Frequently Asked Questions

Aquaponics Cycling

Bacteria are the carburetor of an aquaponics system that takes the otherwise unusable fish waste and creates a near perfect plant fertilizer. In this article I will demystify the process of establishing a beneficial bacteria colony in your aquaponics system. This process is often called system “cycling”. By the end of this article you will fully understand what you MUST do to initiate aquaponics 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 Aquaponics Cycling?

Aquaponics System cyclingCycling starts when you (or your fish) first add ammonia to your aquaponics system. Ammonia (chemical formula NH3) is a compound made of nitrogen and hydrogen. It can come either from your fish or from other sources. Ammonia is toxic to fish and will soon kill them unless it is either diluted to a non-toxic level or converted into a less toxic form of nitrogen. In addition, nitrogen in the ammonia form 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.

The good news is that ammonia attracts nitrosomonas, the first of the two nitrifying bacteria that are present in the air and will populate the surfaces of your system. The nitrosomonas bacteria convert the ammonia into nitrites (NO2) (the golden line in the chart above). This is a necessary step in the aquaponics 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 (shown by the green line in the graph below). 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 ppm or lower, your system will be fully cycled and aquaponics will have officially begun!

Why do I need testing tools?

aquaponics cycling - API Freshwater  Master Test Kit

API Freshwater Master Test Kit

You must have some way of telling where you are in the aquaponics 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 your fish. 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.

To 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.

How do I Start the Cycling Process?

Once you have your aquaponics system set up and your test kit in hand all you need to do to start the cycling process is add a source of ammonia. Traditionally this has been by adding fish and letting their waste be the ammonia, but I’m not a big fan of using fish as an ammonia source. Instead I prefer a technique called “Fishless Cycling” where an external source of ammonia is added to your aquaponics system. Why is this?

aquaponics cycling graph

Typical Nitrogen Cycle

First, both you and your fish will likely experience much less stress because you will not be trying to keep anybody alive during the process. Second, you can more precisely control how much ammonia is added to your system during the process. For example, if you see that your ammonia level is creeping up to 8 ppm, but no nitrites have shown up yet, just stop adding ammonia for a few days and let the bacteria catch up. You can’t do this with fish!

The practical result of this is that with Fishless Cycling you can fully stock your tank once cycling is complete, versus gradually increasing your stocking levels as is recommended when cycling with fish. This is especially beneficial to those who are growing aggressive or carnivorous fish because they are less likely to attack each other if they are all introduced to the tank at the same time.

How do I Cycle Without Fish?

There are several ways to add ammonia to your system, but honestly the best is to simply purchase our Cycling Kits. They come in 3 sizes – Small (< 100 gallons), Medium (100 – 300 gallons) and Large (300 – 500 gallons). They come with all the ammonia you will need to fully cycle the corresponding size tank, powdered seaweed to provide a rich supply of micronutrients to get your plants off to a great start, and detailed instructions.

With Fishless Cycling you can add safely fish to your aquaponics system after your ammonia and nitrite levels drop to zero, or close to it, and you have measurable levels of nitrates. This tells you that both the ammonia converting bacteria (nitrosomonas) and the nitrate converting bacteria (nitrospira) have become fully established and are ready to efficiently process fish waste.

Can I speed up aquaponics cycling?

Unfortunately nitrifying bacteria are some of the slowest growing bacteria in nature, and the cycling process can take as long as six weeks. There are a few things you can do to speed up this process, however.

Temperature – like most microorganisms, nitrifying bacteria multiply more quickly in warmer conditions. Their optimal temperature is between 77-86°F (25-30°C). At 64°F (18°C) their growth rates is decreased by 50%. At 46-50°F (8-10 °C) it decreases by 75%, and stops all together at 39°F (4°C). It will die off at or below 32°F (0°C) and at or above 120°F (49°C).

pH – Bacteria prefer a pH range between 7 – 8. Use hydroponic pH up and down products to keep your pH in this range during cycling.

Oxygen – Nitrifying bacteria are aerobic and will multiply much faster under highly oxygenated conditions. Even if you are cycling without fish be sure to have as much oxygen in your tank water as you would if the fish were there. Think of the bacteria as just another living organism that requires oxygen in your system.

Adding bacteria – You can “jump start” the process by adding bacteria from an existing colony. Good sources of beneficial bacteria are ranked here, leading with the best (the lower you go on the list the more chance you have of introducing a disease into your system):

  • Our Microbe Lift Nitrifying Bacteria product (included with the AquaCycle Cycling Kits)
  • Media from an existing aquaponics system.
  • 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 should be willing to do this…).
  • Rocks from a backyard pond with fish in it.
  • Rocks from a river, lake or wild pond.

When do I add plants?

MaxiCropWe recommend adding plants as soon as you have started the aquaponics cycling process. The reason for this is that it gives the plants some time to put down roots and establish themselves before the fish are introduced and nitrates need to be absorbed. We highly recommend adding MaxiCrop liquid seaweed (about a quart to every 200 – 300 gallons) to your fish tank when you plant because it will give the new plants a boost of micronutrients and encourage them to put down healthy new roots. Our Cycling Kits already include powdered MaxiCrop.

I’ve done all this, but I still don’t seem to be cycling! What could have gone wrong?

We recently wrote a blog post called “The Top 10 Reasons Why Your System Isn’t Cycling“. Hopefully you can find the answer to your cycling mystery in there!


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