Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience

Symbiotic bacteria can boost plant growth, control pathogens, or alleviate abiotic stress. Microbiome engineering incorporated into traditional agricultural practices can improve microbial ecosystem services for crop yield and resilience. New agricultural practices may include microbiome breeding, transplantation, and targeted microbiome engineering, for example by strategic soil amendments in which selective addition of plant exudates attracts and maintains beneficial microbes, or by directly applying microbial consortia as probiotics. Customized microbiome engineering will be necessary to cope with the many variables, including soil type, environmental/climatic conditions, growth stage, and genotype of the plant, to influence the microbiome in a purposeful and effective manner. Breeding 'microbe-friendly' crops can complement microbiome engineering to better attract and maintain beneficial microbiomes. Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications. Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications. an ethylene precursor whose concentration is elevated in plants subjected to biotic and abiotic stresses. It is an important root exudate that plants can release into the rhizosphere to attract plant growth-promoting rhizobacteria (PGPR). ACC deaminase is the enzyme responsible for cleaving the plant ethylene precursor, ACC, into ammonia and α-ketobutyrate. a process by which anaerobic soil conditions are created to disinfest the soil by incorporating soil amendments which are easily degradable, covering the treated area with polyethylene mulch, and saturating the soil by irrigation to provide a 2–6 week treatment period to the soil. naturally occurring organic plant defense metabolites that are produced mainly by the Poaceae plant family, and that have antimicrobial activity against various microbiological threats to plants. comprises groups of microorganisms living in the upper layer of soils; these are typically fungi, cyanobacteria, lichens, mosses, liverworts, and microalgae that play an important role in stabilizing and protecting the soil from erosion and are a rich source of fixed carbon in sparsely vegetative areas. organic chemical compounds that are found naturally in many plants and that have medicinal uses in the pharmaceutical industry. These are also used as a defense against herbivore infestation because they are bitter in taste molecular signatures from small molecules that are present in groups of microbes but are not present in the host, for example flagellin for bacteria, chitin for fungi. microorganisms that assist in plant growth and biocontrol of plant pests or pathogens, respectively. the purposeful manipulation of microbial communities. taxa of closely related microbes that are classified according to a similar specific taxonomic marker gene in their DNA sequence. These are commonly used when analyzing microbiomes using 16S or 18S rDNA (prokaryotes or eukaryotes) marker gene sequences.