Guide to a properly established biofilter

This article is about the details of what I call a “Properly Established Biofilter” (PEB) for freshwater aquariums and specifically for planted aquariums. The basic information is nothing new but rather well forgotten.  The value of this article is in the many years of critical observation of the planted tank system. The article intentionally outlines only the relevant information in a simplified way.


What is a biofilter in general?

The biofilter is a bewildering variety of microorganisms that live everywhere in your tank. That means that the biofilter is on all surfaces of the tank, not just inside the filter.

Processing of waste is happening in every point of the tank at all times. There aren’t exhaustive studies what exact species of microbes make up the planted tank biofilter. What is important to understand is that a Propery Estbalished Biofilter is a biofilter that is functioning properly.

Most modern planted tanks do have a biofilter but it is not established properly.  That can be verified in a very simple way – let the tank by itself for a few days without any care.  Most tank will develop algae and plant deficiency issues within only 3–4 days – especially if the CO2 is reduced or completely shut off.  Tanks that can stay cleaner longer than that – about 10 days – have a better biofilter but still far from what it should be.

Definition of a Properly Established Biofilter

A Properly Established Biofilter consists of a variety of microorganisms that have gradually developed for several months in a tank with minimal interventions.

“Gradually developed for several months”  means at least 8-12 months.

“Minimal interventions” means that the tank was maintained minimally in all senses of this phrase (water changes, light, CO2, etc)

Two things qualify the biofilter as “established”:

1. It consists of a certain variety of microorganisms.
Meaning that the different microbial populations are in a certain ratios that have been allowed to adjust gradually.

2. Its performance is very stable, extremely robust, and very predictable.
Meaning that the microbial processes are not disrupted easily and do not change abruptly leading to a variety of issues  – for example appearance of Black Beard or Staghorn algae.

“Very” and “extremely” are words appropriate for the PEB – it has certain characteristics that make it exceptional. It impacts the aquarium in ways that are uniquely beneficial (closer to Nature) for the animal/plant well being. The result is a great simlification of the maintenance requirements.

Relevance of the Properly Established Biofilter

Since the planted aquarium is an extremely complicated and dynamic system the best approach is to use a set of “best practices” for initial establishment and on-going maintenance. Most planted tank enthusiasts have gotten lost in the details, excessive maintenance efforts have become the norm. Planted tanks have become unnatural in both appearance and functionality.

In the last 15 years a big part of the planted tank hobby has grown toward complication, superficial practices, chemical overdosing, and use of unnecessary equipment. The results are tanks that look very attractive but can not stay algae-free and healthy on their own for more than a few days. A Properly Established Biofilter simplifies the planted tank management and allows for easier maintenance practices that are closer to Nature.

The most important side of the PEB is exactly that – the aquarium becomes more of a natural system  With all the beneficial consequences for plants and animals as well as the subtle beauty of form and function combined that is typical of a any natural environment.

Practical benefits of the Properly Established Biofilter

1. Creates a system that is very stable and free of issues
A tank with a PEB becomes extremely stable. In comparison the average planted tank is normally very unstable and issues are very common. A tank with a PEB can be left literally without any maintenance for prolonged periods of time – several weeks and even months. The water can be changed on a regular basis, or just topped off (or even let to evaporate up to 30%) and there will be no issues at all after refilling it. The tank can be overloaded with fish or have no fish at all. It can be turned into a high tech tank, or into a tank that uses minimal levels of CO2/nutrients, or be ran without any supplementation at all. No issues in either direction.

2. Lower energy conditions for plant growth
Plants can grow with much less light, CO2, and nutrients. That includes “rare” plants and plants that were previously grown in high-tech and extremely high-tech tanks (high or extremely high light/CO2/fertilization/water changes).

3. A very forgiving system
You will have a lot of time to adjust whatever you like or need to adjust. Plants, even fast growing and notoriously picky, will give you plenty of time to make adjustments. Algae is non existent or if it appears in some very limited areas (introduced BGA for example) spreads extremely slowly and it can be dealt easily with minor efforts.

4. Exceptional water clarity
Most people have not seen the unique appearance of the water that is a result of a PEB. The water has a distinct “shimmer” and it appears to be “thicker” – a phenomenon that is hard to explain in words. The clarity is beyond exceptional – when collected in a white bucket the water does not have even a trace of a yellow tinge. At times it is actually almost bluish. Fish appear suspended in “nothing” even when looking through 6 ft. of water (from the side of a big tank).

