and authoritative, Environmental Microbiology: Methods and Protocols, Second Edition aims to provide an unprecedented glimpse into the structure, composition, and activity of microbial communities across diverse environments and illuminate their impact on global ecological processes.

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Part I: Recovery and Investigation of Biological Samples
1. Methods for Isolation and Cultivation of Filamentous Fungi Helena Nevalainen, Liisa Kautto, and Junior Te'o
2. Rapid Extraction of PCR-Competent DNA from Recalcitrant Environmental Samples Michael R. Gillings
3. Quantitative PCR for Detection of mRNA and gDNA in Environmental Isolates Anthony J. Brzoska and Karl A. Hassan

Part II: Describing Microbial Communities
4. Analysis of Community Dynamics in Environmental Samples Using Denaturing Gradient Gel Electrophoresis Claire L. Thompson
5. Terminal Restriction Fragment Length Polymorphism (T-RFLP) Profiling of Bacterial 16S rRNA Genes Catherine A. Osborne
6. Profiling the Diversity of Microbial Communities with Single-Strand Conformation Polymorphism (SSCP) Achim Schmalenberger and Christoph C. Tebbe
7. Human Fecal Source Identification with Real-Time Quantitative PCR Orin C. Shanks, Lindsay Peed, Mano Sivaganesan, Richard A. Haugland, and Eunice C. Chern
8. Next Generation Barcode Tagged Sequencing for Monitoring Microbial Community Dynamics Katy Breakwell, Sasha G. Tetu, and Liam D.H. Elbourne
9. Analysis of Methanotroph Community Structure Using a pmoA-Based Microarray Guy C.J. Abell, Nancy Stralis-Pavese, Yao Pan, and Levente Bodrossy
10. Biolog Phenotype MicroArrays for Phenotypic Characterization of Microbial Cells Amanda M. Mackie, Karl A. Hassan, Ian T. Paulsen, and Sasha G. Tetu

Part III: Investigation of Biological Activities In Situ
11. Visualization of Metabolic Properties of Bacterial Cells Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) Yi Vee Chew, Andrew J. Holmes, and John B. Cliff
12. Single-Cell Raman Sorting Mengqiu Li, Dan G. Boardman, Andrew Ward, and Wei E. Huang
13. Bacterial Whole Cell Biosensors for the Detection of Contaminants in Water and Soils Yun Wang, Dayi Zhang, Paul A. Davison, and Wei E. Huang
14. Stable Isotope Probing to Study Functional Components of Complex Microbial Ecosystems Sophie Mazard and Hendrik Schaefer

Part IV: High Throughput Genomic Approaches for Environmental Microbiology
15. Metagenomics Using Next-Generation Sequencing Lauren Bragg and Gene W. Tyson
16. Targeted Genomics of Flow Cytometrically Sorted Cultured and Uncultured Microbial Groups Sophie Mazard, Martin Ostrowski, Ross Holland, Mikhail V. Zubkov, and David J. Scanlan
17. Quantitative Microbial Metatranscriptomics Scott Gifford, Brandon Satinsky, and Mary Ann Moran
18. Quantitative Metaproteomics: Functional Insights into Microbial Communities Chongle Pan and Jill Banfield

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