Top Ten Microbes of 2009

Drum Roll Please….

So, my post-holiday top ten microbes of the year.

At #11) Pediococcus.  A genus within the lactobacteria family, responsible for sauerkraut!  Present in spoiled beer and wine, including a barley wine we made two summers ago.  Does your funny-tasting wine look oily or ropy?  Possibly this guy.

#10) Brettanomyces.  This little yeast can live in a used oak barrel, or can be brought in on a fruit fly.  It is responsible for making a wine smell like leather, your old baseball mitt, or a band aid.  Thanks Brett!  Its saving grace, in small quantites, it can add complexity and intrigue.  In a lambic farmhouse ale from Belgium, there are up to 86 microbe species present, two predominant ones are Brettanomyces bruxellensis and B. lambicus.

Coming in at #9) Nitrosomonas and Nitrobacter.  One couldn’t do it without the other, give em a hand.  Nitrosomonas converts the ammonium in the soil or a compost pile to nitrite, while nitrobacter takes the nitrite to nitrate, the plant usable form of nitrogen.  Gotta love these guys.  Your doing great work.

At #8) Rhizobium and Bradyrhizobium.  Thse guys (many species, each particular to a certain species of legume) are bacteria that live in the roots of legumes (peas, beans, clover…).  They colonize the plant’s root cell and turn nitrogen gas in the atmosphere into ammonium.  The plant stores the ammonium in little nodules in the roots, that can later be released into the soil for other plants (like grapevines).

#7) Aspergillus oryzae.  Responsible for sake and miso soup.  Better at fermenting rice and soy than other yeasts.  Other aspergilliums make poisonous aflotoxins, but not A. Oryzae.  Miso may be linked to reducing the effects of radiation posioning as was shown in Chernobyl, Hiroshima, and Nagasaki survivors.

#6) Aureobasidium pullulans, responsible for turning the breakdown-resistant lignins in an oak stave into vanillin. Holy shit.  Three years of seasoning the staves maximizes this process.  Read more here http://www.demptos.fr/en_v2/images/J_SCI_TECH_TONNELLERIE_064_A.PDF.  The staves are then formed into a barrel, and then we put our wine into it.  Wondering why your red wine smells like vanilla, butterscotch, or oak?  Thank this guy.

#5) Oenococcus oeni.  This bacteria is responsible for the malolactic fermentation in winemaking.  This process gives acidic wines a creamier mouthfeel, however at the expense of some of the aromatic compounds.  Usually prevented in white wines (by filtration or lots of sulfites).

#4) Penicillium roqueforti.  Umm..What, you don’t like blue cheese?  Fine, go make your own antibiotics.

The top three microbes of 2009,

at #3) Glomeromycota.  A whole phylum of the Fungi kingdom, also known as the mycorrhizae.  These are cool.  Two main types. The endomycorrhiza, or the arbuscular type, actually live inside the plant roots. They live in the intracellular spaces of a root, and grow outwards.  They improve micronutrient intake of the plant by reaching outward from the root, increasing root surface area, and dissolving the surrounding soil.  The other type, the ectomycorrhizae are similar and cover the outside of the plant root. They also fix carbon and increase soil structure by the secretion of a chemical called glomulin (reducing global warming).  

Mycorrhizae coming out of a root

These incredible fungi have even been observed connecting a legume (soil nitrogen fixer) to a non-legume.  Thus, a clover can send excess nitrogen (made by the rhizobium) to a ryegrass, and the clover can receive excess phosphorus from the mycorhizae attaching the ryegrass.  Four species in symbiosis.  Sweet.

Coming in at #2)Lactobacillus acidophilus.  Thank you for cheese, yogurt, and the indigenous flora of the human vagina.  Yes, it is present in all three. In the vagina, a healthy population of Lactobacillus helps prevent infestation of Candida by supporting a balanced ecosystem.   You make life better acidophilus, thank you.

And the 2009, top microbe of the year, drum roll,

#1)Sacchromyces cerevisiae. Thank you for making beer, wine, mead, champagne, and sourdough bread. I love you.