5. Fast settlement of all debries
It takes 10 minutes or less for the mulm to completely settle after pulling plants or rearranging the decorations around.

6. Always a ready-to-go starter biofilter
A new tank can be cycled in a matter of hours using the mulm from a tank with a PEB. The Japanese practice of adding dry bacteria additive after water changes can be followed too but with completely fresh and functional biofilter material. Issues with tanks with unstable biofilters (not-so-clear water, on going algae problems, etc.) can be addressed by simple addition of mulm from a tank with a PEB straight into the water of the problem tank.

7. A PEB-tank can be used to clean algae from plants
A tank with a PEB provides a reliable way to get rid of algae. Just dip the plants in the tank and wait. It takes anywhere from 3-4 hours to 30 days to have the algae disappear. That is right – in some cases it takes only a few hours. Plants like Anubias end up looking artificial – they get an uncommonly clean look. Persistent algae like BBA, Cladophora, and Green Spot are guaranteed to disappear.

Properties of the Properly Established Biofilter

::: What is a biofilter in general?

::: How does a PEB differ from any other biofilter?
A PEB is very stable, extremely robust, and very predictable.
A non-PEB is definitely unstable, could be robust, but it is not predictable.

Different microoranisms “do” different things OR “do” the same thing differently. Some process only certain materials, some process the same materials but in different ways, some process faster, others slower, some develop faster, others slower, etc. That should be obvious but it’s important to emphasize it so we focus on how wildly diverse and dynamic the biofilter is. Because of that complexity a non-PEB biofilter can easily change and not function the way we expect. And because of that complexity you certainly can’t develop a PEB without knowing and following certain practices. Moreover – these practices must be simple and not too precise. Here’s the most important thing you should learn from this article:

::: Stability
The activity of the microorganisms constantly changes. Obvious fact, right? Because different factors affect the microorganisms. A few of the factors considered of great importance are pH, Oxygen, temperature, osmotic pressure. But as we said above – a PEB is stable/robust/predictable. That means a relative independence from the factors that we normally consider of great importance. The PEB is indeed robust – it can actually handle a great and sudden variation of pH, Oxygen supply, and also KH and GH, without any apparent functonal interruption. That means that the PEB can be moved to another tank with very different water parameters (from a hard water tank to a new, soft water tank for example). That stability is a very important practical aspect of the PEB.

::: A closer look at the PEB
The analogies used below are a bit distasteful but easy to remember.

Just like we, ourselves, are covered in microorganisms inside and out at all times the biofilter covers everything in your tank. Look around you – you should be able to imagine the layer of microorganisms covering every single thing you see.  To function properly the human body actually depends on the interaction with certain microorganisms. It is not an exaggeration to say that the microorganisms in an aquarium have the same crucial role.

The microorganisms live in a structure they build called a “biofilm”.  The biofilm is normally invisible in the aquarium but it is there – it covers every single thing you see in the tank. Substrate, decorations, plant roots/stems/leaves, glass, silicone seams, filter media (all of them – mechanical, chemical, biological), the inside of the filter hoses/pipes – they are all covered with biofilm. The film that sometimes develops on the surface of the aquarium water – that is another example of a biofilm. The slimy feel of an aquarium decoration or filter pipe – that is biofilm. When something goes wrong in the tank the microorganisms may leave the biofilm and stay suspended in the water creating an unsightly opalescent look. That state can last for weeks and signals major problems with the microorganisms in your tank.

Dental plaque is an example of a bacterial biofilm too. It is not wanted and we fight it daily by different means. But in an aquarium the biofilm is actually much needed. A PEB has had time to establish a strong and resilient biofilm. A non-PEB tank has biofilm that is much like the dental plaque under daily attack – it does not work very well because it is constantly disrupted by our interventions or by fluctuations of different factors.

The biofilm needs to be properly developed because it provides certain benefits to the microorganisms – a great deal of protection and also better food processing. Disrupt the biofilm and you are disrupting very important ubiquitous processes that must happen in the aquarium. It is not too extreme to say that the biofilter makes or breaks an aquarium. Especially a planted tank which is a special kind of environment that needs to balance the presence of waste (nutrients) with a clean algae-free appearance.