Plant Microbiome Engineering: Principles, Methods, and Current Trends

Global demand for increased food output is predicted to rise by at least 60% in 2050 as a result of climate change and human population development. Plant microbiome engineering involves composition modification and host plant phenotypic enhancement which often results to increased crop yield and healthy agricultural products. As a new strategy to improve agricultural productivity and human health, it is vital to improving global food output and optimization. Impacts of plant microbiome engineering have been reported in enhanced plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance in agricultural practices. Bottom-up or top-down approaches using engineering tools like phage integrases, integrative and conjugative elements (ICEs), chassis-independent recombinase-assisted genome engineering (CRAGE), and host range broad host range (BHR) genome engineering tools have been demonstrated in non-model microorganisms. Emerging areas for microbiome engineering include soil additives, artificial microbial consortia, microbiome breeding and transplantation, and host-mediated microbiome. A common issue with the engineering tools is overcoming restriction/modification of the target bacteria because of their unique restriction/modification systems that defend them from invading DNA, potentially limiting DNA transformation. Although most of the engineering tools are effective for engineering bacteria, their throughput is limited, as only a few hundred organisms can be designed at a time. To reduce the limitations with the engineering tools, synthetic biology offers a more reliable technique for microbiome engineering in situ to recode the metagenome and generate desirable synthetic communities. These techniques allow for the insertion and/or deletion of target activities in native microbial communities with minimal disturbance to the context.