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Remediation of trichloroethylene (TCE) is a major priority for many contaminated sites all over the industrialized world including Hill Air Force Base, UT (HAFB). Phytoremediation as part of a cleanup strategy is an appealing option, and trees at HAFB have been studied to this end. Trees have also been used to delineate groundwater plumes because the passive uptake of organic contaminants by trees generally results in a direct relationship between tree and groundwater TCE concentrations if the trees are using the contaminated groundwater. However, the concentrations of plant-produced TCE metabolites can vary greatly. It was hypothesized that the endophytic microbial community present may be affecting the fate of TCE within these trees. This study was designed to determine if the microbial community present within hybrid poplar trees would change in response to TCE exposure. Trees were grown in a greenhouse to reduce environmental variability. Concentrations of TCE, its degradation products, and its metabolites were then measured in these trees. DNA was extracted from the tree tissues and amplified to determine the quantity of microbial DNA. Diversity of this DNA was determined by fragment analysis. Data were analyzed to determine if there was an effect of TCE treatment on the microbial community composition in the trees. Results showed that all tissues of dosed trees contained TCE. Metabolism of TCE to trichloroacetic acid (TCAA) and trichloroethanol (TCEtOH) in tree tissues was observed by the accumulation of these metabolites. Microbial DNA results revealed that TCE treatment reduced both the quantity and diversity of endophytic bacteria and fungi in several cases. Multivariate statistical analyses also showed that the endophytic microbial community shifted in response to TCE treatment. The endophytic microbial communities present in the hybrid poplar trees of this study were high in concentration and diversity, both of which were affected by TCE treatment. Endophytic bacterial concentrations were observed at over 109 copies/g with diversities of 70+ genetically distinct organisms. Decreases in these values with the addition of TCE showed that the community dramatically changed in some cases, but was able to more quickly adapt to TCE addition in other cases. The effects of these endophytic microorganisms associated with plants should therefore be included when phytoremediation is considered.