Race to the bottom...


Substrates, IMHO, are one of the most often-overlooked components of the aquarium. We tend to just add a bag of  "_____________" to our tanks and move on to the "more exciting" stuff like rocks and "designer" wood. It's true! Other than planted aquarium enthusiasts, the vast majority of hobbyists seem to have little more than a passing interest in creating and managing a specialized substrate or associated ecology.

And, when we observe natural aquatic ecosystems, I think we as a whole tend to pay scant little attention to the composition of the materials which form the substrate; how they aggregate, and what occurs when they do. 

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.

I realize, when contemplating really deep aggregations of substrate materials in the aquarium, that we're dealing with closed systems, and the dynamics which affect them are way different than those in Nature, for the most part.

And I realize that experimenting with these unusual approaches to substrates requires not only a sense of adventure, a direction, and some discipline- but a willingness to accept and deal with an entirely different aesthetic than what we know and love. And this also includes pushing into areas and ideas which might make us uncomfortable, not just for the way they look, but for what we are told might be possible risks.

One of the things that many hobbyists ponder when we contemplate creating deep, botanical-heavy substrates, consisting of leaves, sand, and other botanical materials is the buildup of hydrogen sulfide, CO2, and other undesirable compounds within the substrate.

Well, it does make sense that if you have a large amount of decomposing material in an aquarium, that some of these compounds are going to accumulate in heavily-"active" substrates. Now, the big "bogeyman" that we all seem to zero in on in our "sum of all fears" scenarios is hydrogen sulfide, which results from bacterial breakdown of organic matter in the total absence of oxygen.

Let's think about this for just a second.

In a botanical bed with materials placed on the substrate, or loosely mixed into the top layers, will it all "pack down" enough to the point where there is a complete lack of oxygen and we develop a significant amount of this reviled compound in our tanks? I think that we're more likely to see some oxygen in this layer of materials, and I can't help but speculate- and yeah, it IS just speculation- that actual de-nitirifcation (nitrate reduction), which lowers nitrates while producing free nitrogen, might actually be able to occur in a "deep botanical" bed.

There is that curious, nagging "thing" I have in my head about the ability of botanical-influenced substrates to foster denitrification. With the diverse assemblage of microorganisms and a continuous food source of decomposing botanicals "in house", I can't help but think that such "living substrates" create a surprisingly diverse and utilitarian biological support system for our aquariums.

And it's certainly possible to have denitrification without dangerous hydrogen sulfide levels. As long as even very small amounts of oxygen and nitrates can penetrate into the substrate, this will not become an issue for most systems. I have yet to see a botanical-style aquarium where the material has become so "compacted" as to appear to have no circulation whatsoever within the botanical layer.

Now, sure, I'm not a scientist, and I base this on close visual inspection of numerous aquariums, and the basic chemical tests I've run on my systems under a variety of circumstances. As one who has made it a point to keep my botanical-method aquariums in operation for very extended time frames, I think this is significant. The "bad" side effects we're talking about should manifest over these longer time frames...and they just haven't.

And then there's the question of nitrate. 

Although not the terror that ammonia and nitrite are known to be, nitrate is much less so. However, as nitrate accumulates, fish will eventually suffer some health issues. Ideally, we strive to keep our nitrate levels no higher than 5-10ppm in our aquariums.  As a reef aquarist, I've always been of the "...keep it as close to zero as possible." mindset (that's evolved in recent years, btw), but that is not always the most realistic or achievable target in a heavily-botanical-laden aquarium. You have a bit more "wiggle room", IMHO. Now, when you start creeping towards 50ppm, you're getting closer towards a number that should alert you. It's not a big "stretch" from 50ppm to 75ppm and higher...

And then you get towards the range where health issues could manifest themselves in your fishes. Now, many fishes will not show any symptoms of nitrate poisoning until the nitrate level reaches 100 ppm or more. However,  studies have shown that long-term exposure to concentrations of nitrate stresses fishes, making them more susceptible to disease, affecting their growth rates, and inhibiting spawning in many species. 

At those really high nitrate levels, fishes will become noticeably lethargic, and may have other health issues that are obvious upon visual inspection, such as open sores or reddish patches on their skin. And then, you'd have those "mysterious deaths" and the sudden death (essentially from shock) of newly-added fishes to the aquarium, because they're not acclimated to the higher nitrate concentrations.

Okay, that's scary stuff. However, high nitrate concentrations are not only manageable- they're something that's completely avoidable in our aquairums.

Quite honestly, even in the most heavily-botanical-laden systems I've played with, I have personally never seen a higher nitrate reading than around 5ppm. I attribute this to  common sense stuff: Good quality source water (RO/DI), careful stocking, feeding, good circulation, not disturbing the substrate, and consistent basic aquarium husbandry practices (water changes, filter maintenance, etc.).

