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Environmental Microbiology

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Ian T. Paulsen

    1. Dept. Chemistry & Biomolecular Sciences, Macquarie University, Sydney, Australia

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    You can also search for this editor in PubMed   Google Scholar

  2. Andrew J. Holmes

    1. School of Molecular Bioscience, University of Sydney, Camperdown, Australia

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1096)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
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  2. Recovery and Investigation of Biological Samples

    1. Front Matter

      Pages 1-1
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    2. Methods for Isolation and Cultivation of Filamentous Fungi

      • Helena Nevalainen, Liisa Kautto, Junior Te’o
      Pages 3-16

    3. Rapid Extraction of PCR-Competent DNA from Recalcitrant Environmental Samples

      • Michael R. Gillings
      Pages 17-23

    4. Quantitative PCR for Detection of mRNA and gDNA in Environmental Isolates

      • Anthony J. Brzoska, Karl A. Hassan
      Pages 25-42

  3. Describing Microbial Communities

    1. Front Matter

      Pages 43-43
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    2. Analysis of Community Dynamics in Environmental Samples Using Denaturing Gradient Gel Electrophoresis

      • Claire L. Thompson
      Pages 45-55

    3. Terminal Restriction Fragment Length Polymorphism (T-RFLP) Profiling of Bacterial 16S rRNA Genes

      • Catherine A. Osborne
      Pages 57-69

    4. Profiling the Diversity of Microbial Communities with Single-Strand Conformation Polymorphism (SSCP)

      • Achim Schmalenberger, Christoph C. Tebbe
      Pages 71-83

    5. Human Fecal Source Identification with Real-Time Quantitative PCR

      • Orin C. Shanks, Lindsay Peed, Mano Sivaganesan, Richard A. Haugland, Eunice C. Chern
      Pages 85-99

    6. Next Generation Barcode Tagged Sequencing for Monitoring Microbial Community Dynamics

      • Katy Breakwell, Sasha G. Tetu, Liam D. H. Elbourne
      Pages 101-110

    7. Analysis of Methanotroph Community Structure Using a pmoA-Based Microarray

      • Guy C. J. Abell, Nancy Stralis-Pavese, Yao Pan, Levente Bodrossy
      Pages 111-122

    8. Biolog Phenotype MicroArrays for Phenotypic Characterization of Microbial Cells

      • Amanda M. Mackie, Karl A. Hassan, Ian T. Paulsen, Sasha G. Tetu
      Pages 123-130

  4. Investigation of Biological Activities In Situ

    1. Front Matter

      Pages 131-131
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    2. Visualization of Metabolic Properties of Bacterial Cells Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS)

      • Yi Vee Chew, Andrew J. Holmes, John B. Cliff
      Pages 133-146

    3. Single-Cell Raman Sorting

      • Mengqiu Li, Dan G. Boardman, Andrew Ward, Wei E. Huang
      Pages 147-153

    4. Bacterial Whole-Cell Biosensors for the Detection of Contaminants in Water and Soils

      • Yun Wang, Dayi Zhang, Paul A. Davison, Wei E. Huang
      Pages 155-168

    5. Stable Isotope Probing to Study Functional Components of Complex Microbial Ecosystems

      • Sophie Mazard, Hendrik Schäfer
      Pages 169-180

  5. High Throughput Genomic Approaches for Environmental Microbiology

    1. Front Matter

      Pages 181-181
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    2. Metagenomics Using Next-Generation Sequencing

      • Lauren Bragg, Gene W. Tyson
      Pages 183-201
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Keywords

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. 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.

Editors and Affiliations

  • Dept. Chemistry & Biomolecular Sciences, Macquarie University, Sydney, Australia

    Ian T. Paulsen

  • School of Molecular Bioscience, University of Sydney, Camperdown, Australia

    Andrew J. Holmes

Bibliographic Information

  • Book Title: Environmental Microbiology

  • Book Subtitle: Methods and Protocols

  • Editors: Ian T. Paulsen, Andrew J. Holmes

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-712-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2014

  • Hardcover ISBN: 978-1-62703-711-2Published: 12 February 2014

  • Softcover ISBN: 978-1-4939-5903-7Published: 27 August 2016

  • eBook ISBN: 978-1-62703-712-9Published: 11 February 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 242

  • Number of Illustrations: 16 b/w illustrations, 19 illustrations in colour

  • Topics: Microbiology, Environmental Science and Engineering

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