The rhizosphere microbiome is a major determinant of plant fitness.

The mechanisms driving microbiome assembly are, however, widely unknown, impeding its efficient management.

Here we present free-living protists as an overlooked yet core component of the microbiome that may offer a powerful leverage to improve microbiome function.

Protists shape microbiome structure by consuming bacteria and fungi and can select for plant-beneficial functional traits.

Protist predation increases microbiome provisioning of services required to improve plant growth and health.

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