Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops

Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects—collectively termed “domestication syndrome”—have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.