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Microbial Environmental Genomics (MEG)

  • Book
  • © 2016

Overview

Editors:
  1. Francis Martin

    1. "Tree-Microbe Interactions" (IAM), UMR1136 INRA/University of Lorraine, Nancy, France

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  2. Stephane Uroz

    1. "Tree-Microbe Interactions" (IAM);, UMR1136 INRA/University of Lorraine, Champenoux, France

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1399)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities

    • Lejla Pašić, Ana-Belen Martin-Cuadrado, Purificación López-García
    Pages 1-28

  3. Investigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi

    • Alessandro Desirò, Alessandra Salvioli, Paola Bonfante
    Pages 29-53

  4. GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity

    • Samuel Dequiedt, Pierre-Alain Maron, Lionel Ranjard
    Pages 55-60

  5. Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons

    • Karina Engelbrecht Clemmensen, Katarina Ihrmark, Mikael Brandström Durling, Björn D. Lindahl
    Pages 61-88

  6. Fungal Communities in Soils: Soil Organic Matter Degradation

    • Tomáš Větrovský, Martina Štursová, Petr Baldrian
    Pages 89-100

  7. DNA-Based Characterization and Identification of Arbuscular Mycorrhizal Fungi Species

    • Carolina Senés-Guerrero, Arthur Schüßler
    Pages 101-123

  8. Molecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding

    • G. Arjen de Groot, Ivo Laros, Stefan Geisen
    Pages 125-140

  9. Identification and In Situ Distribution of a Fungal Gene Marker: The Mating Type Genes of the Black Truffle

    • Herminia De la Varga, Claude Murat
    Pages 141-149

  10. Stable-Isotope Probing RNA to Study Plant/Fungus Interactions

    • Amandine Lê Van, Marie Duhamel, Achim Quaiser, Philippe Vandenkoornhuyse
    Pages 151-166

  11. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning

    • Céline Ribière, Réjane Beugnot, Nicolas Parisot, Cyrielle Gasc, Clémence Defois, Jérémie Denonfoux et al.
    Pages 167-182

  12. Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip

    • Joy D. Van Nostrand, Huaqin Yin, Liyou Wu, Tong Yuan, Jizhong Zhou
    Pages 183-196

  13. Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches

    • Anne Schöler, Maria de Vries, Gisle Vestergaard, Michael Schloter
    Pages 197-206

  14. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

    • Kevin P. Keegan, Elizabeth M. Glass, Folker Meyer
    Pages 207-233

  15. Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies

    • Martin Taubert, Carolina Grob, Alexandra M. Howat, Oliver J. Burns, Yin Chen, Josh D. Neufeld et al.
    Pages 235-255

  16. Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes

    • Lisa Ufarté, Sophie Bozonnet, Elisabeth Laville, Davide A. Cecchini, Sandra Pizzut-Serin, Samuel Jacquiod et al.
    Pages 257-271

  17. Metatranscriptomics of Soil Eukaryotic Communities

    • Rajiv K. Yadav, Claudia Bragalini, Laurence Fraissinet-Tachet, Roland Marmeisse, Patricia Luis
    Pages 273-287

  18. Analysis of Ancient DNA in Microbial Ecology

    • Olivier Gorgé, E. Andrew Bennett, Diyendo Massilani, Julien Daligault, Melanie Pruvost, Eva-Maria Geigl et al.
    Pages 289-315

  19. Back Matter

    Pages 317-321
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Keywords

About this book

This volume seeks to understand how organisms and gene functions are influenced by environmental cues while accounting for variation that takes place within and among environmental populations and communities. Microbial Environmental Genomics (MEG) guides readers through methods to analyse the diversity of different organism types (archaea, bacteria, fungi, protists and microfauna), interactions between fungi and trees, and methods to identify and characterize functions and functional diversity of both pro- and eukaryotes. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and practical, Microbial Environmental Genomics (MEG) will serve as a primary research reference for researchers and research managers in environmental microbiology working in the expanding field of molecular ecology and environmental genomics.

Editors and Affiliations

  • "Tree-Microbe Interactions" (IAM), UMR1136 INRA/University of Lorraine, Nancy, France

    Francis Martin

  • "Tree-Microbe Interactions" (IAM);, UMR1136 INRA/University of Lorraine, Champenoux, France

    Stephane Uroz

Bibliographic Information

  • Book Title: Microbial Environmental Genomics (MEG)

  • Editors: Francis Martin, Stephane Uroz

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3369-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3367-9Published: 21 January 2016

  • Softcover ISBN: 978-1-4939-8032-1Published: 31 March 2018

  • eBook ISBN: 978-1-4939-3369-3Published: 20 January 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 321

  • Number of Illustrations: 21 b/w illustrations, 34 illustrations in colour

  • Topics: Human Genetics

  • Industry Sectors: Biotechnology, Pharma

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