When microbiology is a data problem: Putting science together to make better pictures of yeast

Short: A Portuguese-based group is suggesting that winemakers could have more useful information about choosing a yeast strain if scientists did a better job of putting together data from different kinds of experiments.

Longer:

Scientific research generates a lot of different shapes and sizes of data. How does anyone make it work together?

Contemporary scientific research has a lot of big challenges, but here are three: funding, replicability, and integration. Funding is a great big gory topic for another day.

Replicability has seen a lot of attention in recent science news: scientists across disciplines have been reporting difficulty duplicating their colleagues’ results when they try to repeat the same experiments. This is worrisome. (Most) science is supposed to be about making observations about the world that remain the same independent of who is making the observations. Two careful people should be able to do the same experiment in two different places and obtain the same results. Well-trained scientists, however, are finding themselves unable to replicate the results described in scientific papers, and the community isn’t sure what to do about it.

Integration – how to fit together large amounts of lots of different kinds of data – looks like a separate kind of problem. Scientists (microbiologists, biochemists, systems biologists, geneticists, physicists…) study a thing – yeast, say – in many, many different ways. They generate data in many different shapes and sizes, using all manner of different kinds of instruments to make numbers that don’t just tidily line up with each other. But, at least in theory, all of those data are about the same thing – the same yeast – and so finding ways to integrate data from different kinds of experiments should massively improve our understanding of how yeast works as a whole.

Continue reading

Human intervention increases yeast biodiversity? Sort of.

A new article in PLOS ONE (which, being open-access, you can read for yourself) headlines with the promising title “Yeast Biodiversity in Vineyard Environments is Increased by Human Intervention.” Unfortunately, the paper probably doesn’t mean what you’re thinking it means.

The authors collected yeast from vineyards across the Azores, an archipelago off the shore of Portugal where, following the usual story, viticulture arrived with European settlers in the 15th century. The article says that more than 85% of vineyard acreage has recently been abandoned in the course of “social and economic change,” creating an array of cultivated and abandoned vineyards geographically isolated from each other and the rest of the world. This sounds like a fantastic research setting, even if you don’t take into account “doing fieldwork” meaning “walking around vineyards in the Azores.”*

As advertised, the authors took samples across these vineyards and found that the cultivated vineyards harbor higher numbers of individually distinct yeast strains than vineyards that have been abandoned for at least five years. What that means, however, is a little tricky.

The scientists picked bunches of grapes directly from vines into sterile plastic bags, crushed the grapes inside those bags, and then spread the juice onto what microbiologists call rich media** in Petri dishes, and then used DNA sequencing to identify (some of the) yeast colonies that grew on the surface of the media (jello, essentially) in the dishes. So:

  • We’re only looking at yeast on grapes, not in the soil or “in the environment” more generally. A different, maybe more interesting picture of “vineyard diversity” might have come from microbes in the soil.
  • We’re only looking at yeast willing to grow into visible colonies in two days under standard lab conditions (and the scientists also only sequenced some of those colonies). Most yeast will be happy to oblige, but not all yeast cells present in the environment will become visible colonies in dishes (and some will grow slowly. A lot of microbiology research these days side-steps that problem by sequencing all of the DNA present in a sample, but that option is, as one might expect, more expensive and more difficult. These techniques don’t mean that the older grow-in-a-dish options are completely not-useful or wholly obsolete, but they’re a good reminder that growth-in-a-dish always gives us a limited picture of a microbial world.
  • We’re not comparing cultivated vineyards with the untrammelled wilderness. We’re comparing cultivated vineyards with previously cultivated vineyards that are no longer being maintained as such. We don’t actually know anything about environments on this island where human cultivation hasn’t happened.

The authors are right: this study works against the idea that human activity always decreases ecosystem diversity. And it does say something interesting: that (at least in this setting), human maintenance increases the number of yeast species on grapes. This study continues to support the hypothesis that humans and/or their equipment are a source of vineyard yeast. It’s a good reminder, too, that “human intervention” (you could also say “humans living and working as part of the environment,” if you felt like being contrary) isn’t necessarily detrimental. Though it’s also worth remembering that increased biodiversity isn’t necessarily either “natural” or universally beneficial, either. If humans intervened to increase species diversity in the Arctic tundra, would that be a good thing? We might work on finding better ways of listening to environments telling us how they’re feeling. In the meantime, I suppose that this is a start. 

 

*Part of it is also a UNESCO World Heritage site.

**Rich media = lots of nutrients = easy for most yeast to grow.

A new review of familiar news on grape solids

I’ve just finished reading a (short, I’ll admit) review on the “characterization and role of grape solids during alcoholic fermentation under enological conditions,” and I’m delighted to report that there’s little to report. You’re not missing some manner of fascinating spanking new research on grape solids because you don’t have a subscription to the American Journal of Enology and Viticulture. If you got the picture that solids are important for yeast growth from your favorite old textbook for Winemaking 101, you still have the right picture. Chances are that you’re not doing solids wrong.

The major message about grape solids during fermentation continues to be that solids provide yeast with nutrients they need to survive high alcohol concentrations in low- or no-oxygen environments. With plenty of oxygen, yeast can make the lipids they need to maintain good, strong cell membranes. In the absence of oxygen, they can’t and need to absorb those lipids from their environment. Since a fermenting must doesn’t provide a whole lot of oxygen access, wine yeast need those external lipids. Per the classic “oil and water don’t mix” principle, lipids aren’t very soluble in water. (And per the very nouveau classique cocktail principle of fat washing, we’re familiar with the notion that lipids aren’t very soluble in alcohol, either.) The main source of lipids in a wine fermentation that’s essentially water, then, is the solid part.

Ergo, wine solids → lipids for yeast → strong, healthy cell membranes able to withstand the stress of finishing off the last sugars in that 15% alcohol Napa cab.

A few noteworthy points the authors make along the way to that conclusion:

  • Solids aren’t static through fermentation: small particles stick together into larger particles, and larger particles fragment into smaller particles when rising bubbles of carbon dioxide agitate the mix.
  • Solids may also help yeast by helping to remove carbon dioxide. Suspended particles act as nucleation sites for dissolved gases, allowing CO2 to be carried up and out of the must faster and in turn making the environment less yeast-toxic. This, however, seems to be a minor consideration.
  • The more yeast-assimilable nitrogen (YAN) the must contains, the more solid-associated lipids need to be available to support yeast growth to take advantage of all of that nitrogen.

All of which leaves plenty left for scientists to continue investigating. We still don’t have a good picture of how yeast take up lipids from grape solids, either in terms of the mechanism at the cellular level or in terms of how the dynamics of solids settling and mixing matters. Our understanding of how solids move during fermentation could be more detailed (which sounds like a job for the Champagne physicists who study the science of celebratory bubble movement, though I imagine that the CIVC may have them busy enough on other projects). How solids play with wine aroma is a whole category of interesting questions, and research in that arena might even have something useful – and new – to say to winemakers. In the meantime, the news from the research front is that grape solids are still a matter of the good care and feeding of your yeast friends.