How it all works.

We get questions. Lots of questions.

Questions about what we call the "botanical method aquarium."

A sort of a funny name for a rather serious approach to aquarium keeping.

What does it mean. How does it all work? And, doesn't the whole idea seem a bit...well- crazy?

It does seem a bit crazy, doesn't it? I mean, we're telling you to do stuff that seems like it's the perfect recipe for a "dirty" tank.  We espouse literally throwing in leaves, twigs, and seed pods in your aquarium, and allowing them to recruit fungal growths, bacterial biofilms, and ultimately to decompose. We value the resulting detritus and the life forms which accompany it. This is absolutely the opposite of pretty much any "methodology" which has been presented to the aquarium hobby for generations.

Yeah, it's definitely one of those things that does seem to be counter-intuitive- at least, based on the current hobby narrative of what is considered "best practices."

In the aquarium hobby, we seem to have this idea that aquariums should be absolutely pristine and not filled with decomposing organic materials. It's a philosophy that's no doubt grounded in trying to help the greatest number of aquarists develop good habits, and is perpetuated on social media, with thousands of these surgically sterile "natural" aquairums thrown into our news feeds daily.

I can't necessarily trash on the idea of preaching good habits. I mean, proper water quality management and routines are important for long term success. A tank full of uneaten fish food and fish waste is a recipe for trouble. However, I think that somewhere along the way, we went a little overboard and started to obsess about cleanliness of our tanks, to the point where almost any algae, detritus, and heaven forbid, biofilms and fungal growth, would be interpreted as a sign of disaster!

So we scrub and scrape, and siphon...

And I think that this "doctrine of radical cleanliness" has actually caused more problems than it has solved. In our pursuit of this radical cleanliness, we've disrupted beneficial biological processes and dramatically slowed down/limited, or even failed to foster significant microbiomes in our aquaria, which I believe has resulted in a lots of tanks with instability and wildly fluctuating environmental parameters. Ironically, these conditions are the very things that drive many hobbyists to keep their tanks obsessively "clean" in the first place! 

As a result, we've developed a "dependency" on high-priced filters, media and additives- a sort of "crutch" to make up for the self-inflicted biological shortcomings of our systems. 

IMHO, we've sort of lost touch with Nature- and the accompanying skill set required to successfully work with natural processes to manage long-term sustainable aquarium systems. We've taken it to a crazy extreme.

Trust Nature a bit more.

I have almost adapted a radically opposing philosophy to this that says "clean"= "unstable!"

Seriously. On a basic biological level, that's what I think the hobby-accepted definition of "clean" means in practice. Unstable, because it essentially "fights" natural processes in order to keep a physically clean environment. It replaces biology with mechanical cleanliness.

The reality is that we can and should find a "middle ground" between complete disregard for basic aquarium husbandry, and a fanatical effort to create "surgical sterility" in our tanks. For some reason, the hobby as a whole has found it tricky to walk this line. I think our approach can fill that void. If anything, the "botanical method" is sort of a call to pull us back towards the side of Nature, relying on not only good old "hobbyist common sense" and effort, but to form an alliance with the many organisms which comprise the microbiome in our aquariums.


And it starts with understanding what some of these organisms are, why they are beneficial, and allowing them to emerge and proliferate in our aquariums. We talk glowingly about "recruiting" biofilms and fungal growths on these decomposing materials to serve as a nutrient processing "system"

The aquarium itself-or, more specifically- the botanical materials which comprise the botanical-style aquarium "infrastructure" acts as a biological "filter system." Or more precisely, a filter "media" upon which these organisms grow.

The botanical materials present in our systems provide enormous surface area upon which beneficial bacterial biofilms and fungal growths can colonize. These life forms utilize the organic compounds present in the water as a nutritional source.

Oh, the part about the biofilms and fungal growths sounds familiar, doesn't it?

Let's talk about our buddies, the biofilms and fungal growths, just a bit more. One more time. Because nothing seems as contrary to many hobbyists than to sing the praises of these gooey-looking strands of bacterial goodness!

Structurally, biofilms are surprisingly strong structures, which offer their colonial members "on-board" nutritional sources, exchange of metabolites, protection, and cellular communication. They form extremely rapidly on just about any hard surface that is submerged in water.

When I see aquarium work in which biofilms are considered a "nuisance", and suggestions that it can be eliminated by "reducing nutrients" in the aquarium, I usually cringe. Mainly, because no matter what you do, biofilms are ubiquitous, and always present in our aquariums. "Resistance is futile!" We may not see the famous long, stringy "snot" of our nightmares, but the reality is that they're always present in our tanks to a certain extent, regardless.

