For the love of weird substrates...

One of the "cornerstones" of our botanical-method aquarium practice is the use of substrate. Specifically, substrate materials which can influence- or make it easier to influence- water chemistry in the aquarium, as well as to help foster a "microbiome" of small organisms which will provide ecological diversity for the system.

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.


A real pity, especially for those of us who are interested in botanical-method aquariums, which replicate natural aquatic habitats where soils and geology play a HUGE role in influencing the environmental parameters of these ecosystems. And in the hobby, we've largely overlooked the benefits and possibilities which specialized substrates can offer.

So I started to experiment with materials to recreate some of the characteristics of wild aquatic habitats which fascinated me. And an obsession was born.

I started playing with substrates mainly because I couldn't find exactly what I was looking for on the market. This is not some indictment of the major substrate manufacturers out there...I LOVE almost all of them and use and happily recommend ones that I like. I'm obsessed with substrates. I think that the companies which produce them are among the coolest of the cool aquatics industry brands. If I wasn't doing this botanical thing with Tannin, I'd probably have started a company that specializes in substrates for aquariums. Seriously.

And the fact is, the major manufacturers need to market products that more than like 8 people are interested in. It's unreasonable to think that they'd devote precious resources to creating a product that would be geared to such a tiny target. 

And of course, being one of those 8 people who are geeked-out about weird substrates, I decided that I'd "scratch my own itch" (as we did with the botanical thing..) and formulate and create some of my own. Thus, the NatureBase product line was born!

I realized that the specialized world which we operate in embraces some different ideas, unusual aesthetics, and is fascinated by the function of the environments we strive to replicate. These are important distinctions between what we are doing with substrates at Tannin, and what the rest of the aquarium hobby is doing.

Our NatureBase line is not intended to supersede or completely replace the more commonly available products out there as your "standard" aquarium substrate, because: a) they're more expensive, b) they're not specifically "aesthetic enhancements", c) they are not intended to be planted aquarium substrates, and d) because of their composition, they'll add some turbidity and tint to the aquarium water, at least initially (not everyone could handle THAT!)

So, right there, those factors have significantly segmented our target market...I mean, we're not trying to be the aquarium world's "standard substrate", they weren't formatted to grow aquatic plants, we're not marketing them just for the cool looks, and we can't emphasize enough that they will make your water a bit turbid when first submerged. If you have fishes which dig, or which like to "work" the substrate, you may see a near-continuous turbidity in your aquarium!

Oh, joy.

Those factors alone will take us out of contention for large segments of the market!

This is important to grasp.

I mean, these substrates are intended to be used in more natural, botanical-style/biotope-inspired aquariums. Our first two releases, "Igapo" and "Varzea", are specific to the creation of a type of "cyclical" terrestrial/aquatic feature. They do exactly what I wanted them to do, and they were specifically intended for use in specialized set ups, like the "Urban Igapo" idea we've been talking about for a long time here, as well as brackish water mangrove environments, etc.

Let's touch on the "aesthetic" part for a minute.

Most of our NatureBase substrates have a significant percentage of clays and sediments in their formulations. These materials have typically been something that aquarists have avoided, because they will cloud the water for a while, and often impart a bit of color. We also have some botanical components in a few of our substrates, because they are intended to be "terrestrial" substrates for a while before being flooded...and when this stuff is first wetted, some of it will float.

And that means that you're going to have to net it out, or let your filter take it out. You simply won't have that "issue" with your typical bag of aquarium sand!

Shit, you're probably just frothing right now, waiting to cloud and dirty up your aquariums with this stuff, huh?


I can't for the life of me figure out why not? ;)

Remember, some of these substrates were formulated for a very specific purpose: To replicate the terrestrial soils which are seasonally inundated in the wild. As such, these products simply won't look or act like your typical aquarium substrate materials!

Scared off completely yet? I hope not.

Why include sediments and clays in our mixes? 

