Molecular Microbial Ecology Manual

1. Front Matter

   Pages i-xvii

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2. Isolation of microbial nucleic acids

   1. Direct extraction of fungal DNA from soil

      • Ross N. Nazar, E. Jane Robb, Tatiana Volossiouk

      Pages 1-8

   2. DNA extraction from actinorhizal nodules

      • Hugo Ramírez-Saad, Wilma M. Akkermans, Antoon D.L. Akkermans

      Pages 9-20

3. Detection of microbial nucleic acid sequences

   1. Detection and quantification of microbial DNA sequences in soil by Southern and dot/slot blot hybridization

      • Carsten S. Jacobsen

      Pages 21-31

   2. Detection and enumeration of soil bacteria using the MPN-PCR technique

      • Christine Picard, Xavier Nesme, Pascal Simonet

      Pages 33-41

   3. Quantitative PCR of environmental samples

      • Janet K. Jansson, Thomas Leser

      Pages 43-61

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

   1. DNA fingerprinting by arbitrarily primed PCR (RAPDs)

      • Kwong-Kwok Wong, Rita Cheng, Jeffrey Saffer, David Ralph, John Welsh, Michael McClelland

      Pages 63-76

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

   1. The use of phospholipid fatty acids to determine microbial community structure

      • Robert H. Findlay

      Pages 77-93

6. Detection of gene transfer in the environment

   1. Conjugation in aquatic environments

      • Søren J. Sørensen, Niels Kroer, Erik Sørensen, Gitte Sengeløv, Tamar Barkay

      Pages 95-123

   2. Conjugation and mobilization in the epilithon

      • Katja E. Hill, Julian R. Marchesi, John C. Fry

      Pages 125-152

   3. Transduction in the aquatic environment

      • Martin Day, Julian Marchesi

      Pages 153-173

7. Tracking of the speceific microbes in the environment

   1. Lux as a marker gene to track microbes

      • Jim I. Prosser, Elizabeth A. S. Rattray, Kenneth Killham, L. Anne Glover

      Pages 175-191

   2. XylE as a marker gene for microorganisms

      • Jon R. Saunders, Roger W. Pickup, J. Alun Morgan, Craig Winstanley, Venetia A. Saunders

      Pages 193-204

   3. GUS as a marker to track microbes

      • Kate J. Wilson

      Pages 205-229

   4. Antibiotic resistance as a marker for tracking bacteria in the soil ecosystem

      • E. Smit, K. Wernars, J. D. Van Elsas

      Pages 231-245

   5. Subtraction hybridization for the production of high specificity DNA probes

      • A. J. Bjourson, J. E. Cooper

      Pages 247-259

For a long time microbial ecology has been developed as a distinct field within Ecology. In spite of the important role of microorganisms in the environment, 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 cul­ tures. We now realise that only a minor fraction of the microbial com­ munity 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 depo­ sit their new protocols in full detail in the next edition of this Manual. We hope this book finds its place where it was born: at the lab bench! Antoon D.L. Akkermans, Jan Dirk van Elsas and Frans J. de Bruijn March 1995 Molecular Microbial Ecology Manual 1.3.6: 1-8, 1996. © 1996 Kluwer Academic Publishers.

• ecology
• microbial ecology

• 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, Michigan State University, USA

  Frans J. Bruijn

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