Environmental microbiology: methods and protocols

Abstract

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