Thursday, 9 May 2013

Yeast: Species,Strains and Variability

A dendogram showing the genetic/evolutionary relationship
between various species of yeasts. From Reference 1.
So last night I met with the London Homebrewers president, and we planned out something special. I'm not going to say more here - but lets just say once this new project gets rolling it'll blow my blog (and the activities it covers) out of the water.

But, as part of the meeting, our discussion turned to questions like 'what is Brett', 'how does a strain of Brett (or lacto, etc) compare to a yeast strain', etc. In other words, what is the difference between wyeast 1056, 1084 & 2001 (American Ale, Irish Ale and Plisner Urquell respectively), and how does that compare to Brettanomyces bruxellensis or lambicus?

Before going into the details, a brief note on how science organizes species. We organize based on genetic/evolutionary similarity - i.e. if we had two strains that were genetically similar, and one less genetically similar, we would cluster the more similar species together. An example of this can be seen in the attached image - Saccharomyces cerevisiae (top of image) is grouped separate from the Dekkara/Brettanomyces yeasts, while the the Dekkara/Brettanomyces are clustered together The numbers on the lines indicate the relative amount of genetic differences between species, so we can say that Saccharomyces is slightly more similar to Hansenispora occidentalis (71+75 = 146 units of difference) than it is to Brett. bruxellensis (100 + 51 + 100 = 251 units). This mapping allows us to group organisms based on similarity, giving us the ability to separate organisms into strains, species, genera, and higher taxonomical orders. But yeast - being the nightmares of taxonomists - don't play nice...

As always, details below the fold.

Legend:


Why Yeast Give Taxonomists Nightmares

Prior to the genetic revolution - which started in the mid-1990's - yeasts were organized by comparing features like their morphology (shape), biochemistry, the sugars they could eat, and if they engaged in sexual reproduction. The latter may seem odd to a human, but yeasts can do one or the other. Asexually reproducing yeast simply duplicated themselves whole, producing a near-perfect copy (near, because mutations cause a few changes every generation). Sexually reproducing yeasts would divide, but send only half their DNA to each of the resulting cells (spores); these would then fuse with the spores produced by another yeast, leading to mixing of the DNA - AKA yeast sex (not nearly as fun as human sex). When we first started classifying yeast, we thought some species had sex, and that other species didn't, and thus used that criteria to help us separate them into different species.

We were wrong - most yeast can do both; telomorphs are the form of a yeast species which undergoes sexual reproduction, anamorphs are the form of a yeast species which undergoes asexual reproduction. And to make matters worse, the morphology of the two stages of the yeasts life cycle can appear totally different, which for a long time reenforced the idea that the telomorphs & anamorphswere separate species. Instead, yeast 'choose' to be anamorphs or telomorphs based on things like food availability and long-term stress. But given the right conditions anamorphs can be come telomorphs, and vice-versa.

This is why so many yeasts seem to have different names for the same species/genus. Brettanomyces and Dekkara are the same genus of yeast - Brett is the anamorph, Dekk is the telomorph. Likewise, the Hansenispora are telomorph, while Kloeckera is their anamorphs. For reasons that are not entirely clear, anamorphs tend to be the yeast-type that ends up in beer...

Lets Start in the Middle - AKA, WTFerment is a Species?

So the whole anamorph/telomorph thing aside, WTFerment is a species? In simple terms, a species is defined as any group of organisms which can successfully engage in sexual reproduction. This is an imperfect definition as not everything undergoes sexual reproduction (i.e. bacteria such as lacotbacillus) and there isn't always a clear reproductive barrier between species (ring species as an example). We've been trying to find ways around these limitations, and these days tend to use a definition based on genetic clustering, but where one species ends and another begins remains a blurry line.

