Aquarium Nitrogen Cycle | Cycling Methods | Ammonia & Nitrates

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Aquarium Nitrogen Cycle
Sections Included:
The Internets most in depth/updated Nitrogen Cycle article!!

Frequently Asked Questions/Answers

(1) Introduction

(2) What is Nitrogen

(3) Non-Nitrogen wastes

(4) Nitrification; Nitrifying Bacteria, and an Ammonia Chart

Also, *Key Points about Ammonia

(5) De-Nitrification

(6) Bio-Filtration

Including *Use of Medication on Bio-Filtration)

(7) Methods of Aquarium Cycling:

Including *Fishless Cycling

*Seasoned Media

*Fish Food

*Pure Ammonia

*Raw Shrimp

*Cycling Products

*Saltwater Cycling)

(8) Maintaining a healthy nitrogen cycle

(9) What to do for high Ammonia & Nitrites, & Nitrates

(10) References & Downloadable pdf of this article

By Carl Strohmeyer-PAMR 40+ years experience
Updated 3/13/21

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.
Then Nitrates are then either converted to free nitrogen (which is a gas that will not remain in the water) by plants or de-nitrifying anaerobic bacteria, or you remove/lower your nitrates by way of regular water changes, or by using chemical absorbents such as Purigen.

Without this process going on in your aquarium/pond the keeping of fish or other inhabitants would be nearly impossible as ammonia is highly toxic in even small quantities (ammonium is not, but is quickly converted to ammonia at higher pH), nitrites are also toxic although not as much as ammonia. Nitrates are not toxic to most freshwater fish except in high amounts with long term exposure (this is not the case for many saltwater inhabitants though).
So with this in mind it is important to have an established aquarium nitrogen cycle in your aquarium or pond.
Please read on as this article has a lot of updated information about the Nitrogen cycle, including Cycling Methods (and is one of the more accurate and in depth articles available on the internet)!
If any section is difficult to understand, please continue reading, as the article will become more clear after reading as a whole, especially after multiple readings. This is one of the most important, yet most often misunderstood aspects of aquarium keeping, especially among newbies so truly understanding this process is very important, and as well not getting confused by the many anecdotal statements made about this process is important as well.

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.
Nitrogen is essential for organic development; nitrogenous compounds are also required by some organisms for metabolic functions and respiration. Unfortunately, free nitrogen in the atmosphere is not in a form that is usable by plants or animals. Because of its stable structural formula, it is relatively inert and does not combine readily with other elements.
All living organisms, from fish to plants, have great quantities of assimilated nitrogen in their tissues. Nitrogen is a fundamental ingredient for the formation of proteins and nucleic acids. Every organism you place in your aquarium adds nitrogen based compounds; from fish to coral, to live rock, to plants.
The introduction of food also adds nitrogen. Dead or alive, they are organic masses, and possess the same nitrogenous attributes as the fish, plants, invertebrates you added to your aquarium.
Inorganic nitrogen is added two ways: the atmosphere and new water. Atmospheric nitrogen (N2) is incorporated into our aquarium water by way of nitrogen fixing bacteria and by Cyanobacteria (bacteria that obtain their energy through photosynthesis) as ammonia (NH3). Some Cyanobacteria fix nitrogen gas, which cannot be used by plants, into ammonia, nitrites (NO2-) or nitrates (NO3-). Nitrates can then be utilized by plants and converted to nucleic acids and protein.
Inorganic nitrogenous compounds from our tap or well water also enter our aquarium, often as Nitrites or Nitrates. Reverse Osmosis can remove much of this.
For more about tap water, please see this article:
What should I know about tap water for my aquarium? From Chlorine and Chloramines to Phosphates

