Properly Established Biofilter – experience and examples

I am happy to see that you know a lot about all kinds of interactions in the planted tank and inside the plants. And especially how finely balanced they are. But knowing all these details still does not make you capable of setting up a clean tank every time. Do not think I am dismissing what you know and said about CO2 fluctuations, Rubisco, variations of the uptake, and so on.

What follows below is an explanation why I think that all that information is actually secondary – only important if you know how to run the tank “properly” as I like to call it;

The missing factor
In 2009 I discovered a lot of plant physiology information strictly related to the planted tank on a Russian website. The website is the end of all discussions – there are articles about every single aspect and every single topic is supported with multiple scientific references. There are about 130+ pages on the website and practically all of them are packed with information. When a friend of mine suggested that website within 5 minutes of reading it I went crazy with joy. At that point I had spent almost 10 years obsessing about the issues in planted tanks – especially how they can be handled properly repeatedly. I thought that all my questions will be answered and I will be able to setup clean and stable tanks every single time.

That was not so. Not even close. What happened over and over was that I’d setup tanks and some will be fine but others won’t. I could never find a good reason for the difference. All the cool information about chemicals, uptakes, and fine variations of what not during the day meant nothing if I was stuck being unable to setup a tank predictably. And it does not take much to know that every other person is in the same boat. People that always have clean tanks work so much to keep them that way that I do not consider that right. Anything in life is that way – if it takes too much effort something is not being done right.

The biofilter
Since I’ve been in that hobby very long (42 years, I don’t remember if I mentioned that already) when I see something interesting that seems like a possible answer to a problem I can easily refer to all kinds of past related situations. Slowly (apparently I do not know how to focus very well on solving a problem but rather obsess with it) I started to realize that over the years there have been many situations in which the biofilter inside the canister filter has had a profound positive or negative effect on the tank. I can describe many such situations.

A guy that I trust told me that the biofilter mainly handles organics. The Nitrogen cycle is a small part of the biofilter function – only about 10% of what it does. To this day I do not know what are the actual percentages but at that time fighting organics became my main interest.

Artificial removal of organics
I experimented with boatloads of ion exchange resins in a reactor that exposed the media perfectly. There were obvious results in just 2 days. But all resins load very quickly. What I learned was that if there is a way to keep the sequestration of organics (their removal from the tank) stable the tank will stay extremely clean. So I started to think of of ways to remove organics. And as you know – just having a tank full of plants is not really a guarantee for an organics free tank. Yes, the tank stays clean but ONLY after it goes through the usual period of all kinds of issues.

At one point in my efforts to remove organics using resins I was able to literally strip all organics from the water. The tank got extremely clean and the water was so clear that looking through 6 ft of water was like looking through air.That lasted about 1-1/2 days. Then the tank crashed. I mean it started to develop white haze in the morning. I knew that was very bad news and it will progress super fast.

I had disturbed the bacteria. I knew the signs from previous experiences. And I knew that things will start to go down extremely fast. They did. The white haze got real bad in the afternoon of that same day. Literally like pouring a gallon of milk in my 180 gallon tank. By the next day you could not see anything in the tank. Now there was also a starting green tinge – green water along with the suspended microorganisms (the white tinge). The tank could not go back to normal for 3 full months! From previous experiences I knew that the only way to fix that was to let the tank be. No water changes, nothing. Not touching the tank at all. Any water added to the tank to compensate for evaporation lead to a worse green water and haze for about 2 days.

The green water and haze randomly alternated, cleared a bit and got bad again. At one point the green water was so dense that you could only see your fingertip pressing the inside of the glass. Nothing else.

But after 3 months the magic moment came – I saw a bit of clarification that was stronger than usual. And I knew – in 2-3 days the tank will be super clear. That happened exactly like I expected.

I was back to square 1 – to setup a stable and predictable tank I need to load it with plants and wait through a period of instability and unpredictability. That made little sense because I knew that some tanks will eventually get clean but others won’t.

Natural processing of organics
Clearly removing all organics from an aquarium is not a good idea. The lesson of that horrible experience was that you MUST have organics in the tank. You can not just remove them completely and enjoy a clean tank. You must have thriving microorganisms – they process the organics. It’s really as simple as that but that simple truth carries a lot of charge.

So I realized that the goal is not to remove organics but to have them PROCESSED PROPERLY by the microorganisms. Which means one single thing – the biofilter that these microorganisms are must be in a prime state at all times. That is how I came up with the expressions “properly established biofilter” and “properly established planted tank”.

