Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
In answer to the original question, here are some pointers about the nitrifying bacteria:
They need high oxygen. When a filter quits, remove the media, rinse it gently, and let it float, or put it in a mesh bag and keep it in the aquarium wherever there is water movement (air bubbler, power head...)
They need ammonia, but can go several days without. However, your 'overstocked tank' will need the ammonia removal. If there is any way at all to keep the bacteria in contact with the aquarium water, do it.
They do not need to be under water, but do thrive in high humidity, and of course the moving water is bringing them the oxygen and ammonia they need. If you need to store the media away from the tank, I would put it in a bucket so there is a larger volume of air, and just a little water to keep the humidity up. Another way to store it is to dump the media into a bucket of water, add a bubbler or small pump, and add a few drops of ammonia to feed the bacteria. They can be kept alive indefinitely this way. (See the fishless cycle that I have posted quite often for more details)
These bacteria grow on surfaces in a complex layer called a bio film. There are many species of microorganisms in the bio film. It takes several weeks to get a good start, and a couple of months for this complex web of organisms to get fully established. You want to protect this in all possible ways.
Specifically the nitrifying bacteria: They reproduce slowly, and colonize new media slowly. So if you have a dead filter, and the media is not compatible with the new filter you will need to keep using the old media until the new media has a good population of nitrifying bacteria. One of the more conservative ways of doing this is to put the cycled media into several mesh bags in the tank and remove one bag per week for a month or so. This stretches out the loss of the bacteria so there is not too great a loss at any one time. Meanwhile the new filter is growing a good sized population of all the beneficial organisms.
The filter holds roughly 50% of the bacteria that is in the system. The rest of the bacteria live all over the rest of the system: on the substrate, on the plants, on the driftwood, on the ceramic merpeople... depending on which surfaces meet their needs best. In the substrate, for example, there is poor water movement deep in the substrate, not a lot of ammonia or oxygen. So the bacteria live mostly on the upper layer of substrate, but on the bottom of each granule, since they do not like the light.
If you need an emergency source of these bacteria, there are really only 2 sources:
A healthy, cycled aquarium.
A healthy, cycled aquarium can donate up to 25% of its filter media, and not show an ammonia spike. I have taken 25% of the media from several tanks and combined it in one filter and the new tank is pretty close to fully cycled immediately. Taking more than 25% of the filter media is too much, without also removing some fish.
Bottled bacteria: Make sure the ingredients include Nitrospira species of bacteria. This is actually the bacteria that remove the nitrite, turning it into nitrate. A company that bottles that species of bacteria will also have the proper species of ammonia removing bacteria, too. Do not waste money on any product that does not specify Nitrospira. These are delicate bacteria, and do not enter a dormant or hibernating stage. The bottle must not be overheated or frozen, and must not sit on the store shelf too long. If you buy it online, make sure it is shipped with a hot or cold pack, depending on the season.