Bacteria are the magic that takes the unusable aquaponics fish waste and creates a near perfect plant fertilizer. In this article we will demystify the process of establishing a beneficial bacteria colony in your aquaponics system. This process is often called system “cycling”. Today I’ll talk about cycling using fish and next month I’ll go into how to cycle without fish. By the end of these two articles, you will fully understand what you MUST do to initiate cycling and to ensure its success. You will also understand what you CAN do to both make the process less stressful for your fish and your plants, and to speed up the process.

What is Cycling?

Cycling starts when you (or your fish) first add ammonia to your system. Ammonia (chemical formula NH3) is a compound made of nitrogen and hydrogen. It can come either from your fish or from other sources that we will discuss next month. Ammonia is toxic to fish (more on this later) and will soon kill them unless it is either diluted to a non-toxic level or converted into a less toxic form of nitrogen. Unfortunately, nitrogen as found in ammonia is not readily taken up by plants, so no matter how high the ammonia levels get in your fish tank, your plants will not be getting much nutrition from it.

Aquaponics CycingThe good news is that ammonia attracts nitrosomonas, the first of the two nitrifying bacteria that will populate your system. The nitrosomonas convert the ammonia into nitrites (NO2). This is a necessary step in the cycling process; however, nitrites are even more toxic than ammonia! But there is good news because the presence of nitrites attracts the bacteria we are truly after nitrospira. Nitrospira convert the nitrites into nitrates, which are generally harmless to the fish and excellent food for your plants.

Once you detect nitrates in your water and the ammonia and nitrite concentrations have both dropped to .5 or lower your system will be fully cycled and aquaponics will have officially begun!

The Importance Of Testing Tools

You must have some way of telling where you are in the cycling process, typically a four to six week endeavor. Specifically, you must monitor ammonia, nitrite, and nitrate levels as well as pH so that you know that all these elements are in range. If they are not, you may need to take corrective action. This is also the only way that you will know when you are fully cycled and ready to add more fish (or your first fish if you have been cycling with no fish at all). Plus, watching the daily progress of the cycling process is fascinating and something you can only see through the lens of a test kit. By the way, once you reach the point that your system is fully cycled, you will need to do much less monitoring than during the cycling process. So get through the cycling process and look forward to reaping the fruits (or should we say the fish) of your labor.

IMG_0388To do their testing, most aquaponic gardeners use a product by Aquarium Pharmaceuticals Inc. called the API Freshwater Master Test Kit. This kit is easy to use, is inexpensive, and is designed for monitoring the cycling process in fish systems.

You will also need a submersible thermometer to measure your water temperature. Temperature affects both the cycling rate and the health of your fish and plants once you are up and running. See more on this below.

Cycling with Fish

Ammonia (NH3) is the catalyst that starts the cycling process. You must have some means to feed ammonia into the system so that you attract the bacteria that are at the heart of aquaponics.

There are two ways to introduce ammonia into your system with fish and without (fishless). Today we will talk about cycling with fish, and tackle fish-less cycling in the next article.

The Ammonia (NH3)

I used fish to cycle my first aquaponics system and I suspect this is how most people approach cycling. In some ways it is the easier of the two methods because there are no extra inputs, but it is definitely the more stressful of the two options because live critters are involved.

The idea is to add fish on day one and hope that they live through the cycling process. The challenge is to get the system cycled fast enough that the ammonia concentration from the fish waste drops to a non-toxic level before the fish succumb to exposure to their own waste. I strongly recommend that you don’t stock to your tank’s mature capacity (1 lb of fish per 5 – 10 gallons of water) but to less than half that. You might also want to consider these fish as “sacrificial” and perhaps use goldfish from the pet store, which are fairly tolerant of ammonia, rather than the tilapia with which you may ultimately envision stocking your tank. Also, do not feed these fish more than once a day and only feed them a small amount even then.

Fish excrete ammonia through their gills as a bi-product of their respiratory process. Without dilution, removal or conversion to a less toxic form of nitrogen, the ammonia will build up in the fish tank and eventually kill the fish. In addition, ammonia (NH3) continually changes to ammonium (NH4+) and vice versa, with the relative concentrations of each depending on the water’s temperature and pH. Ammonia is extremely toxic to fish; ammonium is relatively harmless. At higher temperatures and pH, more of the nitrogen is in the toxic ammonia form than at lower pH.

Standard test kits measure total ammonia (ammonia plus ammonium) without distinguishing between the two forms. The following chart gives the maximum long-term level of ammonia in mg/L (ppm) that can be considered safe at a given temperature and pH.

Water Temperature

pH 20C (68F) 25C (77F)
6.5 15.4 ppm 11.1 ppm
7.0 5.0 3.6
7.5 1.6 1.2
8.0 0.5 0.4
8.5 0.2 0.1

You will need to monitor your tank water daily during cycling for elevated ammonia levels. If those levels exceed the levels on the chart above you should dilute through a water exchange by pumping out up to 1/3 of your tank’s water and replacing it with fresh, de-chlorinated water.

Adjusting pH

During cycling, especially with fish, you should try and keep your pH between 6.0 and 7.0. The range does not go below 6.0 because most fish prefer slightly alkaline water and few are happy below 6.0. The range does not go above 7.0 because of the ammonia toxicity issue described above (higher pH readings suggest higher ammonia concentrations). So how do you keep pH in such a tight range?

The first rule is: Whatever you do to adjust pH in aquaponics – Do it slowly! Fast, large pH swings are very stressful on fish and will be much more of a problem than having pH that is out of range. Target shifting your pH reading no more than .2 per day and you should be fine.