Well, for one thing, sediments are an integral part of the natural substrates in the habitats from which our fishes come. So, they're integral to our line. In fact, I suppose you'd best classify NatureBase products as "sedimented substrates."

Think about this: Many of our favorite habitats are forest floors and meadows which undergo periodic flooding cycles in the Amazon, which results in the creation of aquatic habitats for a remarkable diversity of fish species.

Depending on the type of water that flows from the surrounding rivers, the characteristics of the flooded areas may vary. Another important impact is the geology of the substrates over which the rivers and streams pass. This results in differences in the physical-chemical properties of the water.

In the Amazon, areas flooded by rivers of black or clear waters, with acid pH and low sediment load, in addition to being nutritionally poor, are called “igapó."

The flooding often lasts for several weeks or even several months, and the plants and trees need special biochemical adaptations to be able to survive the lack of oxygen around their roots. We've talked about this a lot here over the years.


Forest floor soils in tropical areas are known by soil geologists as "oxisols", and have varying amounts of clay, sediments, minerals like quartz and silica, and various types of organic matter. So it makes sense that when flooded, these "ingredients" will have significant impact on the aquatic environment. This "recipe" is not only compositionally different than typical "off-the-shelf" aquarium sands and substrates- it looks and functions differently, too.


You CAN wet them right away; you don't have to do a "wet/dry season" igapo-style tank with them.  However, you should be ready for some cloudy water for a week or more! And again, if you have fishes which like to "work" the substrate, it will be a near-constant thing, the degree to which it will be is based on the habits of the fishes you keep.


And that's where a lot of people will metaphorically "leave the room."Turbid, darker water is a guaranteed "freak out" for a super-high  high percentage of aquarists. 

So, yeah, you'll have to make a mental shift to appreciate a different look and function.

And many hobbyists simply can't handle that. I've been extremely up front with this stuff since the introduction of these substrates, to ward off the, "I added NatureBase to my tank and it looks like a cloudy mess! This stuff is SHIT!" type of emails that inevitably come when people don't read up first before they purchase the stuff. (And trust me- the fact that you're even reading this blog, or listening to this podcast puts you in the tiniest minority of aquarium hobbyists!)

Let's talk a bit about how to "live" with these substrates. 

There are a lot of different ways to use these substrates in all sorts of tanks. I mean, if you want some of the benefits and want to geek out and experiment with them, you can use a "sand cap" of whatever conventional substrate you prefer on top, and likely limit the turbidity somewhat, much like the practice of aquarists who employ "dirted" substrates do.

Oh, and the plant thing...

We're asked a LOT if these substrates can grow aquatic plants. Now, although they were intended to facilitate the growth of terrestrial plants, like grasses, the fact is, both our customers and ourselves have seen pretty damn good plant growth in tanks using this stuff!

Our Igapo and Varzea substrates mimic sandy acidic soils that have a low nutrient content. And, as you know, the color and acidity of the floodwater is due to the acidic organic humic substances (tannins) that dissolve into it. The acidity from the water translates into acidic soils, which makes sense, right?

Now, I admit, I am NOT a geologist, and I'm not expert in soil science. I know enough to realize that, in order to replicate the types of habitats I am fascinated with, it required different materials. If you ask me, "Will this fish do well with this materials?" or, "Can I grow "Cryptocoryne in this?", or "Does this make a good substrate for shrimp tanks?" I likely won't have a perfect answer. Sorry.

Periodically, plant enthusiasts will ask me about the "cation exchange capacity" of our substrate. Cation Exchange Capacity (CEC) is the ability of a material to absorb positively-charged nutrient ions. This means the substrate will hold nutrients and make them available for the plant roots, and therefore, plant growth. CEC measures the amount of nutrients, more specifically, positivity changed ions, which a substrate can hold onto/store for future use by aquatic plants.

Thus, a "high CEC" is important to many aquatic plant enthusiasts in their work.  While it means that the substrate will hold nutrients and make them available for the plant roots. it doesn't indicate the amount of nutrients the substrate contains. 

