The Plant Microbiome Methods and Protocols - Carvalhais, Lilia C.; Dennis, Paul G. (Springer US, 2021)
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.