Lilia C. Carvalhais., Paul G. Dennis The Plant Microbiome

Humana Press, 2021. — 321 p. — (Methods in Molecular Biology 2232). — ISBN: 978-1-0716-1039-8This 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.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 Arabidopsisthaliana
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 Characterize 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