The "players" behind the process...

When we create a new botanical-style aquarium, we need to take into account the stuff that we can't see, but that we know is there. The organisms which make up the "microbiome." 

Every aquarium has a microbiome to a certain extent: An ecological community, comprised of billions of bacteria and other microorganisms, working together to create a diverse, thriving closed ecosystem within the aquarium.

Aquariums- every type- have enormous populations of bacteria, performing all sorts of functions within the system. We are all familiar with the beneficial bacteria which facilitate the nitrogen cycle, and play a vital role in the function of our little worlds. And we know that bacteria and other microorganisms commonly associated with botanical-style aquariums provide numerous other benefits besides denitrification. 

The botanical-style aquarium is no different than any other aquarium type in that regard. These bacteria are ubiquitous in the microbiome. It's an elegant, complex set of interdependencies and relationships on many levels. It is a lot to think about...Like many of you, I have an understanding of the basics, but really delving into this stuff requires a deeper understanding. It's the place where my basic high school and college elective-course biology falls away, and you get into more complex aspects of aquatic ecology in aquariums.

Yet, it's important to at least understand the "biome" concept as it can relate to aquariums. It's worth doing a bit of research and pondering. It'll educate you, challenge you, and make you a better overall aquarist. In this little blog, we can't possibly cover every aspect of this- especially with my lack of scientific training-but we can touch on a few points that are really fascinating and impactful.

An interesting place to start is to simply review a bit about the very composition of the materials that we play with, like seed pods and leaves and such, and how they interact with the aquatic environments that we've created, and the organisms which populate them.

Many seed pods and similar botanicals contain a substance known as lignin. Lignin is defined as a group of organic polymers which are essentially the structural materials which support the tissues of vascular plants. They are common in bark, wood, and yeah- seed pods, providing protection from rotting and structural rigidity.

In other words, they make seed pods kinda tough.

That being said, they are typically broken down by fungi and bacteria in aquatic environments. Inputs of terrestrial materials, like leaf litter and seed pods into aquatic habitats can leach dissolved organic carbon (DOC), rich in lignin and cellulose. Factors like light intensity, mineral hardness, and the composition of the aforementioned bacterial /fungal community all affect the degree to which this material is broken down into its constituent parts in this environment.

Hmm...something we've kind of known for a while, right?

So, lignin is a major component of the "stuff" that's leached into our aquatic environments, along with that other big "player"- tannin.

Tannins, according to chemists, are a group of "astringent biomolecules" that bind to and precipitate proteins and other organic compounds. They're in almost every plant around, and are thought to play a role in protecting the plants from predation and potentially aid in their growth. As you might imagine, they are super-abundant in...leaves. In fact, it's thought that tannins comprise as much as 50% of the dry weight of leaves!


And of course, tannins in leaves, wood, soils, and plant materials tend to be highly water soluble, creating our beloved blackwater as they decompose. As the tannins leach into the water, they create that transparent, yet darkly-stained water we love so much!  

Ecological scientists will tell you that blackwater tends to occur when the rate of "carbon fixation" (photosynthesis) and its partial decay to soluble organic acids exceeds its rate of complete decay to carbon dioxide (oxidation).

Chew on that concept for a bit...Try to really wrap your head around it...I'm still grappling with it, myself! 🤔

It's worth researching and pondering. And sometimes, the research you do on these topics can unlock some interesting tangential information which can be applied to our work in aquariums...

Another interesting tidbit of information from science: For those of you weirdos who like using wood, leaves and such in your aquariums, but hate the brown water (yeah, there are a few of you)- you can add baking soda to the water that you soak your wood and such in to accelerate the leaching process, as more alkaline solutions tend to draw out tannic acid from wood than pH neutral or acidic water does. Or you can simply keep using your 8.4 pH tap water! 

"ARMCHAIR SPECULATION": This might be a good answer to why some people can't get the super dark tint they want for the long term...Based upon that model, if you have more alkaline water, those tannins are more quickly pulled out. So you might get an initial burst, but the color won't last all that long...

Interesting stuff, and all part of the little "stew" we make when we set up a botanical-style aquarium, right?

