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Molecular Microbial Ecology Manual

  • Book
  • © 1995

Overview

Editors:
  1. Antoon D. L. Akkermans

    1. Department of Microbiology, Wageningen Agricultural University, The Netherlands

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  2. Jan Dirk Elsas

    1. IPO-DLO, Wageningen, The Netherlands

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  3. Frans J. Bruijn

    1. MSU-DOE Plant Research Lab, NSF Center for Microbial Ecology and Department of Microbiology, Michigan State University, USA

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    You can also search for this editor in PubMed   Google Scholar

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Table of contents (33 chapters)

  1. Front Matter

    Pages i-xi
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  2. Isolation of microbial nucleic acids

    1. Extraction of microbial DNA from aquatic sources

      1. Extraction of microbial DNA from aquatic sources: Freshwater
        • Roger W. Pickup, Glenn Rhodes, Jon R. Saunders
        Pages 1-11
      2. Extraction of microbial DNA from sewage and manure slurries
        • Kornelia Smalla
        Pages 13-22
      3. Methods for extracting DNA from microbial mats and cultivated micro-organisms: high molecular weight DNA from French press lysis
        • Mary M. Bateson, David M. Ward
        Pages 23-29

    2. Extraction of microhial RNA from aquatic sources

      1. Methods for extracting RNA or ribosomes from microbial mats and cultivated microorganisms
        • David M. Ward, Alyson L. Ruff-Roberts, Roland Weller
        Pages 31-44

    3. Extraction of microhial DNA from bulk soil

      1. Cell extraction method
        • Vigdis Torsvik
        Pages 45-59
      2. Extraction of microbial community DNA from soils
        • Jan Dirk Van Elsas, Kornelia Smalla
        Pages 61-71
      3. Small scale extraction of DNA from soil with spun column cleanup
        • Aimo Saano, Kristina Lindström
        Pages 73-78
      4. Gel purification of soil DNA extracts
        • David D. Myrold, Kendall J. Martin, Nancy J. Ritchie
        Pages 79-87

    4. Extraction of DNA from phytosphere, rhizosphere, rhizoplane

      1. Extraction and PCR amplification of DNA from the rhizoplane
        • Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers, Mark J. Bailey
        Pages 89-108
      2. Extraction of microbial DNA from the phylloplane
        • Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers, Mark J. Bailey
        Pages 109-129

    5. Extraction of RNA from bulk soil

      1. Direct and simultaneous extraction of DNA and RNA from soil
        • Sonja Selenska-Pobell
        Pages 131-147

    6. Nucleic acid extraction from cultures

      1. Extraction of ribosomal RNA from microbial cultures
        • Erko Stackebrandt, Naomi Ward
        Pages 149-159

  3. Detection of microbial nucleic acid sequences

    1. Preparation of radioactive probes

      1. Preparation of radioactive probes
        • Martin Cunningham
        Pages 161-194

    2. Preparation of non-radioactive probes

      1. Detection of nucleic acids by chemiluminescence
        • Martin Cunningham, Bronwen Harvey, Martin Harris
        Pages 195-222

    3. Detection of microbial DNA sequences by colony hybridization

      1. Detection of microbial DNA sequences by colony hybridization
        • Penny R. Hirsch
        Pages 223-234

    4. Detection and quantification of microbial nucleic acid seque Polymerase Chain Reaction (PCR)

      1. Polymerase chain reaction (PCR) analysis of soil microbial DNA
        • Jan Dirk Van Elsas, Anneke Wolters
        Pages 235-244
      2. Detection of mRNA and rRNA via reverse transcription and PCR in soil
        • Sonja Selenska-Pobell
        Pages 245-258

  4. Identification and classification of microbes using DNA and RNA sequences

    1. Partial and complete 16S rDNA sequences, their use in generation of 16S rDN A phylogenetic trees and their implications in molecular ecological studies

      1. Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies
        • Erko Stackebrandt, Fred A. Rainey
        Pages 259-275

    2. Microbial identification and design of phylogenetic trees based

      1. Amplification of ribosomal RNA sequences
        • Richard Devereux, Stephanie G. Willis
        Pages 277-287
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Keywords

About this book

For a long time microbial ecology has been developed as a distinct field with­ in Ecology. In spite of the important role of microorganisms in the environ­ ment, this group of 'invisible' organisms remained unaccessable to other ecologists. Detection and identification of microorganisms remain largely dependent on isolation techniques and characterisation of pure cultures. We now realise that only a minor fraction of the microbial community can be cultivated. As a result of the introduction of molecular methods, microbes can now be detected and identified at the DNA/RNA level in their natural environment. This has opened a new field in ecology: Molecular Microbial Ecology. In the present manual we aim to introduce the microbial ecologist to a selected number of current molecular techniques that are relevant in micro­ bial ecology. The first edition of the manual contains 33 chapters and an equal number of additional chapters will be added this year. Since the field of molecular ecology is in a continuous progress, we aim to update and extend the Manual regularly and will invite anyone to deposit their new protocols in full detail in the next edition of this Manual.

Editors and Affiliations

  • Department of Microbiology, Wageningen Agricultural University, The Netherlands

    Antoon D. L. Akkermans

  • IPO-DLO, Wageningen, The Netherlands

    Jan Dirk Elsas

  • MSU-DOE Plant Research Lab, NSF Center for Microbial Ecology and Department of Microbiology, Michigan State University, USA

    Frans J. Bruijn

Bibliographic Information

  • Book Title: Molecular Microbial Ecology Manual

  • Editors: Antoon D. L. Akkermans, Jan Dirk Elsas, Frans J. Bruijn

  • DOI: https://doi.org/10.1007/978-94-011-0351-0

  • Publisher: Springer Dordrecht

  • eBook Packages: Springer Book Archive

  • Copyright Information: Springer Science+Business Media Dordrecht 1995

  • Hardcover ISBN: 978-0-7923-3698-3Due: 31 October 1995

  • Softcover ISBN: 978-94-010-4156-0Published: 05 November 2012

  • eBook ISBN: 978-94-011-0351-0Published: 06 December 2012

  • Edition Number: 1

  • Number of Pages: XI, 494

  • Topics: Plant Sciences, Soil Science & Conservation, Ecology

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