Biofilms: Learning to love the "gooey stuff..."


As more and more of us start really getting into the idea of botanical-style, blackwater aquariums, we start hearing more and more of the same questions. This is really cool, because it's an obvious sign that we're seeing more and more hobbyists enter the game. What's really interesting to me as that many of the "newcomers" are no longer put off by the dark water, decomposing botanicals, and biofilms.

Well, many of the newcomers, at least. 

I do recall at least two comments by visitors to my office aquarium lately that made me laugh: "Your tank would be so bad-ass if it didn't have that rotting stuff on the bottom!" and "Damn, if your water wasn't all dirty-looking, this tank would be amazing? Is your filter broken?"

(Palm-to forehead moment..)

You've no doubt heard similar comments before?

Remember, for must of us, the aesthetics of the botanical-style blackwater aquarium are radically different than anything others probably intentionally tried to cultivate before, aquarium-wise. We all know that the blackwater, decaying leaves, and degrading botanicals is also the reason why the work so well, look so cool, and function so naturally.

It's all part of that mental shift we've talked about so many times before. And what's the main thing newcomers ask about, besides the blackwater itself?

Biofilm. You know, that "goo" on the botanicals that shows up soon after they're placed in the tank. 


Even the word conjures up an image of something that you really don't want in your tank. Something dirty, yucky...potentially detrimental to your aquarium's health. 

And, let's be honest with ourselves here. The damn dictionary definition is not gonna win over many "haters":

bi·o·film -ˈbīōˌfilm/ noun -a thin, slimy film of bacteria that adheres to a surface.
Some charming and commonly-encountered examples of biofilm include plaque that forms on teeth, and the slime that forms on surfaces in water.
Shit. Really?
Yeah, I guess that's the definition we have to run with.

Well, apart from the unpleasant-sounding description of the stuff, the concept of biofilms and how they form is actually kind of interesting. Not "charming." I didn't say that. But interesting for sure.

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.

Biofilms on decomposing leaves are pretty much the foundation for the food webs in rivers and streams throughout the world. They are of fundamental importance to aquatic life.

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

Yet it does, so we will! :)

Is there a "darkside" to biofilms? Of course. 

Like anything else, too much of a "good thing" can cause problems in rare instances. Frightening, "aquarium armageddon scenarios" could play out. For example, in an extremely overcrowded aquarium (or a very small one) with marginal husbandry and filtration, with a huge amount of biofilm (relative to tank volume) caused by an equally huge influx of freshly-added botanicals, there is always the possibility excessive respiration by biofilm bacteria could lower the water’s dissolved oxygen and increase CO2, asphyxiating your animals and the important aerobic nitrifying bacteria.

Now, that's a true "doomsday scenario"- brought about by: 1)a non-sustainably-managed/populated aquarium, 2)improper preparation and 3) rapid, excessive additions of botanicals, and 4) complete lack of common sense on the part of the aquarist, in terms of husbandry.

So yeah. There IS a darkside to biofilms. If you create circumstances to foster one.

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.

First off, take comfort in the fact that the biggest "blooms" of them occur early on, and that this is typically sort of a passing phase, and can take anywhere from a few days to 2-3 weeks or more before it subsides on it's own to some level that you can live with. Realize that biofilms are present in every aquirium, to some degree. Yeah, even your "Nature Aquarium", guys. Welcome to Planet Earth. It's a gooey place. 

We get it, though- some of you just don't want this stuff, despite its "charms."

Okay, well, when you've got a lot of this material in your aquarium, and it's causing you considerable worry, stress, and just plain giving you a case of the shivers, there are some actions you can take ( besides cursing the whole idea of throwing aquatic botanicals in your system in the first place).

What to do? Here are a few time-tested options:

  • You can wait it out. That's right. Do nothing, except appreciate the wonders of nature, no matter how unsightly they may be at times. I mean, didn't nature make the "Death Flower" and the "Slime Mold?" Seriously. Yeah. And this is nicer to experience than "terrestrial" biofilms, like, oh, let's say... plaque!


  • You can remove the offending botanicals, give them a good scrub with a soft bristle brush (like an old toothbrush), a rinse in fresh water, and put 'em back in.


  • You can remove the botanicals, give them a good scrub, and re-boil/soak them again. Although a bit redundant, and in our opinion, not necessary, this procedure does have the advantage of removing some of the trapped organics that lead to the initial "outbreak", but you may see it happen again.


  • You can leave the botanicals in place, and employ some natural "control", in the form of ornamental shrimp. Yeah, that's right- your "Crystal Red Shrimp", "Bee Shrimp", and the rest of those tiny, overpriced, yet engaging little crustaceans  absolutely adore biofilms, and will attack it voraciously. Alternatively, we've learned that some fishes, like Plecos, some Corydoras cats, Otocinculus, and even Leporinus and other "Headstanders" seem to pick at this stuff fairly aggressively. In fact, I've seen Pencilfishes and other small characins pick at it.


