In part 1, I talked about the bacteria that handle the nitrogenous wastes from the fish. Fine, ammonia is dangerous in tanks. But ammonia is just one waste product. What about all the other things? Fish do produce urine, and they certainly poop. Then there is uneaten food (I know none of us overfeeds, but there are always a few bits too small to interest certain fish, or our wet friends are sloppy eaters). There are dead plant leaves (which of course we always remove one by one as required). There may be dead snails (Ever wonder where they go? Empty shells do not come into being in that form). Perhaps there is even an occasional dead fish (in someone else’s tank, naturally). Even if these things are small enough and light enough to be sucked into the filters, they are still in the tank water until we remove them by cleaning the filters. Only the most naïve would think that out of sight in the filter is out of the water and out of the system. Mechanical filters collect visible or near-visible solid waste material for the hobbyist to remove. Biological filters modify but do not physically remove ammonia or nitrite, they oxidize those to nitrate, still dissolved in the water for the hobbyist to remove by water changes.

Well, there are lot of bacteria and fungi in the world, even (or especially) in aquatic environments. I promise you that you have all you need already in your tank. We are so accustomed to having to wait for development of nitrifying bacteria, and we spend so much time and effort monitoring that development and later the stability of those colonies, that we may never notice that the other bacteria are running fine. No attention, no pampering, and no toxicity – this is easy street. These bugs come through the air, on and inside the fish, in the water around the fish, with the plants, snails, and so on. They, like algae spores, are everywhere. But as is the case for the nitrifying bacteria, they do not start out in the correct numbers needed in your tank. So for these bugs, there also is a development process. There will be an eventual population balance in line with the fairly steady food supply (whatever their particular food may be). Many of these we can call the heterotrophs, or heterotrophic bacteria. By this name, we mean in effect only that they eat other or different things not the dissolved nitrogenous wastes discussed before. There are almost endless numbers of types of these bacteria. They are helped and commonly preceded in trash digestion by the saprophytic fungi and bacteria. The saprophytes eat dead organic matter. If you grossly overfeed, or ever did before you knew better, you are likely to have seen little fuzzy tufts on and between the gravel grains. These were likely clumps of fungus, feasting on the leftover food. They will consume much of such waste, then produce spores (so that there can be future generations of saprophytic fungi) and die. These spores will be everywhere in the tank- and this is not a bad thing. The waste products of the saprophytic fungi or bacteria – their own metabolites- and the breakdown products from the fungi or bacteria themselves are less likely to be harmful than the original organic material. Some of these metabolites and breakdown materials will in turn serve as food or building blocks for heterotrophs which are on all of the surfaces in the tank, or just free-floating in the water column, or even actively swimming in the water. The breakdown of organic matter and wastes is frequently referred to as “mineralization”, i.e., changing organic material to generally simpler inorganic materials. There is likely something to use each stage of the process. These bugs are opportunists – they take advantage of what is present right now in the tank and dissolved in the water. As with the nitrification bacteria, they multiply to consume the materials that are useful to them.


Okay, we are past the first stage of breakdown of organic matter, whether it was excess food, a dead leaf, a dead fish, whatever. We have enriched the water column with nitrates (from nitrogenous wastes), and now have added lots more minerals, some proteins, even some sugars, a whole stew of simpler or some more resistant to breakdown compounds into the water column. Heterotrophs absorb many of these things, or at least the items they want and can use themselves, and grow. Ever heard of cloudy water? A bacterial bloom? This is it. First there is a faint haze, and then it gets denser. It can go to opaque if the necessary nutrient load for that particular organism is high enough. If the bloom is green, it just means that some free-floating alga is having a population explosion rather than a bacterium. Sometimes a bloom looks green, because phagocytic (=capable of ingesting particles) bacteria are devouring an algal bloom, and are “smart” enough not to immediately digest the chlorophyll (or other pigments) by which the alga is using light energy as well as dissolved food sources. All of this can be very, very frightening to the novice aquarist. Their new tank looks like pea soup or a cesspool, and not infrequently smells like something akin to one or the other of those things. This is second only to new tank syndrome with ammonia and nitrite (NTS, cycling a tank) in getting newcomers onto the boards with pleas for help. It is hideous, and appears threatening.

Are blooms (cloudy or green water) dangerous? Like so many other things, it all depends. Many years ago this was more dangerous that it is now, because we know more and our equipment is so much better than it was then. There are several possible dangers. The worst case is a catastrophic crash of the bloom. This is mass death of the bacterium or alga, which has multiplied to such great numbers. Collapse of the bloom causes a massive increase in the oxygen demand on the system- saprophytes will multiply rapidly to eat the dead bugs, (algae or bacteria) and the oxidation (either direct or saprophyte-mediated) of all that bacterial/algal mass can exhaust the tank oxygen down to levels insufficient to support the fish. This is less of a problem than it used to be, due to improvements in our filter and circulation technologies. Collapse can be triggered by exhaustion of any critical nutrient that previously was present in excess, or by intervention by the hobbyist (using medication or physical agents such as flocculants, etc.). If a bloom collapses, be prepared to increase the oxygenation of the system. Also be neurotic about cleaning your mechanical filters (do NOT disturb the biofilter); twice daily rinsing is not excessive. If you have access to diatom filtration, a HOT Magnum with micron filter, even a Quick-Filter and powerhead, this is the time to crank it up, and keep it rinsed or recharged even more often than the routine mechanicals. Getting this biomass out of the system before it is digested and broken down means a lower nutrient load and therefore reduced chance or recurrence of the bacterial or algal bloom (commonly by another species which can best use the resulting new nutrient mixture).

