Arguing “microbial terroir” from microbe to metabolite

Short: New microbial terroir research provides even more evidence that local differences in yeast and bacteria associated with a vineyard make a difference to wine quality.


Bokulich and Mills of UC Davis* have published a series of papers about the communities of yeast and bacteria that live in various winemaking-associated places and arguing for why differences in those communities – usually differences in place; sometimes differences in time – matter to wine as a finished product. Some of their past work outlines distinctive microbial communities around California and connects those communities to climate at a regional level. Their newest publication, out this week, tries to show microbial distinctiveness at the level of near-neighbor wineries and to connect those microbial profiles to wine composition.**

The article is open-access on MBio but, to be honest, it’s a challenging read if you’re interested in following the methods. The study at first seems to involve a two-way comparison between Far Niente and Nickel and Nickel, both in Oakville, California in the Napa Valley. But both of those wineries pulls grapes from multiple vineyards distributed around Napa and Sonoma, and so the comparison is actually among 13 chardonnay and 27 cabernet sauvignon wines, from different vineyard locations, fermented individually in one of those two wineries.

The first part of the study is about showing that grape musts from each of these vineyard sites have unique microbiomes (including bacteria and yeast populations), though their sample size is too small in this case to convincingly argue for a microbial basis to Napa-Sonoma distinctiveness at the AVA level. Unsurprisingly, the diversity of the microbial population and its distinctiveness decreased as fermentation progressed.

The second part of the study is about connecting initial microbial distinctiveness observed in grape musts to wine composition. The authors – and a bunch of statistics – drew some specific connections between the presence of specific metabolites (i.e. chemical compounds created during fermentation by microbial metabolism) with important sensory implications and the presence of specific microbes. On that basis, they argue (they = the authors and the statistics) that they “demonstrate that the microbial composition of grapes accurately predicts the chemical composition of wines made from these grapes and are therefore biomarkers for predicting wine metabolite composition.” That’s true in the sense that they have – in these wines, in this place – created data that mean that identifying X microbe in a must predicts finding Y chemical in a wine, for a limited number of Xs and Ys. It remains a pretty strong way of making the statement.

To be fair, the authors initial frame this as a proof of concept study. Do geographically neighboring vineyards have different microbiologies that matter to wine chemistry? Yes, in these cases, they do. More can be done to substantiate that point, and to follow up on any number of the other questions this paper raises about what some of the microbes linked to specific wine metabolites but with unknown roles in fermentation are actually doing (if they are, in fact, doing anything at all rather than serving as a marker for something else) to make that link happen.

An important note: the framing of this paper, and some others dealing with microbial terroir, can suggest the idea that terroir is quantifiable, reducible to measurable differences in straight-forward wine chemistry. That’s balderdash. Terroir is about regional character. Quantifiable chemical differences are absolutely part of that character, but so is the human history of a place, the character of the people who live there and who make the wine, and the stories that come along with it. Some of those more nebulous influences surely do translate into chemical differences, but not all of them, or at least not all of them in ways contemporary science has an easy time handling. I have no trouble believing that the stories we tell about the wine we’re drinking produce neurochemical changes that affect the sensorineural mechanics of taste perception and that effectually alter the flavor of the wine. Someday soon our sciences may be sophisticated enough to measure those changes. Someday further away, maybe our sciences will be sophisticated enough not to imagine that those measurements explain away why stories are important, too.


*Bokulich has newly moved to Northern Arizona University per the UC Davis press release, though that move is so new that he doesn’t yet seem to have a web presence at his new institutional home.

**Bokulich and Mills’ work is an interesting complement, along different lines, to the microbial terroir work Dr. Matthew Goddard’s group is doing to understand connections amongst regional populations of Saccharomyces cerevisiae, something he presented at the recent International Cool Climate Wine Symposium in Brighton and about which I’ll be writing elsewhere.

