This volume provides lab-oriented protocols to deal the various plant microbiome engineering approaches in a lucid and simple manner. Chapters are divided into four section detailing plant associated microbiomes, single cell genomics, whole community metagenomics, metabolic network monitoring and advanced methods in plant microbiome engineering. Written in the format of the Methods and Protocols in Food Science series, the chapters include an introduction to the respective topic, list necessary materials and reagents, detail well-established and validated methods for readily reproducible laboratory protocols and contain notes on how to avoid or solve typical problems. Authoritative and cutting-edge, Plant Microbiome Engineering aims to provide well-established protocols and procedures largely used by both academics and industrials.