There can be some danger from a bacterial bloom by direct competition for oxygen by the bugs against the fish, but this is uncommon. Some bacteria and algae may release toxins into the water directly or after death, but this too is relatively uncommon. I do not normally use routine carbon filtration, but I would do so if I had a significant bloom in process, just as cheap insurance against toxicity.

Water changes during a bloom are not especially helpful in many to most cases. They can replenish vital minerals that could be becoming limiting factors in the density of the bloom, so sometimes make the bloom worse instead of helping. Bacterial and free-floating algal generation times are very short. Repeated population doubling measured in minutes can cloud a tank with amazing speed. Frequently rinsed mechanical filtration is of much more help, and micron filtration is usually a larger help, even if the bloom has not crashed. Removing the nutrients in excess, even in the form of the bacteria or algae mass itself, is a benefit. Getting excess or imbalanced nutrients out of the system, out of the water, is the goal and take-home lesson here.

If the tank is not opaque and the fish are not gasping at the surface for oxygen, ignoring the bloom while taking extra care of mechanical filtration is just about the best thing to do. If the tank is less than 3-6 months old, it is the best. We may have plenty of saprophytes and heterotrophs, but the various types have not yet established a balance. Overpopulation of one type and then another is almost expected. We can hope the periods of bloom are no worse than a barely detectable haze, but we cannot count on escaping completely. Patience is the most difficult technique to master, or perhaps it is second to learning to feed- I’m still working on that one.

I have mixed feelings about the use of flocculants or clarifiers. These things can work (and if used I would handle the tank as if it were catastrophic collapse of a bloom), but there have been a lot of reports on the web of major fish problems after such treatment. I have not used these myself, so cannot verify or refute any of these successes or failures. My personal guess would be that it is not always the clarifier itself causing the problem, but the resulting strain on the tank filters and oxygen levels from the suddenly dead/dying biomass.

What about the dead fish or the dead snails? Obviously it is better to get them out of the system. But if you “lose” a small fish, or certainly a snail (other than an Apple snail- they are the equivalent of a pretty big fish in mass, and they decay/dissolve really quickly, unlike fish – the smell is, well, impressive), the system can handle it. In the case of the fish there is greater danger of the other fish becoming infected by eating the dead body than there is to the filter. This is a primary infection route for fish TB and for Neon Tetra Disease, and also important for a number of intestinal parasites. Many times on the boards we see posts saying that a pleco was “caught in the act” of killing and eating this or that Tetra, Rasbora, whatever. More often than not, the fish died and was eaten afterward. This sort of thing has little or no importance to the bacterial balance of the tank, but can be highly significant to the health of the fish in the system. A large dead fish behind a rock is an entirely different thing. Anything dead- food, poop, plant, fish- of any significant amount or mass, should be removed from contact with the tank water as soon as possible, and the larger the quantity of the material, the quicker it needs to be out.

Okay, months have passed since we set up the tank; our bacterial/fungal populations have stabilized to the point that we no longer notice their activities. With luck we have even learned to feed and clean the tank. So where do all the bacteria go? Ever heard of infusoria? Ciliated protozoans, rotifers, up to Cyclops and Daphnia, all that fun crowd that made the interesting micrographs in high school biology 101? Guess what they eat? You got it. They eat the bugs we’ve been discussing. And small fish eat them. Ever wonder how baby fish survive in tanks even if they do avoid being eaten by the other inhabitants? They eat exactly this level of the food chain. Also, there will be some (usually very small in numbers) populations of such critters as nematodes – most are not parasites, but free-living – and planaria. Guess what? You have a miniature, although incomplete and grossly simplified ecosystem in your fish tank – your own micro-ecology.

If you happen to have a plenum under the substrate in your tank, the deep levels of your substrate and the plenum under it will be relatively anaerobic – lacking in oxygen. Under these conditions you should eventually have established a denitrification zone. In this area nitrates diffusing down from the water column will be reduced to nitrite and ammonia and finally gaseous N2, with the nitrogen gas bubbling back out into the atmosphere. And guess what does this – more bacteria. Then your tank really would have more of the nitrogen cycle. To be truly complete, we would have to cultivate blue-green algae (BGA), which can fix atmospheric nitrogen (much submerse BGA cannot directly fix dissolved nitrogen), have tank inhabitants that would eat BGA (I don’t know of any) and use that nitrogen for their own nitrogen requirements. The potential drawbacks with in-tank denitrification are the things that happen in similar but deeper anoxia. Have you ever heard of H2S, hydrogen sulfide? Methane (swamp gas)? These are also the bacterial breakdown products from bacteria reducing sulfates or carbon compounds under anoxic (oxygen-free) conditions. And they can do very bad things to the fish in the tank. To me, such added bacterial processes are not particularly needed – water changes are cheaper and easier and faster – and these do have risks of their own. Not all bacterial processes are ones we want in our tanks, but most of them are doing us a favor, and without them we would be in real trouble.

I hope that this gives at least a hint of the complexity of the invisible activities going on constantly in our tanks, and how we really cannot operate our tanks effectively without these processes. I also hope it will make you think twice about casually adding this or that antibiotic or other medication to the tank- even if it doesn’t hit the nitrification bacteria, you can bet it will hit whole populations of some bug of another. After that the entire system is going to have to re-balance itself to compensate for that loss, or to consume the materials those bugs would have used, or because those bugs were the basis of someone else’s diet. Our ecologies may be grossly simplified in relation to the outside world, but that does not mean they are simple themselves.

An earlier version of this article first appeared in AquaSource magazine. It has been edited for this site.

Robert T. Ricketts, a.k.a. RTR


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