The Nitrogen Cycle                
  The Nitrogen Cycle is probably the most important invisible process that goes on within the confines of the aquarium. In essence it is nature's answer to the simple fact that fish and other organisms produce toxins in the environment that can easily build to concentrations that are high enough to kill. The most important organic toxin produced within the aquarium is ammonia [NH3]. The fish release it directly through respiration and more indirectly through urine and eliminated solid wastes. Other sources are from the natural decay processes produced by bacteria acting on dead organic material such as excess food, dead leaves, dead fish and the fluctuating populations of invisible bacteria as well.  
  Ammonia and nitrosomonas                
  Fortunately mother nature has produced organisms which use toxic ammonia [NH3] as an energy source. the result, nitrosomonas bacteria are essentially universal, found most often in soil. They are "lithotrophic" and aerobic. The bacteria form colonies wherever their needs are satisfied, they must have an adequate supply of oxygen passing as well as the ammonia that is their energy source.  
  Ammonia is extremely toxic. It is deadly in relatively small concentrations in the aquarium. The only two reliable ways to eliminate ammonia are with a chemical removal using zeolite (often termed Ammonia Remover) and biologically. Between the two methods, I personally prefer the biological removal by promoting nitrosomonas populations. Most ammonia removers - though rechargeable - never show a color change, so there is no way to know when the product stops working. The biological bed will adjust to environmental changes over time and is the best defense against stress on the fish that I know about.  
  Nitrite [NO2] and nitrobacter                
  Nitrite, the by-product manufactured by nitrosomonas as it reduces ammonia is not as deadly as ammonia, but it was much easier to test in earlier times before a reliable test kit for ammonia became easily available at a reasonable cost. In fact I grew up with the "Nitrite Cycle" simply because the role of ammonia in the cycle was not readily understood. Roughly double concentrations of nitrite can be tolerated before death occurs. Nevertheless, the whole idea is to understand the role of both toxins to control them and keep your fish alive.  
  The New Aquarium and the Nitrogen Cycle            
  The best way to a basic understanding is to discuss the events that occur in a new aquarium set-up - this is time when most novice aquarists endure massive losses without having a clue as to what is wrong, and ultimately becoming discouraged and leave this enthralling hobby.  
  Day 1                      
  Your new aquarium is just set up, think about what you have in front of you. The aquarium is dust free and probably rinsed well. A brand new filter is busy removing non-existent particles and the freshly rinsed gravel sparkles at you. The water from the tap was treated, so it will not kill the fish you already added. Everything is perfect, the tank is ready to keep all those fish you want alive, right?  
  The aquarium, in its brand new state is sterile. It can support fish and other life simply because there is no chlorine or chloramine to kill them. But the tank will not support a full population for quite a while yet!. If there are too many fish they will simply poison themselves. How is this possible? Quite easily, as they live and breathe, the fish will excrete and create ammonia. Unlike a natural pond or river, an aquarium has a limited surface area for ammonia to dissipate, so it builds up in concentration. It doesn't take all that much to cause serious damage.  
  Note the above picture. It shows the main causes of ammonia production. The fish breath in water across the gills, removing some oxygen and exhaling carbon dioxide and ammonia. The fish excrete urine and feces. The urine contains ammonia while the feces is deposited on the bottom of the aquarium as mulm where decay bacteria begin to break it down into ammonia and other by-products. In addition, when live plants are kept, leaves die off and are decayed in their turn. Any fish which expires and is not found rapidly also provides ample food for decay bacteria and creates large amounts of ammonia. The invisible life active at the bacterial level also creates their own quantities of dead material. This also adds to the ammonia production in the aquarium. The aquarium and all the life within it creates an active ammonia factory manufacturing a huge quantity of ammonia solubilized into the water of the tank. The concentration rapidly builds to lethal levels well before the beneficial bacteria nitrosomonas can reach adequate populations to reduce and eliminate the ammonia as rapidly as it is produced.  
