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 life rock in saltwater aquariums though and can play a major 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.

I have moved entire setups many times by moving just the fish and filtration without any issues. This means no decorations 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 besides the filtration did not house any significant amount 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 in otherwise more limited surface area (Bio-Wheel, Bio-Balls, etc.). If this is particularly appealing to you I 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. 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.

Cycling a 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 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 temp 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 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 (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 (not really safe or cycled, is it?).

Use bottled ammonia and measure it properly, you don’t gain much by doing the right thing (fishless cycling) 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 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.

Cycling a Saltwater Aquarium with Live Rock:

Cycling a saltwater tank using live rock is pretty simple and straight forward. Before adding any other livestock, simply add all the live rock you are going to and let it cure in the tank. Curing is the process of allowing anything that died during transport to decay. As the rock cures it will cycle the tank. If the live rock was cured when you bought it you should transport it home completely submerged to keep everything alive. If this is the case it may not need to cure at all and the tank will be instantly cycled, but you should still let it run a few days to make sure. Depending on how bad the rock is it may take a week to a few weeks for live rock to cycle. Just like cycling a freshwater tank you can test ammonia and nitrite daily. Once the nitrite is back down to 0ppm the tank is cycled. Then do a large water change or two to get the nitrate back down as low as possible and start cycling. Do not add ammonia. Once the rock is cured, the tank is cycled, and you do the water changes you can begin stocking.

In addition, please read the article on Live Rock.