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Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems
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  • Published: 16 January 2026

Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems

  • Lena Flörl1,
  • Patrik Schönenberger2,
  • Markus Rienth2 &
  • …
  • Nicholas A. Bokulich1 

npj Biofilms and Microbiomes , Article number:  (2026) Cite this article

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Subjects

  • Applied microbiology
  • Environmental microbiology
  • Food microbiology
  • Microbial ecology

Abstract

Microbial communities play a central role in viticulture, influencing wine characteristics (a concept termed microbial terroir). Yet, the individual factors shaping these microbiomes remain poorly understood. We conducted a multi-year, large-scale survey of Swiss vineyards (95 sites, 680 samples), longitudinally sampling 12 sites (within 2.46 km and identical cultivar and rootstock) over three years. Using 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing, untargeted metabolomics (GC-MS, LC-MS/MS), environmental monitoring, and sensory data, we disentangled environmental factors associated with community assembly and fermentation dynamics. Topography and climate collectively structured microbiomes but affected soil- and plant-associated communities differently. Berry-associated fungi showed the strongest site-specific signature, enabling machine-learning predictions of microclimatic variation. Climatic factors and berry chemistry selectively favor fermentative yeasts, which are each linked to distinct metabolite and aroma profiles. Plant stress metabolites were further associated with microbial and metabolite composition. Our integrative approach thereby fundamentally advances our understanding of microbial biogeography and terroir in viticulture.

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Data availability

Amplicon sequencing data is available from the Sequence Read Archive (SRA) under accession number PRJEB89111 (16S) and PRJEB89112 (ITS).

Code availability

All code used in this study is available on GitHub (https://doi.org/10.5281/zenodo.17530573).

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Acknowledgements

We would like to thank the winegrowers of the Villette AOC Lavaux and Valais for letting us collect samples over 3 years. Further we thank Vivian Zufferey and Jean-Sébastien Reynard of Agroscope for collecting samples in Valais, Serafina Plüss and Julinka Wäsche for technical support, Ondino Azario and Laura Nyström (ETH Zürich) for supporting the GC-MS analysis, and Alfonso Die for supporting HPLC analysis. The authors thank the Genetic Diversity Centre (GDC) of ETH Zurich for supporting the library preparation. The microbiome amplicon sequencing and LC-MS metabolomics analysis were performed at the Functional Genomics Center Zurich (FGCZ) of University of Zurich and ETH Zurich. The authors gratefully acknowledge financial support from the Swiss National Science Foundation [Grant Number: 310030_204275] (to N.A.B.) and the Swiss Government Excellence Ph.D. Scholarship (to L.F.).

Funding

Open access funding provided by Swiss Federal Institute of Technology Zurich.

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Authors and Affiliations

  1. Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland

    Lena Flörl & Nicholas A. Bokulich

  2. Changins College for Viticulture and Enology, Changins—University of Sciences and Art Western Switzerland, Nyon, Switzerland

    Patrik Schönenberger & Markus Rienth

Authors
  1. Lena Flörl
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  2. Patrik Schönenberger
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  3. Markus Rienth
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  4. Nicholas A. Bokulich
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Contributions

The study was conceived by N.A.B. and M.R., and supervised by N.A.B. L.F. and P.S. collected samples, and P.S. recorded viticultural metrics and performed the microvinifications. L.F. processed the samples, performed the analysis, and wrote the article with review and contributions from N.A.B., M.R. and P.S.

Corresponding author

Correspondence to Nicholas A. Bokulich.

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Flörl, L., Schönenberger, P., Rienth, M. et al. Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems. npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-00915-x

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  • Received: 14 May 2025

  • Accepted: 05 January 2026

  • Published: 16 January 2026

  • DOI: https://doi.org/10.1038/s41522-026-00915-x

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