Nitrogen Cycle

The purpose of this article is to provide basic answers to the most common questions asked about the Aquarium Nitrogen Cycle

Much of this information is courtesy of:

"Aquarium Nitrogen Cycle"

Please read the above article for much more accurate and in depth information as there is no more in depth and professional experience based article available free on the Internet (be careful of articles such as by Fish Labs that have show little respect mentoring which show in poor recommendations) 

What is the Nitrogen Cycle?

The nitrogen cycle is the process by which organic protein based wastes are converted from toxic ammonia, to slightly less toxic nitrites, to relatively non-toxic nitrates.

This process is carried out by specific and generally non pathogenic bacteria.

These bacteria include Nitrosomonas and Nitrobacter, both of which are also referred to as Aerobic bacteria.

In some aquarium or pond systems nitrates are converted to free nitrogen (by anaerobic de-nitrifying bacteria) or consumed by plants or algae (or removed by chemical absorbents/resins such as AAP Purigen).

Our Recommended Product Resource:

#American Aquarium Purigen; Controls ammonia, nitrites, nitrates 

What are Organic Protein Based Wastes?

Organic Protein Based Wastes are substances/molecules that contain nitrogen; this includes Urea, Feces, uneaten fish food, and decomposing fish or plant material (fish would have more more proteins than plants, thus having more nitrogen fueling higher ammonia, nitrites, and eventually nitrates). 

What are the stages of the Nitrogen Cycle?

*Initial stage; This starts when fish, plants, food or any organics (even small amounts of air born organics) are introduced to the aquarium. These organics are broken down via aerobic nitrifying bacteria into either ionized (NH3) or unionized ammonia (NH4).

Any amount of NH3 is toxic, however amounts under .05 ppm are generally not an issue and often .0% ppm will appear even in healthy aquariums in the ebb and flow of the nitrogen cycle

*Second Stage; this is when ammonia/ammonium is converted by different aerobic nitrifying bacteria into slightly less nitrites (readings should be still under 40-50 ppm)

*Final Stage; this is the conversion via de-nitrification of nitrites to relatively harmless nitrates (reef aquariums should have nitrates under 40-50, while planted freshwater aquariums should maintain higher nitrates for plants) 

What does Aerobic versus Anaerobic Bacteria Mean?

Aerobic simply means "with oxygen".

In other words the aerobic bacteria needed to convert both toxic ammonia or nitrites require an environment that contains oxygen, generally at least 5 ppm.

Anaerobic bacteria simply means "without oxygen"

These bacteria live in an environment with little or no oxygen, which is of difficult to create in a healthy aquarium.

Very stagnant conditions without oxygen can create the perfect conditions for hydrogen sulfide production which produces th classic "rotten egg" smell.

Please Reference these two articles for further information:

#Aquarium Nitrates; What to Do

#Hydrogen Sulfide in Aquariums 

How does aquarium chemistry affect the nitrogen cycle?

*Maintain carbonate hardness (KH), especially when cycling a new tank, as the process of cycling will use carbonates and without adequate carbonates (KH) your pH can crash which will slow the establishment of nitrifying bacteria as nitrifying bacteria.

As well, at 6.0 pH, the process of nitrification changes which can cause sudden swings in ammonia and nitrites until the bio system stabilizes. The can mean sudden spikes in ammonia NH3 as the pH suddenly climbs or thinking your aquarium has cycled when it has not when the pH suddenly drops!


#Aquarium Nitrogen Cycle; Nitrification traditional and expanded

#Aquarium Chemistry; Carbonate Hardness 

What is the "Best" cycling method?

This is a subjective question that does not necessarily have "one" best answer, however I will attempt to make this as simple as possible.

The method most aquarium professionals prefer is the use of aged/established filter media from healthy well established aquariums.

That said, this method is not always possible, so the next choice would be the liquefied fish food method, possibly blended with a GOOD cycling aid that both aids in establishing the nitrogen cycle AND provides immediate digestions of wastes with facultative bacteria such as SeaChem Stability, Fritz #7, or best; AAP Bacter Plus [which includes USDA approved non-pathogenic and non-toxic strains of domesticated Bacillus Subtillis bacterium]

Our Recommended Product Resource:

#AAP Bacter Plus with Bacillus Subtillis; Premium Cycling Aid

#Stability from American Aquarium

The pure ammonia method is another option, however based on customer emails, phone calls, etc., this method is often more confusing.

