To answer the initial question in post #1, no, beginning aquarists must understand the nitrification cycle and somehow deal with it, or dead fish will result. I wrote an article a couple years back on bacteria, and as my contribution to the discussion I will cut and paste relevant portions, being those directly concerned with nitrification.
The Nitrogen Cycle
Nitrogen comprises about 80% of our atmosphere, and every life form on earth works hard to acquire it. In the aquarium, nitrogen exists in four forms: ammonia [NH3], ammonium [NH4], nitrite [NO2] and nitrate [NO3]. [This excludes the denitrifying aspect where some of the nitrate returns to nitrogen gas.]
Ammonia is a by-product of all aerobic metabolisms—fish, snails, invertebrates, fungi and bacteria; it naturally occurs from continuous biological processes and living organisms in any aquarium, and even at very low levels this ammonia is very highly toxic to all life. At levels between 0.5 and 1 ppm there can be long-term or permanent gill damage. Ammonia is never healthy at levels that can be detected by our standard test kits, and in most cases will have negative effects on the fish. [1]
The fastest uptake of ammonia in an aquarium occurs with live plants; ammonia can be both assimilated (as a nutrient in the ionized form ammonium) and taken up (as a toxin, NH3) by plants. But ammonia is also taken up (though more slowly) by certain nitrifying bacteria, and this produces another form of nitrogen—nitrite, which is also highly toxic to all life at very low levels. Fish readily absorb nitrIte from the water and it combines with the hemoglobin in their blood, forming methaemoglobin. As a consequence, the blood cannot transport oxygen as easily and this can become fatal. At 0.25 ppm nitrite begins to affect fish after a short period; at 0.5 ppm it becomes dangerous; and at 1.0 ppm it is often fatal.
Another group of bacteria take up nitrite, producing nitrate, which is still toxic though much less so. High levels of nitrate, above 40 ppm, have been shown to slow fish growth, suppress breeding, and depress the immune system making the fish much more susceptible to disease. While different fish species show some variation in tolerance, a level below 20 ppm is recommended, and preferably below 10 ppm. After all, most of our fish occur in waters with nitrate so low it can scarcely be measured. Live plants and regular partial water changes both work to achieve this desired state in a balanced aquarium.
The bacteria responsible for this nitrification process of converting ammonia to nitrite to nitrate are termed nitrifying. But the nitrogen cycle is only complete (in aquaria) when it includes de-nitrification; in this stage, different bacteria that are termed denitrifying convert nitrate into nitrogen gas which is released back into the atmosphere. Another component of the complete nitrogen cycle in nature but not present in our aquaria involves the “fixing” of atmospheric nitrogen by cyanobacteria and other life forms.
Nitrifying Bacteria
Nitrification is the oxidation of ammonia/ammonium to nitrite and then the subsequent oxidation of nitrite to nitrate; this is performed by two groups of bacteria known collectively as nitrifying bacteria or nitrifiers. True nitrifying bacteria are autotrophs; they use chemosynthesis to manufacture their energy by using oxygen plus nitrogenous waste (ammonia or nitrite) and carbon (from CO2). There are several different bacterium species involved, all in the family Nitrobacteraceae, that carry out this function in soil, and it used to be thought that these, particularly Nitrosomonas europa and Nitrobacter, were the nitrification bacteria in freshwater. But Dr. Timothy Hovanec led the team of scientists that proved this to be a mistaken assumption. Ammonia is converted to nitrite by bacteria of the Nitrosonomas marina-like strain [2] and nitrite is converted to nitrate by bacteria closely related to Nitrospira moscoviensis and Nitrospira marina. [3] With several subsequent scientific studies by other scientists on wastewater nitrifying bacteria this data is now accepted and confirmed scientific fact. [Ed. This is now believed to be the bacteria in new systems; these disappear as the aquarium establishes, to be replaced by another lifeform, archaea.]
Once established, the population of these bacteria in an aquarium will be in direct proportion to the amount of ammonia or nitrite respectively. Nitrifying bacteria require 12-32 hours to multiply, which they do by binary division [each bacterium divides into two bacteria]. Nitrosomonas multiply in less time (12+ hours) while Nitrospira require more time (up to 32 hours). In a new aquarium, it can take up to eight weeks for the bacteria populations to reach a level capable of eliminating ammonia and nitrite.
The nitrogen cycle bacteria in aquaria are lithotrophic; the word comes from the Greek lithos [= rock] and troph [= consumer], so literally it means “rock eater.” Realistically, it means these bacteria colonize surfaces. The scientific processes that cause this may most simply be described as the bacteria being pulled from the water by several actions occurring on the surfaces. Bacteria are sticky; they exude protein coatings that allow them to build up into a slimy film that we term a biofilm.
Endnotes: [bracketed numbers above]
[1] For more detailed information, see “Nitrogen Cycle,” The Skeptical Aquarist website. Also Neil Frank, “Ammonia Toxicity to Freshwater Fish” on The Krib website. Also Robert T. Ricketts, “Aquarium Microbes, Part 1, Nitrification” on The Aquarium Wiki website.
[2] Paul C. Burrell, Carol M. Phalen, and Timothy A. Hovanec, “Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria,” Applied and Environmental Microbiology, December 2001, pp. 5791-5800.
[3] Hovanec, T. A., L. T. Taylor, A. Blakis and E. F. DeLong, “Nitrospira- Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria,” Applied and Environmental Microbiology, Vol. 64, No. 1, pp. 258-264.
