Molecular microbial ecology manual

Author(s)

Bibliographic Information

Molecular microbial ecology manual

edited by Antoon D.L. Akkermans, Jan Dirk van Elsas, and Frans J. de Bruijn

Kluwer Academic Publishers, c1995-

  • : hbk
  • : set
  • : Suppl. 1
  • : Suppl. 2
  • : Suppl. 3
  • : Suppl. 4

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Note

Loose-leaf in binder; kept up to date by supplements

Includes bibliographical references

Description and Table of Contents

Volume

: hbk ISBN 9780792334101

Description

This text offers general information about molecular techniques relevant to molecular ecological research. Attention is paid to the use of molecular methods for studying the fate of genetically modified and native microorganisms in the environment.

Table of Contents

  • Extraction of Microbial DNA from Sewage and Manure
  • K. Smalla. Cell Extraction Method
  • V. Torsvik. Polymerase Chain Reaction (PCR) Analysis of Soil Microbial DNA
  • J. D. van Elsas, A. C. Wolters. Extraction and pcr Amplification of DNA from the Rhizoplane
  • P.A. Bramwell, R. V. Barallon, H. J. Rogers, M. J. Bailey. Extraction of Microbial DNA from the Phylloplane
  • P. A. Bramwell, R. V. Barallon, H. J. Rogers, M. J. Bailey. Extraction of Ribosomal DNA from Microbial Cultures
  • E. Stackebrandt, N. Ward. In situ Identification of Micro-organisms by Whole Cell Hybridization with RNA-Targeted Nucleic Acid Probes
  • R. I. Amann. Immunofluorescence Colony-Staining (IFC)
  • J. W. L. van Vuurde, J. M. van der Wolf. Fluorescent Staining of Microbes for Total Direct Counts
  • J. Bloem. Natural Transformation in Aquatic Environments
  • J.H. Paul, H.G. Williams. Phage Ecology and Genetic Exchange in Soil
  • P.R. Herron. Design of Microcosms to Provide Data Reflecting Field Trials of GEMs
  • M.A. Hood, R. J. Seidler. Methods for Extracting DNA from Microbial Mats and Cultivated Micro-organisms: High Molecular Weight DNA from French Press Lysis
  • M.M. Bateson, D.M. Ward. Bacterial Community Fingerprinting of Amplified 16S and 16-23S Ribosomal DNA Gene Sequences and Restriction Endonuclease Analysis (ARDRA)
  • A.A. Massol-Deya, D.A. Odelson, R.F. Hickey, J.M. Tiedje. Detection of Gene Transfer in the Environment: Conjugation in Soil
  • E. Smit, J.D. van Elsas. Direct and Simultaneous Extraction of DNA and RNA from Soil
  • S. Selenska-Pobell. Sequence Databases
  • W. Ludwig. Extraction of Microbial Community DNA from Soils
  • J.D. van Elsas, K. Malla. Investigation of Fungal Phylogeny on the Basis of Small Ribosomal Subunit RNA Sequences
  • Y. van de Peer, R. de Wachter. Biodegradation Genes as Marker Genes in Microbial Ecosystems
  • B.M. Applegate, U. Matrubutham, J. Sanseverino, G. S. Sayler. Preparation of Radioactive Probes
  • M. Cunningham. Detection of Nucleic Acids by Chemiluminescence
  • M. Cunningham, B. Harvey, M. Harris. Gel Purification of Soil DNA Extracts
  • D.D. Myrold, K.J. Martin, N.J. Ritchie. Detection of Microbial DNA Sequences by Colony Hybridization
  • P.R. Hirsch. Partial and Complete 16s RDNA Sequences, their Use in Generation of 16s RDNA Phylogenetic Trees and their Implications in Molecular Ecological Studies
  • E. Stackebrandt, F.A. Rainey. Extraction of Microbial DNA from Aquatic Sources: Freshwater
  • R.W. Pickup, G. Rhodes, J.R. Saunders. Slide Immunoenzymatic Assay (SIA)
  • E. C. de Macario, A.J.L. Macario. Designing Release Experiments with GEMs in Foods
  • N. Klijn, A.H. Weerkamp, W. M. de Vos. Heavy Metal Resistances in Microbial Ecosystems
  • M. Mergeay. Detection of mRNA and rRNA via Reverse Transcription and PCR in Soil
  • S. Selenska-Pobell. Methods for Extracting RNA or Ribosomes from Microbial Mats and Cultivated Microorganisms
  • D.M. Ward, et al.
Volume

: set ISBN 9780792334118

Description

This manual provides general information about molecular techniques relevant to molecular ecological research. Attention is paid to the use of molecular methods for studying the fate of genetically modified and native microorganisms in the environment. The book is intended for postgraduate students and research scientists in the plant and soils sciences and plant molecular biology. The first supplement extends the sections published in the basic work.