For reference, scientists measure cation exchange capacity (CEC) in milliequivalents per 100 grams ( meq/100g).

To really get "down and dirty" to analyze substrates scientifically, CEC determinations are often done by a process called "Method 9081A of EPA SW- 846." What the....? CEC extractions are often also analyzed on ICP-OES systems. A rather difficult and pretty expensive process, with equipment and methods that are not something casual hobbyists can easily replicate!

As you might suspect, CEC varies widely among different materials. Sand, for instance, has a CEC less than 1 meq/100 g. Clays tend to be over 30 meq/100 g. Stuff like natural zeolites are around 100 meq/100g! Soils and humus may have CEC up to 250 meq/100g- that's pretty serious!

What nutrients are we talking about here? The most common ones which come into play in the context of CEC are iron, potassium, calcium and magnesium. So, if you're into aquatic plants, high CEC is a good thing!

Of course, this is where the questions arise around the substrates we play with.

It makes sense, right?

Our "Nature Base" substrates do contain materials such as clays and silts, which could arguably be considered "higher CEC" materials, because they're really fine- and because higher surface area generally results in a higher CEC. The more surface area there is, the more potential bonding sites there are for the exchange to take place. Alas, nothing is ever exactly what we hope it should be in this hobby, and clays are often not all that high in their CEC "ratings."

Now, the "Nature Base" substrates are what we like to call “sedimented substrates”, because they are not just sand, or pellets of fired clays, etc. They are a mix of materials, and DO also have some terrestrial soils in the mix, too, which are also likely higher in CEC. And no, we haven't done CEC testing with our substrates...It's likely that in the future, some enthusiastic and curious scientist/hobbyist might just do that, of course!

Promising, from a CEC standpoint, I suppose!

However, again, I must emphasize that they were really created to replicate the substrate materials found in the igapo and varzea habitats of South America, and the overall habitat- more "holistically conceived"-not specifically for plant growth. And, in terrestrial environments like the seasonally-inundated igapo and varzea, nutrients are often lost to volatilization, leaching, erosion, and runoff..

So, it's important for me to make it clear again that these substrates are more representative of a terrestrial soil. Interestingly, the decomposition of detritus and leaves and such in our botanical-method aquariums and "Urban Igapo" displays is likely an even larger source of “stored” nutrients than the CEC of the substrate itself, IMHO. Thus, they will provide a home for beneficial bacteria- breaking down organics and helping to make them more available for plant growth. 

Perhaps that's why aquatic plants grow so well in botanical-method aquariums?

Yeah, the stuff DOES grow aquatic and riparian plants and grasses quite well, in our experience! Yet, again- I would not refer to them specifically as "aquatic plant substrates." They're not being released to challenge or replace the well-established aquatic plant soils out there. They're not even intended to be compared to them!

Remember, our "Igapo" and "Varzea" substrates are intended to start out life as "terrestrial" materials, gradually being inundated as we bring on the "wet season." And because of the clay and sediment content of these substrates, you'll see some turbidity or cloudiness in the water. It won't immediately be crystal-clear- just like in Nature. That won't excite a typically planted aquarium lover, for sure. 

I can't stress it often enough: With our emphasis on the "wholistic" application of our substrate, our focus is on the "big picture" of these closed aquatic ecosystems.

I'll be the first to tell you that, while I have experimented with many species of plants, inverts, and fishes with these substrates, I can't tell you that every single fish or plant will like them. You'll simply have to experiment!

Well, shit- that's not something that you typically hear an aquarium hobby brand tell you to do with their products every day, huh? Like, I'm not going to make all sorts of generalized statements about everything I think that these products can do. It would be very unhelpful. I'd rather focus on how they perform in the types of systems in which they were intended to work in, and what the possible downsides could be!

The whole point here is that these substrates are perfect for a whole range of applications. They're not "the greatest substrates ever made!" or anything like that. However, they are super useful for replicating the soils of some of our favorite aquatic habitats. 