The other unfortunately common method is the Raw Shrimp method. This long ago discredited method found new life in aquarium forums and poorly researched aquatic websites such as Fish Lore. The bottom line is do NOT use this method as your risk of Saprolegina is increased considerably, especially if this method is not carefully performed.

Please reference this excellent article section for MUCH more about these methods:

Nitrogen Cycle; Cycling Methods" 

Where does the Bacteria come from other than cycling aids or Aged/Established Filter Media?

Aerobic Nitrifying bacteria, which includes the nitrite-oxidating Nitrospira, are naturally found in soil and aquatic environments. Airborne Dust in our homes, offices, etc. carries bacteria, fungi, algae, and other microorganisms on minute particles of soil. This is the most common/likely source of nitrifying bacteria in our aquarium when using methods such as fish food or pure ammonia cycling to start our nitrogen cycle.

It is theorized that the bacteria are able to go into a dormant state when conditions are not favorable for metabolism, ready to revive when conditions are right.

For this reason even dried filter media from a previously established aquarium is still going to seed your aquarium faster than nothing at all or even over the pure ammonia or fish food methods.

You will still see that faster cycling using the aged/established filter media method or true cycling products though. 

Will adding any aquarium cycling aids help or hinder the cycling of the aquarium?

Most aids such as "Cycle" and "Stress-Zyme" are primarily Heterotrophic which do not at aid in establishing true Autotrophic Nitrobacteraceae in an aquarium and thus would hinder the establishment of a healthy nitrogen cycle. HOWEVER sometimes a stop gap use of these products that may delay your cycling are necessary to prevent fish deaths.

Better is the use of products such as AAP Bacter Plus which has USDA approved non-pathogenic and non-toxic strains of domesticated Bacillus Subtillis bacterium or AAP/SeaChem Stability which have a synergistic blend of aerobic, anaerobic, and facultative bacteria that is much less likely to hinder your aquariums cycling.

Bio Spira is refrigerated live bacteria products that assuming 100% proper refrigeration can be helpful as a cycling aid or emergency ammonia/nitrite spike treatment. Fritz-Zyme #7 or #9 is non refrigerated live bacteria culture with years of use and documentation by the University of Nevada backing up its effectiveness

Our Recommended Product Resources:

#AAP Bacter Plus with Bacillus Subtillis; Premium Cycling Aid

#Stability from American Aquarium

With the above said, no cycling aid such as the above should be fully depended upon for establishing your nitrogen cycle; as low initial bio loads, time, and patience is still important. As well the use of common Heterotrophic products should NEVER be used for the purpose of establishing an aquariums nitrogen cycle.

Where these aids are best used, especially the better ones such as AAP Bacter Plus or Stability, is for accidental over feedings, or similar emergencies (along with water changes).

The best way to look at these products is as an AID for controlling high ammonia in the presence of fish, as the FACTS ARE the true autotrophic nitrifying bacteria necessary for a healthy aquarium cycle (Nitrosomonas and Nitrobacter), do not store well in a bottle. Your best bet for cycling a new aquarium is with seasoned filter media.

TV shows (such as "Tanked") will make claims to the contrary, but the science and experience of others who are Aquarium "FISH" professionals not "TANK" professionals say quite the opposite!!!

The above noted, one can improve any method of cycling by "squirting" the product "AAP Shieldex" into the bio filter/media that is being primarily used as the main seed bio filter. It should be noted that this is NOT a cycling product, rather is simply "makes life easier" for the bacteria to establish.

The aquarium keeper would squirt some of this product into their bio filter media and it will then make for a base for these bacteria to get a jump start in seeding further.

Resource: #AAP Shieldex Water Conditioner, Beneficial Bacteria Base 

Do the Bacteria need to be fed?

The simple answer is yes!

If the fish or other aquarium inhabitants are removed or lowered in numbers, the nitrifying bacteria will die off. Then if fish are suddenly added, especially in larger numbers, chances are your aquarium will have spikes in ammonia until the bacteria re-establish in numbers needed to meet the change in bio load.

