Cycling Overview

A well-established aquaponic garden needs only simple routine maintenance to stay stable and trouble-free. A new system, however, will need some guidance through the awkward adolescence of cycling, the early days and weeks in which the microbes that process organic waste in your system appear and colonize the environment you've provided for them. During this period, your garden will be biochemically unstable, and the risk of uncontrolled changes in water quality which can harm your fish, plants, and even the developing microbial communities is much higher than in a mature garden.

This guide is intended to help you understand the cycling process, including what you can do to make it quicker, easier, and safer. Because many other cycling guides are freely available online, we'll be focusing on the AquaSprouts garden as our model. While the general principles of this guide will be useful across a broad spectrum of aquatic and aquaponic systems, there are many differences between different types of aquaculture and aquaponic gardening, so be sure to keep in mind ways that the specifics of your system may affect your process if you're cycling something other than an AquaSprouts garden kit!


how does it work?

Cycling is the colonization, in the first few weeks of operation, of your new, relatively sterile system by beneficial bacteria which digest toxic biological wastes into forms that are safer for your fish and easier for your plants to use - the establishment of key steps of the nitrogen cycle. You're likely to hear a lot about the importance of microbes in your aquaponic garden; they’re the engine that allows nutrients to be passed from the food you give your fish to the plants that you eventually harvest. Nothing works without them!

Cycling in an aquatic system is the development of a population of several microbe species which primarily metabolize nitrogen in organic waste in the form of ammonia (NH3) into the much safer and more bioavailable nitrate, (NO3). These microbes, and the material they grow on, are commonly referred to as the system's biofilter.

Cycling typically happens in two distinct stages, each representing a step in the metabolic process:

  1.  The first population of microbes to appear (represented by genus Nitrosomonas) oxidatively metabolizes (eats, loosely speaking) ammonia to produce nitrite. Both ammonia (NH3) and nitrite (NO2-) are quite toxic to fish, seriously interfering with their respiration at concentrations as low as a milligram per liter of water (1 mg/L).
  2. Once the system accumulates some nitrite, a second population of bacteria will begin to grow . These (commonly Nitrobacter species) further oxidize nitrite into nitrate (NO3), which is both much easier for plants to take up and use, and much safer for aquatic animals. Nitrate tolerance varies between organisms, but in general it's safe at concentrations twenty to one hundred times as high as ammonia or nitrite. It is possible for nitrate concentration to build up too high, but in a balanced aquaponic system, your hungry plants will be taking up nitrate long before that. 


Cycling with or Without fish?

In aquaculture, ornamental aquariums, and aquaponics, the same debate has dragged out for decades: what’s the right way to cycle a tank? Specifically, what’s the right way to provide ammonia so that nitrifying bacteria (which are present virtually everywhere and will spontaneously colonize your tank as long as it’s open to the air) will show up and “eat” it? Should you add ammonia directly as a purified chemical, or rely on more natural means and stock your uncycled tank with with, allowing their natural production of waste to start up the cycling process? Both approaches have advantages and disadvantages, but in general, most practitioners of aquaponics seem to lean toward fishless cycling. Whether this is because the process can be hard on fish and lead to sickness or mortalities, or because it’s more precisely controllable varies.

Cycling with Fish - When cycling with fish, the most important thing to keep in mind is that monitoring and maintaining water quality is key to your fish’s health. While water changes are rare in an aquaponic system, during the cycling period, you may need to perform one or more partial water changes to protect your fish from high levels of ammonia or nitrite. This may slow down the cycling process slightly. It’s very important to obtain water testing kits and check your levels of ammonia, nitrite, and nitrate regularly during this time so that you can modify your tank care appropriately.

Cycling with fish is a process of gradually ramping up; have fewer fish in more water gives you more margin for error, so you’ll gradually add more fish to the system as the cycling process continues. This allows your colonies of nitrifying bacteria time to grow and keep up with the waste being produced by more and more fish. The benefits of cycling with fish are simplicity and consistency. All you need to do is feed your fish as normal, and they’ll produce ammonia-rich wastes continuously, keeping a steady supply of nitrogenous wastes available for your bacteria.

Fishless cycling - Fishless cycling requires less aquarium care but more personal diligence on testing and dosing. Instead of relying on fish wastes, you can add ammonia directly (Not just any ammonia, though! See the “What you’ll need” section for details). Cycling this way allows you to measure and dose ammonia in very precise amounts, and it doesn’t risk the health of any fish. It’s also unlikely you’ll need to change the water. However, in order to avoid your new colonies of nitrifying bacteria starving, you will need to test the water for ammonia, nitrite, and nitrate regularly to check your progress, and be diligent about adding ammonia. The changeover point, when you stop adding ammonia and finally add your fish, can also be tricky, but with a little planning, you should be able to stop dosing the day before your fish arrive and seamless switch over to full aquaponics!