The Nitrogen Cycle

02 March 2018

Successful fishkeeping is all about managing the nitrogen cycle; get that right, and everything else will fall into place. The vast majority of premature fish deaths are caused by faulty management of the nitrogen cycle. Besides being toxic in themselves, nitrite and ammonia weaken the ability of fish to combat opportunistic infections. As a result, when water quality declines, problems with fungus, finrot, and whitespot increase. In this article we’ll review the principles behind biological and chemical filtration, the two main methods for removing from the water the nitrogenous wastes produced by the livestock, and look at how each can be best used in the aquarium.

Where do the nitrogenous wastes come from?

Ammonia is the end product of protein metabolism. It is toxic, so all animals have methods for getting rid of ammonia as quickly as possible. Fish mostly get rid of ammonia through their gills. Bony fish excrete the ammonia directly, whereas cartilaginous fish (such as stingrays) produce urea instead. Either way, the ammonia gradually accumulates in the aquarium until it reaches toxic levels, at which point the fish will die. Two factors affect the toxicity of ammonia: pH and temperature. Ammonia becomes more toxic as pH and temperature rises. For this reason, fish in marine aquaria or tanks containing African Rift Valley lake conditions are particularly sensitive to high ammonia concentrations.

One misunderstanding newcomers to the hobby have is between the visible wastes on the bottom of the tank and the invisible wastes in the water. For the most part, the solid wastes are faeces and decaying plant material, neither of which contain much ammonia. Though unsightly, these are not a threat to your fish and can be siphoned away easily at each water change. Paradoxically perhaps, a spotlessly clean aquarium can be a very hostile environment for your fish if the ammonia levels are high, while an established tank with good filtration will be a much healthier place even if it looks a bit messy at first glance.

Chemical filtration

The simplest and quickest solution is removing the ammonia directly using an ammonia-absorbing chemical such as zeolite. Zeolite is inexpensive and effective, and works as well in simple bubble-up box filters as it does in high-pressure canister filters. Although it only works for a few weeks before it 'fills up' with ammonia, it can be easily 'recharged' by a good soak in salty water. Unlike biological filters works at pH 6.0 and less, making it the ideal choice for use in acid water aquaria. Zeolite doesn't need a running-in period either, so a chemical filter can be pressed into use at a moment's notice, making it ideal for use in quarantine, breeding, and hospital tanks. Another advantage of chemical filtration in hospital tanks is that zeolite is not affected by medications or antibiotics, some of which can kill biological filters.

Sounds perfect, right? Zeolite does have its limitations. For a start, although recharging works a few times, eventually the particles become so covered with gunk and bacterial slime that the only option is to throw it away and buy some more. Admittedly, zeolite doesn't cost much, but over the lifetime of an aquarium, replacing the zeolite every few months will need to be factored in. This becomes more tiresome and more expensive the bigger the tank and the messier the fish; while zeolite might be a viable approach for a tank containing a few killifish or a breeding pair of chocolate gouramis, it is much less attractive to an aquarist with a tank full of predatory catfish or Oscars. Standard-issue zeolite is also less effective in salty water than in freshwater, preferring to take up other minerals instead. While there are marine-grade ammonia-absorbers, these are less commonly sold and rather more expensive. The biggest problem with zeolite is that you cannot tell when it is "used up", and at-least weekly ammonia tests are essential to establish the frequency with which the zeolite in your filter will need to be replaced.

Biological filtration

Compared with chemical filtration, biological filtration is cheaper and far easier to maintain over the long run, but more fiddly and temperamental to set up in the first place. Biological filters come in a variety of styles, from the classic undergravel filter through to high-tech wet-and-dry trickle filters, but all work in the same basic way. Water is passed through a porous medium that hosts a large population of bacteria. These bacteria convert the ammonia into less toxic nitrite and then relatively non-toxic nitrate. The nitrate is removed, or more specifically diluted, with each water change, keeping it at a safe level. The microbiology of aquarium filtration is not all that well understood. It is certain that the bacteria converting ammonia to nitrite are different to those converting nitrite to nitrate, but the identity of the species involved is still being studied. Bacteria of the genera Nitrosomonas, Nitrosospira, and Nitrosococcus appear to be involved with the oxidation of ammonia to nitrite, while Nitrobacter bacteria are the ones oxidising nitrite to nitrate.

The differences in bacteria in filters adapted to freshwater, brackish water, and marine aquaria are unknown. As a rule, bacteria from filters matured under one set of conditions cannot be transferred to another. While a freshwater aquarium can be converted to a low-salinity brackish water one (where the SG is 1.003-1.005) without any loss of biological filtration, when the salinity is raised much above this level the filter destabilises and needs to be cycled again. High-end brackish water filter bacteria (SG 1.010 upwards) seem to adapt readily to marine conditions, and vice versa. This seems to suggest saltwater filter bacteria are more tolerant of salinity changes than freshwater ones, but detailed studies are lacking.

Cloning filter bacteria

Regardless of the composition of the bacteria in the filter, they have to get there from somewhere. By far the easiest way to do this is simply take some filter media out of an established filter and put it into the new filter. This process -- called cloning -- kick-starts the colonisation of the rest of the filter media in the filter and should result in a stable aquarium within days. Provided the tank is not overstocked and the fish not overfed, an established aquarium can lose half of its biological filter media and remain healthy, the remaining bacteria will colonise the clean replacement media almost at once, rapidly building up their numbers as they take advantage of the ammonia and nitrite in the water. Conversely, a new filter half-filled with old media from another tank is almost as good as an established filter, and the new tank will certainly be safe enough to carry a moderate loading of aquarium fish.

