Bacteria - It's actually good for your aquarium
The central component of a healthy aquarium is the biological cycle that is continuously present in an aquarium. Often referred to as the nitrogen cycle, this is the process by which ammonia is transformed to nitrite, which in turn is converted to nitrate. Those of you who though that bacteria was something to avoid will be surprised to know that bacteria - nitrifying bacteria - are what keep your aquarium in good health. Rather than embark on another lengthy editorial about the biological cycle of aquariums, I will try and bring to light the ways in which various filtration schemes promote bacterial colonization - this is what can lead to a very healthy biological balance in your aquarium.
The first thing to realize is that the substrate you use in your aquarium allows for bacterial growth. By "substrate" I mean the gravel, crushed coral, sand, etc. that you use for the bottom of your aquarium. The substrate provides the "media" in which the bacteria can colonize. This may seem rather trivial, but the truth is that one of the main components to filtration systems is a "media" where bacterial colonization can occur - this is often achieved with large surface area objects such as sponges and bio-balls.
Box Filters: For those of you that are freshwater aquarists, most likely you have a box filter - the type that hangs on the back of your aquarium. The sponge filter in this type of filtering system provides two (and perhaps more) forms of filtration. First, it provides mechanical filtration. This is simply the removal of debris from the aquarium water because such matter becomes stuck to the sponge and cannot pass through. The second filtration mechanism is to provide a great media for bacterial colonization - bacteria love high surface area materials such as sponges. You may ask how such knowledge can help you. The answer is simple...when you clean your sponge by rinsing it in water, your are in effect removing some of the bacteria that your aquarium has worked so hard to generate. To make a long story short, the best practice is to rinse the sponge, lightly, in water that you have removed from your aquarium. Often a good source of this water is the water that is removed during water changes. Doing so will help preserve the good bacteria that is living in your sponge filter, and at the same time will allow you to remove unwanted debris.
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