One of the most important biological conversions involves the transformation of N2 into a form readily available for plants.
Specialized bacteria that live in soil (Rhizobium) have the capability of converting N2 into NH3 (ammonia) a chemical that plants can absorb through their roots. Ammonia can be used to synthesize amino acids (Rhizobia bacteria require a plant host as they cannot independently fix nitrogen). The process of converting N2 + 3H2 > 2NH3 is called Nitrogen fixation. The bacteria that perform this task are anaerobic (no oxygen required). They possess the enzyme nitrogenase, necessary to catalyze this reaction. Certain plants develop anaerobic nodules on their roots that contain the nitrogenase-producing bacteria such as soybeans.
As well Blue-Green Algae (actually Cyanobacteria) can fix nitrogen and often live symbiotically with some plants; such is the case with the tiny aquatic Azolla fern found throughout the tropical & temperate regions of the world.
Nitrifying bacteria change ammonia (NH3) OR ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-). This is the most important aspect of the nitrogen cycle in an aquarium & pond and will be discussed in depth as this article progresses.
Denitrifying bacteria convert nitrate to nitrogen (N2) gas or Hydrogen sulfide under certain conditions in aquariums or ponds. Denitrifying bacteria are anaerobic, meaning they are active where oxygen is absent. This process is also important to aquariums & ponds (especially marine reef aquariums) and will be discussed in depth as the article progresses.
Reference: Hydrogen Sulfide; a bi-product of anaerobic de-nitrification
Another large group of bacteria are Actinomycetes that grow branching filamentous cells (hyphae) like fungi. These Heterotrophic bacteria are active at high pH levels, are generally gram positive and aerobic. Actinomycetes are common in soil and are responsible for the characteristic smell of freshly turned healthy soil. Actinomycetes decompose large organic substrates/compounds that are hard-to-decompose such as cellulose or Chitin found in exoskeletons of crustaceans.
Fungi/Saprolegnia are more important in degrading these compounds at low pH.
Reference: Fungus, Saprolegnia in Aquariums, Ponds

Here are a few chemical formulas for example:
*Glycerol; a basic sugar and a central component of many lipids: C3-H5-(OH)3
*Glucose; a common sugar: C6-H12-O6
*alpha Linolenic Acid, a fat; Short-chain omega-3 fatty acid: CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH
* Psychosine, a lipid intermediate in the biosynthesis: C24-H47-NO7
* Leucine, an essential amino acid (protein): C6H13NO2

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.
However, ammonia is produced from both metabolism and mineralization. The decomposition (mineralization) process produces large quantities of ammonia (NH3) through the process of ammoniafication.
Heterotrophic microbes (organisms that require organic substrates to get its carbon for their growth and development) utilize the organic compounds of decomposing matter as their carbon source. Ammonia (NH3) is the byproduct of this consumption.
The process of nitrogen cycle was once thought to be a complete linear process, however newer scientific evidence (2008) indicates otherwise.
Newer research indicates that there are three more dynamic processes involved in our aquarium nitrogen cycle, in particular marine aquaria.
I have noticed this in my many both anecdotal observations as well as tests I have performed where many variables were changed, especially during the establishment of a new tanks bio filter (adding plants early on being one), so this new science based theory really helps explain this:

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Recommended Resources

For SeaChem products to help with you aquariums nitrogen cycle, such as:
Prime to neutralize ammonia & nitrites (as well as chlorine and chloramines), Matrix & Purigen for Nitrate control or Stability to aid in your aquarium cycling or for accidental high decaying organics removal (this product does not take the place of full aquarium cycling)

For the latest generation Aquarium LED Lights such as the TMC LED Aquarium Lights, Lighting:

For the best in simple bio filters:TMC Reverse Osmosis Filter System with TDS Meter
The TMC Advanced Aquarium RO Water Filter system includes a TDS meter and operates at less than 2 cents per gallon

Sponge Filters
Premium ATI Hydro Sponge Aquarium Filters for bio and mechanical aquarium filtration.

TMC Fluidized Sand Bed Filters
The TMC Premium Fluidized Sand Bed Filter increases Bio Capacity of any Aquarium system, with unsurpassed Nitrifying Bio-Filtration. Simply the best Bio Filter available!

AAP Wonder Shells
The premier aquarium mineral block from the only supplier with decades of knowledge about the use of this product; Unique version sold NOWHERE ELSE!!

