The "dynamic botanical substrate": Nature unleashed.

Once again, my fascination with aquarium substrates is taking us down to the bottom today! I'm obsessed with the idea of "functionally aesthetic" substrates in our botanical-style aquariums. 

It's because I imagine the substrate as this magical place which fuels all sorts of processes within our aquariums, and that Nature tends to it in the most effective and judicious manner. 

Yeah, I'm a bit of a "substrate romantic", I suppose.😆

I think a lot of this comes from my long experience with reef aquariums, and the so-called "deep sand beds" that were quite popular in the early 2000's.

A deep sand bed is (just like it sounds) a layer of fine sand on the bottom of the aquarium, intended to grow bacteria in the deepest layers, which convert nitrate or nitrite to nitrogen gas. This process is generically called "denitrification", and it's one of the benefits of having an undisturbed layer of substrate on the bottom of the aquarium.

Fine sand and sediment is a perfect "media" upon which to culture these bacteria, with its abundant surface area. Now, the deep sand bed also serves as a location within the aquarium to process and export dissolved nutrients, sequester detritus (our old friend), and convert fish poop and uneaten food into a "format" that is usable by many different life forms.

In short, a healthy, undisturbed  sandbed is a nutrient processing center, a supplemental food production locale, and a microhabitat for aquatic organisms. 

You probably already know most of this stuff, especially if you've kept a reef tank before. And of course, there are reefers who absolutely vilify sandbeds, because they feel that they "compete" with corals, and ultimately can "leach" out the unwanted organics that they sequester, back into the aquarium. I personally disagree with that whole thing, but that's another battle for another time and place! 

Okay, saltwater diversion aside, the concept of a deep substrate layer in a botanical-style aquarium continues to fascinate me. I think that the benefits for our systems are analogous to those occurring in reef tanks- and of course, in Nature. In my opinion, an undisturbed deep substrate layer in the botanical-style aquarium, consisting of all sorts of materials, from sand/sediments to leaves to twigs and broken-up pieces of botanicals, can foster all sorts of support functions.

I've always been a fan of in my aquarium keeping work of allowing Nature to take its course in some things, as you know. And this is a philosophy which plays right into my love of dynamic aquarium substrates. If left to their own devices, they function in an efficient, almost predictable manner.

Nature has this "thing" about finding a way to work in all sorts of situations.

And, I have this "thing" about not wanting to mess with stuff once it's up and running smoothly... Like, I will engage in regular maintenance (ie; water exchanges, etc.), but I avoid any heavy "tweaks" as a matter of practice. In particular, I tend not to disturb the substrate in my aquariums. A lot of stuff is going on down there...

Amazing stuff.

Even in "non-planted" aquariums, playing with this stuff opens up a whole new area of aquarium "exploration."

Like any dynamic habitat, the "botanical-style substrate" relies on a variety of organisms to do the job of processing nutrients. A healthy and diverse assemblage of organisms dwelling in this layer, ranging from bacteria to fungi too worms and small crustaceans comprise what we call the "infauna." Essentially, the infauna is a collective of organisms which do most of the work in keeping a botanical-style aquarium functional and healthy.

These small organisms  do a LOT!  

They will consume excess food, process detritus, and even some algae. During this process, they digest and excrete some of this stuff as waste. In turn, bacteria process the "waste", which keeps the whole  infauna community- and the biological "filtration" of the aquarium- functioning.  

As you know, I've long had a sort of affection for detritus. It's simply not a problem IMHO- particularly in the context of a deep substrate bed. Most of this stuff will be processed by the resident infauna, and consumed by resident fishes.

We talk about the concept of "substrate enhancement" or "enrichment" a lot in the context of botanicals (we tend to use the two terms interchangeably). They're not particularly scientific, yet I think that the monikers work well. We're not talking about "enrichment" in the same context as say, planted aquarium people, with nutritive materials (vitamins, minerals, fertilizers, etc.) put into the substrate specifically for the benefit of plants.