The safest way to do this is to use our AquaDown pH Lowering Solution. Raise pH either by using our AquaUp pH Raising Kit or by alternating alternatively use calcium hydroxide – also known as “hydrated lime” or “builder’s lime” with potassium carbonate (or bicarbonate) or potassium hydroxide (“pearlash” or “potash”). Don’t use citric acid as it is anti-bacterial!

Typically, you will be trying to keep pH down during cycling, and then once your system is cycled you will probably notice that the pH will fall and you will then need to switch to keeping it up. You will probably find that it is easier to increase pH than it is to decrease it. The ideal pH of a mature aquaponics system is 6.8 – 7.0. This is a compromise between what the plants prefer, i.e. a slightly acidic environment of 5.5 – 6.5, and what the fish prefer, i.e. a slightly alkaline environment as we discussed before.

The Nitrite (NO2)

Nitrite is to fish like carbon monoxide is to air breathers. The nitrite will bind with the blood in place of oxygen and keep the fish from getting the oxygen it needs. Fish poisoned with nitrites die of what is called “brown blood disease”. If the nitrite levels in your tank rise above 10 ppm while you are cycling your system with fish, you should do a water exchange as discussed above, but you may also want to add salt to the system in order to further protect the health of the fish.

Do this by adding salt to the system to at least 1 part per thousand (1 kg of salt per 1000 liters of water) using non-Iodized salt. Avoid table salt since it contains potentially harmful anti-caking agents. You can use cheap pool salt or water softener salt available at the grocery or hardware store, but the best product is salt specifically formulated for fish. Make sure to dissolve it completely in a bucket of water before adding it to the fish tank since un-dissolved salt crystals on the bottom of a fish tank can burn a fish that rests against them. Stop feeding your fish until the nitrite levels decline below 1.0 and aerate as much as possible.

How might salt (sodium chloride) help? Sodium Chloride helps mitigate nitrites because the chloride ions bind with the nitrites and thereby help keep some of the nitrite out of your fish.

Adding Plants

seed starting plugI recommend adding plants to your new aquaponic system as soon as you start cycling. Plants can take up nitrogen in all stages of the cycling process to varying degrees; from ammonia, nitrites and nitrates, but they will be happiest when cycling is complete and the bacteria are fully established because so many more nutrients become available at this stage.

When plants are first transplanted, they focus on establishing their root system in their new environment. You may initially see some signs of stress – yellowing and/or dropped leaves – and you will probably not see any new growth for a few weeks. This is fine. Adding plants to your system right away lets them go through the rooting process early on and readies them to start removing the nitrogen-based fish waste from your aquaponics system as soon as possible.

I recommend you use some Maxicrop to get your plants off to a good start during cycling. Maxicrop is derived from Norwegian seaweed, is organic and is used primarily as a growth stimulant, especially to enhance plant root development. It is extremely effective at giving plants a “leg up” after being transplanted into your new aquaponics system, is absolutely harmless to the fish, and probably beneficial for the bacteria. You can find Maxicrop in garden centers, hydroponic stores, and online in both liquid and dry form.

While there are no hard and fast rules about how much Maxicrop to add during cycling, I recommend about a quart of the liquid product for every 250 gallons of water. It will turn your water almost black but don’t worry; this will clear up after a week or so.

Speeding Up the Process

Cycling is in some sense akin to any hunting activity that uses a lure. We start by putting out the ammonia. This attracts the nitrosomonas bacteria which in-turn produces nitrites. The nitrites attract the nitrosprira bacteria which produce the nitrates that are harmless to the fish and delicious to the plants. These two beneficial nitrifying bacteria are naturally present in the environment.

As I stated earlier, this process will take four to six weeks if done with fish, or as little as ten days to three weeks if done fishless. But what if you could speed that up significantly? What if instead of waiting for the bacteria to show up to the party, they actually are part of the party to begin with? You can do this by introducing nitrifying bacteria into your aquaponics system.

Adding Bacteria

While there are many ways to do this, they all boil down to two basic strategies: use bacteria from an existing aquaculture or aquaponics operation or from a near-by pond or instead, purchase bacteria from a commercial source.

Good sources of beneficial bacteria from existing systems are ranked here, leading with the best:

  • Media from an existing aquaponics system
  • Our Microbe-Lift Nitrifying Bacteria product
  • Filter material (floss, sponge, biowheel, etc.) from an established, disease-free aquarium.
  • Gravel from an established, disease-free tank. (Many local pet and aquarium stores will give this away if asked.)
  • Other ornaments (driftwood, rocks, etc.) from an established aquarium.
  • Squeezings from a filter sponge (any pet and aquarium store might be willing to do this…)
  • Rocks from a backyard pond with fish in it

Managing Water Temperature

Water temperature also has a dramatic effect on the speed of cycling. Their optimal temperature is between 77-86° F (25-30°C). At 64°F (18°C) their growth rates is decreased by 50%. At 46-50ºF (8-10°C) it decreases by 75%, and stops all together at 39°F (4°C). It will die off at or below 32ºF (0°C) and at or above 120°F (49°C).

Cycling with Fish – Conclusion

While cycling with fish is the most widespread and straightforward of the cycling techniques, it is stressful on your fish and therefore somewhat stressful for you. But it certainly works. Next month we’ll go over another technique called Fishless cycling that uses pure ammonia to cycle your system.

Either way, it’s time go get up and grow!