Making invisible things visible: Do yeast cells stick to cork during bottle aging?

Yeast do not seem to form biofilms on the bottoms of corks when they’re used, rather than metal crown caps, to secure Champagne bottles during their in-bottle secondary fermentation. This, at least, is the conclusion of an article in the current issue of the American Journal of Enology and Viticulture (paywall), in which Burgundy-based authors investigated the question for the sake of understanding whether Champagne producers, some of whom are using cork for their longer-aging wines, risked upsetting in-bottle fermentation dynamics. After a year of bottle fermentation and aging, a few cells apparently got caught in porous crevices of the cork, but systematic growth presaging the tenacity of a biofilm wasn’t happening.

That finding will no doubt interest the odd sparkling wine producer. Much more interesting is the method they used to make “invisible” cells visible and so reach that conclusion.

How do you determine whether a microbial biofilm is growing somewhere? Continue reading

New, better pictures of what bacteria are doing during fermentation

Short: Microbiologists, using new techniques, are finding that actively fermenting grape musts contain a much wider variety of bacteria than we’ve previously recognized.

Longer: Yeast, being the main actors in alcoholic fermentation, are going to get most of the attention during it. But that’s not the only reason why we don’t know a whole lot about bacteria during fermentation. They’re hard to grow. Doing microbiology the classic way means collecting samples and growing bacteria from them in petri dishes, then identifying whatever grows in the dish. I used to spend measurable fractions of my life “making plates” by mixing Jell-o for bacteria and pouring it into hundreds of little plastic dishes. A main activity of microbiology is waiting for stuff to grow on your plates. The logic here is simple, understandable, and incredibly silly. Bacteria are unbelievably diverse and incredibly specific to their environments. It’s balderdash to think that all of them are going to grow happily, on command, in a dish, in a week or two (if you don’t just throw Monday’s plates out on Friday, which sometimes happens).

The petri dish method is just fine* for working with well-identified and properly house-trained bacteria. It’s pretty horrible for trying to identify all of the unknown bacteria growing in some mystery environment. Only when alternatives became available did microbiology really start coming to terms with the magnitude of what it had been missing. Today, looking for bacterial “unknowns” means identifying bacterial DNA, which is more direct and gives you a better chance of picking up punk microbes that aren’t willing to grow nicely in captivity. Search for bacterial DNA in a vat of actively fermenting grape and you’ll find evidence of a lot more bacteria than the conventional mechanism ever had us thinking about.

Using these techniques, Bokulich, Mills, & co. at UC Davis have been mapping bacterial communities in wineries around the calendar year, wineries across California, and wines with more and less SO2. New research (open-access article), from a (mostly) Washington state-based group, has pointed out something simpler and yet very worth knowing: fermenting wine contains scads more bacteria then we’d ever thought about before. They used “next generation sequencing”** techniques to take snapshots of bacterial communities five times through two weeks of fermentation.

The authors make some questionable comparisons of patterns of bacterial growth between their two study conditions – all the grapes involved were organically grown Riesling, but half were fermented “organically” without added SO2 and the other “conventionally” with SO2. But the experiment involved only a single comparison: two vats, same batch of grapes. Limited replications is no doubt a trade-off with fermenting in realistic 15,000 gallon volumes instead of the completely unrealistic five-gallon carboys too common in much wine research. Regardless, it’s going to take many more comparisons before it’s possible to talk meaningfully about differences in bacterial abundance with and without added SO2.

Here’s why this research is still important. Right now, wine bacteriology is mostly two things: malolactic fermentation, where bacteria are the good guys (unless you’re trying to prevent MLF and it’s happening anyway), and spoilage by a pretty well-known set of culprits, especially acetic acid bacteria. That’s a bit like saying that all Americans are either New York City firefighters or drug dealers. There is a whole lot more going on in both cases. And some of our persistent wine mysteries – why some fermentations stick, some go faster or slower, some produce one aroma and others another – may owe something to that unseen majority. If microbiologists start seeing them, maybe we’ll find out what.

*It’s also time-consuming, labor-intensive, and incredibly wasteful in terms of the masses of plastic that get thrown away. Sometimes you want to do an experiment and can’t because you don’t have enough plates. Or the results you get at 6:00 pm suggest an experiment you should do tomorrow for which you’ll need more plates and you stay until 9:00 pm going through the several-hour process of making more, or someone else uses your plates without telling you, or your plates get contaminated with mold and you have to throw a big batch out.

**As opposed to “deep space nine” sequencing techniques, which are expected to come out next season, will take longer and be more sophisticated, but will never be quite as cool as its predecessor because Patrick Stewart isn’t involved.

Brett + bacteria = worse, or better

Microbiology has gotten a lot wrong studying yeast and bacteria. We’ve assumed, until quite recently, that if a microbe doesn’t grow in a dish it’s not there. And that a microbe is either on/live/growing or off/dead. And that we can study microbes in isolation — “pure culture” — away from other species in little sterile dishes and expect them to behave normally. In all fairness, microbiologists have sometimes seen these as a problems, but have mostly just gone on this way, writing books about what we think we know.

DNA detection and sequencing technology is showing just how many bugs don’t grow in dishes — “high throughput” technology can document (theoretically) all of the species in a drop of [insert favorite liquid here]. That’s pretty routine these days. And we’re slowly beginning to study how mixtures of microbes — you know, the way they live in the wild — behave in the lab. Wine was a bit ahead of the curve here: microbial enologists have been studying the goings-on of spontaneous and mixed fermentations since the late 1980’s.*

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