Diverse soil protists show auxin regulated growth in partnership with auxin-producing bacteria

Predatory protists are single-cell eukaryotic organisms capable of hunting and ingesting bacteria and other microorganisms, which are thought to enrich populations of beneficial bacteria in the rhizosphere, potentially influencing plant health. However, the mechanisms underpinning protist interactions with plant growth promoting bacteria are not well understood. We examined the conservation of plant beneficial traits in bacteria associated with 10 protists of diverse lineages that were isolated from the maize rhizosphere. Metagenomics, whole-genome sequence analysis, and functional assays of 61 groups of protist-associated bacteria identified tryptophan-dependent biosynthesis of the auxin hormone indole-3-acetic acid (IAA) as the most prevalent predicted trait. Mass spectrometry confirmed that all the protist cultures accumulated IAA after tryptophan supplementation, and that IAA production was bacterial-dependent. Hypothesizing that IAA affects protist function, we observed that exogenous IAA significantly increased the culture density and cell size of all 10 protists. Examination of four partial protist genome assemblies identified 13 candidate auxin metabolic gene homologs conserved across plants and protists, and transcriptomic analysis of a Colpoda sp. protist revealed differential expression of thousands of genes in the presence of IAA, further supporting auxin regulation of protist function. These findings demonstrate that soil microeukaryotes can widely host auxin-producing bacteria and that much broader range of eukaryotic lineages perceive and respond to auxin signals than previously recognized. This significantly expands the known breadth of auxin perception as an interkingdom signal, with important implications for soil nutrient cycling and rhizosphere ecology.