Despite the abundance of root-associated endophytic fungi, their function has remained elusive. During experiments to determine the host ranges of common endophytes isolated from a tallgrass prairie, at least two taxa (Microdocchium and
Periconia) were observed to form functional mutualisms with Arabidopsis thaliana and increase the host’s growth. Furthermore, these endophytes reduce A. thaliana susceptibility to a foliar pathogen suggesting induction of systemic plant
defenses. Arabidopsis thaliana does not associate with mycorrhizal fungi and there are only limited examples of endophyte associations in A. thaliana. Accordingly, we have taken advantage of this unique and fortuitous mutualism to further our understanding of the root-associated symbioses. We argue that this system is broadly applicable and the wealth of information available for A. thaliana will allow advances in understanding mycorrhizal and non-mycorrhizal root symbioses alike. Data from unpublished and ongoing microarray (Affymetrix ATH1) experiments indicate that endophytes lead to upregulation of carbon metabolism as well as general plant defenses against potentially pathogenic fungi. Furthermore, metabolome level experiments indicate clear shifts on metabolic profiles. Together, these data indicate that both host transcriptome and metabolome are modulated by the endophyte symbionts.