The nitrogen cycle is, in my opinion, one of the most important things to understand in the aquarium hobby. With a good educational foundation in just the basics a reefer can save a tremendous amount of time and money in the long run. Fish, coral, and invertebrate deaths, cyanobacteria outbreaks, and various types of algae outbreaks are some of the most common results of an unbalanced nitrogen cycle.

Before I go into the specific details of the stages I would like to cover the differences in the bacteria that are responsible for all of the conversions. The 2 basic types of bacteria involved are aerobic and anaerobic bacteria.

Aerobic bacteria are responsible for converting ammonia into nitrites and nitrites into nitrates. All aerobic bacteria require oxygenated water. Generally the more oxygen the better. Aerobic bacteria can be found on the surfaces of live rock, the substrate, sponge filters, and the tank glass to name a few. Pretty much any area of the tank that gets the oxygen rich water and driven by plenty of water flow. This is why trickle filters and bio-balls are so effective at removing nitrites and ammonia. With the constant water flow and the high exposure to air the bacteria can thrive. There is a saying that really annoys me that bio-balls are nitrate factories or that they produce nitrates. It is not that I am an advocate of bio-balls but that this is a misleading statement. Bio-balls in and of themselves produce nothing. The problem with them is that they are not a suitable “home” for anaerobic bacteria leaving the nitrogen cycle incomplete and because of this the nitrates do not get converted and accumulate.

Anaerobic bacteria are responsible for converting the nitrates into nitrogen gas that gets released into the air. This bacteria requires very low oxygen levels. The most common locations for the anaerobic bacteria are in the middle of live rock and the lower levels of the substrate. It is important to note however that not all rock is a suitable home for anaerobic bacteria. First the rock must be of appropriate size and must have the appropriate flow through the rock. Generally the water is transported to the bacteria by either the right amount of water flow over the rock or by the micro-organisms that live in the rock, hence the term “live rock”. If ample locations for anaerobic bacteria to populate are not provided then other steps must be taken to remove the nitrates from the tank. For instance a bare bottom tank with minimal live rock will require more “nitrate supervision” than a tank with a 4” deep sand bed and 150lbs of live rock.

The nitrogen cycle can be broken unto 4 specific stages:

Stage 1: Organic material (detritus, uneaten food, dead organisms) break down into Ammonia (NH3)
Stage 2: Aerobic bacteria convert Ammonia (NH3) into Nitrites (NO2)
Stage 3: Aerobic bacteria (a different strain than in stage 1) convert Nitrites (NO2) into Nitrates (NO3)
Stage 4: Anaerobic bacteria convert Nitrates (NO3) into Nitrogen gas


Stage 1: This stage is important for numerous reasons. First of all this is one of the areas that a reefer can change their husbandry habits and greatly affect the rest of the cycle, thus affecting the health of the tank. One of the biggest actions that can be taken here is to be careful not to overfeed. As a general rule all of the food that you put in the tank should be consumed within 2-3 minutes. How often one should feed the tank will be determined by the livestock inhabiting the tank. For example, most species of Anthias prefer to be fed several (2-4) small meals a day as opposed to some species of Blennies that only need to be fed once a day or Dragonets that will feed all day long on Copepods and (if there is enough pods in the tank) require no supplemental feeding. Only feeding what your livestock can eat will help reduce the dissolved organics in the tank which will in turn reduce the frequency and severity of algae and cyanobacteria outbreaks.

The second reason this is an important stage is the negative effects that high levels of ammonia can have on your livestock, particularly the fish. According to Wilkes University, “Fish may suffer a loss of equilibrium, hyper excitability, increased respiratory activity and oxygen uptake, and increased heart rate. At extreme ammonia levels, fish may experience convulsions, coma, and death. Experiments have shown that the lethal concentration for a variety of fish species ranges from 0.2 to 2.0 mg/l. Trout appear to be most susceptible of these fish and Carp the least susceptible.
At higher levels (>0.1 mg/liter NH3) even relatively short exposures can lead to skin, eye, and gills damage. Slightly elevated ammonia levels falling within the acceptable range may adversely impact aquatic life. Fish may experience a reduction in hatching success; reduction in growth rate and morphological development; and injury to gill tissue (i.e., hyperplasia), liver, and kidneys. Hyperplasia-the gill filaments are swollen and clumped together, reducing the fish's ability to 'breath'.”

Generally after a tank has cycled there will be sufficient bacteria present to convert most (to say all would be too inclusive but the remaining amount is not significant) ammonia in the tank into nitrites. The general exception here is when new livestock is added to the tank. While adding 1 or 2 fish might not affect the cycle, adding 4, 5, or more fish could cause a sudden spike in ammonia levels as a result from the extra detritus and food that will be introduced. Therefore, sudden changes in bioload should be avoided, if it is not steps should be taken to reduce the ammonia levels as quickly as possible should they spike. There are several methods of doing this including water changes, bacterial additives like Seachem’s Stability, and chemical additives like Prime.

Monitoring and controlling this first stage will help you create a balanced nitrogen cycle and will save you and your livestock from a lot of stress.