Saccharomyces under the EM

Wild Fermentation: O’er the winedark sea

Many hip wineries are starting to do what we in the industry call, wild fermentations.  So, what’s the deal?  Are these wines going to be more complex?  Should you pay more for them?  Isn’t this how all wines used to be made?  The short answer, maybe, no, and yes.  The longer answer:

First, lets meet the characters in this story.  If making wine were a Homeric tale, Saccharomyces cerevisiae would be Odysseus.  Saccharo (sugar) myces (yeast) cerevisiae (cerveza, beer) are the tiny, single-celled fungi that eat sugar, and make alcohol, glycerol, acetic acid, and a host of fruity aromatic chemicals called esters.

Next, lets talk about what’s going on in the wine.  Unlike beer or fruit juice, wine is never sterilized or pasteurized.  It is a living system full of molds, yeasts, bacteria, and of course chemicals made by the grapevine.  Whenever you have a source of sugar in nature, undoubtedly someone will take advantage and eat it.  When we crush up the grapes, we introduce a lot of oxygen into our system.  Now that we have oxygen, sugar, amino acids, vitamins, the time is ripe, and it is time to party.

So just who else is invited to this party?  Just as Odysseus arrived home to Ithaca with 100 suitors ready to take his place, we see the likes of Hanseniaspora uvarum, Metschnikowia pulcherrima, Acetobacter spp., Gluconobacter spp., Kluyveromyces spp., Pichia spp., Candida spp., and Torulaspora delbrueckii, Botrytis cinerea, Penicillin spp., and Aspergillus flavus.  Huh?

Those are just a selected few.  I name them to stress a point, there’s a lot of organisms living on grapes.   How did they get there?  They cling on to the legs and hairs of small insects like leafhoppers and flies, they’re floating in the air, or they protect themselves in fungal fruiting bodies and overwinter on the vines.  The first lesson in microbiology, microbes are ubiquitous, they are everywhere.

Saccharomyces begins its journey overwintering in the soil, or as an airborne spore.  As leafhoppers emerge from their wintery shells in the soil, they carry our hero up onto the leaves and berries.  When the ripe grapes are harvested, they are taken into the winery.  If they have been damaged by birds, rain, hail, or mammals, the grapes are likely to be infected by the vinegar bacteria (aceto and gluconobacter) or the molds (Apergillus, Botrytis, and Penicillin), and may be discarded.  If they have managed to hold their form, then they will make it into the crusher/destemmer.

Now here is where the story begins to unfold.  The party begins, and a young winemaker starts to fret.  Three or four days go by, and the vat of $4000 fruit is just sitting there, rotting.  Nothing, seemingly.  However, the various yeasts have already begun.  Torulaspora, Zygosaccharomyces, Kluyveromyces are at their finest hour.  The alcohol begins to rise.  At about 5 to 7 percent, their delicate cell membranes rupture,  they die.  Saccharomyces seizes the day, and begins to spread throughout the small lot.  No other organism can operate as well as he can.  By day 4 or 5, the temperature has risen, and if we were to examine a single drop of must (the fermenting wine), we would find 100 million yeast cells.

How did this happen?  Well made wine has a wonderful property of being 1)acidic (low pH) 2) High in sugar 3) High in alcohol 4)Low in oxygen.  None of the other microbes can survive these conditions, almost none that is.

All wine used to be made in this manner.  In 1866, Louis Pasteur published the book that would give birth to the study of microbes, it was entitled Etudes sur le Vin, Studies over the wine.  He was the first person to describe Saccharomyces, and show how it turned sugar into alcohol.  Ever since then, we’ve been looking at wine in a new way.  Several decades later, we learned how to isolate the spherical shaped yeast, put it into packages, and sell it to winemaker’s across the globe.  These packaged yeasts offered consistency, insurance, reliability.

Let me stress a point.  Most packaged yeasts are not GE, genetically engineered.  They have been isolated from wild yeasts from such far away places as France, Italy, and Germany, and they have been used to make clean wines for many decades.  In the past decade however, scientists ave begun to tamper with yeasts using techniques of genetic modification.  To date, they are illegal to use in the EU, and most winemakers do not use these GMOs.

So, to inoculate (add the package yeasts) or not to inoculate, that is the question.

Some of the wild organisms that start the party create chemicals like acetic acid (vinegar) which leads to ethyl acetate (nail polish remover).  Let me get to the crux.  When Robert Parker called the 1998 Napa Valley vintage the greatest ever, he set off a wave that is still circling the world.  The 1998 was one of the hottest on record.  The wines that resulted were high in flavor and low in acid, hot, voluptuous.  He liked them, and so did the people that only like the wines he likes.  They could be drunk young, they melted in the mouth.

