NITROGEN CYCLE AND AQUARIUM & POND CYCLING;
How the Aquarium Nitrogen Cycle Works
By Carl Strohmeyer
Please click on the picture for a better view, of a BASIC explanation of the "Aquarium Nitrogen Cycle".
Please see a more advanced diagram further in this article.
The aquarium nitrogen cycle is simply put the method by which diffusion from the gills of the fish and their wastes, as well as other decomposing organic matter (such as uneaten fish food) is converted from Ammonia or Ammonium to Nitrites to Nitrates.
What is Nitrogen?
Nitrogen is an element vital to all life processes on Earth. Nitrogen is very important in our biosphere, where nitrogen comprises 78% of the atmosphere, and is part of every living tissue. It is a component of amino acids, proteins and nucleic acids. With the exception of carbon, nitrogen is the most universal element of life. Life could not exist without nitrogen. See Reference Note.
Some Types of Bacteria Important to the Nitrogen Cycle;
• One of the most important biological conversions involves the transformation of N2 into a form readily available for plants.
OTHER ORGANIC WASTEI think it is important to explain that not all organic waste contributes to the nitrogen cycle, (hence high ammonia, etc.). The importance of knowing this is that certain organics may have low amounts or NO nitrogen containing compounds, so controlling the addition of high content nitrogen containing compounds can be important in keeping lower nitrates in established aquariums or lower ammonia/nitrites in less established aquariums (or aquariums that have had their bio cycling process interrupted).
All plant and animals contain proteins (amino acids) and lipids, of which varying amounts of nitrogen atoms are contained depending on the molecule in question.
HOWEVER sugars, carbohydrates (starches) and most fats (fats are a form of lipids, generally without nitrogen atoms though) do not contain nitrogen atoms and therefore CANNOT directly contribute to the nitrogen cycle of your aquarium or pond (bacteria that feed on these oils can multiply and indirectly affect ammonia/nitrites/nitrates).
As well different animal and plant matter have varying amounts of nitrogen containing molecules (with plants in general containing less than animals). The few lipids that contain nitrogen atoms generally have few, and are often less of a factor as well.
It is noteworthy that while these these sugars, carbohydrates, and fats do not contribute to the nitrogen cycle, these do contribute to the aquarium bio load, albeit to a lesser amount than nitrogen containing organics.
See: Aquarium Bio-Load
With this in mind, more fish equals more nitrogen compounds released into an aquarium/pond, as well higher protein foods such as shrimp will also add more nitrogen compounds.
While plants, even decomposing plants generally release fewer nitrogen bearing compounds than a decomposing fish or fish waste. So controlling these molecules via fish numbers vs. plant numbers and diet is important even for an established aquarium (so as to control nitrates).
Here are a few chemical formulas for example:
When an organism dies, nitrogen is moved from plant or animal into the inorganic chemical ammonia by the process of bacterial decay. Ammonia is also produced by bacteria in the breakdown of protein. This process is called Mineralization and is the end result of the metabolism of food.
The Nitrogen Cycle: New Developments and New Prospects
Back to the more Basic/Traditional Explanation:
Ammonia, in its neutral state, exists as ammonium (NH4+). Ammonium (NH4) is formed by the protonation (the addition of a Proton (H+) to the molecule.
What are nitrifying bacteria?
There's a lot of confusion among aquarists about nitrifying bacteria. This is due in large part to the recent emergence of a wide variety of bacterial products claiming to be nitrifying aids.
Another point of disagreement about these bacteria, based on my assertion; since most aquarium diseases are gram negative (especially marine), diseases such as Vibrio, Columnaris, Pseudomonas, Aeromonas and their resulting treatment with antibiotics such as Kanamycin or Nitrofurazone (which are primarily gram negative) will NOT interfere with the nitrifying cycling process when used correctly.
Another commonly used product for aquarium Ich infestation is Malachite Green, despite some common anecdotal comments Malachite Green, as well as Copper Sulfate DO NOT affect nitrifying bacteria (please see references below).
See this article: Aquarium Medications Part 3, Malachite Green
We have ammonia-oxidizers and nitrite-oxidizers in both fresh & saltwater:
AOB ="Ammonia Oxidizing Bacteria"
NOB ="Nitrite Oxidizing Bacteria"
Species of marine nitrifying bacteria are different from those that prefer fresh water, and yet, are very closely related.
