Cycling and Understanding the Good Bacteria

One of the most important aspects of aquarium care is the bacteria that keep the whole system livable. Without them, the water would be lethally toxic in a very short amount of time. Although it’s possible to get by without a proper and full understanding of these bacteria, understanding them better can help every aquarist be that much better at what we do.

What Are They?

The bacteria in question are called nitrifying bacteria. They include Nitrosomonas spp. and Nitrobacter spp.. Nitrosomonas spp. consume ammonia and produce nitrite as a waste product. Nitrobacter spp. consume nitrite and produce nitrate as a waste product (in freshwater). There are some bacteria that consume nitrate and produce nitrogen gas, but they are anaerobic so they do not live where there are high concentrations of oxygen. They only live where there is almost no oxygen, so they are effectively never found in freshwater (a couple biomedias claim to allow for them, but results are usually circumstantial/anecdotal at best). They are common in live rock in saltwater aquariums though and can play a significant role in producing marine aquariums with no detectable nitrate.

Where Do They Come From?

Nitrifying bacteria are actually all around us. They are literally in the air. If you start an aquarium with 100% brand new equipment and add bottled ammonia, the bacteria will start growing. There is no need to add anything to seed them and in most cases, adding bottled bacteria, ‘seeded’ (used) filter media, etc. will not have any significant impact on how well the tank cycles.

Where Do They Live?

The good bacteria can live on any surface in the aquarium. However, like all organisms ever, they concentrate their populations where their limiting factors are best met. In an aquarium, the two things that are the most limited for the bacteria are food and oxygen. Filters provide flow which provides food and oxygen. The surface area of the biomedia provides a surface for the bacteria to grow on where they can sit and allow the oxygen and food to come to them. At the end of the day, it is not the biomedia itself that is anything magical, it is nothing more than surface area per volume. The bacteria are happy to grow on any surface, but they do not simply spread out evenly throughout the aquarium. Although any surface area in the tank (decor, glass, substrate, etc.) are otherwise perfectly acceptable, they do not have the same flow as the filter and therefore will not house significant colonies of bacteria. More precisely, the bacteria in the filter outcompete bacteria elsewhere because they have a better chance of consuming ammonia and nitrite, leaving the other bacteria with little to none. This is why the colony in the biomedia grows to a level where it consumes the ammonia and nitrite as fast as it is produced, resulting in both being undetectable.

I have moved entire setups many times by moving just the fish and filtration without any issues. This means no decorations, water, or even the substrate were moved. The tanks did not re-cycle or go through any sort of mini-cycle. This shows that the substrate, decor, and anything in the tank other than the filtration did not house any significant amount of bacteria. This isn’t to say they were sterile, just that if adequate filtration is provided, effectively all the bacteria will be in the filter.

I have also replaced the entire substrate all at once dozens of times with the exact same results, no re-cycle, mini-cycle, or anything else that indicated any significant amount of bacteria were in the substrate. This again supports the concept that if adequate filtration is provided, effectively all the bacteria will be in the filter.

Surface area doesn’t equal bacteria. Bacteria need much more than surface area to survive, thrive, and establish colonies. Many people focus only on surface area, which is the most ample resource bacteria have, there is no reason at all to think this alone would be a determining factor to where they live. They will grow where their most limited resources are found. Those resources are oxygen and food, both provided by flow, which in any tank is highest in the filter.

Trickle and other filtration methods that expose the bacteria or water to the massive amounts of oxygen in the air can create much more efficient colonies on otherwise more limited surface area (Bio-Wheel, Bio-Balls, etc.). If this is particularly appealing to you, I highly suggest using a sump with a section specifically designed for K2 media. Biowheels stop turning and their filter cartridges are garbage like all other dinky slide-in cartridges. Bioballs are very ’80s and trap tons of debris, which rots and ruins water quality. K2 media is submerged but almost neutral in buoyancy. It is housed in a very aggressively aerated section of a sump that keeps the media tumbling. The aeration provides massive amounts of oxygen and flow. The tumbling keeps the media free of debris and makes it self-cleaning. Together, this means it is no maintenance for you and a superior filtration method. Check out the article on Building Your Own Custom Sump for more details.

Cycling a Tank

Cycling is the process of building up enough beneficial bacteria to handle the full bioload of the tank so that all ammonia and nitrite are processed and quickly as they are produced making both undetectable. Cycling takes time, during which ammonia and nitrite have the potential to easily become stressful and even lethal. This is why so many new aquarists accidentally kill fish or at least make things more difficult for themselves by causing disease to break out in their brand new tank.

