The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic. Differences in the taxonomic composition of eukaryotic and prokaryotic microorganisms were observed between plant types. Our results revealed limited geographic differentiation between the bacterial and fungal communities associated with apples. In contrast, blackcurrant berries harvested from different regions demonstrated high diversity in both bacterial and fungal microbiota structures. Among fungal and bacterial microorganisms, we identified both potentially beneficial (Cryptococcus, Hanseniaspora, Massilia, Rhodotorula, Sphingomonas) and phytopathogenic microorganisms (Cladosporium, Pantoea, Phoma, Pseudomonas, Septoria, Taphrina) indicating their important roles in ecological and evolutionary processes.

Department of Biochemistry and Molecular Biology Institute of Biosciences Vilnius University Saulėtekio al 7 Vilnius LT 10257 Lithuania; Department of Chemistry and Bioengineering Vilnius Gediminas Technical University Saulėtekio al 11 Vilnius LT 10223 Lithuania

Laboratory of Genetics Institute of Botany Nature Research Centre Akademijos str 2 Vilnius LT 08412 Lithuania

Laboratory of Genetics Institute of Botany Nature Research Centre Akademijos str 2 Vilnius LT 08412 Lithuania; Department of Chemistry and Bioengineering Vilnius Gediminas Technical University Saulėtekio al 11 Vilnius LT 10223 Lithuania

Life Science Research Centre and Institute of Environmental Technologies Faculty of Science University of Ostrava Chittussiho 10 70200 Ostrava Czech Republic; Biology Centre Institute of Parasitology Czech Academy of Sciences Branišovska 1160 31 370 05 Česke Budejovice Czech Republic

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