Over the horizon: rewilding microbiomes? Y
ou and I, indeed all organisms, have a genome—an organism’s total genetic makeup. It follows that
there is a proteome, transcriptome, etc. (scientists are studying all of these for many organisms right now). And there is a microbiome. A recent edition of Science (378: 599–560) featured an excellent essay by Raaijmakers and Kiers that focused on a clever use of fungi and other microbes. Tey discuss recent research over the past decade, showing that microorganisms living on and inside eukaryotes—the microbiota—are drivers of host health, enhancing immunity, nutrient acquisition, and tolerance to environmental stresses. From this has emerged a “microbiome rewilding hypothesis” that posits plant and animal health can be improved by reinstating key members of the diverse (ancestral) microbiota that were lost through domestication and industrialization processes, including changes in diet, plant and animal breeding, and the (over) use of antibiotics, pesticides, and fertilizers. A central question is whether the microbiomes of crop
ancestors can be used to “rewild” microbiomes of current crops. Tey argue that rewilding plant microbiomes is similar to restoring diversity lost from the human gut: wild plant ancestors carry microbial partners and functions that modern crops have largely lost. But we still don’t know which microbes disappeared during domestication or how much rewilding could improve crop health. As in animal systems, the effectiveness of microbiome rewilding is debated. Domestication has dramatically reshaped plants—
larger seeds, predictable growth, reduced bitterness— and expanded them into new habitats, but at the cost of increased dependence on fertilizers, pesticides, and irrigation. Naturally, the transition of plants from their native habitats to new ones led to changes in microbiome composition of those plants. For example, the authors note that the domestication of legumes, combined with long-term nitrogen fertilization, has been linked to the evolution of less mutualistic rhizobia (nitrogen-fixing soil bacteria that form nodules in the roots of legumes), and legume varieties that are less able to discriminate between rhizobia that provide nitrogen to the plant versus those that do not. And changes in plant microbiomes are not limited to bacteria, fungi are also affected. Disruption of the symbiotic interaction between plants and their mycorrhizal fungi has also been documented, with domesticated crops showing lower colonization and a decreased growth response to fungal symbionts, especially in fertilized soils. Rewilding involves reinstating key ancestral microbes
in agricultural soils or planting materials, and/or breeding modern crops with specific traits that support
ancestral microbiota colonization. Identifying differences in the microbiomes between crop plants and their wild progenitors—and the mechanisms mediating these differences—is straightforward in theory, but difficult in practice. To unravel plant microbiome interactions, analyses of native soils in a crop’s center of origin are needed to interpret shifts in plant microbiome composition along the domestication path. Next, all possible microbes are tested on wild and cultivar plants. Considering that the effects of plant genotype on microbiome composition may be relatively small, exposure of crops to a suite of different stresses can help amplify the differential recruitment of specific ancestral microbiota. Once the ancestral forms of microbes are found (and “biobanked” for future use), it’s time to do the rewilding—that is, to put them back into the environment. Does all this sound like “woo-woo” or pseudoscience?
So did human fecal transplants just a few years ago … until they were tried. And they worked! Analogous to fecal microbiota transplantation to redirect the dysbiotic composition of human microbiomes, transferring complex microbial communities from root or shoot tissue of wild crop relatives onto seeds or planting material of their domesticated counterparts can initially be used to identify specific microbiome-associated plant phenotypes. If beneficial effects of wild microbiome transplants on crop cultivars are confirmed, approaches to minimize microbiome complexity through dilution to extinction or the design of synthetic microbial communities may help identify the key microbial genera associated with particular plant phenotypes. Te performance of modern crop varieties may also be improved through artificial selection on the native microbiome. Again, exposing plants to specific stresses, such as drought or nutrient deprivation, can expedite the search for specific subsets of ancestral beneficial consortia. Tis can be followed with the identification of specific plant root exudates (or other control mechanisms) in wild relatives that are responsible for the recruitment of these consortia. Existing domesticated crop varieties can then be selected for those particular control mechanisms and used as hosts compatible with the ancestral consortia. Raaijmakers and Kiers conclude by saying that
rewilding approaches can offer a new avenue to harness the benefits of ancestral microbiota, and do not preclude the use of domesticated crop cultivars or agricultural management practices, such as fertilizer. As rewilding research moves between the field and the lab, its value and integration in breeding programs for a new generation of “microbiome-assisted” crops await critical assessment in different agroecologies.
Summer 2026 FUNGI Volume 19:2 29
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