The other reality is that biofilms are something that we as aquarists typically fear because of the way they look. In and of themselves, biofilms are not harmful to our fishes. They function not only as a means to sequester and process nutrients ( a "filter" of sorts?), they also represent a beneficial food source for fishes.

Now, look, I can see rare scenarios where massive amounts of biofilms (relative to the water volume of the aquarium) can consume significant quantities of oxygen and be problematic for the fishes which reside in your tank. These explosions in biofilm growth are usually the result of adding too much botanical material too quickly to the aquarium. They're excaserbated by insufficient oxygenation/circulation within the aquarium.

These are very unusual circumstances, resulting from a combination of missteps by the aquarist.

Typically, however, biofilms are far more beneficial that they are reven emotely detrimental to our aquariums.n

Nutrients in the water column, even when in low concentrations, are delivered to the biofilm through the complex system of water channels, where they are adsorbed into the biofilm matrix, where they become available to the individual cells.  Some biologists feel that this efficient method of gathering energy might be a major evolutionary advantage for biofilms which live in particularly in turbulent ecosystems, like streams, (or aquariums, right?) with significant flow, where nutrient concentrations are typically lower and quite widely dispersed.

Biofilms have been used successfully in water/wastewater treatment for well over 100 years! In such filtration systems the filter medium (typically, sand) offers a tremendous amount of surface area for the microbes to attach to, and to feed upon the organic material in the water being treated. The formation of biofilms upon the "media" consume the undesirable organics in the water, effectively "filtering" it!

What's the hardest part about dealing with biofilms? Accepting their "unique" appearance, and wrapping your head around the fact that these life forms are desirable and normal! 

So, when you are starting up a botanical-method aquarium, you'd be well advised to adopt the mindset that you're creating a small closed aquatic ecosystem, with a variety of unique life forms co-existing at a number of levels. And the point of it all is not just to construct an ecology, but to provide a form of supplemental nutrition for the various inhabitants of your aquarium.

One thing that's unique about the botanical method approach is that we tend to accept the idea of decomposing materials accumulating in our systems. We understand that they act, to a certain extent, as "fuel" for the micro and macrofauna which reside in the aquarium, and that they perform this function as long as they are present in the system.

Our aquariums, much like the wild habitats we strive to replicate, are constantly evolving, accumulating new materials, and creating new physical habitats for fishes to forage among. New food sources and chemical/energy inputs are important to the biological diversity and continuity of the flooded forests and streams of the tropics, and they play a similar role in our aquariums.

So, when you set up your new tank, and add a whole bunch of leaves and seed pods, you're essentially mimicking many of the processes which occur in the wild that foster a growing, dynamic, ecology! And that includes the appearance and proliferation of biofilm and "that other stringy-looking stuff"- fungi.

The fungi which we occur in our botanical method aquariums are known as aquatic hyphomycetes produce enzymes which break down botanical materials in water. Essentially, they are primary influencers of leaf maceration. They're remarkably efficient at what they do, too. In as little as 3 weeks, as much as 15% of the decomposing leaf biomass in many wild aquatic habitats is effectively  "processed" by fungi, according to one study I found!

Aquatic hyphomycetes play a key role in the decomposition of plant litter of terrestrial origin- an ecological process in rain forest streams that allows for the transfer of energy and nutrients to higher trophic levels. 

Read that again, and think about it for a second. This is what ecologists call "nutrient cycling", folks!

These fungi colonize leaf litter and twigs and such soon after they're immersed in water. The fungi mineralize organic carbon and nutrients and convert coarse particulate matter into fine particulate organic matter. They also increase leaf litter palatability to "shredders" (fishes and other aquatic organisms which consume leaf litter as part of their diet), which helps facilitate physical fragmentation.

Fungi tend to colonize wood and botanical materials, because they offer them a lot of surface area to thrive and live out their life cycle. And the abundant cellulose, hemicellulose, and lignin- the major components of wood and botanical materials- are degraded by fungi, which posses enzymes that can digest and assimilate these materials and their associated organics!

Fungi are regarded by biologists to be the dominant organisms associated with decaying leaves in streams, so this gives you some idea as to why we see them in our aquariums, right?

In aquarium work, we see fungal colonization on wood and leaves all the time. And we collectively shit ourselves when it appears in our tanks. Yet, it's really nothing compared to the abundance of this stuff in Nature. Most hobbyists will look on in complete horror if they saw the same extensive amount of fungal growth on their carefully selected, artistically arranged wood pieces as they would in virtually any aquatic habitat in Nature!

Yet, it's one of the most common, elegant, and beneficial life forms which occurs in natural aquatic habitats!

It's everywhere.

