Data from: Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi

While all species interact with multiple mutualists, the fitness
consequences and molecular mechanisms underlying these interactions remain
largely unknown. We combined factorial ecological experiments with
genomewide expression analyses to examine the phenotypic and
transcriptomic responses of model legume Medicago truncatula to rhizobia
and mycorrhizal fungi. We found synergistic effects of these mutualists on
plant performance and examined unique features of plant gene expression
responses to multiple mutualists. There were genomewide signatures of
mutualists and multiple mutualists on expression, with partners often
affecting unique sets of genes. Mycorrhizal fungi had stronger effects on
plant expression than rhizobia, with 70% of differentially expressed genes
affected by fungi. Fungal and bacterial mutualists had joint effects on
10% of differentially expressed genes, including unexpected, nonadditive
effects on some genes with important functions such as nutrient
metabolism. For a subset of genes, interacting with multiple mutualists
even led to reversals in the direction of expression (shifts from up to
downregulation) compared to interacting with single mutualists. Rhizobia
also affected the expression of several mycorrhizal genes, including those
involved in nutrient transfer to host plants, indicating that partner
species can also impact each other's molecular phenotypes.
Collectively, these data illustrate the diverse molecular mechanisms and
transcriptional responses associated with the synergistic benefits of
multiple mutualists.