Why should biofilms have all the fun? Bring on the fungi!

With the botanical aquariums that we play with, there is a very distinct set of occurrences and expectations that we're now quite aware of. And even with these expectations, we still find ourselves having to make mental shifts to adjust to them.

As your botanical aquarium breaks in, you almost always encounter our friend (or nemesis, depending upon how you look at it), biofilm. Now, we've discussed the ins and outs of biofilms in our botanical-style aquariums, and how they arise and propagate in our tanks many, many times in this blog.

To many, the biofilms are a source of consternation, frustration, and out-and-out horror. They look kind of- well, yucky to many. Although by no means harmful, they're simply not everyone's idea of high-quality aesthetics. Of course, biofilms have one extraordinary characteristic that makes them even more important for some in our community: They're a rich and important food source for many fishes and invertebrates.

This is one of the most interesting aspects of a botanical-style aquarium: We have the opportunity to create an aquatic microcosm which provides not only unique aesthetics- it provides self-generating nutritional value on a more-or-less continuous basis.

True "functional aesthetics", indeed!

I feel a great affinity for my friends who keep dwarf shrimp, like CaridinaHalocaridina, etc. These hobbyists understand and appreciate the value of botanicals and the biofilms which colonize them as a food source, and put forth a lot of effort to propagate them in their aquariums.

Some fishes, such as gobies of the genus Stiphodon (Sicydiines) are near-exclusive consumers of biofilms in the wild. Most reside in relatively fast-flowing, well-oxygenated streams which are filled with scattered jumbles of boulders and rocks, filled in with leaf litter. The boulders and rocks are covered in biofilms of various densities and composition.

Granted, the bulk of the biofilms in these habitats is on rocks, but the leaf litter which accumulates in pockets in the habitat is also a substrate upon which they propagate. And in many aquatic habitats, submerged branches and logs and such also recruit these biofilms. 

And biofilms are interesting, in and of themselves. Understanding the reasons they arise and how they propagate can really help us to appreciate them!

We've discussed this before; however, let's revisit the process one more time:

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.


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 for these biofilms to propagate, and that's occasionally what happens - just like in nature.

Of course, we can tell you that a thousand times, and many of you will still be of the opinion that the stuff looks like shit...

And biofilms seem to go hand-in-hand with fungi.

Yeah, those guys.

Not the ones that we vilify for attacking our fish or their eggs, of course. It's easy to just heap them in with the "bad guys" and the nasty implications they have. 


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 aquatic 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! 

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! This is a HUGE point that we can't emphasize enough.

We just have to make that mental shift... As the expression goes, "when life gives you lemons, make lemonade!"

Fungi, although not the most attractive-looking organisms, are incredibly useful...and they "play well" with a surprisingly large number of aquatic life forms to create substantial food webs.

Natural habitats are absolutely filled with this stuff...it's like the whole game here- an explosion of life-giving materials, free for the taking...

Another "mental shift", I suppose...one which many of you have already made, no doubt. I certainly look forward to seeing many examples of us utilizing "what we've got" to the advantage of our fishes! AGAIN: A truly "Natural" aquarium is not sterile. It encourages the accumulation of organic materials and other nutrients- not in excess, of course.

Biofilms, fungi, algae...detritus...all have their place in the aquarium. Not as an excuse for lousy or lazy husbandry- no- but as supplemental food sources to "power" the life in our tanks.

Real gifts from Nature...that you can benefit from simply by "enabling the web" of life which arises without our intervention as soon as leaves, wood, and water mix. Rather than siphoning the stuff out or scraping it off of the seed pods, I think it's so important to actually leave them be- to let them fulfill the role that they are best at.


Stay the course. Don't be afraid. Open your mind. Study what is happening. Draw parallels to the natural aquatic ecosystems of the world. Look at this "evolution" process with wonder, awe, and courage. And know that the pile of decomposing goo that you're looking at now is just a metaphorical "stepping stone" on the journey to an aquarium which embrace Nature in every conceivable way.

Maybe, as the years go by, we as a hobby will overcome generations of fear over stuff like detritus and fungi and biofilms- the life-forms which power the aquatic ecosystems we strive to duplicate in our aquariums. Maybe, rather than attempting to "erase" these things, which go against our "Instagram-influenced aesthetics" of how we think that Nature SHOULD look, we might want to meet Nature where she is and work with her. 

And we just might see the real beauty- and benefits- of unedited Nature.

And of course, the literal "basis" for all of this stuff is the botanical materials themselves, breaking down in our tanks, as they've done in nature for eons.

We've already started to make a "mental shift" which accepts the transient, subtle beauty of decomposing botanical materials, tinted water, biofilms, fungi, and the like. It goes without saying that taking it a little further and allowing these materials to completely break down to serve as the biological "substrate" for our aquatic ecodiversity is simply the next "iteration" in the management of blackwater/brackish botanical-style aquariums.

These small, seemingly "annoying" life forms are actually the most beautiful, elegant, beneficial friends that we can have in the aquarium...

Stay calm. Stay curious. Stay bold. Stay resourceful...

And Stay Wet.


Scott Fellman

Tannin Aquatics 

Scott Fellman
Scott Fellman


3 Responses

Scott Fellman
Scott Fellman

November 15, 2019

Matt, we LOVE the idea of Archaea being in our tanks…In fact, we wrote about our hopes for them in this blog:


Joshua Morgan
Joshua Morgan

November 15, 2019

How intriguing! My blackwater 5 gallon is already developing a substantial biofilm now, less than 3 weeks in. Hopefully the future fishy residents (Coccina complex Bettas?) will find it a useful food source.

Matt Chambers
Matt Chambers

November 15, 2019

You don’t like archaea?

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