Of course, fungal colonization of wood and botanicals is but one stage of a long process, which occurs in Nature and our aquariums. And, as hobbyists, once we see those first signs of this stuff, the majority of us tend to reach for the algae scraper or brush and try to remove as much of it as possible- immediately! And sure, this might provide some "aesthetic relief" for some period of time- but it comes right back...because these materials will provide a continuous source of food and colonization sites for fungal growths for some time!

Ultimately, in the aquarium, it will typically subside a bit to a more "aesthetically tolerable" level, but it will always be present in an aquarium in which botanical materials are available for it to colonize. 

I know that the idea of "circumventing" this stuff by removing it upon initial appearance is appealing to many, but the reality is that you're actually interrupting an essential, ecologically beneficial natural process. And, as we know, Nature abhors a vacuum, and new growths will simply return to fill the void, thus prolonging the process.


Let it play out. Your tan will be just fine. Trust me on this.

Again, think about the role of aquatic hyphomycetes in Nature.

Fungal colonization facilitates the access to the energy trapped in deciduous leaves and other botanical materials found in tropical streams for a variety of other organisms to utilize. 

As we know by now, fungi play a huge role in the decomposition of leaves, both in the wild and in the aquarium. By utilizing special enzymes, aquatic fungi can degrade most of the molecular components in leaves, such as cellulose,, hemicelluloses, starch, pectin and even lignin.

Fungi, although not the most attractive-looking organisms, are incredibly useful...and they "play well" with a surprisingly large number of aquatic life forms to create substantial "food webs", both in the wild and in our aquariums!

Natural habitats are absolutely filled with this stuff...It's like the whole game here- an explosion of life-giving materials, free for the taking...

It doesn't look like the dude's pristine "Nature Aquarium" on Instagram, so we freak the fuck out about it when it shows up. Contest judges would never accept such "sloppiness", so we must remove it immediately!

Just don't. Please.

Think about it for a bit.

Yeah, it's another "mental shift", I which many of you have already made, no doubt. I certainly look forward to seeing many examples of us utilizing "what we've got" to the advantage of our fishes! AGAIN: A truly "Natural" aquarium is not sterile. It encourages the accumulation of organic materials and other nutrients- not in excess, of course.

Fungi are actually an important food item for other life forms in the aquatic environments tha we love so much!  In one study I stumbled across, gut content of over 100 different aquatic insects collected from submerged wood and leaves showed that fungi comprised part of the diet of more than 60% of them, and, in turn, aquatic fungi were found in gut content analysis of many species of fishes!

Now, there is one consideration: Bacteria (ie; biofilms) and fungi that decompose decaying plant material in turn consume dissolved oxygen for respiration during the process.

This is one reason why we have told you for years that adding a huge amount of botanical material at one time to an established, stable aquarium is a recipe for disaster. There is simply not enough fungal growth or bacteria to handle it. They reproduce extremely rapidly, consuming significant oxygen in the process. That is a recipe for the typical "botanical method aquarium disaster" that we see once in a while.

Bad news for the impatient.

Learn to appreciate going slowly and to accept these life forms in your tanks.

Yeah, I admit, decades ago, I freaked out about seeing fungal growths in my tanks, too. I'd get a bit scared, wondering if something was wrong, and why no one else's aquariums ever seemed to look like mine. I used to think something was really wrong!

To reassure myself, I would stare for hours at underwater photos taken in the Amazon region, showing decaying leaves, biofilms,and fungi all over the leaf litter. I'd read the studies by researchers like Henderson and Walker, detailing the dynamics of wild leaf litter zones and how productive and unique they were, and how a wide variety of organisms worked together to make up the ecosystem.

I remember telling myself that what I was seeing in my tanks was remarkably similar to what I saw in images and videos of wild aquatic habitats that I wanted to replicate. They seem to look- and even function- so similarly.

I'd pour over my water quality tests, confirming for myself that everything was okay. It always was. And of course I would watch my fishes for any signs of distress...

I never saw them.

Truth be known, I kind of knew that there wouldn't be any issues, because I created my aquariums with a solid embrace of basic aquatic biology; an understanding that an aquarium is not some sort of underwater art installation, but rather, a living, breathing microcosm of organisms which work together to create a biome..and that the appearance of the aquarium only tells a small part of the story.


There's more going on in our tanks than meets the eye- literally!

Support. Co-dependency. Symbiosis. Whatever you want to call it- the presence of fungi and biofilms in aquatic ecosystems is extremely important to other organisms.

You can call it free biological filtration for your aquarium!

GREAT news for the patient, the studious, and the accepting.

We are creating a big, interwoven set of ecological dependencies in our botanical method aquariums. One which benefits life forms on a variety of levels. 

That's just a very basic, generalized overview of "how it all works." 

Stay curious. Stay intrigued. Stay diligent. Stay brave...

And Stay Wet.


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


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