• To understand the origin of the plant microbiome, we first started by testing the hypothesis that members of the plant microbiome are partially inherited from through seeds and partially acquired from the environment.
• Using culturing device, called Microcosms, for growing plants in microbe-free condition was developed specifically for this work by the ER, we provided experimental evidence of microbial inheritance in plants, from seed to seedling.
• We then identified that the origin of seed microbiome to be combination of both sexual and asexual, i.e. pollen and ovules, and shoot endosphere.
• Based on these results, which provided experimental proof the vertical transmission in plants from parents to offspring (seeds), and from seed to seedling, we tested the hypothesis that this continuous transmission can be tracked back to plant ancestors.
• At this stage, we further aimed to identify the spatial distribution of the plant microbiome at local scale (within the plant) and geographical scale (across the globe). The spatial variation within the plant was evaluated in both fruit and root system.
• To evaluate the geographical distribution of the apple microbiome, we used Gala cultivar sampled from 21 orchards across the globe and analyzed the microbial community associated to its calyx-end, stem-end, and peel using amplicon sequencing. We showed that all apples are not the same.
• The spatial variation within the plant was evaluated in both fruit and root system. The fruit: here we tested the how different part of the fruit vary in their microbial diversity and community composition and how simple agricultural practices such as washing, waxing, and storage time, affect these communities.
• To identify the spatial variation within the root system and examine if these effect are persistent in different genotypes, the microbiota associated with four different apple rootstocks planted in the same soil environment were analyzed.