The problem?  They had no acid, their pH was 4.0  When a wine has a pH between 3.0 and 3.5, none of the other organisms survive except Saccharomyces.  When the pH approaches 4.0, the wine becomes a cess pool.  Wild fermentation leads to spoilage, it is near impossible without spoling.

And so Odysseus arrives at his palace, and begins to slay the evil suitors one by one.   Some winemakers spend hundreds to thousands of dollars every crush to buy packaged yeasts.  They buy several different strains to add complexity to the wine.  Or they go wild.

Here’s the clincher.  A study several years ago showed that no matter if a winemaker used D-254, BM-45, Z-33, Pasteur Red, Prix de Mousse, a combination of all of those in different wines, or let it go wild, if you were to examine the surviving yeasts in all the different wines, it would be the same strain, most likely the strain that lives in the winery and always has.   Truly, our hero has come home.

When you buy a wine that is meant to be aged, (higher acids=lower pH), you support a more sustainable style of winemaking.  In my next story, I will take up unfiltered and unfined, and we will see more of the problems of high pH wine, and learn about winemaking’s dirty little secret, Velcorin.

Mike’s Microbiology: Understanding Wine Aromatics and Flavor

Mike has provided a hugely informative essay on the makeup of wine.

The following essay is the 9th installment in a series of essays entitled “The Top Ten Things I’ve Learned About Wine in the Past Year.”  The idea was to start writing, and maybe someday, write a book. Instead, we’ve started a blog. That dreaded word, more time of your life wasted in front of a blinking screen. Well, this one involves myself, some classmates, and our adventures in wine.

Q: What is wine made out of and why does it taste like it does?

A:  Good question.  I’ll start off the response in simpler terms, and as we go on, I’ll amp it up a bit.

Wine is made out of grapes and the yeast, bacteria, mold, and insects that live on them.

Wine is mostly water.  It got there in several ways.  The grapevine roots absorbed water throughout the growing season, and about 1% of the water that the vine used made it into the grape.  Next, the winemaker added water so that the wine won’t become too alcoholic, he diluted it. We call this post-harvest irrigation.  With that aside, It is often nice when drinking wine to perceive a minerality taste.

Q: What the hell is minerality?

A:  I’m not sure.  I’ve found myself more and more observing the taste of mineral water and sparkling mineral water to see if I can tell a difference.  Check it out.  Calcium, magnesium, potassium, sodium, zinc, copper, chloride, lead, cobalt, manganese, silver, they’re in there.  Doing stuff.  Wines that are described, as the french say, “mineralite, ” often come from old vines, deep soils, and from grapes with subdued “fruit”  complexion.

So, there is water.  What else?  How about acidity.  There are three major acids in wine, and three minors.  Let’s talk the major acids.  The most important is tartaric.  Tartaric is one of the most durable acids in the botanical world.  There are bacteria that can live off of and actually consume many of the acids found in common fruits (apples, cherries, lemons…) Wine is unique.  Hard Apple Cider, Hard Lemonade, Hard Any Fruit, can only survive as a drinkable intoxicant until the indigenous bacteria consume the acids involved.  This is the main reason why wine can survive for more than a hundred years.  Thank you tartaric acid. (There is a rare species of Lactobacillus that can consume tartaric acid.  This rare phenomenon is called “La Tourne.”  I have yet to experience this.)

Q: What does tartaric acid taste like?
A: Sour Patch Kids.  Look at the ingredients.  It’s in there.  It makes your mouth pucker, drool, and then you feel like eating something.

Enter malic acid.  Malus, the latin word for apple.  Malic acid is the sharp and crisp acid of biting into a granny-smith apple.  This acid is in thick supply in apples, crisp Sauvignon Blancs from Loire, France or Marlborough, NZ,, or snappy Pinot Grigio from the Tre Venezie (northeastern Italy).  In the grape, this acid is in high concentration in August.  As the grape begins to shut down in September-October, this acid can actually be consumed by the vine to create ATP(energy).  This is why hotter climates have less acidic wine and cooler climates have more acidic wine.  All because of malic.

Thirdly, there’s lactic acid. Think Lactose – Milk.  This is the acid in milk, and in our bodies after working out too hard.  It is a by-product of bacteria eating the malic acid.  In warmer climates (Spain, California, Southern France) a bacteria eats malic acid and creates lactic.  When a Chardonnay is more creamy, buttery, nutty. Oenococcus, a very small bacteria, has more transformed the malic acid into lactic acid.