And for doing some of those geeky experiments that we love so much. So, that pretty much covers the "sedimented" substrate thing for now. Let's talk about "alternative" substrates for a bit...


In my experience, and in the reported experiences from hundreds of aquarists who play with botanical materials breaking down in and on their aquariums' substrates, undetectable nitrate and phosphate levels are typical for this kind of system. When combined with good overall husbandry, it makes for incredibly stable systems.

I've been thinking through further refinements of the "deep botanical bed"/sand substrate relationship. I've been spending a lot of time researching natural aquatic systems and contemplating how we can translate some of this stuff into our closed system aquaria.

Now, 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 possible 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 just don't think so. 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.

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 personally have yet to see a botanical-method 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 the management of, and close visual inspection of numerous aquariums, as well as 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 accumulation is something a lot of hobbyists are concerned with. 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 was always of the "...keep it as close to zero as possible." mindset, until I realized that corals just grow better with the presence of some nitrate! This was especially evident in my large scale coral grow-out raceways.

It seems that 'zero" nitrate is not always the most realistic or achievable target in a heavily-botanical-laden aquarium, although I routinely see undetectable nitrate reading in my tanks. You have a bit more "wiggle room", IMHO, however, before concern over fish health is a factor. 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 more potentially detrimental readings of 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 moderate 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. Often, as I mentioned above, they're undetectibIe on hobby-level test kits. 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 exchanges, 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.

So yeah, although nitrate is something to be aware of in botanical-method aquariums, it's simply not an ominous cloud hanging over our success.

Relatively shallow sand or substrate beds seem to be optimal for denitrification, and many of us employ them for the aesthetics as well. Light "stirring" of the top layers, if you're concerned about any potential "dead spots" is something that is permissible, IMHO. Any debris stirred up can easily be removed mechanically by filtration, as mentioned above.

But that's it.


Of course, as we already discussed, you don't have to go crazy siphoning the shit (literally!) out of your sand every week, essentially decimating populations of beneficial microscopic infauna -or interfering with their function- in the process.

What I am starting to feel more and more confident about is postulating that some form of denitrification occurs in a system with a layer of leaves and botanicals as a major component of the tank.

Now, I know, I have little rigorous scientific information to back up my theory, other than anecdotal observations and even some assumptions. However, there is always an example to look at- Nature. 

Of course, Nature and aquariums differ, one being a closed system and the other being "open." However, they both are beholden to the same laws, aren't they? And I believe that the function of the captive leaf litter bed and the wild litter beds are remarkably similar to a great extent.

The thing that fascinates me is that, in Nature, leaf litter beds perform a similar function; that is, fostering biodiversity, nutrient export, and yes- denitrification. Let's take a little look at a some information I gleaned from the study of a natural leaf litter bed for some insights.

In a slow-flowing wild Amazonian stream with a very deep leaf litter bed, observations were made which are of some interest to us. First off, oxygen saturation was 6.7 3 mg/L (about 85% of saturation), conductivity was 13.8 microsemions, and pH was 3.5.

Some of these parameters (specifically the very low pH) are likely difficult to obtain and maintain in the aquarium, but the interesting thing is that these parameters were stable throughout a months-long investigation.

Oxygen saturation was surpassingly low, given the fact that there was some water movement and turbulence when the study was conducted. The researchers postulated that the reduction in oxygen saturation presumably reflects respiratory consumption by the organisms residing in the litter, as well as low photosynthetic generation (which makes sense, because there is no real algae or plant growth in the litter beds).

And of course, such numbers are consistent with the presence of a lot of life in the litter beds.




Microscopic investigation confirmed that the leaf litter was heavily populated with fungi and other microfauna. There was also a significant amount of fish life. Interestingly, the fish population was largely found in the top 12"/30cm of the litter bed, which was estimated to be about 18"/45cm deep. The food web in this type of habitat is comprised largely of fungal and bacterial growth which occurs in the decomposing leaf litter. 

