Environmental Microbiology: Methods and Protocols

ISBN-13: 9781627037112 / Angielski / Twarda / 2014 / 242 str.

Ian T. Paulsen; Andrew J. Holmes

Opis

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. This book 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.

Spis treści

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