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Molecular Microbial Ecology Manual

  • Antoon D. L. Akkermans
  • Jan Dirk Van Elsas
  • Frans J. De Bruijn

Table of contents

  1. Front Matter
    Pages i-xi
  2. Isolation of microbial nucleic acids

    1. Extraction of microbial DNA from aquatic sources

    2. Extraction of microhial RNA from aquatic sources

      1. David M. Ward, Alyson L. Ruff-Roberts, Roland Weller
        Pages 31-44
    3. Extraction of microhial DNA from bulk soil

      1. Vigdis Torsvik
        Pages 45-59
      2. Jan Dirk Van Elsas, Kornelia Smalla
        Pages 61-71
      3. Aimo Saano, Kristina Lindström
        Pages 73-78
      4. David D. Myrold, Kendall J. Martin, Nancy J. Ritchie
        Pages 79-87
    4. Extraction of DNA from phytosphere, rhizosphere, rhizoplane

      1. Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers, Mark J. Bailey
        Pages 89-108
      2. Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers, Mark J. Bailey
        Pages 109-129
    5. Extraction of RNA from bulk soil

    6. Nucleic acid extraction from cultures

      1. Erko Stackebrandt, Naomi Ward
        Pages 149-159
  3. Detection of microbial nucleic acid sequences

    1. Preparation of radioactive probes

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

      1. Martin Cunningham, Bronwen Harvey, Martin Harris
        Pages 195-222
    3. Detection of microbial DNA sequences by colony hybridization

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

      1. Jan Dirk Van Elsas, Anneke Wolters
        Pages 235-244
  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

    2. Microbial identification and design of phylogenetic trees based

  5. Detection, identification and classification of microbes using other methods

    1. Detection, identification and classification of microbes using other methods

      1. Jim W. L. Van Vuurde, Jan M. Van Der Wolf
        Pages 347-365
      2. Everly Conway De Macario, Alberto J. L. Macario
        Pages 379-393
  6. Detection of gene transfer in the environment

    1. Gene transfer by transformation

      1. John H. Paul, Haydn G. Williams
        Pages 395-416
    2. Gene transfer by conjugation

      1. Eric Smit, Jan Dirk Van Elsas
        Pages 417-426
    3. Gene transfer by transduction

      1. Paul R. Herron
        Pages 427-438
  7. Tracking of specific microbes in the environment

    1. Marker genes

      1. Bruce M. Applegate, Udayakumar Matrubutham, John Sanseverino, Gary S. Sayler
        Pages 457-470
    2. Designing field and microcosm experiments with GEM’s

      1. Mary A. Hood, Ramon J. Seidler
        Pages 471-486
      2. Nicolette Klijn, Anton H. Weerkamp, Willem M. De Vos
        Pages 487-494

About this book

Introduction

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.

Keywords

RNA biology ecology environment microbe microbes microbial ecology microcosm microorganism molecular biology plant polymer soil

Editors and affiliations

  • Antoon D. L. Akkermans
    • 1
  • Jan Dirk Van Elsas
    • 2
  • Frans J. De Bruijn
    • 3
  1. 1.Department of MicrobiologyWageningen Agricultural UniversityThe Netherlands
  2. 2.IPO-DLOWageningenThe Netherlands
  3. 3.MSU-DOE Plant Research Lab, NSF Center for Microbial Ecology and Department of MicrobiologyMichigan State UniversityUSA

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