Aqua Master Mini Tropical Fish Food-Enhance Immunity
Ultra Premium Dual-color slow-sinking crumbles specially designed for small tropical fish, guppy and tetra to enhance palatability and feeding rate

UV Bulbs
Premium UV Replacement Bulbs at competitive prices!

For those looking for ACCURATE information about stepping up to a higher level of fish care, this article is a MUST READ:
Ultraviolet Sterilizer Use; Facts & Information

Back to the more Basic/Traditional Explanation:

Ammonia is assimilated in more than one way. Plants (such as Hornwort) and algae can assimilate ammonia and ammonium directly for the biosynthesis.

Another group of bacteria (similar to Nitrobacter in function) utilize the enzyme nitrite oxidase that is then responsible for converting nitrite into nitrate (NO3). This nitrate can either be used by plants as a nutrient source, or can be further broken down into nitrogen gas (N2) through the activity of anaerobic bacteria such as Pseudomonas .

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.

Most of these products (all dry products in particular) actually contain species of Heterotrophic bacteria from the genera Bacillus, Pseudomonas, Escherichia, and others (as these bacteria are much easier packaged with a reasonable shelf life under normal conditions/room temperatures).

Product Resources:

True nitrifying bacteria are Autotrophic and considered to be those belonging to the family Nitrobacteraceae whose energy sources are derived from the chemical conversion of ammonia to nitrite, or, nitrite to nitrate (Autotrophic bacteria are organisms that produce complex organic compounds from simple inorganic molecules).

The desired Autotrophic aerobic bacteria of nitrifying bacteria are present everywhere (e.g., in the air), oxygen and at least some moisture is present (not in areas void of oxygen).

Some ammonia oxidizing bacteria can revive more quickly than others.

While many of these nitrifying bacteria (but not all) have been shown to be gram negative; my research and that of my mentor (Dr. John Herzog) have shown these bacteria to react to gram positive treatments such as Erythromycin and not as much to gram negative antibiotics (such as Kanamycin).

For this reason, aquarium keepers need to be careful when treating with medications that are primarily gram positive such as Erythromycin (Maracyn), Ampicillin, or Penicillin. I have also found Tetracycline Hydrochloride to be harsh on nitrifying bacteria as well.

From: The Krib; Erythromycin vs Blue-Green Algae – a short article:

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 short term.

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.

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.

Heterotrophic Bacteria

Heterotrophic Bacteria are an organism that requires organic substrates to get its carbon for growth and development. Some are strictly aerobic, but many are facultative anaerobes (they can survive in either the presence or absence of oxygen).

Another point is growth (which is why Heterotrophic bacteria are favored for cycling products); nitrifying (Autotrophic) bacteria will double in population every 15-24 hours under optimal growth conditions. Heterotrophic bacteria, on the other hand, can reproduce in as little as 15 minutes to 1 hour.

The use of only Heterotrophic Bacteria to cycle an aquarium or pond can result in a bio environment that does not contain the necessary Autotrophic nitrifying bacteria to rapidly adapt to changes in bio load either from added fish, wastes, or similar; thus often resulting in sudden spikes in ammonia or nitrites when these Heterotrophic bacteria cycling products are not added in a timely or regular schedule!

For this reason products that contain only Heterotrophic Bacteria such as “Hagen Cycle” or even the popular Eco-Complete planted substrate SHOULD BE AVOIDED in some aquariums!

Similar with a pond, regular maintenance with sludge removers such as “AAP/ATI Pond Zyme Sludge Remover” in a pond with large amounts of decomposing matter falling into a pond should not present a problem. However, with use of large volumes heterotrophic bacteria pond products, it is easy to over come the healthy bio cycle of autotrophic bacteria and the problem we might be trying to solve might actually get worse.

Low pH and Nitrification Important;

Toxic Ammonia (NH3) changes to ammonium under 6.0 and ammonium (non toxic NH4) switches back to toxic NH3 over 7.0

The cause of this change in the nitrification process is still not clearly understood.

