Say hello to our little friends!

One of the things that we discuss so much around here is the concept of the aquarium as a "microbiome"- a habitat for a wide variety of organisms at many levels.

Over the years, I have thought a lot about how we as botanical-style aquarium enthusiasts gradually build up our systems, and how the entire approach is about creating a biome- a little closed ecosystem, which requires us to support the organisms which comprise it at every level.

Just like what Nature does.

These organisms-our little friends, are priceless additions to our aquairum environments.



Not only does this community of organisms help process nutrients and improve the overall environment for the fishes, it serves as part of their sustenance via the creation of a "food web"- a concept we've talked about more than a few times here.

Yeah, a "food web" in our aquariums. It's not only possible to construct one- I think it's pretty much a "must have" for the serious botanical-style enthusiast. To me, these are fascinating, fundamental constructs which can truly have important influence on our aquariums.

So, what exactly is a food web?


A food web is defined by aquatic ecologists as a series of "trophic connections" (ie; feeding and nutritional resources in a given habitat) among various species in an aquatic community. 

All food chains and webs have at least two or three of these trophic levels. Generally, there are a maximum of four trophic levels. Many consumers feed at more than one trophic level.

So, a trophic level in our case, would go something like this: Leaf litter, bacteria/fungal growth, crustaceans...

In the wild aquatic habitats we love so much, food webs are vital to the organisms which live in them. They are an absolute model for ecological interdependencies and processes which encompass the relationship between the terrestrial and aquatic environments.

So, how would we go about constructing a "food web"in our botanical-style aquariums? For that matter, how do we help create this "microbiome" we keep yapping about?

Well, as you might guess, it all starts with how we set up our aquarium. A typical botanical-style aquarium has a rich substrate, an abundance of leaves and botanicals, and moderate water movement and light. All of these are key ingredients which stimulate the growth and development of a diversity of organisms which make up this milieu.

And the beauty of it all is that you don't HAVE to add cultures of these life forms to get them to colonize your tank. Nature sees to that!

As we all know by now, the first thing that happens when you add botanicals and leaves into an aquarium is that a burst of bacterial biofilms begins to proliferate.

Our other pals, Fungi, arrive on the scene in much the same manner as biofilms. 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!

There are around 3000 species that are known to be associated with aquatic habitats! That's A LOT of species! Aquatic “true fungi” are known as "osmoorganotrophs", a fancy way of saying that they absorb nutrients across their cell wall. Most of them have a "filamentous" morphology at some point during their life cycle. This morphology enables them to invade deep into substrates and to directly digest particulate organic matter (POM) to acquire nutrients for growth and reproduction. 

The fungal community consumes microscopic algae, aquatic macrophytes and terrestrial plant litter (including wood). Aquatic fungi act as very significant decomposers of particulate organic matter (POM), specifically coarse particulate organic matter (CPOM), which includes both plant and animal material . 

We see this in Nature- and absolutely in our aquariums!

Fungi play a huge role in the decomposition of leaves, both in the wild and in the aquarium. By utilizing special enzymes, aquatic fungi can degrade most of the molecular components in leaves, such as cellulose,, hemicelluloses, starch, pectin and even lignin.

Depending on various factors, such as leaf litter type and the local water chemistry, fungal decomposition of leaves can take anywhere from 1 month to 6 months.

The fungi known as aquatic hyphomycetes produce enzymes which cause leaf maceration, and in as little as 2 to 3 weeks, as much as 15% of the decomposing leaf biomass in many aquatic habitats is processed by fungi, according to one study I found.

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, both in the wild and in our aquariums!

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

Fungi are actually an important food item for other life forms in the aquatic environments tha we love so much!  In one study I stumbled across, gut content of over 100 different aquatic insects collected from submerged wood and leaves showed that fungi comprised part of the diet of more than 60% of them, and, in turn, aquatic fungi were found in gut content analysis of many species of fishes!

And of course, there ARE organisms which you can add to your aquarium.

I add bacteria, in the form of Purple Non Sulphur bacteria (PNS) via our product, "Culture", as these highly adaptable Rhodopseudomonas palustris bacteria not only "work" with the nutrients and compounds present in the aquarium via the materials- they will help "kick start" the nitrogen cycle as well.

This is exactly what we envisioned this product to do- To compliment the botanical-style aquarium approach and facilitate the development of a rich microbiome with natural processes.

PNSB consume carbon/nutrients in anaerobic environments, thereby competing with microbes that produce toxic metabolites (e.g. hydrogen sulfide). Unlike nitrifying and denitrifying bacteria, they are capable of performing photosynthesis. In addition, they have been demonstrated repeatedly to possess strong probiotic properties that promote the health of diverse aquatic species.

PNSB is found in freshwater, marine and brackish environments (in the water column, the sediments and even in the guts of animals such as corals). This highly adaptive photosynthetic bacterium balances nutrient cycling in all types of aquatic and terrestrial systems. 