A few key points about ammonia:
Denitrification is the process by which microorganisms convert nitrate (NO3) to nitrogen gas (N2). In terms of the global nitrogen cycle, denitrification serves to balance nitrogen fixation by removing fixed nitrogen (rather than supplying it) to the biosphere.
As a generalization, aerobic nitrification takes place in the top 1-2 inches of substrate (deeper in courser substrate, or more shallow in fine sand). While nitrogen fixing anaerobic bacteria oxidize nitrates in an area of 2-4 inches of substrate (again deeper for course media, more shallow for fine sand). Finally Sulfur fixing anaerobic bacteria that produce hydrogen sulfides generally live in substrate over 3-4 inches in depth.
Nature can pack a lot of bacteria into small places, which is to the advantage of the aquarist. For bacterial growth, all that is required is ammonia and oxygenated water. This is the beginning of the nitrogen process and the growth of bacterial colonies.
As noted earlier, Bio-Wheels are very popular, but in my tests in my maintenance business they are VASTLY overrated. They tend to accumulate hard water deposits and stop and even when they are working my tests have shown little difference in aquariums when they are removed as compared to Sponge filters or Fluidized Filters.
Bio Filtration during use of Medications in Aquariums:
During the use of medications, in particular gram positive antibiotics/antimicrobials your aquarium (or pond’s) important aerobic nitrifying filter bed may be damaged or outright destroyed. However, the majority of aquarium fish diseases are gram negative, so using medications such as Kanamycin are much less likely to damage your aquariums bio filter bed when used properly, including water changes prior to each treatment.
Although systemic treatment of a display aquarium is often necessary, when possible, treatment in a quarantine tank will avoid the above problem in the first place.
In healthy aquarium ammonia and nitrites should be at 0 ppm
In a healthy freshwater aquarium Nitrates should be 15-50 ppm (below 15 ppm is not healthy for planted freshwater aquariums).
METHODS OF AQUARIUM CYCLING:
Many associate fishless cycling with the pure ammonia method, however fishless cycling is ANY method that does not introduce fish immediately or until the aquarium has gone thru the nitrogen cycle. In other words, the ammonia and nitrites have gone up then back down which can take from 10 to as long as 45 days depending on method tank size and temperature. I will note that method one (if done properly) rarely results in an ammonia and nitrite spike, this is why it is my preferred method WHEN possible.I do NOT recommend adding “starter” or cycling fish to start your nitrogen cycle for either freshwater or saltwater.
Regardless of method used, a product that can further aid in establishment of your bio filter is AAP Shieldex. This is NOT a cycling aid, rather it is a slime coat and water conditioner that also works extremely well as base for nitrifying bacteria to cling to.
Finally, before I jump into different cycling methods, I would like to note that testing your and keeping a journal of your water parameters during the cycling process (as well later on, but not at as frequent of intervals) is important in my opinion and will help you note subtle changes. The frequency is a mater of preference/experience, but I would recommend at least every other day for beginners (generally more advanced aquarists can recognize signs and perform cycling as a routine that requires less testing).
 Seasoned Filter Media:
My preferred cycling method is to transfer filter media.
The method of adding “aged” or "seasoned" media is much faster (you still have to take it slow, but this with this method some fish can and should be introduced immediately), and provides all the necessary bacteria, the only negative is adding disease pathogens to your aquarium, but I have rarely encountered this problem. To prevent this transfer of disease pathogens and parasites, only use a media source where no new fish have been added in 30 days, ALL water parameters are good, and if possible has UV Sterilization (although not necessary).
A mistake that is occasionally made is adding a new sponge filter to a fully cycled/seasoned aquarium for a week or two and then adding it to the new tank one is trying to quickly establish via this method.
It is also important to note with this method that you do not rinse filter media/gravel prior to addition to the new tank (especially not with tap water which can kill the nitrifying bacteria).
If fish are not added before 3-7 days, I suggest adding a small amount of liquefied fish food to feed your growing bacterial colonies. I will also note that the 3-7 days seems a bit vague, however this can vary due to temperature, amount of bacterial seed, and other factors, so I would not be overly concerned about the exact timing as I have added fish as soon as 2 days and as long as over a week with no problems.