  Characteristics of Lithotrophic bacteria            
  nitrosomonas (and nitrobacter) are termed lithotrophic bacteria, they require oxygen and their food source to survive. In addition, since they are soil bacteria, they prefer to anchor and build populations on clean hard surfaces. They are quite slow to replicate, as far as the rapid world of bacteria are concerned. In fresh water they tend to replicate geometrically every 8 hours, salt water slows the reproductive rate to about once every 24 hours. Going back to the sterile environment of a new aquarium, and we assume a single bacteria drops in from the outside [it really makes no difference from where], then the reproductive cycle of the bacteria determines the speed at which the aquarium will become optimally able to process ammonia and nitrite as it is produced.  
  Day 1 - 10                    
  Note the first 10 days on the above graph. Ammonia begin a rapid rise up to lethal levels and then drops dramatically to close to a zero level. The replication of the bacteria determine this rise and fall. Since they replicate geometrically, the hypothetical first "bug" becomes 2 in 8 hours, then 4 (16 hours) then 16 (24 hours) the 32 (32 hours) then 64 (40 hours) and so on..... It takes about ten days in relatively ideal conditions for the bacterial to replicate to population where all the ammonia produced within the aquarium is immediately reduced to nitrite. What is shown on the graph is the sudden drop of ammonia concentration slightly after the 10 day maximum.  
  Day 10 to 21                    
  The next 21 days, after the ammonia spike drops to minimal, now show a low to zero level of ammonia residue, but a steadily increasing concentration of nitrite, rising much higher in concentration than the ammonia graph, about double in fact. Nitrite is toxic, but not as toxic as ammonia, thus the simple fact that the concentration can rise so high without a total loss of fish. As nitrite becomes more evident, so do the populations of nitrobacter removing the nitrite from the system and changing it into nitrate [and energy for the bacteria]. As the populations grow, they gradually become able to reduce nitrite as soon as it is created by nitrosomonas acting on ammonia production. After 21 days from the beginning of nitrite build-ups the spike falls rapidly to the low levels of the graph. From there the nitrate levels start to rise over time.  
  There's a Glitch                  
  There is a problem with the above simplistic view, Mother Nature has thrown a curve into the straightforward Nitrogen Cycle reviewed above. The bacteria that reduces nitrite to nitrate, nitrobacter is inhibited by a free concentration of ammonia in the water. This is the reason that the nitrobacter population is essentially kept at a zero level until day ten when the ammonia spike reaches the minimum level. Once the ammonia inhibition is removed, then (and only then) nitrobacter can begin to replicate. They are also lithotrophic so they require the same things that nitrosomonas require, oxygen, their food source and clean hard places to attach and populate.  
  After Day 31                    
  Once the nitrite is removed as fast as it is produced by nitrosomonas, the final by-product of the Nitrogen Cycle is nitrate. It is a compound which is not easily reduced any further by aerobic bacteria. Because of this, the nitrate levels begin to slowly rise and continue to build over the rest of th life of the aquarium. The best way to get rid of nitrate is simply to practice proper water maintenance procedures. With regular water changes, nitrate is diluted, removing water with high nitrate concentrations and replacing it with low nitrate conditioned tap water is one of the most effective ongoing ways to eliminate nitrate. A second method tried in various ways is to promote anaerobic bacterial growth, this takes nitrate and reduces it to nitrogen and other by-products. In my opinion, this is dangerous, and extremely difficult to control. If it doesn't go correctly, hydrogen sulfide and pother toxic gasses are released into the water column in bubbles. I have found proper water maintenance is much better than relying on questionalble anaerobic techniques to remove nitrate.  
  Biological Innoculation                  
  When biological innoculation products such as Hagen's Cycle, Hagen's Waste Control and Amtra's Clean are created, they must take into account this little glitch. It precludes a "magic potion" where you simply add a culture of bacteria and suddenly the Nitrogen Cycle's run-in period is eliminated. Cycle does noticeably reduce the run-in time of a new aquarium, and it dramatically lessens the ammonia and nitrite spikes within the run-in period, but it must be regularly added to the aquarium to overcome the fact that ammonia inhibits nitrobacter. Using a regular weekly dose, the little glitch mentioned earlier is overcome by the regular addition of high numbers of both nitrosomonas and nitrobacter.