Plant Genetics as a Tool for Manipulating Crop Microbiomes: Opportunities and Challenges

Growing human population size and the ongoing climate crisis create an urgent need for new tools for sustainable agriculture. Because microbiomes have profound effects on host health, interest in methods of manipulating agricultural microbiomes is growing rapidly. Currently, the most common method of microbiome manipulation is inoculation of beneficial organisms or engineered communities; however, these methods have been met with limited success due to the difficulty of establishment in complex farm environments. Here we propose genetic manipulation of the host plant as another avenue through which microbiomes could be manipulated. We discuss how domestication and modern breeding have shaped crop microbiomes, as well as the potential for improving plant-microbiome interactions through conventional breeding or genetic engineering. We summarize the current state of knowledge on host genetic control of plant microbiomes, as well as the key challenges that remain.

Automated summary

The growing human population and climate crisis call for new tools for sustainable agriculture, with a focus on manipulating agricultural microbiomes due to their profound effects on host health. Genetic manipulation of host plants is proposed as another method for microbiome manipulation, alongside current methods like inoculation of beneficial organisms or engineered communities, which have faced challenges in establishment in complex farm environments. Opportunities lie in improving plant-microbiome interactions through host genetic control, but challenges remain.