Indigenous yeast in Sauternes, multi-species family wineries, and Casale’s Trebbiano orange wine

A group of French scientists, mostly based in Bordeaux, have recently published evidence* that the same Saccharomyces cerevisiae populations have lived at their winemaking homes in Sauternes for at least 23 years.** Two decades is a brief moment, whether you’re measuring in human-history-of-Sauternes time or in yeast-evolution time, but their work still supports the idea that yeast populations become associated with wineries and stick to them.

A main point the scientists aim to make is that these longstanding, tradition-following Sauternes estates haven’t been badly polluted by modern, commercial winemaking yeasts. Only seven percent of the S. cerevisiae strains they collected could be clearly connected to specific commercially produced strains. This news is excellent for those in the natural wine camp who want to call spontaneous ferments “natural” or “wild.” In this little corner of Sauternes, at least, it seems that wines allowed to ferment spontaneously aren’t just being fermented by commercial yeasts persistent in the environment. Most of the work of fermentation is indeed being done by yeasts which very likely existed in the area prior to Lallemand and the rest introducing their tidy little foil packets of active dried specimens.

A good case can be made, I’d argue, for calling those non-commercial yeast something like “domesticated indigenous” rather than “wild:” human winemakers have selected and bred them up for desirable winemaking characteristics over many generations, just as human dog-keepers have bred up select canine features or orchid aficionados have carefully developed new plants. Domestication can happen even if living things are never bought and sold.

Regardless of what we choose to call these yeast species, though, this sort of research says that those species are part of the traditional winemaking environment, part of the terroir. Terroir is apt because that complex term incorporates human traditions and activities, the way winemakers and the rest of the community have shaped the land and its various characteristics: soil, plant life, microbial life, architecture, machinery, maybe some canines. Terroir doesn’t force us to make a choice between those winery-associated yeasts being wild or cultivated. They’re both, and winemakers and winemaking have evolved with them.

The Casale orange trebbiano*** I opened last night is made by a winery with whose winemaking history in their neck of Chianti can be traced back to 1770. The wine itself is a 2012 vintage and the current release, kept on the skins for 30 days and in stainless steel for two years. The property is biodynamic, the wine spontaneously fermented.

Even if the mid-palate is fairly empty, the nose and the finish are more than enough to rescue that deficiency: savory, nutty, sweetly orange blossomy and honeyed up front all at once, and acidity with great energy and tension (minerality, if you wish) on the tail, with a pleasant light astrigency across the breadth of the middle. This isn’t just a wine for thinking with, and I’d readily pour it for anyone who thinks that all biodynamic orange wines must smell like hair salons and taste like dirt, because it doesn’t. But it’s a beautiful example of a wine good both for drinking and for thinking, that tastes pleasant and nourishing and that provokes pleasant and nourishing trains of thought.

When we care about family wineries – for the purely aesthetic value of tradition as well as the economic value of maintaining local businesses and the winemaking value of passing down knowledge and physical infrastructure – we should care about the extended family, not just the humans but the yeast (and maybe even other species) who have also lived on a winemaking property for generations, who make the wine with their human coworkers. Taking care of the family can’t be just about loving your brothers, or even about supporting the other families who might work with you, but about caring for your non-human brothers and coworkers. Now, that’s a pleasant and nourishing train of thought.

*Full text of the article behind an academic journal’s paywall, unfortunately.

**A bit more detail on that point: the team collected samples from three Sauternes estates over 2012, 2013, and 2014, isolating 653 individual yeast strains, and compared them to commercial strains and to 102 “library” isolates collected from one of the three estates between 4 and 23 years ago. The comparisons to determine which strains are related to which other strains rely on 15 “microsatellites,” or specific, small sections of DNA the sequence of which is highly and characteristically variable amongst strains. Much could be said about how we define what constitutes an individual “strain” on the basis of the tools we have available to do so – appearance (phenotype, in biology jargon) in the past, genetic today – but I’ll forgo that conversation for today.

***Purchased for £15.50 from Wood Winters in Edinburgh.

Effects of grapevine leafroll disease on wine quality (and when is a disease a disease?)