In a new aquarium, this is even more worthy of note as any fragile new bacterial colonies that are present can easily disappear without "food" from fish waste. If the seasoned fish filter method is used, but no fish or other means of feeding these bacteria are added, the bacteria will quickly die off and the cycling will fail.

How do I know when my Aquarium has cycled?

When you are cycling your aquarium, you will want to monitor your water parameters. Doing so will help you determine when your aquarium has cycled. Typically, when your Ammonia and nitrites have gone up, and come back down, your aquarium has cycled. This can take anywhere from 10 to 45 days, depending on the cycling method, tank size, and temperature. 

What aquarium parameters (test kit result) are considered "correct"?

his is a somewhat "loaded" as different aquatic life have different tolerances. However for simplification, I will list each parameter and what is generally acceptable:

*Ammonia: No more than .5 ppm.

Although 0 is best, often occasional spikes of .5 in a healthy/cycled aquariums will occur and over reacting can cause more harm than good. This said any increases should turn on a "yellow caution light" resulting in temporary more frequent tests and looking for dead fish, over feeding, etc.

*Nitrites: the same as ammonia, no more than .5 with 0 being desirable

*Nitrates: 50 ppm or less is best in more basic community aquariums. However reef, planted, shrimp, and more MAY require much lower numbers.

I recommend reading these articles for much more understanding of nitrate levels:

#Aquarium Nitrates

#What are aquarium Nitrates?- Fish Beginner

#Marine Aquarium Basics, Care

#Planted Aquarium Care 

How should I clean my filters and change water to maintain a healthy Nitrogen Cycle?

*Rinse filter media in used tank water or de-chlorinated tap water so as to not kill nitrifying bacteria.

*Add de-chlorinators when changing water over 10%

*Do NOT vacuum all ‘dead’ spots under live rock in the live sand of a “Marine Tank ONLY”. (This can destroy anaerobic bacterial colonies in Marine Tanks needed for de-nitrification). Even then try and vacuum only the top layer in open areas of live sand in marine tanks, with only occasional “dips” into deeper sand (the use of a ½ inch layer of #3 crushed coral makes this process easier and quite bluntly makes for better aerobic and anaerobic filtrations and as well trapping of detritus).

*Do NOT wash gravel or totally change water, again this will destroy or hamper establishment of bio bacterial colonies.

*Rotate filter media changes so as to always have older media with bacterial colonies. In a HOB filter with a cartridge, place a second cartridge in 7-10 days before changing the old one of install a sponge pre-filter on your HOB filter such as a Filter-Max Pre-Filter.

Our Recommended Product Resource:

#Filter Max Sponge Prefilters from American Aquarium 

What affect does a healthy biological nitrogen cycle have on other aquarium chemistry parameters, especially in bowls or small tanks?

This is a common question and the simple answer is that a well established nitrogen cycle constantly produces acids that deplete your aquariums alkaline reserve which in turn slowly lowers pH over time unless alkaline buffers or water changes with buffers are performed (natural or added).

This is quite healthy and having an established and balanced nitrogen cycle along with good aquatic chemistry practices generally results in tanks with few pH/KH bounces.

The problems often occurs in small tanks where parameters are generally less stable simply because it is more difficult to maintain a healthy nitrogen cycle.

This is considerably amplified in bowls or small tanks where no bio filter is present or when the bio filter is so weak that regular water changes are needed just to keep ammonia and nitrite levels in check.

Reference our other Fish Beginner Article:

#Aquarium GH, KH, PH; Chemistry, What to Know 

Will Water Conditioners that Remove Chlorine Affect the Aquarium Nitrogen Cycle?

Normal use will not affect your aquariums nitrogen cycle.

This said normal use should not be more than once per day as ALL Water Conditioners are "Redox Reducers" which is actually a "good thing" as these reduce oxidative stress in fish.

However if over used, these chlorine removing water conditioners, such as AAP Prime, Amquel Plus, etc., will interfere with nitrogen cycle since this process is basically an oxidizing Redox process. You want to achieve a "Balanced" Redox, not constant Reduction nor high oxidation.


#Aquarium Water Conditioners Information

#Aquarium Nitrogen Cycle; Nitrification

#Aquarium Redox

#American Aquarium Products Prime