The Plant Microbiome, 1st ed. 2021 Methods and Protocols Methods in Molecular Biology Series, Vol. 2232

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.

1. Studying Seed Microbiomes

Birgit Wassermann, Daria Rybakova, Eveline Adam, Christin Zachow, Maria Bernhard, Maria Müller, Riccardo Mancinelli, and Gabriele Berg

2. Sampling Microbiomes Associated with Different Plant Compartments

Henry W. G. Birt, Anthony B. Pattison, andPaul G. Dennis

3. Sampling of Bacteria Associated with Plant Vascular Tissues

Anthony J. Young

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

Jed Calvert

5. Preparation of Samples for Characterization of Arbuscular Mycorrhizal Fungi

Alberto Guillén

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

7. Fast Screening of Bacteria for Plant Growth Promoting Traits

Bruna Durante Batista, Maria Letícia Bonatelli, and Maria Carolina Quecine

Kenneth Dumackand Michael Bonkowski

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

10. 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, and Amy E. Zanne

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

Akitomo Kawasaki and Peter R. Ryan

12. Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by quantitative-PCR

Aimeric Blaud, Abadie Maïder, and Ian M. Clark

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

Yun Kit Yeoh

14. Inference and Analysis of SPIEC-EASI Microbiome Networks

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

Everthon Fernandes Figueredo and Maria Carolina Quecine

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

Eugenie Singh, Peer M. Schenk, and Lilia C. Carvalhais

17. Soil-borne Legacies of Disease in Arabidopsis thaliana

Gilles Vismans, Jelle Spooren, Corné M.J. Pieterse, Peter A.H.M. Bakker, aned Roeland L. Berendsen

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

Nina R. Ashfield‑Crook, Zachary Woodward, Martin Soust,and D. İpek Kurtböke

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

20. Functional Soil Biological Measurements to Support Healthy Soils

21. A Bait-Trap Assay to Characterise Soil Microbes that Exhibit Chemotaxis to Root Exudates

22. Methods for Root Exudate Collection and Analysis

Hugo A. Pantigoso, Yanhui He, Michael J. DiLegge, and Jorge M. Vivanco

23. Collection of Sterile Root Exudates from Foliar Pathogen-Inoculated Plants

Yang Song, Corné M.J. Pieterse, Peter A.H.M. Bakker, and Roeland L. Berendsen

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts