Background Many studies have been carried out on the growth-modulating efficiency of plants by the colonization of an endophytic fungus Piriformospora indica. However, studies involving the co-culture of alga with endophytic fungal strains for enhanced biodiesel production are rare. In this study, the interaction between P. indica and Parachlorella kessleri -I, a marine algal strain, was assessed at metabolic level. Results In association with an endophytic fungus, the algal biomass enhanced from 471.6 to 704 mg/L, and the fatty acid methyl ester (FAME) profile of P. kessleri -I increased substantially. In case of FAME profile of co-cultured P. kessleri -I, two essential components of biodiesel, i.e. elaidic acid and oleic acid, increased by 1.4- and 1.8-fold, respectively. To ascertain changes in the metabolic profile of P. kessleri -I by P. indica co-culture, gas chromatography–mass spectrometry (GC–MS)-based untargeted metabolomics study was performed to identify the metabolites involved; and differential nature of the essential metabolites was also confirmed using HPLC and LC–MS. Significant modulation of the bioactive metabolites such as succinate, oxo-propanoate, l -alanine, glutamate, acetate and 1,2 propanediol, hydroxy butane was observed. Conclusion The metabolites like glutamate and succinate that usually belong to the GABA shunt pathway were observed to be upregulated. The pathway links nitrogen metabolism and carbon metabolism, thus influencing the growth and lipid profile of the algae. These differential metabolites thus indicated the important commensal association between the endophytic fungus and autotrophic marine alga, and established that endophytic fungus can be handy for the sustainability of algal biofuel industries. Electronic supplementary material The online version of this article (10.1186/s13068-019-1516-6) contains supplementary material, which is available to authorized users.
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