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A plant’s microbiome is a dynamic collection of microbial communities, including bacteria, fungi, viruses, protists, and nematodes, that colonize various tissue types and ultimately coevolve with the host plant. Plant-associated microbes harbor enormous potential to provide economical and sustainable solutions to current agricultural challenges. Phytomicrobiome engineering through CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology is a burgeoning field aiming to manipulate plant-associated microbial communities for enhanced symbiotic relationships. It is possible to engineer phytomicrobiomes by a top-down or bottom-up approach. The bottom-up method separates microorganisms from environmental microbiomes that are linked to specific plant types, strains, or organ; they are further assembled again as artificial microbial communities (SynComs) following their genetic engineering in order to carry desired characteristics. After that, the engineered strains—which are capable of vigorously recolonizing their hosts—are injected into the plants. Horizontal gene transfer, also known as HGT, is used in the top-down strategy for introducing desired traits into a variety of hosts in situ. Using mobile genetic elements (MGEs) is one top-down method to study PGP traits holistically. MGEs transfer and integrate exogenous genes into a random subpopulation of microbiomes. Creating bacteriophage (phage) systems to modify or eradicate specific species is another top-down tactic. The delivery of CRISPR edited tools takes place usually by three main methods: agrobacteria delivery, protoplast delivery, and biolistic/gene gun delivery. Genome-wide functional genomics increasingly allows discovery of new genes that are responsible for PGP activities including biocontrol, biofertilization, and biostimulation. Moreover, interdisciplinary methods offer a predictive framework for developing a dependable and long-lasting plant–microbiome for nutrient recycling, stress physiology, and high-yielding genotypes resistant to disease.

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Phytomicrobiomes Engineering Using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)

  • 章节

  • 发表日期：

    2025年

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  • Pratishtha Jain,
  • Lokesh Ravi

摘要

A plant’s microbiome is a dynamic collection of microbial communities, including bacteria, fungi, viruses, protists, and nematodes, that colonize various tissue types and ultimately coevolve with the host plant. Plant-associated microbes harbor enormous potential to provide economical and sustainable solutions to current agricultural challenges. Phytomicrobiome engineering through CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology is a burgeoning field aiming to manipulate plant-associated microbial communities for enhanced symbiotic relationships. It is possible to engineer phytomicrobiomes by a top-down or bottom-up approach. The bottom-up method separates microorganisms from environmental microbiomes that are linked to specific plant types, strains, or organ; they are further assembled again as artificial microbial communities (SynComs) following their genetic engineering in order to carry desired characteristics. After that, the engineered strains—which are capable of vigorously recolonizing their hosts—are injected into the plants. Horizontal gene transfer, also known as HGT, is used in the top-down strategy for introducing desired traits into a variety of hosts in situ. Using mobile genetic elements (MGEs) is one top-down method to study PGP traits holistically. MGEs transfer and integrate exogenous genes into a random subpopulation of microbiomes. Creating bacteriophage (phage) systems to modify or eradicate specific species is another top-down tactic. The delivery of CRISPR edited tools takes place usually by three main methods: agrobacteria delivery, protoplast delivery, and biolistic/gene gun delivery. Genome-wide functional genomics increasingly allows discovery of new genes that are responsible for PGP activities including biocontrol, biofertilization, and biostimulation. Moreover, interdisciplinary methods offer a predictive framework for developing a dependable and long-lasting plant–microbiome for nutrient recycling, stress physiology, and high-yielding genotypes resistant to disease.