Aquarium biofilter facts

The aquarium biofilter consists of thousands of species of microorganisms.

What they do should not be viewed as just “waste processing” but as processing of anything that is available. The biofilter does much more than convert Ammonia to Nitrate. Among other things a well functioning biofilter improves the utilization of nutrients by both plants and fish. Another example is the processing of invisible “dissolved organics” which are the main cause of algae outbreaks.

The interactions of the microorganisms are very dynamic – both between themselves and with the environment. The fundamental role of the biofilter in the aquarium maintenance can not be overstated. All other filtration (mechanical, chemical, UV) is secondary. This is a video is an introduction to the invisible universe of the aquatic microorganisms:

Where is the biofilter?
The aquarium biofilter is not just the active microbes in the biofilter media inside your canister, sponge, or HOB filter. Look at your tank – everything that you see is covered with an invisible layer of microorganisms. Just like your skin and everything we see around us. In an aquarium the biofilter is on the plants, rocks, wood, substrate, glass, equipment, inside the hoses, on the fish themselves.

A practical way to look at the biofilter
For aquarium purposes – maintenance and problem solving – thinking of the biofilter as a large group of diverse creatures is not enough.

A more practical mindset is to focus on the PROPER RELATIONSHIPS between them. Meaning that I can have a 10 year old tank and yes, it is full of all kinds of microbes. But they are still struggling to establish balanced relationships. The tank has always had ongoing problems and I never had a good idea how to solve them once and for all. That is a very common situation among aquarium enthusiasts. It is literally solely based on the lack of knowledge what is the biofilter, how it works, and what needs to be done to be established properly. Below are the main facts in a nutshell. References to the scientific articles that the points summarize are written at the end of this article.

What every aquarist should know about the biofilter

1. The biofilter in aquarium is very different on Day 1, Day 30, Day 60.
That means that the combination of species changes wildly in the first 2 months. What is more important – the species are not even related evolutionary on these different days.

That means that the biofilter has a natural development timeline. If the progression from one set of microorganisms to another is interrupted the biofilter never matures. The result is ongoing problems. The common way to solve them is through constant mandatory maintenance. The bottom line is that the aquarist is ignoring (and harming) fundamental natural processes – the natural stages of the establishment of an ecosystem. The aquarium is kept in a perpetual state of imbalance.

2. Biofilter (BF) in aquarium 1 is a completely different make up from BF in aquarium 2. And the BF in aquarium 3 is totally different from 1 and 2.
But all 3 biofilters work the same way if they are established – processing the same things in the same efficient way. All 3 tanks stay stable and clean.

That means that if we want to make a new tank stable and clean we can transfer some of the biofilter from an existing stable tank to the new tank. That was a common practice in the aquarium hobby many years ago that has been very much forgotten. In modern terms – we can “copy and paste” the biofilter from one tank to another. But do remember – the two biofilters will provide the same function but end up having a different microbial make up. For that reason manufacturing, packaging, and selling “the best biofilter” is a questionable effort.

There is an important detail in making the transfer work; We need to get A LOT of the old tank creatures AND /their food/their waste. That is done by syphoning the “dirt” on the bottom of the established tank. What we’re doing really is transferring the living creatures along with their own environment into the new tank. Such a biofilter “injection” has the ability to stop algae from growing literally immediately – because of the active established interaction of the microbes.

Examples of actual use of biofilter material to eradicate algae can be seen here:

Biofilter effect on algae

3. Not a single species dominates.
In the established biofilter there are thousands of species but not one species dominates.

It would be logical to say that in a tank that has issues some species do dominate. That means that any issues we have can be viewed as an imbalance that lets a single or a few microbial species to take over. But the rule can be applied to algae, plants and fish too. Most aquarists have seen an example of that when one or more algae takes over the tank. Also for aesthetic purposes aquarists create such an imbalanced environment intentionally. One example is the popular Asian style planted tank layout known as “Iwagumi”.

We can say that Nature is all about diversity and the domination of one or a few species is only a temporary period toward establishing diversity and balance. In the context of the aquarium biofilter that means that while the biofilter is establishing we should allow for smooth and gradual development. Without constant and sudden changes (big water changes, adding and removing chemicals, fish, plants).

4. Most creatures in the biofilter are not Bacteria.
Usually when aquarist talk about the biofilter they refer to “bacteria”. But that is not correct. Bacteria are one of the 3 domains of life – Archaea, Bacteria, Eucariota. The biofilter consists mainly of species of Archaea, not Bacteria.

Archaea maybe the most ancient creatures on Earth. Refert to the Wikipedia entry if you’d like to know more:

4. A scientific-based approach to aquarium cycling.

The article below is not what I follow. It is someone else’s approach.

It describes steps and details to establish the aquarium biofilter that are based on actual scientific research. The approach as a whole may not be what you want to do because you find it too complicated. But the information is very valuable because it makes you understand that the aquarium biofilter is not just about “microbes converting Ammonia to Nitrate”.


More scientific articles about the aquarium biofilter: