Environmental Microbiology

Methods and Protocols

  • Ian T. Paulsen
  • Andrew J. Holmes

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

Table of contents

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

    1. Front Matter
      Pages 1-1
    2. Helena Nevalainen, Liisa Kautto, Junior Te’o
      Pages 3-16
    3. Anthony J. Brzoska, Karl A. Hassan
      Pages 25-42
  3. Describing Microbial Communities

    1. Front Matter
      Pages 43-43
    2. Orin C. Shanks, Lindsay Peed, Mano Sivaganesan, Richard A. Haugland, Eunice C. Chern
      Pages 85-99
    3. Katy Breakwell, Sasha G. Tetu, Liam D. H. Elbourne
      Pages 101-110
    4. Guy C. J. Abell, Nancy Stralis-Pavese, Yao Pan, Levente Bodrossy
      Pages 111-122
    5. 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
    2. Mengqiu Li, Dan G. Boardman, Andrew Ward, Wei E. Huang
      Pages 147-153
    3. Yun Wang, Dayi Zhang, Paul A. Davison, Wei E. Huang
      Pages 155-168
  5. High Throughput Genomic Approaches for Environmental Microbiology

    1. Front Matter
      Pages 181-181
    2. Lauren Bragg, Gene W. Tyson
      Pages 183-201
    3. Sophie Mazard, Martin Ostrowski, Ross Holland, Mikhail V. Zubkov, David J. Scanlan
      Pages 203-212
    4. Scott Gifford, Brandon Satinsky, Mary Ann Moran
      Pages 213-229
  6. Back Matter
    Pages 241-242

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.


Biological activities in situ Ecological processes Environmental microorganisms High throughput “omics” approaches Microbial communities

Editors and affiliations

  • Ian T. Paulsen
    • 1
  • Andrew J. Holmes
    • 2
  1. 1.Dept. Chemistry & Biomolecular SciencesMacquarie UniversitySydneyAustralia
  2. 2.School of Molecular BioscienceUniversity of SydneyCamperdownAustralia

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2014
  • Publisher Name Humana Press, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-62703-711-2
  • Online ISBN 978-1-62703-712-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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