M O L E C U L A R M I C R O B I A L E C O L O G Y M A N U A L

MOLECULAR MICROBIAL ECOLOGY MANUAL

Edited by

A N T O O N D.L . A K K E R M A N S Department of Microbiology, Wageningen Agricultural University, The Netherlands

J A N D I R K V A N ELSAS IPO-DLO, Wageningen, The Netherlands

and

F R A N S J. D E B R U I J N MSU-DOE Plant Research Lab, NSF Center for Microbial Ecology and Department of Microbiology, Michigan State University, U.S.A.

Springer-Science+Business Media, B.V.

L i b r a r y o f Congress C a t a 1 o g i n g - i n - P u b 1 i c a t i o n Data

M o l e c u l a r l i c r c ^ ^ a l e c o l o g y manual / e d i t e d by A n t o o n D.L. A k k e r m a n s ,

J a n D i r k V/an E l s a s , and F r a n s J . De B r u i j n .

p . cm .

ISBN 978-94-010-4156-0 ISBN 978-94-011-0351-0 (eBook)

DOI 10.1007/978-94-011-0351-0 1. M o l e c u l a r m i c r o b i o l o g y . 2 . M i c r o b i a l e c o l o g y . I. A k k e r m a n s ,

A. D. L . I I . E l s a s , J . D. van ( J a n D . ) , 1951- I I I . De B r u i j n ,

F . J . ( F r a n s J . )

QR74.M64 1995b

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ISBN 978-94-010-4156-0

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Contents

Preface

SECTION 1: Isolation of microbial nucleic acids

1.1. Extraction of microbial DNA from aquatic sources

1.1.2. Extraction of microbial DNA from aquatic sources: Freshwater Roger W. Pickup, Glenn Rhodes and Jon R. Saunders

1.1.3. Extraction of microbial DNA from sewage and manure slurries K. Smalla

1.1.4. Methods for extracting DNA from microbial mats and cultivated micro-organisms: high molecular weight DNA from French press lysis

Mary M. Bateson and David M. Ward

1.2. Extraction of microhial RNA from aquatic sources

1.2.3. Methods for extracting RNA or ribosomes from microbial mats and cultivated microorganisms

David M. Ward, Alyson L. Ruff-Roberts and Roland Weller

1.3. Extraction ofmicrohial DNA from hulk soil

1.3.1. Cell extraction method Vigdis Torsvik

1.3.3. Extraction of microbial community DNA from soils J. D. van Elsas and K. Small a

v

VI

1.3.4. Small scale extraction of DNA from soil with spun column cleanup Aimo Saano and Kristina Lindstrom

1.3.5. Gel purification of soil DNA extracts David D. Myrold, Kendall J. Martin and Nancy J. Ritchie

1.4. Extraction of DNA from phytosphere, rhizosphere, rhizoplane

1.4.2. Extraction and PCR amplification of DNA from the rhizoplane Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers and Mark J. Bailey

1.4.3. Extraction of microbial DNA from the phylloplane Penny A. Bramwell, Rita V. Barallon, Hilary J. Rogers and Mark J. Bailey

1.5. Extraction of RNA from bulk soil

1.5.1. Direct and simultaneous extraction of DNA and RNA from soil Sonja Selenska-Pobell

1.6. Nucleic acid extraction from cultures

1.6.2. Extraction of ribosomal RNA from microbial cultures Erko Stackebrandt and Naomi Ward

SECTION 2: Detection of microbial nucleic acid sequences

2.2. Preparation of radioactive probes

2.2.1. Preparation of radioactive probes Martin Cunningham

2.3. Preparation of non-radioactive probes

2.3.1. Detection of nucleic acids by chemiluminescence Martin Cunningham, Bronwen Harvey and Martin Harris

2.6. Detection of microbial DNA sequences by colony hybridization

2.6.1. Detection of microbial DNA sequences by colony hybridization Penny R. Hirsch

Vll

2.7. Detection and quantifIcation of microbial nucleic acid seque Polymerase Chain Reaction (PCR)

2.7.2. Polymerase chain reaction (PCR) analysis of soil microbial DNA J.D. van Elsas and A. Wolters

2.7.5. Detection of mRNA and rRNA via reverse transcription and PCR in soil

Sonja Selenska-Pobell

SECTION 3: Identification and classification of microbes usmg DNA and RNA sequences

3.1. Partial and complete 16S rDNA sequences, their use in generation oj" 16S rDNA phylogenetic trees and their implications in molecular eco­logical studies

3.1.1. Partial and complete 16S rONA sequences, their use in generation of 16S rONA phylogenetic trees and their implications in molecular eco­logical studies

Erko Stackebrandt and Fred A. Rainey

3.3. Microbial identij"ication and design oj"phylogenetic trees based

3.3.1. Amplification of ribosomal RNA sequences Richard Devereux and Stephanie G. Willis

3.3.2 Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA)

Arturo A. Massol-Deya, David A. Odelson, Robert F. Hickey and James M. Tiedje

3.3.4. Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA sequences

Yves van de Peer and Rupert de Wachter

3.3.5. Sequence Databases Wolfgang Ludwig

3.3.6. In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes

Rudolf I. Amann

Vlll

SECTION 4: Detection, identification and classification of microbes using other methods

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

4.1.3. Immunofluorescence colony-staining (IFC) J.W.L. van Vuurde and J.M. van der Wolf

4.1.8. Fluorescent staining of microbes for total direct counts Jaap Bloem

4.1.9. Slide immunoenzymatic assay (SIA) Everly Conway de Macario and Alberto J.L. Macario

SECTION 5: Detection of gene transfer in the environment

5.1. Gene transfer by transformation

5.1.1. Natural transformation in aquatic environments John H. Paul and Haydn G. Williams

5.2. Gene tramier by conjugation

5.2.3. Detection of gene transfer in the environment: Conjugation in soil Eric Smit and Jan Dirk van Elsas

5.3. Gene transfer hy transduction

5.3.2. Phage ecology and genetic exchange in soil Paul R. Herron

SECTION 6: Tracking of specific microbes in the environment

6.1. Marker genes

6.1. 7. Heavy metal resistances in microbial ecosystems M. Mergeay

6.1.8. Biodegradation genes as marker genes in microbial ecosystems Bruce M. Applegate, Udayakumar Matrubutham, John Sanseverino and Gary S. Sayler

lX

6.2. Designing field and microcosm experiments with GEM's

6.2.1. Design of microcosms to provide data reflectin field trials of GEMS Mary A. Hood and R.J. Seidler

6.2.3. Designing release experiments with GEM's in foods: Risk assessment of the use of genetically modified Lactococcus lactis strains in fermented milk products; a case study

Nicolette Klijn, Anton H. Weerkamp and W.M. de Vos

Xl

Preface

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 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 micro­bial 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.

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