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 Two Stage vs. Single Stage Fermentation. Why, when, or why not?
Because there are a lot of newer brewers out there, and since we often recommend dry-hopping and secondary fermentation, it seemed like a good idea to discuss the benefits of Two Stage Fermentation.

First let's define it and then explain why. Two Stage Fermentation, commonly called Primary and Secondary Fermentation, is nothing more than transferring the beer via siphoning into another fermenting vessel part way through the fermentation process. The reasons for doing this are three-fold:
1.) Removal of the partially fermented beer from contact with the worst of the waste by-products, most of which form during the early and most active part of the fermentation.
2.) Giving the (still mildly active) yeast some exposure to oxygen, which it used to help build a large and healthy population at the very beginning of fermentation... but may not have had as much as needed to maximize the population. This second breath of oxygen sometimes allows for a more complete fermentation.
3.) Breaking up the suspension of solids in the beer which are in no hurry to drop out or "flocculate". Eventually most of them would drop out, but this way more do and in the end we have cleaner looking beer in the bottles, with less sediment. And if gelatin has been used to help that flocculation, the sediment will be very well compacted.

Now that we have determined this is a positive step we need to discuss when the step should be taken. We'll use your imagination, and knowledge of how a fermentation activity curve looks to illustrate the typical fermentation. Fermentation activity is most easily evidenced by increasing and then decreasing airlock activity. After adding yeast and an initial lag while the yeast wakes up, there is a quick rise in CO2 production followed by a nearly equally quick drop, and finally a long period of relative inactivity until the beer is ready to bottle or keg. Since CO2 production goes hand in hand with sugar conversion and alcohol production, we can make some important estimations regarding fermentation progress. While we can't actually measure the amount of gas being produced, we definitely see the airlock bubble frequently and then slow down. If we were to literally count all of the airlock bubbles produced in a complete fermentation, we could at any time calculate how far along the fermentation was, in terms of % of completion. Without actually having to take a week of vacation and stare at your fermenter, we can tell you that by the time your airlock has slowed to bubbling only every 15 to 30 seconds, you will have seen 80% to 90% fermentation completion and resultant alcohol formation in a healthy fermentation. It is at this period that we recommend transferring your beer to secondary, and if "dry-hopping", do so. To synopsize, if there has been 80% to 90% of the potential CO2 produced, then that same % of total sugars have been converted, and that % of total potential alcohol has been produced.

So why is that important? Because we can remove the beer from the majority of waste materials that will ultimately be produced, at a time when the yeast might benefit from oxygen exposure but, ...if the oxygen is not needed there is enough CO2 still being produced from late fermentation to scrub or purge oxygen from the environment and, ...there is adequate alcohol in the beer to defend it against airborne contaminants. Yup, that's a mouthful, but that is exactly what we want to do, when, and how we want to do it. Read that over, carefully.

Now for the brief balance of the title's topic: "why not?". The biggest reason to not transfer into a secondary container is if we wait until it's basically too late to be beneficial. If fermentation has effectively ceased we can only slightly benefit beer clarity by transfering it. We will have allowed too long an exposure to the ugliest waste by-products, possibly allowing flavor to suffer. Any unnecessary exposure to oxygen at that time, when it is not likely to be purged if unneeded, is likely to cause some level of oxidation.... again a flavor degradation. And lastly, if the fermentation is over... well, why bother? Pretty sensible question, huh?

Irish Moss and Gelatin clarifier (optional but strongly recommended).

Just what is Dryhopping?