After several readers inquired about leaving headroom when bottling, I felt obligated to experiment.
I had always learned to fill the kombucha all the way to the top when bottling for a secondary fermentation. This stops the activity of the bacteria because of the exclusion of oxygen, while the yeast can continue to ferment the sugars to create CO2 and an effervescent drink, because yeasts can function with or without oxygen (1).
After being prompted to do some experimenting on my own, I left around an inch of headroom in several kombucha bottles for a secondary fermentation. I left the bottles out for a few days, and then I refrigerated them. I didn't open the bottles right away because I already had some kombucha bottles open, but I pulled one out from the refrigerator a week or so later and found that the kombucha bottled with around an inch of headroom was more fizzy than a good number of my previous batches!
Although Happy Herbalist mentions to fill the kombucha to the top of the bottles in their Brewing Guide (look under "Bottling"), on their Bottling Tips page there is a section "Choosing to leave an airspace." According to their Bottling Tips page, if you leave oxygen and airspace in the bottle and if the temperatures are between 70-85 degrees F, the bacteria will continue to remain active and the kombucha will continue to sour, which makes sense because the bacteria require oxygen.
Meanwhile, the yeasts can function with or without oxygen. However, according to Happy Herbalist, yeasts only form carbon dioxide and fizz when oxygen is present (2). "Carbon dioxide suffocates/diminishes the bacteria, but produce[s] the fizz and sparkling brew. Without oxygen the yeast produce more alcohol...The yeast may be active in temperatures as low as 40F (5C) with or without oxygen" (2). In other words, if you leave headspace when bottling, the yeasts can create more carbon dioxide and fizz because of the oxygen present in the airspace. But if there is no airspace, the ability of the yeasts to produce an effervescent drink is limited because of the limited availability of oxygen.
Unfortunately, I was perfectly happy with this explanation until I returned to this formula from my previous post, Kombucha + Fizz, and could not find oxygen needed in the equation for the yeasts to form carbon dioxide:
The yeasts convert sugar to alcohol + carbon dioxide (3, p. 40)
C6H1206 -> 2C2H5OH + 2CO2
sugar -> alcohol + carbon dioxide
Thus, I am somewhat still confused about the exact relationship between the yeasts, oxygen, carbon dioxide, and kombucha fizz. Perhaps the presence of oxygen helps to encourage the yeasts to form more carbon dioxide and fizz, but its presence is not necessary?
Something to note is that kombucha that is bottled all the way to the top will taste different than kombucha that is bottled with airspace, such as in the amount of fizz produced and in others ways as well, such as the acidity of the drink.
I have not found much information on the recomended amount of airspace if you decide to bottle kombucha this way. However, beer brewers tend to leave 1-2 inches of headspace in their bottles according to this thread. Again, experimentation is key, and do whatever you prefer according to personal preference and taste!
As always, I am continuing to learn more about kombucha day by day, and I hope to share that information. If you have any more information or tips on the bottling process and kombucha fizz, please send the information my way or leave a comment!
All my posts related to bottling can be found here.
References
1. http://www.happyherbalist.com/brewing_kombucha.htm
2. http://www.happyherbalist.com/bottlingtips.aspx
3. Frank, Gunther W. Kombucha - Healthy beverage and natural remedy from the Far East. 4th ed. Austria: Wilhelm Ennsthaler, 1994.
***Update July 12, 2010***
I was able to get to talk to a brewer who brews beer and kombucha. Here is what I learned:
- Confirmation that headroom helps prevent the bottle from exploding from the buildup of carbon dioxide.
- You can still increase the fizz in your brew whether or not you leave headroom in your bottle.
- You won't lose fizz by leaving headspace in the bottle.
- You lose more fizz the more you transfer the kombucha from container to container. You can actually decarbonate your brew by transferring your kombucha from container to container.
Part of the reason why there doesn't seem to be a clear answer to the question about whether it is better or not to leave headroom to create more fizz, is because kombucha ferments and SCOBYs contain different strains of bacteria and yeasts and in different proportions. Wild and airborne bacteria and yeasts, which differ according to the location and environment, add even more variation to the mix. Here is one Analysis of a Kombucha Ferment by Happy Herbalist as an example for what may be in your brew.
I personally prefer to bottle with headroom at the moment. But it is up to you, and based on your experiences, to decide whether or not you want to leave headroom in your bottles. I recommend experimenting with both. If anyone wants to share their experiences with bottling, please do so!

