ORIGINAL ARTICLE Versatility of the green microalga cell vacuole function as revealed by analytical transmission electron microscopy Anastasia Shebanova 1 & Tatiana Ismagulova 1 & Alexei Solovchenko 1,2,3 & Olga Baulina 1 & Elena Lobakova 1 & Alexandra Ivanova 4,5 & Andrey Moiseenko 1 & Konstantin Shaitan 1 & Vladimir Polshakov 6 & Ladislav Nedbal 7 & Olga Gorelova 1 Received: 15 June 2016 /Accepted: 8 September 2016 # Springer-Verlag Wien 2016 Abstract Vacuole is a multifunctional compartment central to a large number of functions (storage, catabolism, maintenance of the cell homeostasis) in oxygenic phototrophs including microalgae. Still, microalgal cell vacuole is much less studied than that of higher plants although knowledge of the vacuolar structure and function is essential for understanding physiol- ogy of nutrition and stress tolerance of microalgae. Here, we combined the advanced analytical and conventional transmis- sion electron microscopy methods to obtain semi-quantitative, spatially resolved at the subcellular level information on ele- mental composition of the cell vacuoles in several free-living and symbiotic chlorophytes. We obtained a detailed record of the changes in cell and vacuolar ultrastructure in response to environmental stimuli under diverse conditions. We suggested that the vacuolar inclusions could be divided into responsible for storage of phosphorus (mainly in form of polyphosphate) and those accommodating non-protein nitrogen (presumably polyamine) reserves, respectively. The ultrastructural findings, together with the data on elemental composition of different cell compartments, allowed us to speculate on the role of the vacuolar membrane in the biosynthesis and sequestration of polyphosphate. We also describe the ultrastructural evidence of possible involve- ment of the tonoplast in the membrane lipid turnover and exchange of energy and metabolites between chloro- plasts and mitochondria. These processes might play a significant role in acclimation in different stresses in- cluding nitrogen starvation and extremely high level of CO 2 and might also be of importance for microalgal biotechnology. Advantages and limitations of application of analytical electron microscopy to biosamples such as microalgal cells are discussed. Keywords Analytical electron microscopy . Microalgae . Nitrogen . Phosphorus . Polyphosphate . Stress responses . Vacuole Abbreviations DAPI 4′,6-diamidino-2-phenylindole EDX Energy-dispersive X-ray spectroscopy EELS Electron energy loss spectroscopy EFTEM Energy-filtered transmission electron microscopy EMS Epichloroplast membrane structure HAADF- STEM High angle annular dark-field scanning trans- mission electron microscopy NMR Nuclear magnetic resonance Handling Editor: Tsuneyoshi Kuroiwa Electronic supplementary material The online version of this article (doi:10.1007/s00709-016-1024-5) contains supplementary material, which is available to authorized users. * Alexei Solovchenko solovchenko@mail.bio.msu.ru 1 Lomonosov Moscow State University, Moscow, Russia 2 Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia 3 Faculty of Biology, Moscow State University, Leninskie Gori 1/12, 119234 GSP-1 Moscow, Russia 4 Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russia 5 St. Petersburg State University, St. Petersburg, Russia 6 Faculty of fundamental medicine, Lomonosov Moscow State University, Moscow, Russia 7 Institute of Bio- and Geosciences / Plant Sciences (IBG-2), Forschungszentrum Jülich, Jülich, Germany Protoplasma DOI 10.1007/s00709-016-1024-5