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The purpose of bacteria in aquarium

Brief Description

This page explains the purpose of beneficial bacteria in fish tanks and in a case something isn't clear or if you'd like to ask, use a form at the bottom of this page! Additionally we'd like you to visit the following articles too: Biological Cycle in the Aquarium and Ways how to Cycle an Aquarium with FAQ.


When an aquarium is first set up it is incapable of supporting any livestock until it has built up large enough colonies of beneficial bacteria that will convert all traces of toxic ammonia and nitrites into nitrates that are removed during water changes or consumed by plants that have been added to the tank. But what are these beneficial bacteria and how do they keep our aquariums healthy?

Cycling a fish tank

To understand the processes that are taking place in the aquarium, we have to first learn a little about water chemistry and what it involves. We have heard the phrase “cycling the tank” but what does that mean. When we first set up an aquarium we are actually setting up an artificial ecosystem that hangs on a fragile balance. If we get everything right then the tank looks great but if the balance tips against us and the water parameters take a dive we will start losing fish.

The phrase “cycling the tank” refers to the nitrogen cycle that is being created in our small ecosystem i.e. the aquarium.

A new tank has just been filled with water, the filter has been switched on and the water is up to temperature, the only missing factor is the bacteria that will inhabit the filter, live in the substrate and even cover the tank ornaments and tank glass. The nitrogen cycle will now start to be created. Fish waste will always break down to create ammonia in the tank water, this is highly toxic to the fish so the first stage of the nitrogen cycle is to slowly build up a colony of “nitrosomonas bacteria” to break down the ammonia into nitrites. These bacteria are found naturally in all water but in very small concentrations, nowhere near enough to cope with our tank. They are lithotrophic bacteria that can only survive on clean, hard surfaces such as the media in filters, and as stated previously, tank ornaments and tank glass. As well as needing a food source from the ammonia they also require an adequate supply of oxygen to thrive and multiply. To obtain a large enough colony of these bacteria in our aquariums there are a couple of methods that we can use. Fishless cycling is where drops of pure ammonia are added to the water to feed the bacteria or we can lightly stock the tank with a couple of fish to provide the ammonia from the fish waste. Decaying matter and uneaten fish food will also break down to produce ammonia but this can also affect the overall water quality. Whilst the colony is expanding it is quite common to experience bacterial blooms in the water as the nitrosomas bacteria are free floating and consuming the ammonia present. The water will take a milky appearance but one the colony has established itself the water will clear. Algae may also appear all over the aquarium as ammonia is also a food for this micro organism.

Converting ammonia to nitrites and nitrates

Our colony of nitrosomas bacteria has now grown large enough to deal with all of the ammonia present; it has now been converted to nitrites. These are less toxic to the fish but still dangerous. Another colony of bacteria will start to grow in our filters and aquarium to convert the nitrites to nitrates. These are the nitrobacter bacteria. They will do the same job as the nitrosomonas bacteria except they will deal with the nitrites. They too need food from the nitrites and oxygen to thrive so this must be provided by the fish keeper. At this stage the ammonia will be almost non-existant but do not be tempted to add any more fish. All this will do is increase the ammonia level again and this will in turn slow down the multiplication of the nitrobacter, they can only thrive at low ammonia levels. Once the colony has established, your ammonia levels and nitrite levels are almost at zero, this is what you are aiming for. Nitrates have risen but these are kept under control with water changes, even if a reading is showing on your test kits they are not immediately toxic to your fish.

In our filters and aquarium there are now thriving colonies of nitrosomas and nitrobacter bacteria, now we have to look after them. As stated earlier, they need oxygen to thrive. This is why the filters should be rinsed on a regular basis to prevent clogging. This should only be done with old tank water as fresh water will wipe out most of your established bacterial colonies.

The bacterial colonies are always on a constant balance with each other; this is why too many fish should not be added to the tank at any one time. Upsetting the balance of the bacterial colonies can result in mature aquariums going through mini cycles where the nitrosomas bacteria need to rebuild to control the ammonia levels to prevent them from stunting the nitrobacter colonies.

Bacteria cultures in shops

There are bacterial cultures that are available to buy which are supposed to “kick start” your filters. At the moment there are two schools of thought as to their usefulness, some keepers are praising them but some keepers are doubting the ability of suppliers to bottle a colony of bacteria and provide them with enough food, oxygen etc. to keep the colony alive until they are used.

We have covered the beneficial bacteria, what we must be aware of is that harmful bacteria can enter the aquarium and thrive in places like the substrate if the gravel or sand is not cleaned on a regular basis. These harmful bacteria can bring diseases and infections to your fish so every precaution must be taken to eliminate their introduction. They can be introduced by your hands touching the fish food, tank maintenance when your hands are in the water, lack of tank maintenance allowing a build up of detritus in the substrate and even in the water. Washing your hands prior to tank maintenance and feeding will help - do not use soap as this can affect your tank water!

Quarantining any new fish that are to be added to your tank will allow you to spot if they are infected before they are added to the tank, there is nothing worse than one infected fish wiping out all of your stock.

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