What's the alternative?

Back in 2015, we talked about the idea of "substrate enrichment" in botanical-style aquariums. In other words, adding botanical materials to the more traditional substrates of sand, etc. Now, at first glance, this idea seems rather "normal" in many respects. I mean, planted aquarium enthusiasts have been adding various supplements to their substrates for decades, with the intention of providing beneficial trace elements and nutrients for plants.

However, we're talking about enriching the substrate for the purpose of providing tannins, humic substances, and nutrition- for the cultivation and growth of microbial and crustacean life forms that could reside in the substrate. Not primarily for aquatic plants.

As a means to enhance the ecology of the aquairum.

When you examine the substrates found in many natural habitats, they often appear to be a mixture of a variety of materials, including sands, sediments, muds, clays, and botanical materials. These materials not only look different- they function in unique ways, not only influencing the water chemistry, but the biology and ecology of the aquatic systems as well.

Now, in Nature, there are numerous factors which contribute to the composition of substrates, including geology, the flow velocities of the body of water, the surrounding topography, the seasonal variations in water level (ie; inundation/dessication cycles), and accumulation of materials from the surrounding terrestrial environment.

Nature utilizes almost everything at her disposal in order to create and maintain aquatic ecosystems. So, why do we as hobbyists, who want to create the most realistic approximations of wild habitats possible, just sort of "mail it in" when it comes to substrate? I mean, just open a bag of aquairum sand or whatever, and call it a day and move on to he more "exciting" parts of our tank?

As I just mentioned, 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). We're not talking about "enrichment" in the same context as say, planted aquarium people, with materials 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 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. There is something oddly compelling to me when I look at both aquariums and natural biotopes with a diverse, interesting bottom structure.

I'm fascinated by alternative substrates in our aquariums.  Not just for plants, mind you, but for creating more realistic representations of what we find in nature...We've talked a lot about the composition of substrates within the waters of the natural habitats we love so much.

There are virtually unlimited options for alternative substrate materials. Particularly, stuff like twigs, leaves, and the like. I was looking at one of my tanks the other day and it hit me how happy the fishes seemed, poking and grazing through the bed of broken twigs and leaves that makes up the majority of the substrate in the tank.

To me, beyond the simple aesthetics. Yeah, a tank 'scape in this manner (we jokingly call it a "no-scape") has a different look. And a function which is significantly different than what we're used to. And of course, I find the function part equally- if not more- fascinating than the aesthetic part.

It's very much a representation of what we see in Nature. And to our fishes, it's what they're evolved to exist in.

And our fishes take to aquariums set up to recruit life forms like biofilms and fungal growths easily. And guess what, not only do you ultimately learn to love the look (well, geeks like me do!), you begin to notice the incredible stability of an aquarium managed with what I half-jokingly call an "active substrate" (to borrow a term from our vivarium friends...)!

Obviously, the key to the "functional" part of a "substrate-centric" aquarium is...wait for it- the substrate materials that you use!

I like stuff like little twigs and root pieces, mixed with leaves. I think that when laid down loosely on the bottom of the tank (with or without a thin layer of sand), these materials serve as a sort of "matrix" to capture detritus, foster microorganism growth, and facilitate the growth of our BFF's, biofilms and fungal growths!

Yeah, those guys again.

Biofilms form when bacteria adhere to surfaces in some form of watery environment and begin to excrete a slimy, gluelike substance, consisting of sugars and other substances, that can stick to all kinds of materials, such as- well- in our case, botanicals.

Biofilm growth occurs rather quickly, too.

It starts with a few bacteria, taking advantage of the abundant and comfy surface area that leaves, seed pods, and even driftwood offer. The "early adapters" put out the "welcome mat" for other bacteria by providing more diverse adhesion sites, such as a matrix of sugars that holds the biofilm together.

Since some bacteria species are incapable of attaching to a surface on their own, they often anchor themselves to the matrix or directly to their friends who arrived at the party first.

Sorta sounds like a Facebook group, huh?

(The above graphic from a scholarly article illustrates just how these guys roll.)

And we could go on and on all day telling you that this is a completely natural occurrence; bacteria and other microorganisms taking advantage of a perfect substrate upon which to grow and reproduce, just like in the wild. Freshly added botanicals offer a "mother load"of organic material and surface area upon which these biofilms propagate, and that's typically what happens - just like in Nature.  

Yet it does, so we will! :)

The real positive takeaway here: Biofilms are really a sign that things are working right in your aquarium! A visual indicator that natural processes are at work.

Yet, understandably, it may not make some of you feel good. Again, I ask you to make a mental shift to accept them as a perfectly natural occurrence, which is ubiquitous in the natural habitats from where most of our fishes hail.

And then there are the fungi.

Fungi reproduce by releasing tiny spores that then germinate on new and hospitable surfaces (ie, pretty much anywhere they damn well please!). These aquatic fungi are involved in the decay of wood and leafy material. And of course, when you submerge terrestrial materials in water, growths of fungi tend to arise. Anyone who's ever "cured" a piece of wood for your aquarium can attest to this!

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?