Gut reaction: Viruses cause disease. Disease is bad. Viruses are bad.

Gut reaction muted by a lot of recent genetics research: Viral DNA seems to be embedded in genomes all over the place. We’re not sure why a lot of it is there, or stayed there, or what it does while its there. Some viruses cause disease. Some don’t. Viruses are complex, and we probably don’t know the half of it yet.

A name like “grapevine leafroll-associated virus” gets you thinking about negative consequences. Rolled leaves don’t collect light efficiently, which means that they won’t contribute to the plant’s photosynthetic metabolism efficiently, which means that the plant may be malnourished, grow slowly, and/or not have enough energy to ripen fruit. Rolled leaves are bad. A virus that’s associated with rolled leaves is bad. But the virus is only associated, not causative. Some viruses in this general family of leafroll-associatedness aren’t associated with vine symptoms. And infected vines only show symptoms post-veraison (the stage of ripening at which grapes change color), even though they carry the virus in detectable quantities year-round.

Ergo, a group of vine and wine scientists headquartered in eastern Washington state designed an experiment to ask (published in PLOSOne, and therefore open-access to everyone): do grapes from vines with grapevine leafroll disease, and carrying one of these viruses (GLRaV-3), lag behind their undiseased counterparts throughout ripening, or only when vines show symptoms? Being particularly conscientious*, they also improved on existing studies of grapevine leafroll disease by collecting data for three consecutive years from a commercial vineyard, sampling grapes throughout the season but also harvesting grapes at the typical time and making wine from diseased and undiseased pairs, and subjecting those wines to (limited) chemical and sensory analysis. They also used own-rooted rather than grafted vines, which eliminates some potentially confounding variables.

Their conclusions, after collecting data over the 2009, 2010, and 2011 growing seasons:

  • Grapevine leafroll disease decreases vigor (as measured by cane pruning weights) and fruit yield in own-rooted Merlot vines in Western Washington.
  • Grapes from diseased/infected vines have lower total soluble solids (TSS) and higher titratable acidities (TA) (and, to a less dramatic degree, lower anthocyanin concentrations) than grapes from undiseased/uninfected vines, but only after vines begin displaying symptoms post-veraison.
  • Wines made from diseased grapes were browner and less intensely colored, earthier and less fruity, and more astringent compared with their undiseased counterparts.
  • However, panelists only correctly distinguished diseased from undiseased wines when served side-by-side in black glasses, removing the notable color differences from consideration and forcing them to differentiate on smell and taste alone.
  • Soluble solids, TA, and pH were all more dramatically affected than anthocyanins in diseased vines, which reflects the decoupling of anthocyanin development and sugar accumulation that happens late in ripening during which environmental conditions play heavy in anthocyanin development.

These conclusions probably do more for plant scientists than for commercial growers: data from one Merlot vineyard near Prosser can’t be precisely extrapolated to you, wherever you are, and thresholds for usable fruit are always a matter of context (the authors note that future studies should document the effects of grapevine leafroll disease on specific sensorily-important compounds). The study does add data points to a collection of statistically robust data that might help large companies make judgments about what they can include in their generic red blends before pH or some other parameter becomes a problem. But maybe the most interesting line of thinking here has to do with the nature of disease, and of relationships between viruses and diseases and symptoms. Do vines have leafroll disease before they exhibit symptoms? Where do we want to draw lines between normal or acceptable variation and disease symptoms? If a vine looks sad but makes grapes that make wine indistinguishable from happy-vine wine, and if genetic testing says that the plant also happens to have a virus, does that mean that the vine has a disease, or is it healthy?

Disease” can mean something different to the plant pathologist who looks at a vine, a geneticist who looks at the DNA of a vine, a commercial grower who looks at the fruit of the vine or a winemaker who looks at the juice it makes. That vine may be infected with viruses. Is the virus bad?


*Full disclosure: I know and think highly of several of the scientists on this team.