I wish I knew how to take measurements of the bacterial colonies. I'd really like to know just how much of it is in the filter vs in the substrate, on the glass and on the plants. I'd especially like to know just how much less of a role the filter plays in a heavily planted tank as far as bacteria are concerned.
Q
Since you asked.... (this will teach you he.. he... he...)
There are actually several methods for determining the number of bacteria that is in a sample.
Sampling any media is always difficult but remember you don't have to include every single bacteria from a given region. A consistent reasonable sampling across all treatments it required. To test the glass a cotton swab rubbed against a measured surface of glass would work. To test the substrate physical agitation with the addition of some salts may loosen the bacteria from the substrate. Even using a mild surfactant may be usable.
The most common, cheapest, but least accurate is to use growth media and serial dilution techniques to estimate the bacterial counts. To make my explanation easy lets say we sample 1 gram of a sponge. To that 1 gram of sponge we will at 9ml of buffered water this makes a 1/10 dilution. We can then put it in a piece of equipment called a stomacher (this beats the sample up to loosen the bacteria from the substrate). We will then use a set of 9 more tubes of 9ml of buffered water. So we tank 1ml of water from the 1/10 solution and add it another test tube of 9ml of buffer to make a 1/100 solution. We then repeat these steps to make a 1/1,000, 1/10,000, 1/100,000, 1/1,000,000, 1/10,000,000, 1/100,000,000 and 1/1,000,000,000 solutions. We can then take 1ml from each of these solutions and plate using a good very general bacterial media. We then incubate these plates at 25C until we can distinguish clear bacterial colonies (I'd say 10-15 days). We then count how many bacterial colonies are on the plate. We can skip all those with <10 or > 200 on them. This usually leaves only one or two plates countable. Then multiply the number of colonies times the dilution factor. So if we had 145 colonies on the 1/1,000,000 it would equal 145,000,000 bacteria per 1 gram of substrate.
The limitations to this method is sampling accuracy, whether the bacteria species will grow on the media, and the accuracy of the dilution.
Another method uses a machine that passes the buffered sample between two electrodes. The bacteria will complete the circuit and send a signal that can be counted. This works only if the sample is really quite pure because many different particles will complete the circuit.
Now if you have a lot of money that you want to throw at the project you can buy equipment that can detect bacteria by running them through a glass capillary tube. It then shines a focused beam of light through the capillary tube and detects the refracted light from the bacteria. This is highly accurate and much faster than the old dilution method. It can also differentiate between bacteria and other junk in the solution because of the way it refracts the light.
For anyone who read this entire thing, didn't you have anything better to do you fool?