Microbial activity is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial ecology influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.

微生物活动是农业生态系统的组成部分，并影响农产品的质量。微生物生态学会影响葡萄的健康和农作物产量，发酵过程中糖会转化为乙醇，从而影响葡萄酒的香气和风味。葡萄树中存在着区域差异的微生物模式，并且必须确定，但是微生物模式如何在小规模（<100 km）范围内对葡萄酒的区域特色（风土）产生影响尚不清楚。在这里，我们使用宏基因组学和种群遗传学来研究自发发酵过程中的真菌群落，酵母菌种群和酿酒酵母种群，以研究微生物分布和真菌对所得葡萄酒的影响。我们发现了真菌，酵母菌和酿酒酵母在地理起源（地产/葡萄园）之间，受到葡萄品种的影响。酿酒酵母在发酵过程中的生长和优势重塑了真菌群落，并在菌株水平上显示了地理结构。真菌微生物群多样性与葡萄酒化学物质之间的关联表明，酿酒酵母在确定次区域规模的葡萄酒香气特征中起主要作用。小于12 km的地理分布支持不同的微生物群落，包括主要的发酵酵母S. cerevisiae在本地环境中可能是不同的。这些发现为微生物对酒土的贡献提供了进一步的证据。以及可持续农业实践的观点，以保持微生物多样性并优化发酵功能以提高饮料质量。