Temporal and spatial dynamics within the fungal microbiome of grape fermentation
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Abstract
Over 6 years, we conducted an extensive survey of spontaneous grape fermentations, examining 3105 fungal microbiomes across 14 distinct grape‐growing regions. Our investigation into the biodiversity of these fermentations revealed that a small number of highly abundant genera form the core of the initial grape juice microbiome. Consistent with previous studies, we found that the region of origin had the most significant impact on microbial diversity patterns. We also discovered that certain taxa were consistently associated with specific geographical locations and grape varieties, although these taxa represented only a minor portion of the overall diversity in our dataset. Through unsupervised clustering and dimensionality reduction analysis, we identified three unique community types, each exhibiting variations in the abundance of key genera. When we projected these genera onto global branches, it suggested that microbiomes transition between these three broad community types. We further investigated the microbial community composition throughout the fermentation process. Our observations indicated that the initial microbial community composition could predict the diversity during the early stages of fermentation. Notably, Hanseniaspora uvarum emerged as the primary non‐ Saccharomyces species within this large collection of samples.
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Hi Rachel, Thank you for your positive comments! Only 91 of 4309 otus were unassigned against the qiime_ver8_dynamic_10.05.2021 database. These accounted for approximately 1.4% rel abundance of the T1 samples. Most of the data was assigned to the genus level.
Cris.
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Relative to other open ecosystems, where the assembly of the communities is initiated by a multitude of species, grapes appear to display a very low number of core OTUs
Congrats on such a comprehensive and impressive study! I am curious to what extent the UNITE database was able to classify your ITS sequences (eg fraction of sequences unclassified vs classified, and to what taxonomic level)? Is it possible that fungal species found in these types of cultivated fruit environments are not well-represented in databases? In any case, it would be interesting to know how much diversity is yet to be characterized in grapes!
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