Table of Contents

  • Supplement 1: 1.1.1. Extraction of microbial DNA from aquatic sources: Marine environments
  • J.H. Paul. 1.2.1. Extraction of microbial RNA from aquatic sources: Marine environments
  • S.L. Pichard, J.H. Paul. 1.3.2. Direct extraction of microbial DNA from soils and sediments
  • W.H. Johnston, et al. 1.4.1. Detection of microbial genes from the rhizosphere by magnetic capture hybridization and subsequent amplification of target genes by PCR
  • C. Jacobson. 2.1.1. Quantification of nucleic acids
  • V. Torsvik. 2.1.2. Parameters of nucleic acid hybridization experiments
  • C.N. Nakatsu, L.J. Forney. 2.8.2. Soil
  • E. Baath. - Basic Work: Extraction of Microbial DNA from Sewage and Manure
  • K. Smalla. Cell Extraction Method
  • V. Torsvik. Polymerase Chain Reaction (pcr) Analysis of Soil Microbial DNA
  • J.D. van Elsas, A.C. Wolters. Extraction and pcr Amplification of DNA from the Rhizoplane
  • P.A. Bramwell, et al. Extraction of Microbial DNA from the Phylloplane
  • P.A. Bramwell, et al. Extraction of Ribosomal DNA from Microbial Cultures
  • E. Stackebrandt, N. Ward. In situ Identification of Micro-organisms by Whole Cell Hybridization with RNA-Targeted Nucleic Acid Probes
  • R.I. Amann. Immunofluorescence Colony-Staining (IFC)
  • J.W.L. van Vuurde, J.M. van der Wolf. Fluorescent Staining of Microbes for Total Direct Counts
  • J. Bloem. Natural Transformation in Aquatic Environments
  • J.H. Paul, H.G. Williams. Phage Ecology and Genetic Exchange in Soil
  • P.R. Herron. Design of Microcosms to Provide Data Reflecting Field Trials of GEMs
  • M.A. Hood, R. J. Seidler. Methods for Extracting DNA from Microbial Mats and Cultivated Micro-organisms: High Molecular Weight DNA from French Press Lysis
  • M.M. Bateson, D.M. Ward. Bacterial Community Fingerprinting of Amplified 16S and 16-23S Ribosomal DNA Gene Sequences and Restriction Endonuclease Analysis (ARDRA)
  • A.A. Massol-Deya, et al. Detection of Gene Transfer in the Environment: Conjugation in Soil
  • E. Smit, J.D. van Elsas. Direct and Simultaneous Extraction of DNA and RNA from Soil
  • S. Selenska-Pobell. Sequence Databases
  • W. Ludwig. Extraction of Microbial Community DNA from Soils
  • J.D. van Elsas, K. Malla. Investigation of Fungal Phylogeny on the Basis of Small Ribosomal Subunit RNA Sequences
  • Y. van de Peer, R. de Wachter. Biodegradation Genes as Marker Genes in Microbial Ecosystems
  • B.M. Applegate, et al. Preparation of Radioactive Probes
  • M. Cunningham. Detection of Nucleic Acids by Chemiluminescence
  • M. Cunningham, et al. Gel Purification of Soil DNA Extracts
  • D.D. Myrold, et al. Detection of Microbial DNA Sequences by Colony Hybridization
  • P.R. Hirsch. Partial and Complete 16s RDNA Sequences, their Use in Generation of 16s RDNA Phylogenetic Trees and their Implications in Molecular Ecological Studies
  • E. Stackebrandt, F.A. Rainey. Extraction of Microbial DNA from Aquatic Sources: Freshwater
  • R.W. Pickup, et al. Slide Immunoenzymatic Assay (SIA)
  • E.C. de Macario, A.J.L. Macario. (Part contents).
Volume

: Suppl. 1 ISBN 9780792336907

Description

This manual provides general information about molecular techniques relevant to molecular ecological research. Attention is paid to the use of molecular methods for studying the fate of genetically modified and native microorganisms in the environment. The book is intended for postgraduate students and research scientists in the plant and soils sciences and plant molecular biology. The first supplement extends the sections published in the basic work.

