Abstract
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.
Highlights
As the human population grows, food production must increase despite global climate change presenting more challenging conditions for crop production
Engineering microbiomes via the host genome has a major advantage over current microbial products in that it does not require changes to infrastructure or management, since plant breeding and genetic improvement is already common practice (Bakker et al, 2012)
The improvement of crop microbiomes via genetic manipulation of the host is a promising approach because it has the potential to promote plant-driven enrichment of beneficial microbes from any environment and any soil community
Summary
As the human population grows, food production must increase despite global climate change presenting more challenging conditions for crop production. 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. One potential method to circumvent these limitations of microbial inoculants is to alter host genetics to promote the recruitment and growth of beneficial microbes.
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