Rather, "enrichment" in our context refers to the addition of botanical materials for creating a more natural-appearing, natural-functioning substrate- one which provides a suitable haven for microbial life, as well as for fungi, small crustaceans, biofilms, and even algae, to serve as a foraging area for our fishes and invertebrates. There is something oddly compelling to me when I look at both aquariums and natural biotopes with a diverse, interesting bottom structure.

They are diverse harbors of life, ranging from fungal and biofilm mats, to algae, to epiphytic plants. Decomposing leaves, seed pods, and tree branches compose the substrate for a complex web of life which helps the fishes we're so fascinated by to flourish. And, if you look at them objectively and carefully, they are beautiful.

Detritus ("Mulm") located in the sediments is the major source of energy and/or nutrients for this dynamic habitat. The bacteria which perform all the important chemical reactions, such as converting ammonia to nitrite, nitrates to nitrogen, releasing bound-up nutrients, neutralizing hydrogen sulfide, etc. will obtain  essential nutrients from the detritus (this is what autotrophic bacteria that metabolize ammonia/ammonium or hydrogen sulfide for energy do).

These bacteria may also "harvest" those nutrients, as well as metabolize (aerobically or anaerobically) the organic compounds present in the detritus for energy, just like heterotrophs do.

The processing of nutrients in the aquarium is a fascinating one; a real "partnership" between a wide variety of aquatic organisms.

Yes, there is a lot of amazing biological function occurring in these layers. Now, hobbyists have played with deep sand beds in aquariums for many years, and knowledgable proponents of natural aquarium management, such as Diane Walstad, have discussed the merits of such features in far more detail, and with a competency that I could only dream of! That being said, I think the time has never been better to experiment with this stuff!

Again, we're talking about utilizing a wider variety of materials than just sand, so the dynamics are quite different, offering unique functions, processes, and potential benefits.

I'm fascinated by the different types of soils or substrate materials which occur in blackwater systems, and how they influence the aquatic environment. Keep in mind that many of the habitats we obsess over, like Amazonian "igapos" and "igarapes" are seasonally-inundated forest-floor features, so it goes without saying that the terrestrial soil composition and associated biomass have significant influence on the aquatic environments that emerge during the wet season.

Yeah, we know a little about that stuff, right?

So, the idea of a "dynamic substrate", comprised of a variety of materials, will create a very efficient functionally aesthetic habitat for a variety of life forms. Higher organisms such as "Blackworms", "Trumpet Snails", Planarians (not the nasty parasitic ones), GammarusDaphnia, etc. will compliment the bacteria, fungi, and other life forms which live in sediments and sand.

And I should once again point out that my vision of a "dynamic "botanical-style substrate is one comprised of materials like leaves and bits of botanicals mixed in with, on top of, or in place of traditional sand. My obsession with botanical materials to influence and accent the aquarium habitat caused me to look at the use of certain materials that are reminiscent of those found in the wild aquatic habitats, to augment the more "traditional" sands and other substrates used in aquariums. 

And in some instances, as mentioned above-to replace them entirely.  

We have sourced materials which we feel recreate some of the appearance, texture, and function of the tropical streams and rivers that we obsess over. Some, like "Fundo Tropical" and "Substrato Fino" are coconut-derived, and will not only "tint" the water, but will impart those humic substances and such that seem to be so beneficial for many fishes. And then we have our more "leaf-centric" materials, such as Mixed Leaf Media and "MLM2", which provide a different look and function.

We are getting ready to release several more botanical materials that we think will be perfect for this purpose, so stay tuned. 

The texture of these types of materials tends to facilitate the growth of small life forms, like  bacteria and higher organisms (like worms, creatures like Gammarus, and other crustaceans) can thrive and reproduce, processing uneaten food and other materials, which providing the occasional "snack" for foraging fishes. 

Obviously, we're not advocating just recklessly throwing "stuff" into your tank and waiting for something good to happen. I suppose the "con"side of incorporating these types of materials would be that you could overdo it, at least at the outset. You know, adding too much too soon, possibly overwhelming the resident bacteria population in an established aquarium, potentially rapidly reducing pH or even oxygen with excess enthusiasm! It's possible- perils that are well-known to most in our community.

