Skip to main content
SpringerLink
Log in
Book cover

The Plant Microbiome

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Lilia C. Carvalhais

    1. Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Paul G. Dennis

    1. School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Australia

    View editor publications

    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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2232)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (23 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Studying Seed Microbiomes

    • Birgit Wassermann, Daria Rybakova, Eveline Adam, Christin Zachow, Maria Bernhard, Maria Müller et al.
    Pages 1-21

  3. Sampling Microbiomes Associated with Different Plant Compartments

    • Henry W. G. Birt, Anthony B. Pattison, Paul G. Dennis
    Pages 23-29

  4. Sampling of Bacteria Associated with Plant Vascular Tissues

    • Anthony J. Young
    Pages 31-35

  5. Sampling of Plant Material to Study Endophytes in Small, Large, and Woody Plants

    • Jed Calvert
    Pages 37-42

  6. Preparation of Samples for Characterization of Arbuscular Mycorrhizal Fungi

    • Alberto Guillén
    Pages 43-51

  7. Culture-based Methods for Studying the Bacterial Root Microbiome of Wheat

    • Rebekah J. Robinson, Vanessa N. Kavamura, Penny R. Hirsch, Ian M. Clark, Tim H. Mauchline
    Pages 53-60

  8. Fast Screening of Bacteria for Plant Growth Promoting Traits

    • Bruna D. Batista, Maria Letícia Bonatelli, Maria Carolina Quecine
    Pages 61-75

  9. Protists in the Plant Microbiome: An Untapped Field of Research

    • Kenneth Dumack, Michael Bonkowski
    Pages 77-84

  10. Plant-associated Fungi: Methods for Taxonomy, Diversity, and Bioactive Secondary Metabolite Bioprospecting

    • Mariana Costa Ferreira, Camila Rodrigues de Carvalho, Marina Bahia, Débora Luiza Costa Barreto, Rafaela Nogueira Azevedo, Betania Barros Cota et al.
    Pages 85-112

  11. Extraction and Purification of DNA from Wood at Various Stages of Decay for Metabarcoding of Wood-Associated Fungi

    • Jeff R. Powell, Michaela Blyton, Brad Oberle, Gillian L. Powell, Jessica Rigg, Darcy Young et al.
    Pages 113-122

  12. Peptide Nucleic Acid (PNA) Clamps to Reduce Co-amplification of Plant DNA During PCR Amplification of 16S rRNA Genes from Endophytic Bacteria

    • Akitomo Kawasaki, Peter R. Ryan
    Pages 123-134

  13. Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by Quantitative-PCR

    • Aimeric Blaud, Abadie Maïder, Ian M. Clark
    Pages 135-146

  14. Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes

    • Yun Kit Yeoh
    Pages 147-153

  15. Inference and Analysis of SPIEC-EASI Microbiome Networks

    • Henry W. G. Birt, Paul G. Dennis
    Pages 155-171

  16. Gene Knockout of Beneficial Plant-associated Bacillus spp. Using the CRISPR-Cas9 Double Plasmid System

    • Everthon Fernandes Figueredo, Maria Carolina Quecine
    Pages 173-191

  17. Sample Preparation for Culture-Independent Profiling and Isolation of Phyllosphere Bacteria to Identify Potential Biopesticides

    • Eugenie Singh, Peer M. Schenk, Lilia C. Carvalhais
    Pages 193-208

  18. Soil-Borne Legacies of Disease in Arabidopsis thaliana

    • Gilles Vismans, Jelle Spooren, Corné M. J. Pieterse, Peter A. H. M. Bakker, Roeland L. Berendsen
    Pages 209-218

  19. Bioactive Streptomycetes from Isolation to Applications: A Tasmanian Potato Farm Example

    • Nina R. Ashfield-Crook, Zachary Woodward, Martin Soust, D. İpek Kurtböke
    Pages 219-249

  20. Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops

    • Acacio Aparecido Navarrete, Rita de Cássia Bonassi, Juliana Heloisa Pinê Américo-Pinheiro, Gisele Herbst Vazquez, Lucas William Mendes, Elisângela de Souza Loureiro et al.
    Pages 251-263
Back to top

Keywords

About this book

This volume provides methods, protocols, and reviews that are useful for new and experienced plant microbiome researchers. Chapters guide readers through the investigation of microbiomes associated with seeds, sampling microbiomes from plant compartments and tissues, culture-based methods, culture-independent metabarcoding methods, methods to obtain DNA and perform metabarcoding, protocols to block PCR amplification from the plant host, qPCR-based methods, editing of specific genes in Bacillus genomes, and Streptomycetes and plant microbial indicators. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, The Plant Microbiome: Methods and Protocols aims to ensure successful results in the further study of this vital field.


Editors and Affiliations

  • Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia

    Lilia C. Carvalhais

  • School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Australia

    Paul G. Dennis

Bibliographic Information

  • Book Title: The Plant Microbiome

  • Book Subtitle: Methods and Protocols

  • Editors: Lilia C. Carvalhais, Paul G. Dennis

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1040-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1039-8Published: 08 November 2020

  • Softcover ISBN: 978-1-0716-1042-8Published: 08 November 2021

  • eBook ISBN: 978-1-0716-1040-4Published: 07 November 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 321

  • Number of Illustrations: 9 b/w illustrations, 57 illustrations in colour

  • Topics: Plant Sciences

Publish with us

Policies and ethics

Back to top

Search

Navigation