Adding "living rock" to a marine aquarium is similar in effect to cloning a filter. The living rock brings in a load of bacteria along with all the other life forms that infest them, and these bacteria will quickly spread to the filter. Good-quality living rock itself has a substantial ability to perform as a biological filter medium itself, and for this reason many marine aquarists mature their tanks by installing large amounts of living rock.

Cycling with fish

If you don't have another filter from which to grab some established filter media, you'll need to cycle the aquarium instead. The required bacteria are on plants and in the air and water, and will multiply rapidly in an aquarium provided they are given some 'food'. The stuff they need is ammonia, and that has to come from somewhere. Cycling with fish essentially means putting in a few, very hardy species to act as ammonia donors. In the process, these fish are exposed to dangerously high levels of ammonia and nitrite. These fish can and do end up being "sacrificed" if they cannot tolerate these conditions, and for this reason cycling with fish has begun to fall out of use. That said, if done properly it can work and the fish needn't end up dying if only the hardiest species are chosen. Zebra Danios (in freshwater aquaria) and black mollies (in marine or brackish aquaria) have generally proven to be the best species for cycling tanks, showing little apparent discomfort from elevated levels of ammonia or nitrite provided substantial (50%) water changes are regularly performed (i.e, at least weekly).

Besides fish, cycling also requires an ammonia or nitrite test kit. Many aquarists use both. With the first fish installed, the ammonia levels will rapidly rise, followed shortly afterwards by the nitrite levels. The ammonia comes from the fish of course, but the nitrite indicates that the bacteria are starting to convert the ammonia into nitrite. As they do so, the ammonia levels will start to decline. Once there is nitrite in the water, the bacteria that convert nitrite to nitrate will start to appear, and the nitrite concentration will begin to decline. After about four to six weeks, the ammonia and nitrite levels should be close to zero, and you can add a few more fish. The filter bacteria will more quickly ramp up their efforts this time, and any spikes in ammonia or nitrite levels will be short-lived. As the weeks pass, you can add more fish, and the aquarium will be fully cycled within 2-3 months in the case of a freshwater tank, and anything up to 6 months for marine aquaria.

Fishless cycling

To avoid using fish as the ammonia source, many aquarists have added ammonia directly to the water. The bacteria don't care where the ammonia comes from, and such an approach can work well. Ammonia is nasty stuff though, and should be kept away from pets and children. The ammonia is added to the water until a reasonably high concentration around 5 mg/l) is attained. Because bottles of ammonia vary in concentration, this is very much a process of trial and error: add some ammonia, let the water get pushed around by the filter for ten minutes, do a test with the ammonia test kit, and add more ammonia if required. Make a note of how much you added to get to the desired concentration. Repeat this dose each day. The basic result will be similar to that of cycling with fish: a couple of weeks of high ammonia levels, then a few weeks of high nitrite levels, and then everything will settle down. Once you're happy the tank has cycled (no ammonia or nitrite) you can add some hardy fish, safe in the knowledge that the filter is working properly and the fish will not be stressed.

Optimal water conditions

The ideal water conditions for all fish are these: zero ammonia, zero nitrite, and nitrates that are as close to zero as possible. In an established aquarium, ammonia and nitrite should not be a problem, but nitrates can be. The water coming out of the tap may well have nitrate levels above the tolerances of certain freshwater aquarium fish and well above those preferred by marine fish and invertebrates. Thames Water, for example, aims for a standard nitrate concentration of 50 mg/l, well above that which is acceptable in a properly-run reef tank. Nitrate-removing chemical filter media are available but these are more for "polishing" essentially nitrate-free water than bulk removal of nitrate, and the nitrate-removing biological filters are cumbersome and expensive since they need to create anaerobic conditions for the required variety of bacteria. For all practical purposes, adding nitrate-free water during water changes is the preferred option for aquarists keeping nitrate-intolerant species. Reverse-osmosis filters are the best tools for this, producing about 1 litre of nitrate- and mineral-free water for every 10 litres of regular tap water. This water can be hardened as required with tap water or freshwater "salts" for use in freshwater tanks or turned into brackish or salt water by adding marine salt mix. A cheaper, but less secure, way to obtain relatively clean water is to collect rainwater.

Although not really suitable for use in marine tanks because of the leaf litter and other gunk that collects in the gutters and water butts, once strained and filtered rainwater works very well with freshwater fish. Again, it may need to be mixed with tap water to get the right pH and hardness, and filtering through carbon will remove any unwanted organic compounds, but rainwater is at least plentiful in the UK, and a rainwater butt is cheap to buy from any garden centre.

Even if you stuck with using tap water, high nitrates are not too serious a problem. Ordinary community tank tropicals are fine at 50-100 mg/l, and adding vigorously growing plants to a tank will reduce the nitrate levels to some degree. Performing at least weekly water changes of 50% will keep the nitrates low enough that the fishes will be happy and healthy. Though often overlooked in favour of fancy equipment and chemical additives, the value of regular water changes cannot be overstated. Proper filtration and generous, regular water changes are the keys to managing the nitrogen cycle in the aquarium, and together form the royal road to successful fishkeeping.

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