CRISPR/Cas9 mediated genome engineering in microbes and its application in plant beneficial effects

Various microbes has been used in food, agricultural and other industries across the world due to their beneficiary role, fast growth and ease of genetic manipulation. Plant microbe’s interaction may be agriculturally good or bad depending upon the species of bacteria or fungi. Different mutants have been created for plant microbe’s interaction by means of traditional genetic engineering, which is time consuming and laborious. However, different mutants of important microbes often produce desired or agricultural beneficiary product in very low content. Therefore, editing of genome of these microbes using CRISPR/Cas9 system greatly improve these different strains of bacteria, yeast and fungi due to its easiness and efficiency. This tool has been abundantly used in bacteria such as E. coli, C. beijerinckii, Mycobacterium, Streptomyces, rhizobacteria such as, B. subtilis, B. mycoides and yeast such as Saccharomyces cerevisiae, Yarrowia lipolytica, Pichia pastoris, Candida albicans, Kluyveromyces lactis, and Ustilago maydis. The CRISPR/Cas9 mediated manipulation in microbe’s biosynthetic pathway for targeted by product such as ethanol, β-carotene, and 2,3-butanediol (plant growth promoting siderophore) etc. has done. The variants of CRISPR/Cas9 and its derivative tool such as CRISPRi, CRISPRa, Multiplexing and CRISPR based tagging makes this as a valuable for genome and metabolic engineering in various microbes. The present chapter describes the basic of CRISPR mechanism, to genome/gene editing tool, different kind of tool kit and metabolic engineering in agriculture important bacteria such as Bacillus subtilis HS3 and Bacillus mycoides EC1.