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Research Article

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Nicholas A. Bokulich, John H. Thorngate, Paul M. Richardson, and David A. Mills
PNAS January 7, 2014 111 (1) E139-E148; first published November 25, 2013; https://doi.org/10.1073/pnas.1317377110
Nicholas A. Bokulich
Departments of aViticulture and Enology and
bFood Science and Technology, and
cFoods for Health Institute, University of California, Davis, CA 95616;
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John H. Thorngate
dConstellation Brands, Inc., Saint Helena, CA 94574; and
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Paul M. Richardson
eMicroTrek, Inc., San Francisco, CA 94104
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David A. Mills
Departments of aViticulture and Enology and
bFood Science and Technology, and
cFoods for Health Institute, University of California, Davis, CA 95616;
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  • For correspondence: damills@ucdavis.edu
  1. Edited by Robert Haselkorn, University of Chicago, Chicago, IL, and approved October 25, 2013 (received for review September 16, 2013)

See related content:

  • Microbial terroir for wine grapes
    - Dec 05, 2013
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Significance

We demonstrate that grape-associated microbial biogeography is nonrandomly associated with regional, varietal, and climatic factors across multiscale viticultural zones. This poses a paradigm shift in our understanding of food and agricultural systems beyond grape and wine production, wherein patterning of whole microbial communities associated with agricultural products may associate with downstream quality characteristics. Elucidating the relationship between production region, climate, and microbial patterns may enhance biological control within these systems, improving the supply, consumer acceptance, and economic value of important agricultural commodities.

Abstract

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom “microbial terroir” as a determining factor in regional variation among wine grapes.

  • viticulture
  • agriculture
  • metagenomics
  • next-generation sequencing

Footnotes

  • ↵1To whom correspondence should be addressed. E-mail: damills{at}ucdavis.edu.
  • Author contributions: N.A.B., J.H.T., P.M.R., and D.A.M. designed research; N.A.B. performed research; D.A.M. contributed new reagents/analytic tools; N.A.B. analyzed data; and N.A.B., J.H.T., and D.A.M. wrote the paper.

  • Conflict of interest statement: N.A.B., P.M.R., and D.A.M. all own shares of MicroTrek, Inc. a service laboratory serving the food and beverage industry.

  • This article is a PNAS Direct Submission.

  • Data deposition: Raw data are publicly deposited in QIIME-db (www.microbio.me/qiime/) as studies 2019 (bacterial 16S rRNA sequences) and 2020 (fungal ITS sequences).

  • See Commentary on page 5.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1317377110/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Microbial biogeography of wine grapes
Nicholas A. Bokulich, John H. Thorngate, Paul M. Richardson, David A. Mills
Proceedings of the National Academy of Sciences Jan 2014, 111 (1) E139-E148; DOI: 10.1073/pnas.1317377110

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Microbial biogeography of wine grapes
Nicholas A. Bokulich, John H. Thorngate, Paul M. Richardson, David A. Mills
Proceedings of the National Academy of Sciences Jan 2014, 111 (1) E139-E148; DOI: 10.1073/pnas.1317377110
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