I've encountered different schools of thought about that matter. Some researchers claim that covering the mouth of an erlenmeyer flask with cotton + aluminum foil will reduce the oxygen transfer to the fermentation medium, so they use only cotton to seal the flask. Others use cotton + aluminum foil to reduce the risk of contamination. I am just curious about which one of the above two most researchers prefer when they carry out an aerobic fermentation.
After sterilization, simply remove the aluminum foil, and use with only cotton (erlenmeyer flask should move up, when cotton gently is pulled up)
By the way, that's my personal experience and I had never encountered any contimination with this.
The reason for covering the cotton wool bung with aluminium foil is to prevent it becoming soaked with condensation during autoclaving. Use of waterproof cotton wool also helps prevent this problem. The foil should be removed immediately the flask is taken out of the autoclave, to allow the bung to dry. The dry cotton wool bung acts as a filter to prevent air-borne microbes from gaining entry to the nutrient medium!
You can also get re-usable foam bungs now that are a big improvement, in terms of ease of use and wettability.
There is no advantage whatsoever to use aluminium foil covering the cotton plug. Gases still escape from the flask. Moreover, condensation of water vapor coming from the flask in contact with the cotton will moisten the cotton, which might lead to contamination. With time, thewhole cotton plug may become wet and, from then on, contamination becomes more probable.
If you fill your Erlenmeyer flasks quite a bit, and if you have a long fermentation time growing high-oxygen consumer strains to high biomass, then oxygen consumption may be so significant, that the oxygen in the headspace is depleted. If you make a short experiment, if you have little liquid, i.e. less cells and more headspace, you may not see an effect. But if there is no need for the aluminium foil, then it is not worth contemplating this approach.
Covering Erlenmeyer flasks with aluminium foil will not help in any way for transfer of oxygen . Erlenmeyer flask plugged with Cotton during fermentation help transfer of oxygen.
When I grow shake flasks I either grow them to take a lot of samples over several days or just overnight to inoculate a bioreactor.
I do not like the foil only covering because the growth rate does seem to be inhibited and the cap tends to fall off more easily than the other types. I do not like cotton plugs because they are inconsistent and annoying to remove more than once.
In the autoclave, whatever closure I choose is covered with foil to protect it from moisture in the autoclave and removed after the flask has been inoculated.
I prefer to use milk filters secured with an elastic band. They are cheap but a bit hard to find (in the US some dairy supply companies sell them). They are also annoying to remove and replace several times with one hand.
The next type of closure I prefer is a foam plug since again they are cheap and can be found at general lab supply companies in various sizes. If the flask is too full and the neck of the flask is short they can get wet. They are easier to remove and replace several times with one hand than milk filters.
The flask closures that can be autoclaved many times are good, but I find them to be very expensive because if the cells start to grow on them then you can't clean them properly and you have to throw them out. These closures are made of silicon and sit over the neck of the flask, there is a foam section in the middle to allow for gas exchange.
The most expensive, but most convenient, shake flask closure is the single use disposable cap with a gas permeable membrane that comes with a screw thread. You can get glass shake flasks to fit these caps or you can get single use sterile polycarbonate flasks with the screw cap in place.
And lastly, if you wish to maximise the gas transfer rate, use baffled shake flasks. They come with side and/or bottom baffles. The bottom baffles only are not as good as the side baffles. The ones that have both side and bottom baffles are better.
Sorry for the long response. I have grown thousands of shake flasks with various microbes and suspended plant cell cultures. Thank you and good luck.
I should add the following to my answer. Aluminum foil loosely put on top of the mouth of an Erlenmeyer flask will likely leave sufficient space for gas exchange (from inside of the flask to the ambient). For gas exchange to occur, there is no need of 'huge gaps'. If however the aluminum foil is closely wrapped and held in place, for example with a flexible rubber band, gas exchange will be prohibited.
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