From the above article and quote, I would postulate that a change in Heterotrophic bacteria along with possible Redox Reactions or lack there of (a low pH below 6.0 is very oxidizing with little/no reduction which for this reason alone is not a healthy environment.

Further pH/Nitrification Information:

Keeping a low pH/KH can be a double edged sword where by a simple procedure such as a water change with slightly higher pH water can result in an immediate conversion of ammonium (NH4) to deadly ammonia (NH3) with disastrous results.

See References:

Further References for the Previous Section:


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.

This process can take place in an environment of very limited oxygen by anaerobic bacteria. This process is more common in Marine aquaria and takes place in fine #00 sand, live rock, or aquarium mud.

This generalization can very by substrate size, amount of plant roots and depth thereof as well as how deep certain worms, copepods dig into the substrate. Use of airline deep under sand beds over 5-6 inches that products very limited and controlled bubbles can allow for more de-nitrification while further limiting sulfur reduction.

It is also noteworthy that many premium aquarium/pond cycling aids or waste digesters such as SeaChem Stability or API PondCare Pond Zyme contain anaerobic heterotrophic bacteria and can be useful to add during spikes in the bio load of an aquarium or pond to aid in nitrate reduction and lower incidence of Hydrogen Sulfide production from decaying organic wastes (which can also affect water clarity and algae blooms).

The production of Hydrogen Sulfide in aquariums (both salt and even more so freshwater) is a controversial subject, often with unclear answers as to whether anaerobic de-nitrification is beneficial in freshwater due to the POSSIBLE production of Hydrogen Sulfide.

One key to allow de-nitrification without production of Hydrogen Sulfide is to allow some oxygen penetration of the substrate and as well. In saltwater aquariums, worms, copepods, etc often help perform this work. In freshwater, plant roots achieve this well and also remove raw ammonia as well as nitrates.


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.

Relatively new scientific evidence shows nitrifying bacteria to be sticky and adheres to the surfaces like glue (using exopolymeric substances), so agitation of filter media when rinsing (no tap water), or vacuuming of gravel will not destroy these colonies.

Remember you need oxygen (5-7 ppm dissolved oxygen) and a lot of surface area for bacterial colonies. Wet/dry filters, sponge filters, ceramic media, and loosely packed upper layers of gravel are all sources for bacterial accumulation. If there is not adequate surface area in oxygenated areas filter media or gravel, nitrification will be poor.

However the oxygen aspect is where old anecdotal information has resurfaced on the Internet.
Besides the Bio Wheel; DIY bio filters have popped up in Internet forums and videos (these have been around before in some form or another long before the Internet).

Reference & Product Links:

Canister filters can also be good sources for nitrification as long as the proper media is used (such as ceramic rings OR BETTER volcanic rock or SeaChem Matrix) and the media is not packed too tight and is rinsed regularly.

Bio Filtration during use of Medications in Aquariums:

During the use of medications, in particular gram positive antibiotics/antimicrobials your aquarium (or ponds) 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.

Sometimes it is necessary to treat with wide spectrum (mixed antibiotic treatments) or strong gram positive antibiotics such as Erythromycin for unknown problems or diseases such as Streptococcus or Eye Infections.

Further Reference Information:

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.

Please see this article for further information about medications: Aquarium Medications/Treatments


In healthy aquarium ammonia and nitrites should be at 0 ppm.



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.

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).

[1] 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.

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.

For marine tanks the use of seasoned or cured live rock serves 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 Store’s (or even a friend’s) aquarium health for obtaining aged/seasoned filter media. In this case, I would recommend one of the next two methods.

Further seasoned media cycling method tips

An ammonia spike is not uncommon with the use of seasoned media for there to be an ammonia spike when more fish are added, often this spike may take a several days depending on the amount of fish added as well as the bio load that the seasoned media has grown to handle.

Generally this is not too much of a concern, but the use of AAP/SeaChem Prime, cutting back on feeding, and definitely placing the addition of any other fish “on hold” until the nitrifying bacteria “catch up” with the new bio load are good practices.

As an example of what happens (and this is NOT scientific, just an analogy):

If say you added a sponge filter from a 20 gallon tank that is fully seeded to another 20 gallon tank that is brand new or restarted after bleaching.

