Comparative metataxonamic analyses of seeds and leaves of traditional varieties and hybrids of cucumber (Cucumis sativus L.) reveals distinct and core microbiome

Profiling the endophytic microbiome of different tissues and varieties of agricultural crops can help to understand i) the tissue specific and varietal specific microbes associated with the plants ii) their potential role in growth, stress tolerance, disease resistance, and yield of the plants. Comparative microbiome profiling across various varieties and hybrids will also be useful to identify the plant's core microbiome. The main objective of the work is to profile and study the microbiome of traditional varieties in comparison with hybrids of cucumber, which would help to understand the microbiome structure in developing consortia to engineer the microbiome of modern hybrids, for useful phenotypes. Metataxonomic sequencing of bacteria and fungi using 16S rRNA gene and ITS regions respectively were carried out in seed and leaf samples of cucumber traditional varieties and modern hybrids. Among bacteria, Prevotella, Bacteroides, Lactobacillus, Dialester, and Fecalibacterium, and among fungal genera, Pichia, Aspergillus, Phaeoisariopsis, Candida, and Malassezia belonged to the core microbiome of cucumber. Modern hybrids were rich in antibiotic producing and toxic pollutant degrading bacteria. Many of the fungi and bacteria observed in the study are well known plant growth promoting microorganisms and play role in offering disease resistance. Some of the bacteria and fungi have beneficial roles in human gut thus revealing the dietary importance of cucumber. The microbes identified in the current study will be useful starting point to develop a consortia to engineer the cucumber microbiome for growth, yield and stress tolerance traits.