Like nitrifying bacteria, PNSB metabolize ammonium and nitrite and nitrate. And they're not just important to the nitrogen cycle. They're also capable of aerobic organoheterotrophy - a process of removing dissolved organics from the water column- just like other microbes!

As "extremophiles", they're ideal for our "botanical-centric" aquarium systems. 

And of course, you can even culture some organisms, like Paramecium, to help "prestock" your tank.

You know, by creating an "Infusoria" culture!

"Infusoria"-a delightful catch-all term, from the "Golden Age" of aquarium keeping, may be described as a real "catch-all" term for small aquatic organisms, like euglenids, protozoa, unicellular algae, tiny invertebrates, and that are commonly found in freshwater environments, like ponds, creeks, and drainage ditches, used as a first food for tropical fish fry. Sometimes, it's referred to as "green water" in older hobby literature- a kind of vague descriptor.

In modern formal biological classification, the term "infusoria" is considered an antiquated, obsolete descriptor, as  most of the organisms previously included in the collective term "Infusoria" are assigned to a different assemblage of taxonomic groups.

Nonetheless, it's a charming, albeit somewhat antiquated term that is still used in aquarium circles to describe the tiny organisms that arise when you soak some blanched lettuce, vegetable skin, or other plant matter in a jar of water. They're perfectly sized for young tropical fish fry as the first food when they are free swimming. In fact, at around 25-300 microns, these organisms are consumable by most fishes as soon as they've absorbed their yolk sac.

Sounds good, but how do you "make" the stuff?

Well, traditionally, it was done in the most low tech way: You would take some blanched lettuce leaves, old flower clippings, hay, etc. etc. and basically let the stuff decompose in water, and after several days, a smelly solution of cloudy water will arise, driven by bacteria. Ultimately, after a few more days, the water will clear when creatures like Paramecium and Euglena arrive on the scene and consume the rampant bacteria population. Voila, in theory, you have an "infusoria culture."

You can simply add this culture to your new botanical-style aquarium, and, in theory, you've started to inoculate your tank with a variety of organisms which can help create a "foundation" for the ecology in our tanks.

Embracing these life forms as a key pillar of what we do really stands out in aquarium practice.

Far different than the "typical" approach to starting an aquarium, which is really more reliant on filtration, external food inputs (from us!), and the execution of consistent maintenance to get it through the "startup" period, when a typical system is almost "sterile" compared to our botanical-style ones.


The next set of organisms you could add would consist of some well-known to us in the aquarium hobby. You can obtain pure cultures of Daphnia and perhaps some of the other commonly available live freshwater crustaceans, like copepods, Gammarus, Cylcops, etc., and let them "do their thing" before you add your fishes.

This way, you've got sort of the makings a little bit of a "food web" going on- the small crustaceans helping to feed off of some of the available nutrients and lower life forms, and the fish at the top of it all. 

I've experimented with the idea of "onboard food culturing" in several aquariums systems over the past few years, which were stocked heavily with leaves, twigs, and other botanical materials for the sole purpose of "culturing" (maybe a better term is "recruiting) biofilms, small crustaceans, etc. via decomposition. I have kept a few species of small characins in these systems with no supplemental feeding whatsoever and have seen these guys as fat and happy as any I have kept.

And it's the same with that beloved aquarium "catch all" of infusoria we just talked about...These organisms are likely to arise whenever plant matter decomposes in water, and in an aquarium with significant leaves and such, there is likely a higher population density of these ubiquitous organisms available to the young fishes, right?

Now, I'm not fooling myself into believing that a large bed of decomposing leaves and botanicals in your aquarium will satisfy the total nutritional needs of a batch of characins, but it might provide the support for some supplemental feeding! On the other hand, I've been playing with this recently in my "varzea" setup, stocked with a rich "compost" of soil and decomposing leaves, rearing annual killifish with great success.

Of course, the more daring among you may want to go even further in your "pre-stocking" work, introducing various worms, like "Black Worms" or Tubifex worms, if you can find clean cultures of them. For that matter, even "blood worms", which are actually the larval phase of the midge.

Some organisms, such as nematodes and chironomids ("Bloodworms!") will dig into the leaf structures and feed on the tissues themselves, as well as the fungi and bacteria found in and among them. These organisms, in turn, become part of the diet for many fishes.

A food web.

And the resulting detritus (here we go again!) produced by the "processed" and decomposing plant matter is considered by many aquatic ecologists to be an extremely significant food source for many fishes, especially in areas such as Amazonia and Southeast Asia, where the detritus is considered an essential factor in the food webs of these habitats.

It performs the same function in an aquarium- if we allow it to.

It's really important to consider our botanical-style aquariums- or any type of aquarium, for that matter- as small ecosystems, which have inputs, outputs, cycles, and rhythms, all of which are dictated by the fungi and bacteria which are the real "workers" in our aquariums. 

Our little friends.

By taking a little extra time to educate ourselves about the organisms and processes which occur in wild aquatic habitats, as well as in our aquariums, we are able to facilitate their growth- and enjoy their benefits.

Stay curious. Stay diligent. Stay observant. Stay creative...

And Stay Wet. 


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


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