That said, among brewing yeasts there are some pretty clear species divisions. Saccharomyces cerevisiae (ale yeast) & Saccharomyces pastorianus (lager yeasts) are different species. Likewise, within the Brettanomyces genus of yeasts, there are two separate species used in brewing - B. bruxellensis (which includes B. lambicus) and B. anomalus. But within those species are a lot of unique strains: all the various ale yeasts - everything from good ol' American Alethrough to the hefewisen yeasts, funky trappist ale yeasts and saison yeasts are all S. cerevisiae. Over a dozen strains of B. bruxellensis are commercially distributed, with aromatic characteristics ranging from the barnyard to a tropical pineapple plantation.

What Makes a Strain a Strain?

So in the species discussion we've run into the concept of a strain - but what exactly is that? In many ways, some strains seem like they should be different species (a banana/clovy/cloudy hefeweizen yeast is, in our fermenter, hugely different from a clean/crisp American ale yeast), while some strains are so similar to each other as to be hard to tell apart (e.g. American ale 1056 from wyeast vs. WLP001 from White Labs).

Darth Stella - a truly fearsome
breed of dog
Dog breeds are a good analogy of how yeast strains relate to each other - all dogs are the same species; even a Chiwawa can be crossed with a German Shepard (yes, this has happened) - but despite being of the same species, they vary greatly in their characteristics. But as different and diverse as they are, all dogs are dogs.

So where do these (yeast) strain differences come from? How is it an American strain can produce nearly no esters, while a trappist strain of the same species produces them by the bucketful? The answer is 'a small number of mutations'. A mutation which causes a cell to produce slightly smaller amounts of esters may be sufficient to rid a beer of fruity esters, while a small change in the way a yeast assembles its cell wall can lead to huge changes in flocculation & attenuation.

I find it astounding that such small changes in a yeast genome can lead to such huge changes in the fermenter - but that is how it works. Flavour/aroma compounds work at very low concentrations, so even minor genetic changes can lead to large changes in the resulting beer.

So where do these strains come from? The answer is two-fold:
  1. The vast majority of these strains were selected by brewers as having desired characteristics. The underlying evolution is quite complex - involving crosses between species (like I said, the concept of species is vague), duplications of parts of the genome, and more. Long story short - funky genetic stuff happened, brewers liked the results, and vola - a strain is born!
  2. For the more 'wild' species used by brewers - brettanomyces, Lactobacillus, Pediococcus, and so forth, are naturally-occurring strains. In many cases these strains are the particular form of the yeast/bacteria that happens to inhabit the trees and air of a brewing area - for example, the 5 or so strains of Brettanomyces lambicus you can buy are simply the strains that happened to occupy the 5 or so Belgian valleys where lambic beers are brewed.

Genus? Family?

In the previous paragraphs I've occasionally used the word genus - so what is that? A genus (plural = genera) is a group of related strains. For example, Saccharomyces cerevisiae & Saccharomyces pastorianus are different species, with very different fermentation profiles, flavour/aromatic production, etc. But, despite being separate species, they are not enormously different - they're nearly sisters compared to their cousin Brettanomyces. Scientists cluster similar species to together into a Genus - so S. cerevisiae & S. pastorianus belong to the same genus - 'Saccharomyces'. Indeed, that is how we name species - <Genus> <species> - so the name Saccharomyces cerevisiae indicates the genus (Saccharomyces) and the specific species within that genus (cerevisiae).

You can probably see where this is going - similar genera can be grouped together - we call these groupings 'families', families get grouped into 'orders', orders into 'class', class into 'phylum', phylum into 'kingdoms', and kingdoms into 'domains'. Every time we step 'up' the taxonomic scale we group ever more disparate groups of organisms together.

References


  1. Boekhout T et al. (1994). Phylogeny of the Yeast Genera Hanseniaspora (Anamorph Kloeckera), Dekkera (Anamorph Brettanomyces), and EenieZZa as Inferred from Partial 26s Ribosomal DNA Nucleotide Sequences. Int. Jour. System. and Evol. Microbiol. Vol 44 #4.

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