Plant domestication does not reduce diversity in root microbiomes
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Domestication has profoundly shaped human civilization and the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. Root microbiomes play crucial roles in nutrient acquisition, pathogen defense, and biotic stress tolerance, yet the influence of domestication on their diversity and assembly is still debated. Two primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. To evaluate these hypotheses, we conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities, while others show no significant change. Overall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. Based on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing not only diversity but also microbiome function, and considering how root morphology might affect microbiome recruitment. Finally, we highlight the need for research on the potential adaptive or maladaptive consequences that introgression between wild and domesticated plants could have from a microbiome perspective.
SIGNIFICANCE STATEMENT
Plant domestication has had profound impacts on plant traits and their genetic makeup. These traits are likely to influence microbial interactions with the plants, but the overall effect of domestication on plant microbiomes is still subject to debate. In this work, we challenge two primary hypotheses regarding the effects of domestication on root microbiomes; we compared published microbiomes of wild and domesticated plants and found that domestication does not reduce microbial diversity or the plant’s contribution to their associated microbial communities. Instead, these effects vary between plant species and environmental conditions. This work provides insights into how domestication shapes plant-microbe relationships and discusses new approaches that are critical for advancing this area of research.
