Bacterial endophyte antagonism toward a fungal pathogen in vitro does not predict protection in live plant tissue

Endophytic microbiota are potentially useful plant symbionts for conferring biotic or abiotic stress tolerance. Common approaches to identify putatively beneficial functions of endophytes rely on lab-based assays. However, if functional roles are context-dependent, lab-based assessments may not accurately represent functional outcomes under variable field conditions. Our objective was to test whether antagonism by bacterial endophytes towards a plant pathogen in vitro would be predictive of disease outcomes in live plant tissue. We challenged Fusarium graminearum, a fungal pathogen of wheat, against bacterial endophytes isolated from wheat plants in two in vitro assays. A subset of isolates, with in vitro antagonistic activity ranging from weak to strong, was selected for testing in live plant tissue (detached wheat heads). Assays were performed under different temperature and/or carbon dioxide conditions to test environmental dependency in the plant-endophyte-pathogen interactions. The two in vitro assays produced contrasting measures of pathogen inhibition, and neither predicted pathogen load reductions in the detached wheat head assay. Additionally, outcomes were environment-dependent and varied among bacterial isolates. Thus, endophytic impacts on plant performance cannot be easily inferred from simplified in vitro assays, and environmental gradients should be incorporated into future testing of microbial interactions in plant hosts.