Establishing the nitrogen cycle, AKA “cycling”, is the hardest, most frustrating, part of aquaponics, in part because the activity is all invisible to the naked eye.  We hope that the nitrifying bacteria are finding our system, and then moving in and reproducing, but the only way that we know what is happening is through sometimes subtle changes of color in a test kit test tube.  And when that test tube stays the same color day after day, sometimes week after week, it is very frustrating.

Over the past few years of handling customer calls about cycling we’ve developed a checklist of what to ask to help them identify the problem and cycle successfully.  Hopefully you will see the solution to your own cycling mystery somewhere on this list.

1. Temperature – During the colder months of the year, this is the number one issue we see, especially with people who are cycling without fish.  The optimal temperature for bacteria reproduction is between 77-86° F (25-30°C).  At 64°F (18°C) their growth rates is decreased by 50%.  This means that the rate at which you cycle will be twice as long as it would be with warmer temperatures.
2. pH Too Low – We had a call just yesterday from someone who has spent the past two months cycling with no trace of nitrites or nitrates.  The average temperature of his system was between 65 and 70, so that could have had something to do with it, but when we asked him what his pH was he said 4.0!  That is essentially an acid bath and there is no way that the nitrifying bacteria are going to colonize in that kind of environment.  Bacteria actually prefer a pH closer to 8.0.  While this is too high for your plants to be happy, during cycling the bacteria are the main focus so targeting a higher pH than you will want during the rest of your system’s life makes sense.As an aside, if you are using the API Freshwater Master Test Kit, and you see a reading of 6.0 that means that your water is at 6.0 or below. You might want to find another means to test to an even lower range to see what your actual, true pH reading is.
3. Chlorine– This chemical is added to municipal water supplies for sterilization (i.e.,to kill the bacteria).  It is easy to remove because it dissipates from the water as a gas.  If you don’t already have a dechlorinating filter on your incoming water supply you can get rid of chlorine by simply holding the water in a separate tank for a day or two.  Oxygenating the water using an aerator will speed up the process.
4. Chloramine – While you can assume your city water supply has chlorine in it, chloramine is more rare. But it is also much more difficult to get rid of.  There are two ways that I know of.  The first is a double mechanical filtration method where you send the water through both a charcoal filter and a reverse osmosis filter.  The second is to remove it chemically by adding a product such as ChlorAm-X.  If you are using the chemical method you should do this in a separate holding tank before the water enters your aquaponics system.
5. Stop Adding Ammonia – The next problem we see only occurs during fish-less cycling, and the scenario unfolds as follows.  You add enough ammonia to reach 4.0 ppm then you start testing your system every day.  After a while the ammonia disappears and nitrites show up.  Good news!  The problem starts, however, when you don’t replenish the ammonia.  Think of the ammonia as food that you set out to attract the first set of nitrifying bacteria (nitrosomonas), and those bacteria come to the party bringing the food (nitrites) for the second set of bacteria (nitrospira).  If the food runs out, the party is over and everyone goes home!  You need to keep up a steady supply of ammonia in the front end of the process to keep everyone happily reproducing and colonizing your system. That steady supply can come either from an ammonia compound or from the addition of fish to your system.
6. Too Much Ammonia – Some aquapons believe that ammonia levels higher than 6 ppm will actually retard the cycling process.  Some don’t.  I don’t know enough to form a strong opinion either way, but I thought I would add it to the list of possibilities.
7. Sterile Environment – Occasionally we find a system that is being started in an indoor environment that is so shut off from outside air and a natural supply of nitrifying bacteria that it will never cycle on its own without the addition of purchased bacteria.
8. Lack of Oxygen – Nitrifying bacteria are aerobic. The more oxygen you have flowing through your system the faster your system will cycle.  Be aware that this is challenged by #1 above.  Liquids at higher temperatures have a harder time holding gas, so if you are heating your water to encourage bacteria growth be sure to pump up the oxygen as well.
9. Time – Cycling is a natural process that we can certainly encourage by establishing favorable conditions, but after that Mother Nature is on her own schedule.  You might be doing everything right, and the bacteria just need a bit more time.
10. You really are cycled; you just don’t know it – This is my favorite, because it is so easy to fix and the customer is usually delighted to discover that his problem was not really a problem at all!  The instructions for your test kit need to be followed to the letter.  If you don’t follow them, you won’t get accurate readings.  The Nitrate test is by far the most complex, and therefore the most likely to tell you that you don’t have any nitrates when in fact you actually do.  Do yourself a favor.  Read and carefully follow the instructions!

Cycling an aquaponics system can be a trying time, but the good news is that once you are fully cycled, you can safely add fish and plants and will never need to go through this again!  Good luck.

Enjoyed this post? Here are some others you might like:

1. Starting your Aquaponics System Using Fishless Cycling
2. Starting Up (Cycling) an Aquaponics System Using Fish
3. Speeding Up Cycling (Starting) an Aquaponics System
4. Aquaponics Fishless Cycling – revisited
5. Aquaponics Cycling and the Case of the Missing Ammonia