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In the present study, FTIR spectroscopy and hyperspectral imaging was introduced as a non-destructive, sensitive-reliable tool for assessing the tripartite kernel-fungal endophyte environment interaction. Composition of coleorhizae of  Triticum durum  was studied under ambient and drought stress conditions. The OH-stretch IR absorption spectrum suggests that the water-deficit was possibly improved or moderated by kernel’s endophytic partner. The OH-stretch frequency pattern coincides with other (growth and stress) related molecular changes. Analysis of lipid (3100–2800 cm −1 ) and protein (1700–1550 cm −1 ) regions seems to demonstrate that drought has a positive impact on lipids. The fungal endosymbiont direct contact with kernel during germination had highest effect on both lipid and protein (Amide I and II) groups, indicating an increased stress resistance in inoculated kernel. Compared to the indirect kernel-fungus interaction and to non-treated kernels (control), direct interaction produced highest effect on lipids. Among treatments, the fingerprint region (1800–800 cm −1 ) and SEM images indicated an important shift in glucose oligosaccharides, possibly linked to coleorhiza-polymer layer disappearance. Acquired differentiation in coleorhiza composition of  T. durum , between ambient and drought conditions, suggests that FTIR spectroscopy could be a promising tool for studying endosymbiont-plant interactions within a changing environment.

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Spectroscopy and SEM imaging reveal endosymbiont-dependent components changes in germinating kernel through direct and indirect coleorhiza-fungus interactions under stress