The invention concerns a method for the phytoremediation treatment of a medium contaminated with at least one element selected from the group consisting of (preferably water soluble and volatile) organic pollutants, heavy metals, radionuclides or a mixture thereof, comprising the step of cultivating upon the contaminated medium a plant associated with an endophytic microorganism able to improve the phytoremediation of the plant, to reduce phytotoxicity of chemicals. The invention further relates to methods for improving phytoremediation by directly modifying members of the endogenous endophytic community of a plant, via horizontal gene transfer. Another part of the invention relates to plants associated with such endophytes and/or plants with a modified endogenous endophytic community.