For marine tanks the use of seasoned or “cured” live rock serve this purpose quite well.
This method (added media) will give you more instant bio bacterial colonies and this is method that is used by far the most by the professional aquarium maintenance community (which needs faster more sure results for their clients), despite the internet popularity of the next two cycling methods.
Also keep in mind that many pathogens such as pseudomonas are usually present in a healthy aquarium, but when fish are stressed, the fish are in poor health due to poor feeding and lack of proper minerals, and/or water conditions are less than desirable- these pathogens will be opportunistic and cause a disease in the fish.
A product that does not necessarily help speed up the cycling process itself, but de-toxifies the ammonia and nitrites during this process, allowing for less stress on fish while leaving the ammonia/nitrites still bio available to nitrifying bacteria is Prime.
As a negative to the aged bio-filter media, this simply may not be possible for a new aquarium owner who has no friends to obtain aged filter media or if one does not trust a Fish Stores (or even a friend) aquarium health for obtaining aged/seasoned filter media. In this case, I would recommend one of the next two methods.
 Ammonia Method;Another method is fishless cycling where un-scented pure ammonia is poured into the aquarium.
As noted, 4 ppm is a typical fishless cycling target. Higher (7 ppm) or lower (3 ppm) is also OK for healthy bacterial colony growth (based on mine and others in the maintenance communities experience).
This process usually takes about 3-6 weeks for the aquarium to cycle (when your ammonia and nitrites have dropped to 0).
However, please check your ammonia purchase by shaking the bottle at the store, if it foams or bubbles, it has detergents and should not be used.
This method is growing in popularity, however it is not without a few drawbacks.
Here are some pluses and minuses to this method;
*This method does not add actual bacteria (and is not really any quicker than the method below: adding fish food to a fishless aquarium) and because human nature is to want to add fish sooner than the 3-6 weeks it takes for this method.
*It is still not as quick as my preferred method above (seeded media, gravel, sand, live rock).
*This method is especially dangerous when used with live rock and/or sand that have already been added as the ammonia will kill me organisms that reside in live rock adding even more ammonia and pollution to your tank thus defeating the reason for this method.
*As a positive, if patience can be observed, this method is very safe when one considers the possibility of disease pathogen introduction from the aged media method (no matter how remote the risk).
*The pure ammonia method also has a positive over the fish food method in that there is no risk of Saprolegnia (mold) introduction to the new aquarium (although the “raw shrimp method” is of vastly higher risk for this than the fish food method).
*With both this and the dissolved fish food method, addition of any medications during the cycling process can and most often will interrupt correct establishment of a bio filter
 Fish Food Method;
Another method is the gradual addition of fish food to an otherwise empty aquarium (no fish). This can be a very effective means of cycling that is preferred by many experienced aquarists. This method takes about the same time as the pure ammonia method (2-6 weeks, usually about 3).
The only risk of the fish food method is the possibility of Saprolegnia (mold) growing on rotting fish food which can become pathogenic to new fish that will be introduced later.
TIP/NOTE: I suggest for even better utilization of the fish food cycling method to add this liquified fish food toa baster or syringe and in inject directly into a runnig high capacity sponge filter (such as the AAP Hydro Sponge Filter) or simlar quality bio filter.
Regardless of fishless cycling method chosen, the bio load is always going to be in flux (higher or lower). When higher is needed, nitrifying bacteria double in population in 18 to 24 hours. When less are needed, they die back and are consumed by each other.
*Please note, that with both this and the pure ammonia method, addition of any medications during the cycling process can and most often will interrupt correct establishment of a bio filter
 Other fishless cycling methods;
There are other methods of fishless cycling being recommended or used however one method being pushed on the internet by "cut & paste", anecdotal websites and forums is the use of Raw Shrimp; however this is a recycled idea (which included the use of silversides, frozen shrimp, and even dead feeder fish) and has reappeared on the internet even though it was debunked in the early 1990's!
Another note/point is that even the fish food method (as noted earlier) can allow for Saprolegnia to get a foothold in an aquarium if food is simply dumped into an aquarium, making this method not any better than the “Raw Shrimp or Silversides” method as its decay will also attract Saprolegnia (or heterotrophic bacteria), so make sure to liquefy fish food prior to addition to your aquarium when used for cycling.
