REGULAR ARTICLE Global metabolomics analysis reveals distinctive tolerance mechanisms in different plant organs of lentil (Lens culinaris) upon salinity stress Dimitrios Skliros & Chrysanthi Kalloniati & Georgios Karalias & George N. Skaracis & Heinz Rennenberg & Emmanouil Flemetakis Received: 13 November 2017 /Accepted: 17 May 2018 # Springer International Publishing AG, part of Springer Nature 2018 Abstract Background and Aims Omic technologies in the past years have provided a variety of data in model plants. In legumes, results οn Lotus japonicus and Medicago truncatula have highlighted the biochemistry which takes place inside cells under a variety of abiotic stress- es. Here we conducted metabolomics in the forage legume lentil (Lens culinaris) upon salinity stress on acclimated and non-acclimated plants and compared results from leaf and root analyses. Methods We used two lentil varieties, originated from different geographical locations and studied differences in their global metabolite profile i) using gradual or initial application of salt stress, ii) between leaves and roots, and iii) between the varieties. Results Most important differences were noted in salin- ity induced diminished abundance of organic acids in both varieties’ leaves and roots, accumulation of sugars and polyols in leaves, and accumulation of other key- metabolites, such as L-asparagine, D-trehalose, allanto- in and urea in the roots. We also demonstrated the driver of deleterious Cl - accumulation in leaves for potential compartmentalization in the vacuole, a defensive mech- anism for withstanding salinity stress in plants. Finally, a model is suggested of how legumes upregulate a meta- bolic pathway, which involves purines catabolism in order to assimilate carbon and nitrogen, which are lim- ited during salinity stress. Conclusions Future omics works with lentil can help understanding the regulation of the biochemical Barsenal^ against abiotic stresses such as salinity and render the selection of better crops. Keywords Lens culinaris . Lentil . Metabolomics . Abiotic . Salinity . Stress . Purines . Legumes Plant Soil https://doi.org/10.1007/s11104-018-3691-9 Responsible Editor: Wieland Fricke. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11104-018-3691-9) contains supplementary material, which is available to authorized users. D. Skliros : C. Kalloniati : G. Karalias : E. Flemetakis (*) Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera odos street, 75, 11855 Athens, Greece e-mail: mflem@aua.gr G. N. Skaracis Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece H. Rennenberg Fakultät für Umwelt und Natürliche Ressourcen (UNR), Institut für Forstwissenschaften, Professur für Baumphysiologie, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 053/ 054, 79110 Freiburg, Germany H. Rennenberg College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia