The start of the journey...And the direction it takes us...

It seems incredible to me that the world of blackwater, botanical-style aquariums is still “finding its tribe”, with lots of hobbyists trying this approach for the first time. And as the techniques evolve, the processes become more refined..or even more unusual.... I was thinking about this today when I was playing with a new tank I'm starting up in my office.

I utilized some mangrove wood which was not really "cured"- something I've done before with this wood, and the inevitable cloudiness and tint came quickly. And it got me thinking...

When you add botanicals to an aquarium, particularly a brand new one, there is almost always some sort of cloudiness initially. This is caused by several factors, ranging from good old “dirt” coming off of their surfaces, to dissolving lignin, cellulose, and of course, tannins. It’s a complex organic “brew”, which is released into the water as the materials begin to break down.


Of course, all of this material dissolving into the aquarium can create cloudiness.That's probably your first sign that "things" are happening! We often see such cloudiness in aquariums when we may not have fully prepared our botanicals, or wood. 

Will it go away on its own, without our intervention?

In my experience, it will...eventually. And of course, "eventually" can be days, weeks...or longer. No guarantees. And "without our intervention" is a sort of vague thing. You can let Nature sort it out, as she's done for eons. I mean, you could...could- even "cure" wood and botanicals "in situ." I've done it before. I wouldn't recommend it, however.

"Well, shit, Scott- you said you 'could'- so how would you?"

Damn, I did. And I can run the risk of being pretty irresponsible here, I know. Let me elaborate further. 

Well, there are a few approaches you can take to managing this stuff.

You can employ some chemical filtration media, such as activated carbon, to help clear up the cloudiness and perhaps remove some of the organics. You could perform water exchanges, with the knowledge that this may disrupt or slow the development of a significant population of beneficial bacteria. 

You can do this. You won't be adding fishes for a while, but you can do this. You can add bacteria, however. In fact, this is where our bacterial inoculant, "Culture", can excel. It is comprised of the hardy, incredibly versatile Purple Non-Sulphur Bacteria (PNSB), Rhodopseudomonas palustris.

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!

PNSB are useful for their ability to carry out a particularly unusual mode of metabolism: anaerobic photoheterotrophy. In this process, they consume organic wastes while inhabiting moderately illuminated and poorly oxygenated microhabitats (patches of detritus, leaf litter beds, shallow depths of substrate, deeper pores of expanded clay media, etc.).

By competing with other anaerobes such as methanogenic archaeans  (more about them later) and sulfate-reducing bacteria for food, these voracious "sludge-eaters" significantly reduce the production of toxic byproducts such as methane and hydrogen sulfide!

It’s important to understand that your best allies in the cause of establishing a new aquarium are bacteria and fungi, as we’ve talked about repeatedly.

Bacteria will arrive in your aquarium through a number of means- on leaves and seed pods, in substrate (particularly if you’re using material from an established one), wood, etc. The nitrifying bacteria that we admire so much are present in almost every aquatic system- even a brand new aquarium. However, there simply aren’t enough of them in a new aquarium to process the waste produced by a significant fish population.  And of course, to grow the population of these beneficial bacteria, you need to supply then with their major energy source- ammonia.


Without re-hashing the whole well-trodden nitrogen cycle stuff, we know by now that these bacteria will oxidize the ammonia and convert it to nitrite, which a second group of bacteria process and convert to less harmful compounds, specifically, nitrate. When both of these types of bacteria reach a population sufficient to process the available energy sources, you’ve got an aquarium that’s “cycled.”

"Aquarium Keeping 101", right?

Yeah, it should be.

Of course, with the pH in blackwater aquariums generally falling into the range of 6.0-6.8, you’ll see a slower processing of ammonia and nitrite. And when you get really low pH, as we’ve talked about before (like 5.5pH or lower), these organisms essentially shut down, and a new class of organism, Archaens, take over. Now, that;’s a whole different thing for a different blog, but suffice it to say, the lower pH, botanical-style/blackwater aquarium is a different animal altogether! 