Q:  Water, acid, anything else?
A:  Good question.  Yes.  Sugar.  Glucose and Fructose are made by the leaves in the ever-popular “photosynthesis.” These two sugars are put together in the leaf cells and shipped to the grape berry in the form of sucrose, “cane sugar.”  Yeast eat glucose easier than fructose.  A wine with “residual sugar” has sugar that was not consumed by the yeast and turned into alcohol.  A wine that is “Dry”, has no remaining sugar, it has all been turned into alcohol.  A “sweet” wine is a wine where the yeast get too stressed, go on strike, and stop making alcohol leaving behind uneaten sugar.  This is what makes Sauternes from France, Trockenbeerenauslesen from Germany, Lush Zinfandels, Stickies from Austalia, and any other sweet wine, sweet.  Unionized yeast. Alternatively, brandy can lead the way.  Another way of making a sweet wine is to kill the yeast with booze.  This is how one makes a Port.  Stop the fermentation by adding distilled, hard, booze.

Q: This sounds interesting, I’ve heard of this so called, “alcohol.”
A: Ethanol, Grandpa’s ol’ Cough Medicine, C2H5OH.  Whatever you call it, it has been helping you get laid for years.  Yeast make ethanol when they eat sugar in the absence of oxygen.  Wine tends to be anywhere from 11 to 16 percent alcohol.  Eventually, the yeast die because they made too much alcohol (their cell membranes get stretched out like an accordian, poor fool).  As you may or may not know, pure ethanol can almost taste sweet, hot, or viscous.

Q:  Wow, anything else?
A: Tannin.  Tannins are complex ring shaped molecules (phenolic compounds), sometimes occuring in chains (polyhphenolic compounds), and are what makes tea and wine taste, bitter.  They are found in the skins and seed.  As they pass over your tongue, the draw out your salivary proteins.  This makes your mouth feel like you are “chewing on a rug.”    Good?  Yes.  Tannins are a diverse family of molecules, of which nature and plants are abundant in.  They make wine “complex,” and tannins help break down the fats in rich steaks (this is why syrah goes with a New York Steak so nicely).

Among the tannin family is a chemical called resveratrol, one of the best chemicals from “nature” that helps our cholesterol stay low.  Another branch of the “tannin” family tree includes anthocyanins.  These are the color pigments of cranberries, raspberries, blueberries, pomegranates, grapes, etc.  They act as antioxidants when we consume them, scavenging crazy radicals.

Q: Is this essay supposed to be boring?

A:  Hmmm…I was starting to get excited, I was talking about radicals.  Want to hear about aromatic compounds?  Alright, I thought you would.  Let’s get this party started.

As grapes ripen, first they are very acidic.  From July-September, the sugars are rising.  Also, amino acids, vitamin B and C, and potassium salts are being formed,   Finally, October. The skies start to grey and the temperature starts to drop.  This is when the winegrower and all the people who enjoy wine start to pray.  The last thing to develop in a grape is the aromatic compounds.  These are unique, and what makes a grape taste like the Earth has stood still, and a bright light from above is shining down good will to mankind.  Aromatic compounds tend to exist in the space between the flesh and the skin of the berry.  Their average weight is about 702 nanograms.  They are delicate, they go away with too much heat and sun, and they are what make wine taste like the earth is new again.  They are what give a wine “varietal character.”

Here’s the game, you drop a flavor, I tell you the chemical and where it came from.  Caught your attention?

Q: Aight.  Bell pepper.
A:  2-Methoxy-3-isobutylpyrazine.  This compound is found in Merlot, Cabernet Sauv and Franc, Carmenere, Sauv Blanc.  It is made in the photosynthesis process and is transported to the grapes.  This flavor can be reduced by picking late.  It is deteriorated by sunlight.  These varieties are genetically dispositioned to make this flavor.

Q: Not bad.  How  about flowers, like in a muscat for example.
A:  The abundance of floral compounds in a pretty white wine numbers from about 10-20 compounds.  First, linalool(lin-a-lo-o-o-o-o-ol).  This chemical is common in many flowers such as basil, lavender, coriander, and hops.  Widely found in varieties like Riesling, Muscat, and Gewurtztraminer.  It is a delicate chemical, and these wines need to be treated accordingly.  These grape varieties have a genetic predispostion to make this compound in the cells of the leaves and place this delicate, floral, aromatic, unique, chemical into the berries as they approach their ideal ripeness.  Its sensory threshold is about 7.2 parts per billion, or 7 micrograms per liter of wine.

