Environmental microbiology : methods and protocols / edited by Ian T. Paulsen, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia, Andrew J. Holmes, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia.

Includes bibliographical references and index.

Methods for isolation and cultivation of filamentous fungi / Helena Nevalainen, Liisa Kautto, and Junior Te'o -- Rapid extraction of PCR-competent DNA from recalcitrant environmental samples / Michael R. Gillings -- Quantitative PCR for detection of mRNA and gDNA in environmental isolates / Anthony J. Brzoska and Karl A. Hassan -- Analysis of community dynamics in environmental samples using denaturing gradient gel electrophoresis / Claire L. Thompson -- Terminal restriction fragment length polymorphism (T-RFLP) profiling of bacterial 16S rRNA genes / Catherine A. Osborne -- Profiling the diversity of microbial communities with single-strand conformation polymorphism (SSCP) / Achim Schmalenberger and Christoph C. Tebbe -- Human fecal source identification with real-time quantitative PCR / Orin C. Shanks ... [and 4 others] -- Next generation barcode tagged sequencing for monitoring microbial community dynamics / Katy Breakwell, Sasha G. Tetu, and Liam D.H. Elbourne -- Analysis of methanotroph community structure using a pmoA-based microarray / Guy C.J. Abell ... [and 3 others] -- Biolog phenotype microarrays for phenotypic characterization of microbial cells / Amanda M. Mackie ... [and 3 others] -- Visualization of metabolic properties of bacterial cells using nanoscale secondary ion mass spectrometry (NanoSIMS) / Yi Vee Chew, Andrew J. Holmes, and John B. Cliff -- Single-cell Raman sorting / Mengqiu Li ... [and 3 others] -- Bacterial whole-cell biosensors for the detection of contaminants in water and soils / Yun Wang ... [and 3 others] -- Stable isotope probing to study functional components of complex microbial ecosystems / Sophie Mazard and Hendrik Schäfer -- Metagenomics using next-generation sequencing / Lauren Bragg and Gene W. Tyson -- Targeted genomics of flow cytometrically sorted cultured and uncultured microbial groups / Sophie Mazard ... [and 4 others] -- Quantitative microbial metatranscriptomics / Scott Gifford, Brandon Satinsky, and Mary Ann Moran -- Quantitative metaproteomics : functional insights into microbial communities / Chongle Pan and Jillian F. Banfield.

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.--