Stage 2: This is the step that a reefer can take a breath on. Nitrites are the least harmful to all tank inhabitants and because the bacteria that convert them are aerobic there is generally not much in the tank. I should note here that this varies between fresh and saltwater aquariums. With some freshwater species nitrite levels at 1ppm can be toxic. However with most marine species the tolerance was much greater. According to a study done by Randy Holms-Farley “Tests in marine species, however, showed the toxicity to be much lower. None of the thirteen marine fish species for which I could find nitrite toxicity data had LC50 values below 100 ppm, and half had LC50 values of 1,000 - 3,000 ppm or more.” The amount of nitrites required to be considered toxic for a reef combined with the natural resistance more livestock have to it make nitrites low on the list of things to worry about. In the same article Randy Holms-Farley wrote, “In reality, nitrite probably is not toxic enough to warrant measuring in most marine systems.” But if you have the test (which is standard in most kits) you might as well. It just might alert you to a problem that needs to be addressed.

Stage 3: This is the stage that produces one of algae’s favorite reef tank elements…nitrates. This stage, similar to the previous, does not usually have any problems getting established due the responsible bacteria being aerobic and the abundance of suitable locations in most reef tanks.

Like ammonia there are, at least, two significant reasons to monitor this stage of the cycle. First, nitrates are a significant variable in the frequency and severity of algae and cyanobacteria outbreaks which can not only make the tank look bad but can kill corals. Along with light, phosphates and nitrates are algae’s main food sources. Keeping the nitrates under control will significantly help with this issue. There are several methods of reducing nitrates including the use of a nitrogen sponge, water changes, and macro algae.

The second reason to monitor this stage is the sensitivity of the invertebrates to high levels of nitrates. Corals and fish as actually pretty resilient to nitrates. This natural resistance is not as strong as it is to nitrites but in fish only tanks nitrate levels of 10-30 ppm is acceptable. Like fish, most corals can tolerate elevated levels of nitrates and some have shown better growth with slightly elevated levels. The exception however is calcerous corals as they showed a decreased growth rate. At excessive levels of nitrates almost all corals show a decreased growth rate. An article in the Advanced Aquarist by Randy Holmes-Farley stated, “elevated nitrate can excessively spur the growth of zooxanthellae, which in turn can actually decrease the growth rate of the host coral.” Many invertebrates however cannot tolerate high levels of nitrates and excessively high levels can kill them. As with most livestock some inverts, like starfish, are more susceptible than others. This high sensitivity is frequently noted in the description if purchased from an online retailer.

There are several methods for lowering nitrates in the reef tank. Some of these methods will have inhibiting factors such as space or cost. A few of the methods utilized are water changes, nitrogen sponges, activated carbon, refugiums stocked with macro algae or mangroves, and algae scrubbers. Having a skimmer (also known as a foam fractitioner) that is powerful enough to handle the bioload will also make a huge difference in the entire nitrogen cycle by removing dissolved organics from the water column.

Stage 4: This is the stage that most reefers struggle with. Anaerobic bacteria in the reef tank are solely responsible for the conversion of nitrates into nitrogen gas. The problem with this stage usually arises when there are not enough locations available for the anaerobic bacteria to colonize. As mentioned earlier these locations are most commonly the interior of live rock and the lower levels of the sand bed. Water transportation to these areas is also a factor. Studies have shown that if there are sufficient micro organisms (worms, pods, etc) living on the rock that the movement of their bodies in and out of the holes on the rock can provide enough water movement to facilitate this process. Conversely if the rock in your tank is not “live” then it may not be sufficient for nitrate reduction. This same logic can be applied to the substrate.

This stage is also the reason most reefers will now tell you to remove your bio-balls if you are using them. As stated earlier it is not that the bio-balls themselves are producing nitrates but that they are not capable of hosting anaerobic bacteria in any significant numbers, if at all. Recently I heard an explanation as to why this is more of an issue with bio-balls than with smaller rock in the tank. It was hypothesized that when the nitrates are produced at the bio-balls that the nitrates must travel through the filtration, back into the tank, and into the anaerobic zones before being converted. Since there is not a direct route to these zones many of the nitrates just continue to float around the tank and do not get converted resulting in elevated levels. When the nitrates are produced on the surfaces of the substrate and live rock it is already in position to be transported to the anaerobic zones for conversion. Since there will be a finite amount of aerobic bacteria in the tank (limited by the available “food”, in this case nitrites) you want to them to colonize on the substrate and rock, not the bio-balls. In other words, if 80% of the nitrates in your tank are produced at the bio-balls then 80% of the nitrates in your tank must travel a greater distance to be converted reducing the changes that they will be converted at the same rate that the nitrites and ammonia are being converted throwing off the equilibrium and resulting in elevated levels of nitrates.

That is a general overview of the nitrogen cycle. Any of these stages could be discussed in much greater detail but this post is already long enough. If anyone would like more information on anything specific please ask. If anyone would like the links to articles referenced in this post please ask. I hope this was helpful!

Nice write up kid....excellent work.

+2... Good Info!!!