| Summary: | Onion (Allium cepa) bulb rot is an important pathological problem worldwide, as it is caused by diverse pathogens, bacterial and fungal. The diversity and structure of microbial communities associated with apparently healthy and diseased onion bulbs were analyzed. The community-based approach allowed identification of a number of potential pathogenic microorganisms associated with onion bulbs affected by disease under storage environments. Enterobacteriaceae, Burkholderia, Gluconobacter, Acinetobacter, Pseudomonas, Citrobacter, Nectriaceae, Botrytis, Wickerhamomyces, Penicillium, and Candida were the most relatively abundant bacterial and fungal taxa in the diseased onion bulb dataset. It was found that these taxa are also widely distributed in the bulbs without apparent disease symptoms. Additionally, several potential fermenters were detected in onion tissue. These data suggest that, in addition to abiotic factors, fermentation plays a role in the storage spoilage of onion bulbs. It was also shown that bacterial and fungal communities differ in their diversity and structure between individual onions affected by bulb rot. The identification of dinoflagellates Symbiodinium in onion bulbs suggested that this eukaryote might have a much broader spectrum of habitats and eukaryotic hosts.
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