I came across this recent PNAS paper during my weekly bioenergy search on pubmed. It confused me because the topic of this paper has NOTHING to do with bioenergy. However, I want to present this paper because (1) I think this paper’s findings have important implications for the field of bioenergy and (2) the main topic of this paper focuses on another favorite topic of mine – BEER!
HISTORY: The domestication of beer yeast
Before I get into the great finding in this paper, I’d like to backtrack a little bit to the history of beer production to introduce the problem.
It’s well understood that crops used to make beer, bread, and the like were domesticated by humans during the agricultural revolution, and that as we cultivated those plants, they changed. What is less understood is how the microbes we used in the brewing process were unwittingly cultivated by our ancestors, long before the discovery of microbes themselves.
Early in our brewing history, wild yeast fermented our grains for us. These yeast still exist today, and still brew for us. These yeast are called ale yeast, and (obviously) produce ale-type beer. You could go to many groceries (or basically any specialty beer store) and find some of my favorite ales like Redhook ESB, Fat Tire Ranger IPA, and La Fin Du Monde Belgian-style ale. These yeast ferment grain into alcohol at near room temperature (about 65 degrees F), grow at the top of the fermentation vessel , and either are, or directly evolved from the baker’s yeast Saccharomyces cerevisiae.
Up until the 15th century, ale yeast were the only game around. No problem for me, those are my favorites. But, if you’re like most people, you prefer lager beer. These beers, which were first brewed around modern Germany, ferment grain at a much colder temperature than ale yeast (45 - 60 F), live at the bottom of the fermentation vessel, and have not been found naturally in the environment – only in the brewing environment. These yeast are named Saccharomyces pastorianus. More commonly, it’s known as lager yeast, and it produces some of the most popular beers in the world, including Budweiser, Coors, and PBR. Some of the existing European ancestors to these American giants include Stella Artois, Heineken, and Budvar.
PROBLEM: Whence the lager?
We know that lager yeast arose in the 15th century from historical accounts. We also know some about its biological history. Two completely separate species of yeast (or more) can combine their genetic codes in a process known as hybridization. We know that lager yeast has the genetic code from multiple wild yeast inside of it. Part of its code comes from the ale yeast S. cerevisiae. Some of its code matches up with a yeast known to contaminate the brewing process known as S. bayanus. However, the origin of much of its genetic code remains unknown. It has been hypothesized that lager yeast is made of a hybrid of ale yeast, the contaminant yeast, and some third lager yeast, or possibly it is a hybrid of ale yeast and some yet undiscovered strain of contaminating S. bayanus yeast. The authors of this paper set out to find the origin of the lager yeast species.
THE HUNT: Know your oaks
The S. bayanus contaminants can be found naturally in the wild. They like to grow in the bark of oak trees in the northern hemisphere and beech trees in the southern. How do these yeast manage to contaminate beer? Well, brewing equipment was often made of sturdy oak in the days long before sterilization. It stands to reason that our modern contaminants arose from oak trees and oak casks millennia ago.
The authors chose related beech trees to look for the parent of the lager yeast. Others have looked in the oak forests of Europe to find the lager yeast. These authors chose to look someplace else. Because lager yeast are a cold tolerant species, the authors decided to look in the consistently cold beech forests of Patagonia, in Peru. Lo and behold these authors found and named a new species (S. eubayanus for true bayanus) all the way in the forests of South America. So, now we can thank South America for potatoes, tomatoes, and lager beer!
This is the first article I’ve ever read with a new species classification in it. I highly recommend skipping to the end where the species is classified in both English and latin. Pretty classy stuff, science!
HOW THEY DID IT: The yeast needle in the beech haystack
You can’t just stroll around the forests of Patagonia with a magnifying glass expecting to find lager yeast. Here’s what these authors did to see the forest of microbes in the trees. The authors took 133 samples of bark and soil that grew around three different species of beech trees as well as yeast that grow on fungi on top of beech trees. From these 133 samples, the authors isolated yeast species and purified the DNA from individual strains. They then chopped up the DNA using a restriction enzyme and compared the resulting banding pattern of the new yeast with the known cold-tolerant yeast S. bayanus (that old contaminant) and S. uvarum (a yeast involved in cider production). The authors were able to group their selected yeast strains into two populations (Pop. A and Pop. B)using this analysis. Finally, they found the lager yeast ancestor by sequencing the complete genome of one representative strain from populations A and B, and comparing those sequences to the modern lager yeast, the S. uvarum cider yeast, and the S. bayanus brewing contaminant yeast. The authors found that their Patagonian species A and B differed from each other in sequence by about 6-8%. They also showed these species are different species experimentally by showing their spores are highly inefficient at hybrid crosses. They found that species B only differs from S. uvarum cider yeast by 0.52%. Interestingly, they found that the sequence of species A almost perfectly matches the non-ale-yeast portion of S. Pastorianus lager yeast (a divergence of only 0.44% by sequence). Thus the new species S. eubayanus was identified and named.
CONCLUSIONS: What on earth does this have to do with biofuel?
Half a millennium ago, some brewers must have unwittingly brewed their favorite ales in Patagonian beech casks. Their haphazard use of dirty, yeast-ridden equipment resulted in a blockbuster yeast strain that produces some of the most popular beers in the world.
We are now in the process of actively domesticating microorganisms like oil-producing algae, methane-producing bacteria, and alcohol-producing yeast. Many of these organisms can be hybridized with their cousins and genetic modification can make even more precise changes and include even more diverse genes from far-distant organisms. However the question remains: will we be able to rationally beat what our ancestors were able to do by chance? Are we limiting ourselves by using clean equipment? Maybe we need to roll the dice, throw some muck into our experiments, and see what happens.
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