17Plant microbiomes have important roles in plant health and productivity. However, 18 despite flowers being directly linked to reproductive outcomes, little is known about the 19 microbiomes of flowers and their potential interaction with pathogen infection. Here, we 20 investigated the temporal dynamics and spatial traits of the apple stigma microbiome 21 when challenged with a phytopathogen Erwinia amylovora, the causal agent of fire blight 22 disease. We profiled the microbiome from the stigmas of a single flower, greatly 23 increasing the resolution at which we can characterize shifts in the composition of the 24 microbiome. Individual flowers harbored unique microbiomes at the OTU level.
25However, taxonomic analysis of community succession showed a population gradually 26 dominated by bacteria within the families Enterobacteriaceae and Pseudomonadaceae. 27 Flowers inoculated E. amylovora established large populations of the phytopathogen, 28 with pathogen specific gene counts of >3.0 x 10 7 in 90% of the flowers. Yet, only 42% of 29 inoculated flowers later developed fire blight symptoms. This reveals pathogen amount 30 on the stigma is not sufficient to predict disease outcome. Our data demonstrate that 31 apple flowers represent an excellent model in which to characterize how plant 32 microbiomes establish, develop, and interact with biological processes such as disease 33 progression in an experimentally tractable plant organ.34 35 36 37 38 39 40 Flowers, the reproductive organs of angiosperms, play a critical role in the plant's 41 lifecycle. The most important function of flowers is to provide a mechanism for 42 pollination, the union of sperm contained within pollen, to the ovules contained in the 43 ovary. The fertilized ovules produce seeds that will later germinate to become the next 44 generation of plants. Yet, unlike other vegetative organs such as the roots, stems, and 45 leaves that are present through a large part of the plant's lifecycle, flowers develop on 46 mature plants and are typically present for the limited period during bloom. As such, 47 research characterizing the microbiome of the flower is generally less developed than for 48 other plant organs. 49 Flowers of apple (Malus domestica) have been subject to considerable research 50 attention as they are the direct precursors of apple fruits, one of the most consumed fruits 51 worldwide (1). The ephemeral nature of apple flowers, with mature flowers from petal 52 open to petal fall only lasting for 5-10 days in spring, offers a unique environment in 53 which to study community succession (1, 2). During bloom, petals open up in a relatively 54 short period of time, typically within one day, which exposes the internal flower parts to 55 the environment and microorganisms. Several of these internal flower parts exude various 56 types of nutrient-rich secretions including nectar, stigmatic exudate, and pollen exudate, 57 for the purpose of attracting pollinators, and inducing the germination of pollen grains (1, 58 3). These secretio...