Schematic summary of the mechanisms by which the endobacterium affects G. margarita metabolism. Starting from the left on the top, the drawing illustrates how in the presence of the endobacterium, the fungus G. margarita upregulates genes involved in respiration, leading to higher ATP production. This status is mirrored by morphological changes in the mitochondrial ultrastructure. Thanks to the upregulation of SOD, H2O2 is produced and further detoxified to water by ROS-scavenger enzymes, like glutathione peroxidase. Intracellular calcium homeostasis is efficiently maintained. Treatment with GR24, a synthetic SL induces some transcriptional responses that mimic the endobacterium presence, suggesting that there is interference between the microbe presence and the plant hormone treatment. The oxidative burst is correlated with higher spore production in many fungi: this feature is indeed present in G. margarita, which contains endobacteria. As G. margarita exclusively colonises plants starting from spores, this feature represents an evolutionary benefit. Red font, transcriptome results; green font, data from biochemical, cellular and physiological experiments; interrupted line, hypotheses based on the literature. A full colour version of this figure is available at The ISME Journal online.