Let’s talk more about these floral chemicals sent from heaven.  A couple more at you, Beta-damascenone, geraniol, Cis-rose oxide, beta-ionone.  A vial of these would trigger your memory to think of roses, violets,or geraniums,  The same chemicals in these flowers are made by the grape berry cells as they approach their ideal ripeness.  Could creation be any more beautiful?

Q:  Alright.  How about coconut.
A: Cis and trans lactones.  These are chemicals leached by oak barrels into the wine.  Its a chemical found in oak wood and it smells like coconut.  American oak contains more cis than trans.  What does that mean?  A more pronounced coconut in American oak than French oak.

Q:Shit. Are you serious? What’s going on here.  Are you about to get jiggy?
A: Yes.  I am.  I could list about 100 compounds that are found in oak barrels, grapes, grape stems, compounds made by yeast, made by bacteria, made by mold.  Such compounds create aromas like litchi, grapefruit, cat pee, honey, black pepper, cotton candy, white pepper, black currant, apricot, ginger bread, cloves, bananas, cigar box, blackberries, fresh-bread and more.  Each one of those is an ester, or a monoterpene, or some other electrochemical-magnetic resonance sent from heaven to make life worth living.

Let me break it down.  Ethanol is the playing field, and these various chemicals are the players.  Some players are synergistic, and some are masking. Some aromas are made by spoilage organism and make wine smell like shit, or barnyard, or bandaids, or vinegar.  I’m not going to talk about those anymore tonight, they make me feel like rotting fruit.  Others are from the oak, some from the grape, some from the yeast, some from the Lactic acid bacteria, others can be from eucalyptus trees on the property, or even stones in the soil.

If I were to place a vial of Ethyl 2-methyl butyrate in your face, you’d tell me it smelled like chemically treated strawberries, like at the dentist’s office.

Q: Wierd, sounds like science, or New Jersey.  Aight, so If that same vial had some cysteinil-related mercaptans, what would it smell like?
A: Great question.  Fresh strawberries.

Q: Really?  Like straight from the farm?
A: Yeah.  This is an example of a synergistic aroma relationship.  The grape made a compound that made the other compound smell better, so that the birds want it more, so that they spread the seeds.

Q: Shit.  Alright.  Go on, tell me some more crazy stuff..
Oak:
Guiacol and 4-Methyl Guaicol– smoky, charred, toasty aromas.  Made when the oak staves are toasted in the fire
furfural and 5-methyl furfural– sweet, butterscotch, caramel, almond.  Made when cellulose and hemi-cellulose are combusted during the toasting
Eugenol and Iso-eugenol– Cloves.  Increases as a white-rot fungi “seasons” the oak staves over a process of 2-3 years.
Bacteria:
Diacetyl–  Butter.  Bacteria that eat the malic acid create this chemical, and then reabsorb it.  Think California chardonnay.  Thank you Oenococcus oeni.
Yeast: Isoamyl Acetate– Banana/Fruity.  Yeasts make chemicals that become esters in the presence of alcohol.  The majority of young wines smell fruity because of the yeasty esters.  As wines age, the grape esters are unlocked.

There are a lot of different compounds found in different wines, and this is why wine is so beautiful.  This is the palette that the winemaker paints his canvas.  Life likes to make life better, biophilia.  In young wines, many of the compounds are ready to be smelled in the ester form.  Meanwhile, a lot of the aromas are locked away, tied to a sugar, or known as a glycosicidic precursor.  As the wine ages, these vine created chemicals become available to the nose.

You’ve been reading for a while now, and I don’t want you to feel overwhelmed, plus I need to go to sleep and bottle wine in the morning.  Wine is meant to be enjoyed, and the main point of this essay is that wine tastes like the Earth that it comes from.  Forest floor, roses, passion, and love itself.  With enough popular demand, I could compile a complete list of aromatic compounds. Until then, our blog is about to get lit up.  Stay tuned for the top 10 microbes of 2010.

Michael Penn

Footnote: Much of this information is sourced from a presentation available here.