And of course, fishes and invertebrates which live amongst and feed directly upon the fungi and decomposing leaves and botanicals contribute to the breakdown of these materials as well! Aquatic fungi can break down the leaf matrix and make the energy available to feeding animals in these habitats. And look at this little gem I found in my research:

"There is evidence that detritivores selectively feed on conditioned leaves, i.e. those previously colonized by fungi (Suberkropp, 1992; Graca, 1993). Fungi can alter the food quality and palatability of leaf detritus, aecting shredder growth rates. Animals that feed on a diet rich in fungi have higher growth rates and fecundity than those fed on poorly colonized leaves. Some shredders prefer to feed on leaves that are colonized by fungi, whereas others consume fungal mycelium selectively..."

"Conditioned" leaves, in this context, are those which have been previously colonized by fungi! They make the energy within the leaves and botanicals more available to higher organisms like fishes and invertebrates! 

The aquatic fungi which will typically decompose leaf litter and wood are the group known as “aquatic hyphomycetes”. Another group of specialists, "aero-aquatic hyphomycetes," colonize submerged plant detritus in stagnant and slow- flowing waters, like shallow ponds, puddles, and flooded forest areas. Fungal communities differ between various environments, such as streams, shallow lakes and wetlands, deep lakes, and other habitats such as salt lakes and estuaries.

And we see them in our own tanks all the time, don't we? Sure, it's easy to get scared by this stuff...and surprisingly, it's even easier to exploit it as a food source for your animals! We just have to make that mental shift... As the expression goes, "when life gives you lemons, make lemonade!"

 I remember the first few botanical-style tanks I created, almost two decades ago now, would hit that phase early on when biofilms  and fungal growths began to appear on my "botanical substrate", and I'd hear my friends telling me, "Yeah, your tank is going to turn into a big pile of shit. Told you that you can't put that stuff in there."

Because that's what they've been told. The prevailing mindset in the hobby was that the appearance of these organisms was an indication of an unsuitable aquarium environment.

Anyone who's studied basic ecology and biology understands that the complete opposite is true. The appearance of these valuable life forms is an indicator that your aquatic environment is ideal to foster a healthy, diverse community of aquatic organisms, including fishes!

Exactly like in Nature.

I remember telling myself that this is what I knew was going to happen. I knew how biofilms and fungal growths appear on "undefended" surfaces, and that they are essentially harmless life forms, exploiting a favorable environment. I knew that fungi appear as they help break down leaves and botanicals. I knew that these are perfectly natural occurrences, and that they typically are transitory and self-limiting to some extent.

Normal for this type of aquarium approach.

I knew that they would eventually subside, or even largely go away, but I also knew that there would be a period of time when the tank might look like a big pool of slimy shit. Or, rather, it'd look like a pile of slimy shit to those who weren't familiar with these life forms, how they grow, and how the natural aquatic habitats we love so much actually function and appear!

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 leaf litter zones and how productive and unique they were.

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.

Just like in Nature, the habitats we have created are optimal for our fishes. And looking at the wild habitats as models for functional ecology opens up a whole new opportunity for us as aquarists. 

Ecologically, the productivity and diversity of these habitats make them perfect subjects for replication in our aquariums. Not only do they offer unique aesthetics- they offer really cool opportunities to see how they canfunction in a closed system like an aquarium!

When fishes are kept in a representation of a habitat which mimics its form and function, enormous potential for discoveries and success present themselves! Materials like twigs, roots, and seed pods incorporated into the substrate in our aquariums creates a remarkably faithful recreation of the ecology and appearance of these natural habitats. 

It all starts with looking at some of the features of natural aquatic habitats.

Look at the way rocks, soil and branches come together in flooded forests to form interesting physical spaces that fishes utilize for protection, foraging, and reproduction. By happenstance, these formerly terrestrial features become important and unique underwater microhabitats that fishes can exploit for food, protection, and spawning sites.

By replicating the complex look and physical attributes of these features, including rich substrate, roots of various thickness, and leaves, we offer our fishes all sorts of potential microhabitats. In the aquarium, we tend to focus on the "macro" level- creating a nice wood stack, perhaps incorporating some rock- but we seldom see the whole picture allowed to come together in a more natural way.

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 and creating the ecology of the aquairum. A healthy and diverse assemblage of organisms dwelling in this layer, ranging from bacteria to fungi to 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.

Be kind to your substrate, and it will be most kind to you.

Trust me on that. 

There's a lot more to the bottom than a pile of clean white sand...that's for sure! Think about the ecology of your tank...and think about the alternatives to "plain old sand."

Stay creative. Stay bold. Stay curious. Stay patient. Stay focused...

And Stay Wet.


Scott Fellman

Tannin Aquatics 


Scott Fellman
Scott Fellman


2 Responses

Scott Fellman
Scott Fellman

September 23, 2021

Hi Brandon,

Super cool idea, Sphagnum moss! Worth an experiment, right? Glad you enjoyed the articles…keep experimenting!



September 23, 2021

Great article, I’ve always thought of botanicals as a top dresser for substrate although I have often thought about a Sphagnum moss substrate.

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