Achieving food security in a context of environmental sustainability is one of the main challenges of the XXI century. Two competing strategies to achieve this goal are the use of genetically modified plants and the use of plant growth promoting microorganisms (PGPMs). However, few studies assess the response of genetically modified plants to PGPMs. The aim of this study was to compare the response of over-expressing the vacuolar H
+
-PPase (AVP) and wild-type rice types to the endophytic fungus;
Piriformospora indica
.
Oryza sativa
plants (WT and AVP) were inoculated with
P. indica
and 30 days later, morphological, ecophysiological and bioenergetic parameters, and nutrient content were assessed. AVP and WT plant heights were strongly influenced by inoculation with
P. indica
, which also promoted increases in fresh and dry matter of shoot in both genotypes. This may be related with the stimulatory effect of
P. indica
on ecophysiological parameters, especially photosynthetic rate, stomatal conductance, intrinsic water use efficiency and carboxylation efficiency. However, there were differences between the genotypes concerning the physiological mechanisms leading to biomass increment. In WT plants, inoculation with
P. indica
stimulated all H
+
pumps. However, in inoculated AVP plants, H
+
-PPase was stimulated, but P- and V-ATPases were inhibited. Fungal inoculation enhanced nutrient uptake in both shoots and roots of WT and AVP plants, compared to uninoculated plants; but among inoculated genotypes, the nutrient uptake was lower in AVP than in WT plants. These results clearly demonstrate that the symbiosis between
P. indica
and AVP plants did not benefit those plants, which may be related to the inefficient colonization of this fungus on the transgenic plants, demonstrating an incompatibility of this symbiosis, which needs to be further studied.