The Plant Microbiome Methods and Protocols

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.

Studying Seed Microbiomes.- Sampling Microbiomes Associated with Different Plant Compartments.- Sampling of Bacteria Associated with Plant Vascular Tissues.- Sampling of Plant Material to Study Endophytes in Small, Large and Woody Plants.- Preparation of Samples for Characterization of Arbuscular Mycorrhizal Fungi.- Culture-based Methods for Studying the Bacterial Root Microbiome of Wheat.- Fast Screening of Bacteria for Plant Growth Promoting Traits.- Protists in the Plant Microbiome - An Untapped Field Of Research.- Plant-associated Fungi: Methods for Taxonomy, Diversity, and Bioactive Secondary Metabolite Bioprospecting.- Extraction and Purification of DNA from Wood at Various Stages of Decay for Metabarcoding of Wood-Associated Fungi.- Peptide Nucleic Acid (PNA) Clamps to Reduce Co-Amplification of Plant DNA during PCR Amplification of 16S rRNA Genes from Endophytic Bacteria.- Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by quantitative-PCR.- Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.- Inference and Analysis of SPIEC-EASI Microbiome Networks.- Gene Knockout of Beneficial Plant-associated Bacillus spp. using the CRISPR-Cas9 Double Plasmid System.- Sample Preparation for Culture-Independent Profiling and Isolation of Phyllosphere Bacteria to Identify Potential Biopesticides.- Soil-borne Legacies of Disease in Arabidopsis thaliana.- Bioactive Streptomycetes from Isolation to Applications: A Tasmanian Potato Farm Example.- Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops.- Functional Soil Biological Measurements to Support Healthy Soils.- A Bait-Trap Assay to Characterise Soil Microbes that Exhibit Chemotaxis to Root Exudates.- Methods for Root Exudate Collection and Analysis.- Collection of Sterile Root Exudates from Foliar Pathogen-Inoculated Plants.