I think just having a bit more than a superficial understanding of the way botanicals and other materials interact with the aquatic environment, and how we can embrace and attempt to replicate these systems in our own aquariums is really important to the hobby. The real message here is to not be afraid of learning about seemingly complex chemical and biological nuances of blackwater systems, and to apply some of this knowledge to our aquatic practice.

Yeah, it's the "jumping off point" for one of my favorite speculative areas in our little hobby speciality:

With botanicals breaking down in the aquarium as a result of the growth of fungi and microorganisms, I can't help but wonder if they perform, to some extent, a role in the management-or enhancement-of the nitrogen cycle.

In other words, does having a bunch of leaves and other botanical materials in the aquarium foster a larger population of these valuable organisms, capable of processing organics- thus creating a more stable, robust biological filtration capacity in the aquarium?

With a matrix of materials present, the bacteria (and their biofilms, as we've discussed a number of times here) have not only a "substrate" upon which to attach and colonize, but an "on board" food source which they can utilize as needed? Facultative bacteria, adaptable organisms which can use either dissolved oxygen or oxygen obtained from food materials such as sulfate or nitrate ions, would also be capable of switching to fermentation or anaerobic respiration if oxygen is absent.


We've talked about that before, right?

And I'm not talking about this in regards to making kambocha, either!  Botanical "layers"- particularly, leaf litter beds- in the wild, offer an interesting study in nutrient processing and food production for the surrounding aquatic ecosystems. And, although botanicals accumulate to significant depth in some areas, the processes which we are fascinated with even occur at surprisingly shallow depths...

One study of wild leaf litter beds in Amazonia indicated that the majority of the aerobic decomposition probably occurs in the upper 10 cm of the leaf litter bed, as lower material is more tightly packed, reducing O2 diffusion, and is generally older and already well decomposed. It is also thought that fermentation processes release acids (specifically, acetic acid), which help reduce the pH substantially within these beds. 

So, we have biological processes occurring in botanical/leaf litter beds which a)facilitate nutrient processing in the habitat, b)contribute to the food chain, and c)potentially influence the chemical parameters of the water.

That's just like what happens in the wild habitats, isn't it?

Studying the influences of Nature on aquatic environments, and how to replicate and incorporate these influences into our aquariums is the key. Building a specialized aquatic microcosm in our tanks will unlock somany secrets and lead to amazing breakthroughs with our fishes.

The thing that's unique about the botanical-style 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.

I have long been one the belief that if you decide to let the botanicals remain in your aquarium to break down and decompose completely, that you shouldn't change course by suddenly removing the material all at once. Personally, I consider this an essential practice in the management of botanical-style aquariums.

The point is, 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.

In the case of our fave aquatic habitats, like streams, ponds, and inundated forests, epiphytes are abundant, and many fishes will spend large amounts of time foraging the "biocover" on tree trunks, branches, leaves, and other botanical materials.

The biocover consists of stuff like algae, biofilms, and fungi. Although most animals use leaves and tree branches for shelter and not directly as a food item, grazing on this epiphytic growth is which occurs on them is very important.

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

I am of the opinion that a botanical-style aquarium, complete with its decomposing leaves and seed pods, can serve as a sort of "buffet" for many fishes- even those who's primary food sources are known to be things like insects and worms and such. Detritus and the organisms within it can provide an excellent supplemental food source for our fishes!

It all seems to go back to food, doesn't it?

We have the opportunity to create an aquatic microcosm which provides not only unique aesthetics- it provides soem supplemental nutritional value for our fishes, and perhaps most important- nutrient processing- a self-generating population of creatures that compliment, indeed, create the biodiversity in our systems on a more-or-less continuous basis.

True "functional aesthetics", indeed!

Natural materials, submerged in water, processed by a huge diversity of organisms, working together. A microbiome.  

Gaining a superficial understanding of the processes, the "players", and the benefits which occur in healthy botanical-style aquariums is one of the most important things we can do to create beautiful, biologically diverse, and highly successful systems.

Get to know those players. Study the processes. Embrace the aesthetics. Enjoy.

Stay informed. Stay excited. Stay curious. Stay observant...

And Stay Wet.


Scott Fellman

Tannin Aquatics 

Scott Fellman
Scott Fellman


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