Table of Contents

  • Supplement 1: 1.1.1. Extraction of microbial DNA from aquatic sources: Marine environments
  • J.H. Paul. 1.2.1. Extraction of microbial RNA from aquatic sources: Marine environments
  • S.L. Pichard, J.H. Paul. 1.3.2. Direct extraction of microbial DNA from soils and sediments
  • W.H. Johnston, et al. 1.4.1. Detection of microbial genes from the rhizosphere by magnetic capture hybridization and subsequent amplification of target genes by PCR
  • C. Jacobson. 2.1.1. Quantification of nucleic acids
  • V. Torsvik. 2.1.2. Parameters of nucleic acid hybridization experiments
  • C.N. Nakatsu, L.J. Forney. 2.8.2. Soil
  • E. Baath. - Basic Work: Extraction of Microbial DNA from Sewage and Manure
  • K. Smalla. Cell Extraction Method
  • V. Torsvik. Polymerase Chain Reaction (pcr) Analysis of Soil Microbial DNA
  • J.D. van Elsas, A.C. Wolters. Extraction and pcr Amplification of DNA from the Rhizoplane
  • P.A. Bramwell, et al. Extraction of Microbial DNA from the Phylloplane
  • P.A. Bramwell, et al. Extraction of Ribosomal DNA from Microbial Cultures
  • E. Stackebrandt, N. Ward. In situ Identification of Micro-organisms by Whole Cell Hybridization with RNA-Targeted Nucleic Acid Probes
  • R.I. Amann. Immunofluorescence Colony-Staining (IFC)
  • J.W.L. van Vuurde, J.M. van der Wolf. Fluorescent Staining of Microbes for Total Direct Counts
  • J. Bloem. Natural Transformation in Aquatic Environments
  • J.H. Paul, H.G. Williams. Phage Ecology and Genetic Exchange in Soil
  • P.R. Herron. Design of Microcosms to Provide Data Reflecting Field Trials of GEMs
  • M.A. Hood, R. J. Seidler. Methods for Extracting DNA from Microbial Mats and Cultivated Micro-organisms: High Molecular Weight DNA from French Press Lysis
  • M.M. Bateson, D.M. Ward. Bacterial Community Fingerprinting of Amplified 16S and 16-23S Ribosomal DNA Gene Sequences and Restriction Endonuclease Analysis (ARDRA)
  • A.A. Massol-Deya, et al. Detection of Gene Transfer in the Environment: Conjugation in Soil
  • E. Smit, J.D. van Elsas. Direct and Simultaneous Extraction of DNA and RNA from Soil
  • S. Selenska-Pobell. Sequence Databases
  • W. Ludwig. Extraction of Microbial Community DNA from Soils
  • J.D. van Elsas, K. Malla. Investigation of Fungal Phylogeny on the Basis of Small Ribosomal Subunit RNA Sequences
  • Y. van de Peer, R. de Wachter. Biodegradation Genes as Marker Genes in Microbial Ecosystems
  • B.M. Applegate, et al. Preparation of Radioactive Probes
  • M. Cunningham. Detection of Nucleic Acids by Chemiluminescence
  • M. Cunningham, et al. Gel Purification of Soil DNA Extracts
  • D.D. Myrold, et al. Detection of Microbial DNA Sequences by Colony Hybridization
  • P.R. Hirsch. Partial and Complete 16s RDNA Sequences, their Use in Generation of 16s RDNA Phylogenetic Trees and their Implications in Molecular Ecological Studies
  • E. Stackebrandt, F.A. Rainey. Extraction of Microbial DNA from Aquatic Sources: Freshwater
  • R.W. Pickup, et al. Slide Immunoenzymatic Assay (SIA)
  • E.C. de Macario, A.J.L. Macario. (Part contents).
Volume

: Suppl. 2 ISBN 9780792339434

Description

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. (c) 1996 Kluwer Academic Publishers.
Volume

: Suppl. 3 ISBN 9780792346555

Description

This manual provides general information about molecular techniques relevant to molecular ecological research. Attention is paid to the use of molecular methods for studying the fate of genetically modified and native micro-organisms in the environment.

Table of Contents

  • Direct ribosome isolation from soil, A. Felske, et al
  • genotyping of bacterial isolates from the environment using Low-Molecular-Weight RNA fingerprints, M.G. Hofle
  • in situ PCR methodologies for visualization of microscale genetic and taxonomic diversities of prokaryotic communities, Feng Chen, et al
  • characterization of the diversity of ecologically important microbes by rep-PCR genomic fingerprinting, J.L.W, Rademaker, et al
  • denaturing gradient gel electrophoresis (DGGE) in microbial ecology, G. Muyzer
  • extraction of proteins from aquatic environments, O.A. Ogunseitan
  • detection of microbes by laser confocal microscopy, A. Hartmann, et al
  • in situ hybridization to detect microbial RNA in plant tissue, Katharina Pawlowski, et al
  • siderophore receptor as a marker to track fluorescent pseudomonas spp., P.A.H.M. Bakker, et al
  • the celB marker gene, A. Sessitsch, et al
  • GFP as a marker gene, A. Unge, et al.

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