
In this month’s blog, we’re sticking with the microbes that are essential to operating a healthy, productive aquaponics system.
Imagine you’re at a county fair. As you walk down the rows of carnival games, you notice a stand packed with small, water-filled plastic bags, each containing a colourful goldfish. For $10, you get a chance to throw 3 rings at a stick. If you land one, you get a fish. If you land all three, you get two. You hand your funnel cake to your partner and give it a try. Two minutes later, you have a goldfish in each hand, and you’re rushing out of the fairgrounds to the nearest pet store in a panic. They can’t stay in those bags for long. You buy a tank kit, and the cashier warns you about “new tank syndrome.” So, what is new tank syndrome, and how do you keep it from killing your new fish friends?

“New Tank Syndrome” can impact aquaponics systems just like it can aquariums. Art by Ross.
From previous blogs, we know that after your fish and solid-waste processing microbes have eaten, the protein in your fish feed is released as ammonia. This ammonia and the process of filtering it is why new tanks/systems are so prone to fish kills and failures.
Ammonia will exist in different forms depending on the acidity of your water. At higher acidities (lower pHs, e.g. pH 6.0 – 7.0), there are extra hydrogen ions available in your water. These hydrogen ions will attach to your ammonia ions and the ammonia will be in its ionized form (NH4, also called “ammonium”). When the water becomes basic (higher pHs, e.g. pH 7.0 – 8.0), there are fewer hydrogen ions available in solution, so the ammonia shifts more into its “un-ionized” form (NH3). Ionized ammonia isn’t that bad, but un-ionized ammonia is incredibly toxic to fish. Levels as low as 20 particles per billion will damage their gills; that’s less than a pinch of salt spread across 10 standard bathtubs. As the un-ionized ammonia concentrations increase, it will lead to convulsions, comas, and death in your fish.
If you have one fish in a huge pond, that fish won’t be able to make enough ammonia to get itself sick. In the same way, if you are constantly replacing the water in your fish tanks with fresh, ammonia-free water (called a flow-through system), ammonia also can’t build up to toxic levels. But with systems like aquariums or coupled aquaponics systems, with smaller amounts of water that recirculate and aren’t constantly replaced, the ammonia will quickly build up to levels that can poison and kill your fish. This is the first fatal step in new tank syndrome.
Constant water changes can be very stressful for fish. And for aquaponics, we don’t want to be constantly bringing in fresh water, because that would dilute the nutrients our plants need to grow. This means we need another way to keep our ammonia levels down.
Luckily, there is some energy left in the ammonia molecule, and certain species of bacteria have evolved to take advantage of this. These “ammonia oxidizing bacteria” (AOBs) take in ammonia, pop off the hydrogen ions and replace them with two oxygen ions. This releases energy the bacteria can use to grow/reproduce, and creates nitrite (NO2-).
Unfortunately, nitrite is also very, very toxic to fish. It gets absorbed by the gills and takes the place of oxygen molecules in the fishes’ bloodstream, turning their blood a brown colour and causing them to suffocate (similar to how carbon monoxide poisoning works in humans). This is the second fatal step in new tank syndrome.
But there’s still hope! A second type of bacteria, “nitrite oxidizing bacteria” (NOBs) can still get a little bit of energy out of the nitrite molecule, by adding on a third oxygen molecule and creating “nitrate.” You can have 100x more nitrate in the water compared to ammonia and nitrite, without hurting your fish. The process of ammonia getting converted to nitrite and nitrate is called “nitrification.”

Concentration of ammonia, nitrite, and nitrate as niitrifying organisms and nitrification become established. Source.
By nurturing a healthy biofilter, filled with AOBs and NOBs, ammonia and nitrite will get converted so fast that they never have the chance to hurt your precious fish friends. The problem with this whole process is that it takes time. A lot of time. Because there isn’t a lot of energy in ammonia or nitrite compared to other energy sources (e.g. carbon), the bacteria that eat them grow very slowly. For example, populations of carbon-eating bacteria like e-coli can double every 20 minutes. Meanwhile, ammonia and nitrite-eating bacteria only double every 10-24 hours. This means it takes 2-3 months for AOBs and NOBs to become established enough to keep your fish safe.
What can you do in the meantime? How can you make sure your two county fair goldfish don’t get sick, or your aquaponics system starts up without losing fish? Prepare, treat, and take it slow. Below are a few helpful tips:
Prepare:
- Get your filter cycling well before you put in fish by adding small amounts (e.g. 1 tsp in 100L) of scent-free household ammonia to your tank, and cycling water through the filter until your water tests positive for nitrite and nitrate.
- Get some filter media from a friend with a disease-free freshwater aquaponics system or aquarium, and add it to your filter to seed your system with beneficial AOBs and NOBs.
Treat:
- Do slow, partial water changes to keep ammonia and nitrite below toxic levels.
- Keep your system pH on the acidic side. This might slow down your AOB/NOB growth a little, but it will make the ammonia that does build up much less toxic to your fish.
Take it slow:
- If your system can handle 100 fish, start with 2 or 3. Let them eat, make ammonia, and establish your biofilter bacteria.
- Feed your fish less than they want, at least at first, to keep ammonia/nitrite levels lower while your biofilter becomes established.
- Increase your feed rate and fish count slowly, keeping an eye on the ammonia and nitrite levels, and feeding less if the levels start to creep up.
Eventually, your biofilter will mature and become established, and you will have a system with a bunch of happy fish, and concentrated nutrients. In the next blog, we’ll talk about how plants suck those nutrients out of the water.
