The Plant Microbiome: Methods and Protocols

ISBN-13: 9781071610398 / Angielski / Twarda / 2020 / 321 str.

Lilia C. Carvalhais; Paul G. Dennis

Spis treści

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, and Paul 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

Rebekah J. Robinson, Vanessa N. Kavamura, Penny R. Hirsch, Ian M. Clark, and Tim H. Mauchline

 

7. Fast Screening of Bacteria for Plant Growth Promoting Traits

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

 

8. Protists in the Plant Microbiome - An Untapped Field Of Research

Kenneth Dumack and Michael Bonkowski

 

9. 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, Carlos Leomar Zani, Ana Raquel de Oliveira Santos, Carlos Augusto Rosa, and Luiz Henrique Rosa

 

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

Henry W. G. Birt and Paul G. Dennis

 

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

Acacio Aparecido Navarrete, Rita de Cássia Bonassi, Juliana Heloisa Pinê Américo-Pinheiro, Gisele Herbst Vazquez, Lucas William Mendes, Elisângela de Souza Loureiro, Eiko Eurya Kuramae, and Siu Mui Tsai

 

20. Functional Soil Biological Measurements to Support Healthy Soils

Hazel R. Lapis-Gaza and Anthony B. Pattison

 

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

Katherine V. Weigh, Bruna D. Batista, and Paul G. Dennis

 

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

 

 

Blurb

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.