Of course, with this type of experimentation, we need to employ a healthy dose of common sense and good habits. It's important to have adequate water movement, creation, and overall good husbandry when attempting such a substrate.

Well, yeah.

This kind of combination of natural materials can create a potentially messy substrate area if you are not a careful feeder, over-stock your aquarium, and tend to let things go. So, just be conscientious about maintenance! Makes sense, right?

Working with ideas like this always requires that we proceed slowly and cautiously- looking at the potential for issues as thoughtfully as we do at the opportunity to do "evolutionary" things. Building a botanical-style aquarium system is not simply about a different "look."

It's about creating a biological system optimized for the blackwater environment. With a substrate comprised of botanical materials which specifically compliment the overall aquarium habitat, the possibilities for success with these unique systems are significant!

It will require some responsible experimentation, patience, observation, reflection- and occasionally failure. Personally, I have not had any disasters with my years of experimenting with botanical-style substrates and sediments/sands. That doesn't mean that you'll be immune to problems. It just means that if I can pull it off- you certainly can, too. The "learning curve" with this type of stuff is likely a bit unpredictable, but I think it's well worth taking on!

We're literally just "scratching the surface" of the idea of dynamic botanical substrates, and the next set of insights, discoveries, and even breakthroughs- is out there for the taking.

Let's get after this!

Stay brave. Stay curious. Stay open-minded. Stay innovative. Stay resourceful. Stay observant. Stay patient...

And Stay Wet.


Scott Fellman

Tannin Aquatics 


Scott Fellman
Scott Fellman


2 Responses

Scott Fellman
Scott Fellman

January 16, 2020

Hi there! Thanks for the kind words.

Good to hear of your experience! I think the cyanobacteria is a sort of inevitable thing in a high nutrient/highligh/low-to-moderate flow aquarium. Personally, I Have not experienced cyan in a freshwater aquarium before, although thousands of hobbyists do. And I[ve experienced it many times in reef tanks, where there is often a “perfect storm” of optimum conditions in newer tanks for their growth and proliferation. They’re the most adaptable life forms on the planet!

There are a few things you can do to slow it down…Not one of my recommendations, BTW, will be to use any kind of algicide. These of course work, and the "collateral damage: is equivalent to “nuking” the tank, as you’d imagine.

So, you could decrease the photoperiod/intensity (is the water “tinted?” That could help a bit…), increase the water flow, add some faster-growing plants, stepped-up water exchanges, and incorporate some activated carbon or other chemical filtration media in your filter. And of course, you can wait it out. These types of algae, although almost always “present” in any aquarium, are opportunistic; waiting for optimum circumstances to rear their ugly head (do they have a head? 😆) . Those circumstances are typically a lot of light, lack of competition (I; fast-growing higher plants) lower water movement, and suitable substrate upon which to grow…

And again, the passage of time. SO it’s about increased nutrient export mechanisms, DECREASED light intensity/period, and the passage of time. And of course, you could sort of “enjoy” their appearance while they’re there…an ultimate “mind shift”…

It’s about finding a “balance”, and you’ll get there over time. These blooms seldom last forever. They last until conditions for their appearance are not optimum…

Hope this at least gives you a starting point. Good luck in your battle.

Nicolas Hanrez
Nicolas Hanrez

January 16, 2020


Fantastic podcast !

I’m work on deep sand bed for 18 months. The tank is 975L + 240L sump. I layered different kind of sand (thicker to finer) and pouzzolane to achieve a 20cm bottom substrate. Then I applied leaf, wood and pods litter on top. Also growing Epipremnum Aureum, Monstera and Echinodorus. And I’m working on a greenwall on top of the tank to finish natural filtration and bring some green in the house.

Water parameters are good as it’s really soft and acidic, really low nitrates even without water changes. But I have issues with phosphates and black beard algae and, most concerning, CYANOBACTERIA… I keep adding wide range of enzymes and bacterias (aerobic and anaerobic) to the tank but I can’t get rid of it…

Do you have any advice?

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