[2] 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 method is growing in popularity, however it is not without a few drawbacks.

*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

[3] Fish Food Aquarium Cycing 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 to a baster or syringe and in inject directly into a running high capacity sponge filter (such as the AAP Hydro Sponge Filter) or similar quality bio filter (beware of the cheap Chinese knock offs now flooding the market that have much lower capacity than the original made in USA Hydro Sponge Filters).

With this method, you want to with just a pinch of fish food for every 10-20 gallons per day with testing prior to each addition of liquified fish food.

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

[4] 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!

I do not recommend this method, not because it does not work for cycling, but because it may also allow a Saprolegnia infection to get started in your new aquarium (or at the very least; heterotrophic bacteria which is not a desirable nitirfying bacteria as discussed earlier).

I should note back when this method was making its rounds in popularity that it worked fine in many instances and with a 100% water change and vacuuming of gravel can reduce this risk even further, however some risk still remains as per my many tests of pathogens and as per the often misunderstood lifecycle of Saprolegnia.

Please Reference for further information: Saprolegnia in Aquariums

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.

As a final point, this article has a section dealing with water changes and their affect on pathogens or similar: Aquarium Disease Prevention; Section 1, Cleanliness

[5] Cycling Products;

Fritz also has a less concentrated live nitrifying bacteria, #7 and #9, that does not require refrigeration and has a much longer shelf life.

Product Resource: Fritz-Zyme #7 from AAP

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.

Most other products are Heterotrophs, which cannot truly cycle an aquarium and are at best useful for spikes in bio loadsof established aquariums.

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.

Liquid Cycle, Quick Start, 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).

An excellent aquarium cycling product brought back by AAP is Bacter Plus.

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.

What SeaChem provides is an autotrophic nitrifying bacteria that would normally shut down and become dormant until oxygen and ammonia/nitrite again become available that normally takes considerable time to revive (they can last for years in this state), that revive relatively quickly.

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 that I will not share).

One major positive of these products over other products such as Stress Zyme or Microbe-Lift that also employ Heterotrophs is that its synergistic blend does not “dump” these into the aquarium/pond thus taking over any true nitrifying Autotrophs that may be present, thus it allows for establishment of your bio filter while it also takes care of immediate and slowly released nitrogenous wastes (‘Microbe-Lift Nite Out’ is similar to Stability as it is primarily ‘aerobic encapsulated oxygen’ Autotrophs).

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.

Here is a link to this study, please note that the data records are very well documented and there is no fudging of data as well as is so common today’s politically and corporately driven science!

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).

Quote from a fish forum about the use of Stability, Cycle, Stress-Zyme

*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”.

PLEASE reference this article for more information to back up what I am saying:

[6] Marine Aquariums;

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.

Product Resource: Seio Reliable High Performance Propeller Aquarium Pump

I would point out that live sand does not add nitrifying bacteria in significant amounts to help jump start your nitrogen cycle nearly as well as live rock due to the fact of oxygen depth penetration.

*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:

As mentioned earlier, many plants such as Hornwort also remove nitrogenous waste.

I personally like to see at least some bacteria establish it self before a full load of plants are added (but there are others with have no problem with such a method). Having plants in the beginning does help keep the dangers of ammonia (NH3) or Nitrites (NO2) from building to toxic levels, which allows for a quicker addition of fish to your aquarium.

What heavily planted aquarium keepers should be aware of is that if the plants suddenly shut down their photosynthesis and all nutrient uptake, this can result in sudden ammonia spikes. This includes light failures, medication or certain medication combinations, or any other factor that neutralizes plant bio functioning. For this reason, having a seeded bio filter, even if in another aquarium that can be moved over is important. The AAP Hydro Sponge Filters are excellent for such a use.

Cycling Summary:

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).

Please note the ammonia will still test after using these products as most test kits do not differentiate between ammonia and ammonium (ionized ammonia), with the exception being the SeaChem Ammonia Alert Test.

* 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;

* 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).


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.


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