Argentinian fruit surface microbial ecosystems

Fruits are an important part of a balanced human diet because of their fiber, vitamin, and antioxidant contents. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting oversupply. To avoid food waste, fruit fermentation can provide a solution for this, ideally using strains coming from the fruit environment. However, little is known about the microbial communities present on the surfaces of fruits. Further, flowers, where the fruits originate from, are also an underexplored niche. In the present study, the microbial ecosystems associated with the surfaces of tropical fruits from Northern Argentina (white guava, passion fruit, and papaya), different stages of ripening of certain fruit types (passion fruit and papaya), and Japanese medlar flowers, both open and closed, were investigated using a shotgun metagenomic sequencing approach. Overall, the microbial community compositions largely differed between the different fruits, both at genus and species level, showing very heterogenous fruit surface microbial ecosystems. The microbial fruit and flower communities unraveled contained mainly bacteria, as most metagenomic sequence reads corresponded with bacteria, whereas only a small number corresponded with yeasts. Species of lactic acid bacteria, which are of importance for future controlled fermentation processes were very restricted. The fact that a fraction of the metagenomic sequence reads could not be identified suggests that either not all species present have been sequenced, or that there are still new species to be discovered in fruit surface microbial ecosystems.