Filtration - Back to Biological Basics

We're back for part III of Filtration Basics, and this chapter is probably the most important aspect of successfully filtering marine aquarium water: Biological Filtration. Pretty much every biological filtration method in the world works the same way; water is passed through some type of material that allows for oxygen and water to move through it and is capable of being colonized by a few different kinds of related bacteria. Whether we are treating aquarium water, or running a municipal wastewater treatment plant, we rely on nitrifying bacteria to remove nitrogen-based waste, in a process called nitrification.

We're not going to get into the actual equations and chemical math of these interactions, for fear of making many of you doze off. Technically, what is happening is a process called oxidation and it goes like this:

In the first step of this process, nitrifying bacteria from a few different genera (the plural of genus) but usually Nitrosomonas take ammonia and oxygen and turn them into nitrite, hydrogen and a couple free electrons, mmm electrons.

In step two of nitrification another genus of bacteria called Nitrobacter (and less commonly a few others) take nitrite and water and turn them into nitrate, hydrogen and a couple more electrons (still mmmm).

As this relates to your aquarium, ammonia is the primary waste product of the animals you house, both fish and invertebrates. This ammonia (and nitrite) is very toxic in very low concentrations. Why we cycle aquariums is to give the tank time to develop colonies of these bacteria. They grow in the sand, on the rocks, and importantly, in and on the media of your filter systems. These bacterial colonies take time to develop and multiply. Without them, the water in your aquarium would quickly be toxic to all the non-bacterial critters in there!

The third step of this process is a little bit trickier and gets frequently overlooked in conversations about biological filtration and is never talked about with nitrification, because this step is actually called denitrification. You see, there isn't anything to turn nitrate into except for nitrogen gas. This is a process where, yet another bacterium (or series of bacteria) takes nitrate and some free electrons to make nitrogen gas, which is the vast majority of the atmosphere here on earth. Yes, you read that right, mostly what you breath is nitrogen, not oxygen (78% nitrogen, 21% oxygen, and 1% everything else.)

The tricky bit here is that the first two bacteria need oxygen, and the last process is much more efficient without it, and even at peak efficiency it is a much slower process than nitrification. Regardless, nitrate can still be toxic, though in much higher concentrations than Ammonia or nitrite and it needs to be removed. The time tested and true way to deal with nitrate is by having a healthy amount of very porous, real live rock in the aquarium. The water holding the nitrate penetrates and migrates through the rock, but so slowly that the oxygen gets left behind and so the internal environment of the rock is conducive to denitrification. Once popular DSB, or deep sand beds worked in a similar fashion, the lowest levels of the sand bed were also devoid of oxygen and the same processes happened. There are some porous filter media on the market today which also function this way. You can use things like rock rubble, or sintered stone in a sump, and they will also reduce nitrates through this pathway.

Another way to deal with excess nitrate is through uptake. Nitrate is a form of nitrogen that is very available for plants, algae and bacteria to utilize. As such, the aquariums with a copious amount of rock offer many surfaces for different algae to grow on. Even the coralline algae we all love in our tanks utilizes nitrates for growth, and you guessed it, more rocks = more surfaces and more algae growth = less free nitrate.

Some aquarists utilize plants in their displays as well, and mangrove shoots grow very well in aquariums, though they need a lot of light and vertical space above the tank, and their effect on available nitrate is limited. Algal scrubbers are a technology that are very common in larger scale water treatment, and indeed are often seen in home aquariums as well. One of the primary benefits of a refugium is that a hobbyist can grow algae in a part of the tank that is sheltered from fish and inverts that would otherwise eat it, and the algae grows without interruption. This is a very effective way to deal with nitrates. If you've ever seen a sump with a ball of chaetomorpha, in it, nitrate removal is the chaeto's number one job. There are lots of other types of algae-based filters around the world being used for a variety of things, but they are not very popular in aquariums. For those of you looking to pioneer new pathways in filtration, there are probably some opportunities here!

In the end, no matter how you decide to lower your nitrate levels, there is one method you should all be using. It was the first process ever used to keep marine aquariums healthy. The very earliest marine holding tanks in the history of the world used water changes to keep tidal pools full of water that was suitable for marine life. Beyond the water change's capacity to remove off colors, and to boost the buffers and trace minerals that your aquarium requires to stay healthy and balanced, a 20% water change will reduce the nitrates in the water by 20%. Now, new nitrates are being made, and if you have a large buildup of organic material in your tank that isn't also getting removed, your numbers after the water change will not show a 20% reduction, but over time, it will keep your nitrates down like nothing else can. Do the water changes, and use a quality salt like Tropic Marin that you know won't bring more nitrogen-based pollutants back in.

Now, we would be remiss if we didn't talk about the seeding tanks with bacteria. Obviously, there are many different biological boosters you can use these days, and if you've been reading any of our tank care articles in the last ten years, you know we're big fans of the Dr. Tim's line of bacterial products, especially their One-and-Only. This product can take the cycling time of an aquarium from weeks down to a day, or even hours. We still suggest running an aquarium dosed with One-and-Only for 24 hours to let that bacterial colony settle in and reproduce, but many aquarists report success with immediate stocking after dosing it.

Regardless of how you plan to start your biological filter, it remains a critical, and perhaps the most critical, aspect of your filter system. Take care of the bacteria you want, and they will keep the bacteria you don't want in check (as well as your nutrients!). Use plenty of good, porous live rock, and never skip your water changes and you should have an aquarium that is stable, clear and healthy for decades to come.