The Plant Microbiome: Methods and Protocols

✍ Scribed by Lilia C. Carvalhais, Paul G. Dennis

• Publisher: Springer US;Humana
• Year: 2021
• Tongue: English
• Leaves: 320
• Series: Methods in Molecular Biology 2232
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xii
Studying Seed Microbiomes (Birgit Wassermann, Daria Rybakova, Eveline Adam, Christin Zachow, Maria Bernhard, Maria Müller et al.)....Pages 1-21
Sampling Microbiomes Associated with Different Plant Compartments (Henry W. G. Birt, Anthony B. Pattison, Paul G. Dennis)....Pages 23-29
Sampling of Bacteria Associated with Plant Vascular Tissues (Anthony J. Young)....Pages 31-35
Sampling of Plant Material to Study Endophytes in Small, Large, and Woody Plants (Jed Calvert)....Pages 37-42
Preparation of Samples for Characterization of Arbuscular Mycorrhizal Fungi (Alberto Guillén)....Pages 43-51
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
Fast Screening of Bacteria for Plant Growth Promoting Traits (Bruna D. Batista, Maria Letícia Bonatelli, Maria Carolina Quecine)....Pages 61-75
Protists in the Plant Microbiome: An Untapped Field of Research (Kenneth Dumack, Michael Bonkowski)....Pages 77-84
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
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
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
Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by Quantitative-PCR (Aimeric Blaud, Abadie Maïder, Ian M. Clark)....Pages 135-146
Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes (Yun Kit Yeoh)....Pages 147-153
Inference and Analysis of SPIEC-EASI Microbiome Networks (Henry W. G. Birt, Paul G. Dennis)....Pages 155-171
Gene Knockout of Beneficial Plant-associated Bacillus spp. Using the CRISPR-Cas9 Double Plasmid System (Everthon Fernandes Figueredo, Maria Carolina Quecine)....Pages 173-191
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
Soil-Borne Legacies of Disease in Arabidopsisthaliana (Gilles Vismans, Jelle Spooren, Corné M. J. Pieterse, Peter A. H. M. Bakker, Roeland L. Berendsen)....Pages 209-218
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
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
Functional Soil Biological Measurements to Support Healthy Soils (Hazel R. Lapis-Gaza, Anthony B. Pattison)....Pages 265-281
A Bait-Trap Assay to Characterize Soil Microbes that Exhibit Chemotaxis to Root Exudates (Katherine V. Weigh, Bruna D. Batista, Paul G. Dennis)....Pages 283-289
Methods for Root Exudate Collection and Analysis (Hugo A. Pantigoso, Yanhui He, Michael J. DiLegge, Jorge M. Vivanco)....Pages 291-303
Collection of Sterile Root Exudates from Foliar Pathogen-Inoculated Plants (Yang Song, Corné M. J. Pieterse, Peter A. H. M. Bakker, Roeland L. Berendsen)....Pages 305-317
Back Matter ....Pages 319-321

✦ Subjects

Life Sciences; Plant Sciences