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