This article will briefly discuss the bacteria related to what we term the nitrogen cycle. The information herein is my summation of the scientific and practical data in various sources including those mentioned in the endnotes. Endnote references are identified in the text by the number in square brackets [x]. Due to text limits, the article is separated into successive posts; the endnotes are in the third part.
Bacteria are essential for life on the earth, and they exist everywhere; in only one milliliter of freshwater there are a million bacteria cells, invisible to the naked eye. The name bacteria is the plural of bacterium, which is the Latinized form of the Greek bakterion [bakteria] which means a staff or cane, so named because the first bacteria discovered were rod-shaped. They are single-celled prokaryote microorganisms; prokaryotes are organisms that lack a cell nucleus. Bacteria occur in two forms, autotrophic and heterotrophic.
Autotrophic bacteria synthesize their own food, and they require oxygen so they are termed aerobic. Some do this via photosynthesis using sunlight, oxygen and water. Others use chemosynthesis, a process whereby they manufacture carbohydrates from carbon dioxide (CO2) and water using chemical nutrients rather than sunlight as the energy source. Science now believes that chemosynthesis was what allowed life to begin on earth, a view supported by the fairly recent discovery of the remarkable ecosystems around the hydrothermal vents on the ocean floor that have absolutely no relationship with sunlight—conditions very similar to those that initially existed on the earth for hundreds of millions of years before any form of life appeared.
Heterotrophic bacteria cannot synthesize their own food so they need organic material such as fish waste, dead bacteria, fish and plant matter, etc., and while some are aerobic, many are facultative anaerobes, meaning that they can survive in either the presence or absence of free oxygen. Anaerobes are organisms that do not require free oxygen for growth. This has significant consequences in aquaria.
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. These also attract and bind fungi and algae. Snails, shrimp and fish seen grazing these mats are feeding on the countless microscopic creatures and algae that live there. But this is not their most important function; these biofilms are absolutely essential to a healthy aquarium because of the bacteria they contain.
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].
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.
Bacteria are essential for life on the earth, and they exist everywhere; in only one milliliter of freshwater there are a million bacteria cells, invisible to the naked eye. The name bacteria is the plural of bacterium, which is the Latinized form of the Greek bakterion [bakteria] which means a staff or cane, so named because the first bacteria discovered were rod-shaped. They are single-celled prokaryote microorganisms; prokaryotes are organisms that lack a cell nucleus. Bacteria occur in two forms, autotrophic and heterotrophic.
Autotrophic bacteria synthesize their own food, and they require oxygen so they are termed aerobic. Some do this via photosynthesis using sunlight, oxygen and water. Others use chemosynthesis, a process whereby they manufacture carbohydrates from carbon dioxide (CO2) and water using chemical nutrients rather than sunlight as the energy source. Science now believes that chemosynthesis was what allowed life to begin on earth, a view supported by the fairly recent discovery of the remarkable ecosystems around the hydrothermal vents on the ocean floor that have absolutely no relationship with sunlight—conditions very similar to those that initially existed on the earth for hundreds of millions of years before any form of life appeared.
Heterotrophic bacteria cannot synthesize their own food so they need organic material such as fish waste, dead bacteria, fish and plant matter, etc., and while some are aerobic, many are facultative anaerobes, meaning that they can survive in either the presence or absence of free oxygen. Anaerobes are organisms that do not require free oxygen for growth. This has significant consequences in aquaria.
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. These also attract and bind fungi and algae. Snails, shrimp and fish seen grazing these mats are feeding on the countless microscopic creatures and algae that live there. But this is not their most important function; these biofilms are absolutely essential to a healthy aquarium because of the bacteria they contain.
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].
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.