 Cycling Products;
There are many products for cycling available too, but most in my experience/tests do not work well with the exception of SeaChem Stability, Fritz #7 or #9, Microbe-Lift Nite Out, Dr Tim's One & Only , & possibly BioSpira.
It is also noteworthy that many I know in the aquatic community such as others in aquarium maintenance profession as well as aquatic forums have not had all that good of results in tests with BioSpira, possibly due to poor storage, etc.
Another problem with many cycling products is due to the fact that aerobic nitrifying bacteria cling to media and gravel (this has been PROVEN scientifically) and do not work while suspended in water. Also poor storage and shelf life undoubtedly play a role as well, and proper since storage and handling cannot often be well verified, this explains the often mixed results especially with BioSpira.
Liquid Cycle and Stress-Zyme are just preserved bacteria (mostly Heterotrophs) that are more useful for over feeding or other bio over loads in an established aquarium (as aerobic bacteria needed for nitrification do not store well in liquid form at room temperature without oxygen).
Tetra Safe Start is another newer product, that makes many claims, but without any real proof to date (as well previous experience with most of their products over the last 3 decades leaves me with LITTLE trust of any product with a Tetra Label).
Another product on the market by a VERY reputable company; SeaChem, is “Stability”.
SeaChem claims this to be a synergistic blend of aerobic (including encapsulated oxygen Autotrophs), anaerobic, and facultative bacteria.
Dr Tim's One & Only & Microbe-Lift Nite Out are similar, both with "lab developed" aquarium nitrifiers that can be stored at room temperature in sealed bottles (although I personally do NOT recommend Dr. Tim's for reasons of business practices).
My recommendation in the past as it pertains to Stability & the other similar products is to use it as an aid in cycling of new aquariums or (better) as a boost when the bio load of an aquarium suddenly “jumps’ for whatever reason, NOT a primary way to cycle your aquarium.
If any non-refrigerated cycling product is to be used in an aquarium, as I noted earlier, Stability would be the first choice I would recommend for an aquarium that already has fish and is encountering cycling problems (whether an established aquarium that had a spike in bio load for whatever reason or a newer tank that had a set back for whatever reason).
*Note; With any cycling product (especially the more proven products such as Fritz Turbo Start and Stability), it is best to add these products only when “food” in the form of raw ammonia or fish waste is present; so my recommendation is to wait a day or two after adding fish or to add pure ammonia immediately prior to these products.
* "Dry" Cycling Products; there are many powered cycling products such as API Pond Zyme and the aquarium "EcoBio-Block".
 Marine Aquariums;
Seasoned Live Rock is an excellent way to jump start your marine tank nitrogen cycle.
This live rock should likely also have some “food” for the nitrifying bacteria as well as healthy colonies of Nitrosococcus, Nitrospira, & Nitrococcus nitrifying bacteria in the outer areas where oxygenated water circulation can reach these bacteria. It is important to keep good circulation around your live rock with a power head or propeller pump once introduced into your new aquarium.
*Also the use of “live saltwater” is NOT based in any real scientific evidence since nitrifying bacteria secrete glue like substance to adhere to substances such as live rock and are generally not found in real quantity in the water column.
*Finally I will note as to different cycling methods; I have used these different methods in my Aquarium maintenance and research business in controlled tests and still found that the added media/sand/gravel/seasoned live rock method works fastest and with the best results, although I have also had good results with this method combined with the fish food method (do not combine with the pure ammonia method).
*Effect of plants on Aquarium Cycling:
Water changes are helpful during cycling, whether fishless or with methods such as “seasoned filter media” that allow for fish to be present. This is a point that is often missed due to inaccurate information that is still disseminated about lowering bacteria in the water column or in the gravel by performing water changes since aerobic Autotrophic nitrifying bacteria secrete a glue like substance (please see the section near the beginning of this article: “Biofiltration”).
Another important point as to the use of cycling products, whether it be Cycle or the overly touted Bio Spira; often aquarists (even so called experts, and I have to admit to being guilty to this at times myself), will base an opinion on whether a product or method is effective or is not effective on non-controlled observations.
