Temporal and spatial dynamics within the fungal microbiome of grape fermentation

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Wine fermentation is a highly complex and competitive environment, imposing harsh selective pressures on fungal community ecology and diversity. The composition of fungal communities inhabiting the surface of grapes will directly impact fermentation progression, wine quality, and contribute to the distinctiveness between wines from different geographical regions. Despite this, the extent of microbial community diversity between geographies, termed ‘microbial terroir,’ remains highly debated. We amassed a large survey of grape spontaneous ferments over six years, encompassing 3105 fungal microbiomes across 14 geographically separated grape-growing regions, and nine grape cultivars. Investigation into the biodiversity of these ferments identified that few high abundance genera form the core of the initial grape microbiome. In line with previous studies, various consistent taxa were linked to specific geographical locations and grape varieties. However, these taxa accounted for a small portion of the overall diversity in the dataset. Through unsupervised clustering, we identified three distinct community types in the grape fungal microbiome, each exhibiting variations in the abundance of key genera. Analysing ferments across temporal and spatial scales revealed significant differences in species richness and compositional heterogeneity between wineries and grape growing regions. However, microbial communities were transient between years in the same winery, regularly transitioning between the three broad community types. We then investigated microbial community composition throughout the fermentative process and observed that initial microbial community composition is predictive of the diversity during the early stages of fermentation, with Hanseniaspora uvarum detected as the main non- Saccharomyces species within this large cohort of samples. Our results help to formulate a clear understanding of the spatial and temporal characteristics of the grape juice fungal microbiome and suggest that these communities are mainly defined by the grape niche and in a minor way shaped by local environmental conditions.

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  1. 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.


  2. 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!