Now, that's just me. I'm no scientist, certainly not a chemist, but I have a basic understanding of maintaining a healthy nitrogen cycle in the aquarium. And I am habitual-perhaps even obsessive- about consistent maintenance. Water exchanges are not a "when I get around to it" thing in my aquarium management "playbook"- they're "baked in" to my practice.

And I think that a healthy, ecologically varied substrate is one of the keys to a successful botanical method aquarium.

I'm really into creating substrates that are a reasonable representation of the bottom of streams, tributaries, and igapo, as found in the Amazon basin. Each one of these has some unique characteristics, and each one presents an interesting creative challenge for the intrepid hobbyist. Until quite recently, the most common materials we had to work with when attempting to replicate these substrates were sand, natural and colored gravels, and clay-comprised planted aquarium substrates.

I reiterate a "manifesto" of sorts that I played out in  "The Tint" back in 2015: 

"If I have something to say about the matter, you'll soon be incorporating a wide variety of other materials into your biotope aquarium substrate!"

Damn, did I just quote myself?

I did!

If you've seen pictures and videos taken underwater in tropical streams (again, I'm pulling heavily from the Amazonian region), you'll note that there is a lot of loose, soil-like material over a harder mud/sand substrate. Obviously, using an entirely soil-based substrate in an aquarium, although technically possible and definitely cool- could result in a yucky mess whenever you disturb the material during routine maintenance and other tasks. You can, however, mix in some of these  materials with the more commonly found sand.

So, exactly what "materials" am I referring to here?

Well, let's look at Nature for a second.

Natural streams, lakes, and rivers typically have substrates comprised of materials of multiple "grades", including fine, medium, and coarse materials, such as pebbles, gravels, silty clays and sands. In the aquarium, we seem to have embraced the idea of a homogenous particle size for our substrates for many years. Now, don't get me wrong- it's aesthetically just fine, and works great. However, it's not always the most interesting to look at, nor is it necessarily the most biologically diverse are of the aquarium.

A lot of natural stream bottoms are complimented with aggregations of other materials like leaf litter, branches, roots, and other decomposing plant matter, creating a dynamic, loose-appearing substrate, with lots of potential for biological benefits. Of course, we need to understand the implications of creating such "dynamic" substrates in our closed aquariums.

When we started Tannin, my fascination with the varied substrate materials of tropical ecosystems got me thinking about ways to more accurately replicate those found in flooded forests, streams, and diverse habitats like peat swamps, estuaries, creeks, even puddles- and others which tend to be influenced as much by the surrounding flora (mainly forests and jungles) as it is by geology.

And of course, my obsession with botanical materials to influence and accent the aquarium habitat caused me to look at the use of certain materials for what I generically call "substrate enrichment" - adding materials reminiscent of those found in the wild to augment the more "traditional" sands and other substrates used in aquariums to foster biodiversity and nutrient processing functions.

Again, look to Nature...

If you've seen pictures and videos taken underwater in tropical streams (again, I'm pulling heavily from the Amazonian region), you'll note that there is a lot of loose, soil-like material over a harder mud/sand substrate. Obviously, using an entirely mud-based substrate in an aquarium, although technically possible- will result in a yucky mess whenever you disturb the material during routine maintenance and other tasks. You can, however, mix in some other materials with the more commonly found sand.

That was the whole thinking behind "Substrato Fino" and "Fundo Tropical", two of our most popular substrate "enrichment" materials. They are perfect for helping to more realistically replicate both the look and function of the substrates found in some of these natural habitats. They provide surface area for fungal and microbial growth, and interstitial spaces for smalll crustaceans and other organisms to forage upon.

Substrates aren't just "the bottom of the tank..."

Rather, 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 were so fascinated by flourish. And, if you look at them objectively and carefully, they are beautiful.

I encourage you to study the natural environment, particularly niche habitats or areas of the streams, rivers, and lakes- and draw inspiration from the functionality of these zones. The aesthetic component will come together virtually by itself. And accepting the varied, diverse, not-quite-so-pritinh look of the "real thing" will give you a greater appreciation for the wonders of nature, and unlock new creative possibilities.

In regards to the substrate materials themselves, I'm fascinated by the different types of soils or substrate materials which occur in blackwater systems and their clearwater counterparts, and how they influence the aquatic environment.

For example, as we've discussed numerous times over the years, "blackwater" is not cased by leaves and such- it's created via geological processes.

In general, blackwaters originate from sandy soils. High concentrations of humic acids in the water are thought to occur in drainages with what scientists call "podzol" sandy soils. "Podzol" is a soil classification which describes  an infertile acidic soil having an "ashlike" subsurface layer from which minerals have been leached.

That last part is interesting, and helps explain in part the absence of minerals in blackwater. And more than one hobbyist I know has played with the concept of "dirted" planted tanks, using terrestrial soils...hmmm.