Okay, I"m throwing a lot of information here, and doing what I hope is a slightly better-than-mediocre attempt at tying it all together. The principal assertions I'm making are that, in the wild, the leaf litter bed is a very productive place, and has a significant impact on its surroundings, and that it's increasingly obvious to me that many of the same functions occur in an aquarium utilizing leaf litter and botanicals.

"Enriching" a substrate with botanicals, or composing an entire substrate of botanicals and leaves is a very interesting and compelling subject for investigation by hobbyists.

So, three areas of potential investigation for us:

*Use of botanicals and leaves to comprise a "bed" for bacterial growth and denitrification.

*Understanding the chemical/physical impact of the botanical "bed" on an aquarium. (ie, pH, conductivity, etc.)

*Utilization of a botanical bed to create a supplemental food source for the resident fishes.

We've also touched on the idea of a leaf litter/botanical bed as "nursery" for fry, something more and more hobbyists/breeders are confirming is a logical "go-to" thing for them. 

Interesting semi-anecdotal observations from my friends in the know suggest that the biofilms for decaying leaves form a valuable secondary food for the fry of fishes such as Discus, Uaru, (after they’re done feeding on their parent’s exuded slime coat) and even Loricariid catfishes. And I've seen juvenile fishes  of a variety of species "appear" from my botanical-rich aquariums over the years, fat and happy, apparently deriving some nutrition from the fungi, bacteria, and small crustaceans which live in, on, and among the leaf litter bed.

My own experience with creating leaf-litter-bed-focused aquariums has proven that supplemental food production for the resident fishes is a real "thing" that we need to consider. It's a valid and very exciting approach to creating a functional closed aquatic ecosystem.


We talk about the concept of "substrate enhancement" or "enrichment" a lot in the context of aquatic botanicals (we tend to use the two terms interchangeably).

Again, we're not talking about "enrichment" in the same context as say, planted aquarium guys, with materials put into the substrate specifically for the benefit of plants. However, the addition of botanical and other materials CAN create a sort of organic "mulch" which benefits many aquatic 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 haven for microbial life, as well as for small crustaceans, biofilms, and even algae, to serve as a foraging area for our fishes and invertebrates.

We've found over the years of playing with botanical materials that substrates can be really dynamic places, and benefit from the addition of leaves and other materials. For many years, substrates in aquarium were really just sands and gravels. With the popularity of planted aquariums, new materials, like soils and mineral additives, entered into the fray.

With the botanical-method aquarium starting to gain in popularity, now you're seeing all sorts of materials added on and in the substrate...for different reasons of course.

I think the big takeaway is that we should not be afraid to experiment with the idea of mixing various botanical materials into our substrates, particularly if we continue to embrace solid aquarium husbandry practices.

In my opinion, richer, botanically-enhanced substrate provides greater biological diversity and stability for the closed system aquarium. 

Is it for everyone?

Not for those not willing to experiment and be diligent about monitoring and maintaining water quality. Not for those who are superficially interested, or just in it for the unique aesthetics it affords. 

However, for those of you who are adventurous, experimental, diligent, and otherwise engaged with managing and observing your aquariums, I think it offers amazing possibilities. Not only will you gain some fascinating insights and the benefits of "on-board" nutrient export/environmental "enrichment"- you will also get the aesthetics of a more natural-looking substrate as well.

Like so many things we do in our niche, the "weird" alternative and botanical-enriched substrate approaches are fascinating, dynamic, and potentially ground-breaking for the aquarium hobby. For the adventurous, diligent, and observant aquarist, they present numerous opportunities to learn, explore, and create amazing, function-first aquatic ecosystems.

Who's in?

Stay creative. Stay observant. Stay diligent. Stay thoughtful...

And Stay Wet.


Scott Fellman

Tannin Aquatics 


Scott Fellman
Scott Fellman


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