I think that the real key ingredient to managing a low pH system (like any system) is our old friend, patience! It takes longer to hit an equilibrium and/or safe, reliable operating zone. Populations of the organisms we depend upon to cycle waste will take more time to multiply and reach levels sufficient to handle the bioload in a low-pH, closed system containing lots of fishes and botanicals and such.

This certainly gives the bacterial populations more time to adjust to the increase in bioload, and for the dissolved oxygen levels to stabilize in response to the addition of the materials added-especially in an existing aquarium. Going slowly when adding are botanicals to ANY aquarium is always the right move, IMHO.

And at those extremely low pH levels?


They sound kind of exotic and even creepy, huh?

Well, they could be our friends. We might not even be aware of their presence in our systems...If they are there at all.

Are they making an appearance in our low pH tanks? I'm not 100% certain...but I think they might be. Okay, I hope that they might be. 


Archaeans include inhabitants of some of the most extreme environments on the planet. Some live near  vents in the deep ocean at temperatures well over 100 degrees Centigrade! true "extremophiles!" Others reside in hot springs, or in extremely alkaline or acid waters. They have even been found thriving inside the digestive tracts of cows, termites, and marine life where they produce methane (no comment here)  They live in the anoxic muds of marshes (ohhh!!), and even thrive in petroleum deposits deep underground.


(Image used under CC 4.0)


Yeah, these are pretty crazy-adaptable organisms. The old cliche of, "If these were six feet tall, they'd be ruling the world..." sort of comes to mind, huh?

Yeah, they’re fucking beasts….literally.

Could it be that some of the challenges in cycling what we define as lower ph aquariums are a by-product of that sort of "no man's land" where the pH is too low to support a large enough population of functioning Nitrosomanas and Nitrobacter, but not low enough for significant populations of Archaea to make their appearance?


I'm totally speculating here. I could be so off-base that it's not even funny, and some first year biology major (who happens to be a fish geek) could be reading this and just laughing…

I still can't help but wonder- is this a possible explanation for some of the difficulties hobbyists have encountered in the lower pH arena over the years? Part of the reason why the mystique of low pH systems being difficult to manage has been so strong?

Could it be that we just need to go a LOT slower when stocking low pH systems?

Yeah, we should go slower.

And yes, you can "cure" everything in situ, fi you understand what's happening, what the potential downsides are, and how to manage this process. You need to just be patient. 

Right after the initial "break in" and "cycling" process comes the next phase- 


Decomposition of plant matter-leaves and botanicals- occurs in several stages.

It starts with leaching -soluble carbon compounds are liberated during this process. Another early process is physical breakup or fragmentation of the plant material into smaller pieces, which have greater surface area for colonization by microbes.

And of course, the ultimate "state" to which leaves and other botanical materials "evolve" to is our old friend...detritus.

And of course, that very word- as we've mentioned many times here- has frightened and motivated many hobbyists over the years into removing as much of the stuff as possible from their aquariums whenever and wherever it appears.

Siphoning detritus is a sort of "thing" that we are asked about near constantly. This makes perfect sense, of course, because our aquariums- by virtue of the materials they utilize- produce substantial amounts of this stuff.

Now, the idea of "detritus" takes on different meanings in our botanical-style aquariums...Our "aquarium definition" of "detritus" is typically agreed to be dead particulate matter, including fecal material, dead organisms, mucous, etc.

And bacteria and other microorganisms will colonize this stuff and decompose/remineralize it, essentially "completing" the cycle.

Decomposition is so fundamental to our "game" that it deserves mentioning again and again here!

Now, a lot of people may disagree, but I personally feel that THIS phase, when stuff starts to break down, is the most exciting and rewarding part of the whole process! 

And perhaps- one of the most natural...

How we start our systems- the approach that we take, the way we react and adjust- are fundamental parts of the equation. And yeah, there ARE a lot of different ways you can go. Some will raise a few eyebrows. Some will make fellow hobbyists think that you're crazy. But you CAN take different routes.

And you should at least think about them now and then.

Stay creative. Stay studious. Stay engaged. Stay excited...

And Stay Wet.


Scott Fellman

Tannin Aquatics 





Scott Fellman
Scott Fellman


Leave a comment