Here is my explanation, the Heterotrophic Bacteria contained in Cycle will decompose some of the organics, thus lowering initial ammonia output, but this is not actually “seeding” your aquarium because as soon as you cease using this product your ammonia will go right up due to the lack of Autotrophic nitrifying bacteria.
Of course my example also shows where these products can be useful as well, just do not depend on them for cycling. I might also make the point that by either employing fishless cycling or aged filter media, this should never come down to the use of such products (unless your bio filter has been disrupted by the use of gram positive medications, extended, power failures, etc.).
WHAT TO DO FOR HIGH AMMONIA OR NITRITES (when Fish are already present):
Steps to temporarily improve high ammonia problems (emergency ammonia poisoning procedures)
HOWEVER, make sure that 100% water changes are NOT performed, even with small Betta bowls.
Be aware that if your aquarium has copious amounts of decomposition in the absence of correct KH Buffers likely will result in a low pH. A pH under 6.5 will convert much of your aquarium ammonia to non toxic NH4 all the while slowing the nitrogen cycle and thus natural removal of ammonia.
* Use SeaChem Prime (removes chlorine/chloramines, detoxifies ammonia & nitrite) or Amquel Plus or to a lesser extent many other older generation Ammonia/Nitrite de-toxifiers such Ammo Lock, or Amquel. These products do not remove ammonia they change the ammonia from highly toxic NH3 to less toxic Ammonium (NH4).
* Add a cycling aid, such as SeaChem Stability which interferes the least with establishment of a healthy bio filter in your substrate or filters as it provides both Autotrophic and Heterotrophic bacteria as well, unlike competing products, the bacteria employed by Stability are non-sulfur fixing and will not produce toxic hydrogen sulfide.
* Add salt (NaCl); this is a popular method for "nitrite poisoning" and should be added at 1 tablespoon per 5 gallons to 1 teaspoon per gallon depending upon fish sensitivities. The addition of salt will prevent methemoglobin that forms in the blood due to nitrite exposure from building up.
* For high ammonia or nitrite exposure (common in fish shipped from long distances), the use of Methylene Blue in 30 minute baths is very effective and also counters the effects of methemoglobin in the blood by increasing the hemoglobin oxygen carrying abilities.
* It is also common for ammonia and/or nitrite spikes after moving or transferring an aquarium.
Steps for a long term solution to lower ammonia levels
* Add "seasoned" by bio media such as sponge or filter fiber from another healthy tank to kick start your bio filtration.
* Add filter media with high abilities to maintain nitrifying bacteria such as Volcanic Rock, Ceramic Bio Media, and especially SeaChem Matrix
* Consider zeolite in the filters to absorb some of the ammonia (FRESHWATER ONLY!).
* Use of chemical absorbents such as SeaChem Purigen placed in a filter or other high flow areas (even placed in a bag at the base of a sponge filter).
* Cut back on feeding and do not use fish foods high in non-aquatic proteins, which are mostly un-digestible by fish and add to your ammonia.
* Increase pH slowly and more importantly KH, as a pH below 7.0 slows the growth of nitrifying bacteria (as stated earlier in this article).
* Increase Bio-Filtration;
This is a much more common problem with bowl/small aquarium filters, as many buy poorly designed under gravel filters with small carbon (& sometimes a few grains of zeolite added) under the mistaken belief these can remove much ammonia/nitrites, which in controlled tests are very inadequate.
* Although as explained earlier that products such as "Cycle", or "Stress Zyme" are not good choices for "kick starting" your aquarium or pond nitrogen cycle (in other words used as a biological cycling product), they DO contain Heterotrophic Bacteria than can at least consume some of the organic waster while your nitrogen cycle is still in the process of establishing itself or re-establishing itself if the bio filter has been interrupted by gram positive medications (assuming fish are present, otherwise I would not use them).
WHAT TO DO FOR HIGH NITRATES:
Although not generally toxic, high nitrates over 50 ppm can stunt fish growth and lead to health issues if fish are exposed to high nitrates for an extended time in freshwater.
Please note that these suggestions/points are NOT an exhaustive list, please follow the links at the end for more complete information.
FREQUENTLY ASKED NITROGEN CYCLE QUESTIONS & ANSWERS:
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