Again, the reality here is that in an otherwise well-managed, sustainably-populated aquarium, at best the largest blooms of the stuff will be a temporary nuisance, subsiding to a tolerable level, or even being almost unseen, for as long as you have the aquarium in operation.

Remember, it's all part of the game with a blackwater, botanical-influenced aquarium. A part of that "mental shift" towards accepting and appreciating a more truly natural-looking, natural-functioning aquarium. The "cost of admission", if you will- along with the tinted water, decomposing leaves, etc., the dues you pay, which ultimately go hand-in-hand with the envious "ohhs and ahhs" of other hobbyists who admire your completed aquarium when they see it for the first time.

Now, there are a lot of you who have come to admire, and even love the whole idea of biofilm. Like, those of you who love the aforementioned ornamental shrimp. You understand the value of having a periodic "crop" of this stuff available for your shrimp to "graze" upon. You actually are wanting to foster it. 

So, what are the botanicals which seem to give you the best shot at purposely "recruiting" the stuff? Well, pretty much all of them- in fact, almost anything you put underwater- will recruit some biofilms at some point. However, in our experience, there are a few which seem to "recruit" more biofilms initially than others. They are:

"Teardrop Pods"- which also tend to soften more quickly on their interior than many other botanicals, rendering them more attractive to biofilms in the early phases of their "run" in an aquarium.


Magnolia leaves- Yup, these most beloved, tannin-imparting leaves have that waxy "cuticle" that seems to recruit biofilm more quickly than other leaves during their first weeks of submersion. It seldom lasts very long, generally subsiding dramatically on it's own quite fast. 

"Concha Pods"- Another lightweight botanical with an interior that seems to soften very quickly, recruiting a good amount of biofilm in the process. Like the "Teardrop Pods", the biofilms tend not to linger very long, so "make hay while the sun shines" and let your shrimp have at 'em quickly!"

Jackfruit Leaves - These Indian leaves tend to be attractive to shrimp anyways; however, with the "value added" benefit of rapid biofilm recruitment, your shrimp will feel like you really appreciate them, and no longer any harbor resentment for the shrimps' ridiculous $400USD per gram price tag. (sorry, couldn't resist!)

Now, you may have other favorites for this purpose, and we could probably devote a whole damned article to it (Why not, I've just written a thousand-plus words on biofilm! Where else in the aquarium world are you going to find that kind of content every day- for free, nonetheless? And yet, some of you still buy generic, "non-romanced" Catappa leaves from some clown on E-Bay. Really? Huh? How DO you sleep at night? Have I guilted you yet?)

Okay, this is getting a bit "long-winded", and even a bit nasty- but you get the idea. Biofilms are  common in nature, and a part of pretty much any aquarium, yet a bit more significant (and noticeable) when you play with aquatic botanicals. They are not to be feared- although they should be respected- and ultimately, utilized as food by your animals!

And, I actually have this theory...

I think that decomposing pods, leaves, and even the biofilms, function as a sort of "biological filter", much in the way live rock does in the reef aquarium. I think that we've just started getting into this idea, and that there may be more functional advantages to layers of botanicals than we think!

More on this in future installments, for sure! 

In the mean time...

Stay calm. Stay brave. Stay curious. Stay devoted.

And Stay Wet.

Scott Fellman

Tannin Aquatics




Scott Fellman
Scott Fellman


2 Responses

Scott Fellman
Scott Fellman

February 23, 2017

Hi Gerald,

Thanks so much for the kind words and GREAT edit suggestions! I re-read that section on CO2 myself and though, “What was I trying to say?” Made the changes per your suggestion; much more logical! Somethings the coffee doesn’t kick in at 5:30AM, lol Thanks again for the suggestions!


Gerald Pottern
Gerald Pottern

February 22, 2017

Hi Scott - Very nice article, although this part is a bit confusing:

“… there is always the possibility that bacteria within the biofilms can multiply extremely rapidly, reducing the level of oxygen in the rest of the aquarium, which could lead to a dramatic reduction of CO2 being released out of the water. This, in turn, could lead to CO2 levels rising quickly and sharply … "

You might want to revise that to something like: “excessive respiration by biofilm bacteria could lower the water’s dissolved oxygen and increase CO2, asphyxiating your animals and aerobic nitrifying bacteria”. (These effects happen at the same time, rather than one “leading to” the other). Also, the phrase about “reduction of CO2 being released out of the water” was a bit confusing.

Might also include a statement (probably near the beginning) that leaf-decomposing biofilms are THE foundation of the food web in most streams and rivers; a long-accepted principle in stream ecology.

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