Fishless cycling is generally the ideal method. With this, no fish are present so there is no stress or risk of harming them in any way. Once you have your tank running, you add bottled ammonia (no additives, colors, fragrances, etc.) in very small amounts. You need to give it a couple of minutes to mix and then test your ammonia. Track how much you add. Ideally, you should use a syringe so that the measurements are very accurate (Lixit makes good ones, but eBay and other places are full of good options). You want to bring the concentration up to 4ppm. Add up how much ammonia you added, this is the amount of ammonia you need to add every day, just be sure not to let the concentration in the tank go over 4ppm. It will go over 4ppm if you add it blindly before the bacteria start to develop, which will actually inhibit the growth of the bacteria.

Raise the temperature up to 88-90F or as high as your heater can get it. This is a good time to realize how powerful your heater is. Imagine if it got stuck on with fish in the tank. This is why I suggest keeping the power of heaters to only about 2 watts per gallon. It is also good to keep the tank very well aerated. The nitrifying bacteria thrive in high oxygen, warm water.

Test ammonia and nitrite daily. Test before you add that day’s ammonia so that you don’t allow the ammonia to go over 4ppm. You will notice the ammonia begin to go down and the nitrite will begin to go up. Then the nitrite will go down. Once the nitrite is down to 0ppm, the tank is cycled you need to keep adding the same amount of ammonia daily until the day you add fish, otherwise, all the bacteria you worked so hard to build up will starve. Before you actually add fish, you need to do a large water change or two to get the nitrate back down to the same or only slightly above the tap water (ideally under 20ppm).

Done properly, this entire process can take as little as 12-15 days, but don’t worry if it takes longer.

Sources of Ammonia

The ideal source of ammonia is bottled ammonia. It should have no fragrances, dyes, or anything else. For some reason, some people like to let stuff such as fish food or frozen seafood (usually shrimp) rot in the tank as a source of ammonia. This is a horrible idea. For one, you have no measure of how much ammonia is being added. Secondly, it is inconsistent since as it rots the amount of ammonia produced will go down until none is being given off. So although it was a source at some point, by the end (once it is all gone and rotted away), there is no more ammonia being added to the tank. So whatever bacteria did develop subsequently starved by the time it is safe to add fish. That’s not really safe or cycled, is it?

Use bottled ammonia and measure it properly, you don’t gain much by doing the right thing the wrong way.

Silent Cycle

In larger tanks (about 75 gallons or above), it is possible to have what I call a silent cycle. This is when a small amount of fish is added and the amount of ammonia produced stays low enough to not cause any issues due to the large volume of water diluting it. For example, you may add two small peacock cichlids to a 75 and their bioload in that large of a tank won’t cause any issues.

You still need to track ammonia and nitrite and watch the fish closely. If there are any signs of anything off at all, do water changes, it isn’t worth risking the fish.

Changes in Bioload

Once the tank is cycled, it will generally stay matched to the bioload of the tank. However, if the bioload changes, you could have a situation where the tank is only partially cycled. Any significant, sudden increase in the bioload can be enough to cause a mini-cycle where you may see ammonia and/or nitrite. Usually, the spikes aren’t as high as they will be in a new, completely uncycled tank, but they can still be problematic, especially with more sensitive species. This is why it is vital to stock the tank slowly. Don’t suddenly double the bioload or even add 50% more fish all at once. Spread them out and do an extra water change or two in the few days after adding anything close to a significant amount of fish.

Another problem can be un-cycling a tank by removing too much of the biomedia at once. This usually occurs with small tanks that have a HOB filter with just a slide-in cartridge that is replaced monthly. This removes all the bioload every month and can cause issues maintaining the cycle. This is a big reason to not use any of those types of HOBs (I only use and recommend AquaClears, but the Seachem Tidals are a good option as well).

If you have issues with ammonia or nitrite once fish are in the tank, first look at the fish. Sometimes, they are actually okay and you can take a minute to breathe and realize it’s not as bad as it could be. Next, like any time anything is wrong with an aquarium, do a water change. Do the same size as normal or only slightly larger, doing a much larger water change than usual can shift the chemistry of the tank too much too quickly and add a problem rather than relieve one. Then, add salt. Salt is amazing at helping when anything’s wrong. In addition, it’s particularly effective against nitrite poisoning making it even more powerful when there’s an issue with nitrite. Do a water change every 1-3 days until the ammonia and nitrite are back to undetectable adding salt each time for the amount of water changed. Stop adding salt once things are good again.

Other Articles You May Be Interested In

Types of Aquarium Filters

Filter Media Types Guide

Freshwater Chemistry

Stocking an Aquarium

Sand as a Superior Substrate

Heaters – The Ticking Timebomb in Every Tank

Salt in Freshwater Aquariums