I setup a new tank and dumped a thick layer of mulm in it. Here are pictures: The idea was that if the biofilter eats organics before anything else I will dump it over everything inside the tank and I should have a situation in which every point of the tank is gobbling up organics. Little did I know that was going to lead to great things. Below are pictures of that tank in the first day of setup. It shows the amount of mulm and the clarity of the water the next day (impossible to really show on a picture):

What I saw the very next morning was shocking. The water was so clear that it looked as if it was not there. Also I did the “white bucket test” – when you syphon water from the tank in a white bucket. If it has any kind of tinge of color then there are organics in the water. I was shocked to see that my new tank water looked literally bluish. Not a speck of yellow.It is not possible to take a good picture of that:

One day I compared a white bucket of tap water to a white bucket with water from the tank. There was a tiny difference – but it was a difference between 2 shades of blue!

The biofilter and plant health
After that experiment I got a ton of rare plants. I intentionally bought them from people that I knew grow them in extremely high tech tanks. Huge PAR, CO2, ferts, water changes… What I saw happening in my tank is impossible to describe – it does not fit the common experience and knowledge:

Not a single one of the 22+ species of rare plants ever died. The only way most of them died was because a few species grew faster , got out of the water, and shaded everybody else. All that happened with very low CO2, no fertilizers, no water changes. There were no fish in the tank. The light was low to medium light (70PAR for only 3 hours a day). The new Amazonia supplied a lot of Ammonia and that saved the day someone knowledgeable told me. But there is no way anybody can keep such high tech plants alive for more than a few days in such “mediocre” conditions. Today, 3 years later, the tank is still running. There never, ever, was any algae in it. Only once I introduced a small piece of wood that had a little BGA on it. The algae never spread. It just sat there never growing. Eventually it disappeared. This is the tank today – I like the very wild look and it fits the all-white room very well. The plants are the same plants from 3 years ago:

Making it work
I hope you follow what I write. It is a long story but I am trying to explain to you how I started to understand that simplifying the aquarium setup and maintenance practices is the way to go. All the cool details we can find about physiology etc are only second.

Studies (I can send you links) show that the microorganisms that form the biofilter change completely from Day 0, to Day 30, to Day 60. In fact it has been found that the populations on these different days are made of species that are not even related evolutionary. Meaning that an older, well developed biofilter is a very special thing. For example – not a single species dominates but there is a great variety of species.

You can not interrupt that natural development and expect to have a problem-free tank. But that is exactly what most aquarists do when using fertilizers, water changes, adding/trimming/removing plants. The biofilter has no chance to develop smoothly. Problems are always around the corner. In the last 20 years – since year 2000 – the lack of understanding has been so deep that tank stability and the state of the biofilter are seldom discussed. And when they are discussed it is usually on a very superficial level.

That same study also shows that biofilters in different aquariums are actually comprised by different species of microorganisms. So you can not say “Aha, this here mix of microorganims is The One!”. And there is more – in all aquariums the developed biofilter is the same functionally, but not as species. Meaning that a well developed filter will process waste very well but the creatures that do that are not the same from one tank to another. All that means one thing – the same thing again – the biofilter must be left to develop properly and not be interrupted. You are literally letting Nature do her thing. As opposed to constantly interrupting.

The above two findings also explain what I found by accident – that dumping a bunch of old “mulm” in a new tank not only cycles it overnight, but also renders it stable and clean. Because you are populating the brand new area with life that has had time to establish and develop. You are making a new tank old in a matter of hours. There is no initial period of issues, need for clean up, maintenance. You can literally not change much water. The biofilter does all the cleaning.


I hope all that was not hard for you to read and follow. I wrote it partly because I will show you a video that will be of much greater interest to you if you knew what it is about. The things I described above are shown working in the video. A severely algae infested tank is rendered beyond clean without any work, water changes, fertilizers, reduction of light. And no, that is not the only tank I have setup and observed to do that once a properly established biofilter is added to it. Today, 3+ weeks after the tank became clean some of the plants have become 3 foot long, and there is a lot of shading going in. Not a speck of algae anywhere. The tank looks as if it was setup 10 minutes ago – just like it looked when it cleared up.

And the coolest but very reasonable thing about using the power of the biofilter (adding mulm): The tank does not need to be new. It can be a tank with ongoing problems. You can clean it without any work. The results will be not just far better than any manual cleanup and special filtration you can do but will also render the tank stable. VERY stable. Think about letting it evaporate 50% or add more light to it or shut off the CO2 or add CO2 or add more fish or reduce the fish. No problems, ever. Sounds like a pipe dream. But it is the reality of a properly established biofilter. Over the years I have had neglected tanks that acted exactly like that. But I never had the mindset to see what was going on in front of my eyes.

Now. I will have to ask you to not share the video with anybody. What will happen is what I have seen many times – intellectual theft. There are people that would claim that was their idea and promote it as such for personal gain and profit. Please respect my trust in you and do not share the video.

(Video is private. Shared only by request.)

Also – that miraculous transformation without any work other than dumping some mulm in the tank hides some important details. But they are not water changes or other such common practices. The details have to do with the big picture. Is the tank actually in a state to support the newly introduced mulm? Is the tank in a state to actually grow plants? Things like that.