Also interesting to note is that fact that soluble humic acids are adsorbed by clay minerals in what are known as"oxisol" soils, resulting in clear waters."Oxisol" soils are often classified as "laterite" soils, which some who grow plants are familiar with, known for their richness in iron and aluminum oxides. I'm no chemist, or even a planted tank geek..but aren't those important elements for aquatic plants? 



Let's state it one more time:

We have the terrestrial environment influencing the aquatic environment, and fishes that live in the aquatic environment influencing the terrestrial environment! T

his is really complicated stuff- and interesting! And the idea that terrestrial environments and materials influence aquatic ones- and vice-versa- is compelling and could be an interesting area to contemplate for us hobbyists! 


When ecologists study the substrate composition of aquatic habitats like those in The Amazon, they tend to break them down into several categories, broad though they may be: Rock, sand, coarse leaf litter, fine leaf litter, and branches, trunks and roots.

Studies indicate that terrestrial inputs from rainforest streams provide numerous benefits for fishes, providing a wide range of substrate materials that supported a wider range of fishes than can be found in non-forested streams. One study concluded that,  "Inputs from forests such as woody debris and leaf litter were found to support a diversity of habitat niches that can provide nursing grounds and refuges against predators (Juen et al. 2016). Substrate size was also larger in forest stream habitats, adding to the complexity and variety of microhabitats that can accommodate a greater and more diverse range of fish species (Zeni et al. 2019)."

But wait- there's more! Rainforests create uniquely diverse aquatic habitats.

"Forests can further diversify and stabilize the types of food available for fish by supplying both allochthonous inputs from leaf litter and increased availability of terrestrial insects that fall directly into the water (Zeni and Casatti). Forest habitats can support a diverse range of trophic guilds including terrestrial insectivores and herbivores (Zeni and Casatti).

Riparian forests deliver leaf litter in streams attracting insects, algae, and biofilm, each of which may be vital for particular fish species (Giam et al., Juen et al. ). In contrast, nonforested streams may lack the allochthonous food inputs that support terrestrial feeding fish species..."

Leaf litter- yet again. 

And then there are soils...terrestrial soils- which, to me, are to me the most interesting possible substrates in wild aquatic habitats.

So, the idea of a rich soil substrate that not only accommodates the needs of the plants, but provides a "media" in which beneficial bacteria can grow and multiply is a huge "plus" for our closed aquatic ecosystems. And the concepts of embracing Nature and her processes work really well with the stuff we are playing with.


As you've seen over the past few years, I've been focusing a lot on my long-running "Urban Igapo" idea and experiments, sharing with you my adventures with rich soils, decomposing leaf litter, tinted water, immersion-tolerant terrestrial plants, and silty, muddy, rich substrates. This is, I think, an analogous or derivative  concept to the "Walstad Method", as it embraces a more holistic approach to fostering an ecosystem; a "functionally aesthetic" aquarium, rather than a pure aesthetic one.

The importance of incorporating rich soils and silted substrates is, I think, an entirely new (and potentially dynamic) direction for blackwater/botanical-style tanks, because it not only embraces the substrate not just as a place to throw seed pods, wood, rocks, and plants- but as the literal foundation of a stable, diverse ecosystem, which facilitates the growth of beneficial organisms which become an important and integral part of the aquarium.

And that has inspired me to spend a lot of time over the past couple of years developing more "biotope-specific" substrates to compliment the type of aquariums we play with.

When we couple this use of non-conventional (for now, anyways...) substrate materials with the idea of "seeding" our aquariums with beneficial organisms (like small crustaceans, worms, etc.) to serve not only as nutrient processing "assistants", but to create a supplementary food source for our fishes, it becomes a very cool field of work.

As creatures like copepods and worms "work" the substrate and aerate and mix it, they serve to stabilize the aquarium and support the overall environment.

Nutrient cycling.

That's a huge takeaway here. I'm sure that's perhaps the biggest point of it all. By allying with the benthic life forms which inhabit it, the substrate can foster decomposition and "processing"of a wide range of materials- to provide nutrition for plants- or in our case- for the microbiome of the overall system. 

There is so much work to do in this area...it's really just beginning in our little niche. And, how funny is it that what seems to be an approach that peaked and fell into a bit of disfavor or perhaps (unintended) "reclassification"- is actually being "resurrected" in some areas of the planted aquarium world ( it never "died" in others...).

And a variation/application of it is gradually starting to work it's way into the natural, botanical-method aquarium approach that we favor.

Substrates are not just "the bottom." 

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.

Stay curious. Stay ob servant. Stay thoughtful. Stay bold...

And Stay Wet.


Scott Fellman

Tannin Aquaitcs 

Scott Fellman
Scott Fellman


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