Reefkeeping 101 -
Natural Filtration

Busting a Myth

A long, long time ago in a tank not too far away a single little fishy swam around and around. He was a fearless little fish as he was added to this bleak tank to slay the ugly Ammonia Monster. Now all good fish keepers knew about this ugly monster and they knew a single brave fish would need to be sacrificed to appease its hunger. After all, once the good nitrate-making fairies took over, the dread monster would never return. For this, the little fish was made the hero, although posthumously…

That story has been around so long that most (new to the home aquarium hobby) believe it whole-heartedly. It is based on some facts however. In the early years of tropical fish keeping, fish were often added to nearly sterile tanks. A clean tank was a disease-free tank so why add anything that would harbor filth. The problem was that ammonia is a true monster in a sterile environment. The good guys (nitrifying bacteria) are slow growing, taking almost ten days to become effective, while the bacteria that convert protein and other organic nitrogen compounds into toxic ammonia appear overnight. The net result is that the beneficial bacteria needed to effectively process the toxic ammonia never secure a foothold in the super clean tank. It didn't take too long for that fact to be realized, and aquarists soon began to manage nitrogen in all sorts of ingenious ways.

Freshwater Biofiltration

In February, I talked about some types of mechanical or chemical filtration. Namely skimmers, a form of mechanical filtration and canister filter, which depending on the media employed, can be mechanical (micron filter) or chemical (activated carbon or phosphate sponge). These are important means of filtration but in any aquarium, biological filtration is the most important filtration method.

For those of you that skipped biology classes, or only paid attention when they were discussing the birds and the bees; when an organic waste enters the water column, bacteria start to feed on that waste and in doing so use oxygen to break down and consume that waste. In the early 1950's that fact became well-known and filters were developed that encouraged bacteria to grow on a fixed substrate, such as gravel, and would help in removing dissolved organic materials. This allowed far more fish to be housed safely in the limited volume of an aquarium. In the world of freshwater, they still reign supreme.

In a freshwater tank, we can use an under-gravel filter, wet/dry or bio-wheel. These mechanically-aided biological methods are the important means of having a successful freshwater tank. An under-gravel filter provides a very large surface area (the gravel itself) but has the drawback that the oxygen for those bacteria comes from the water column. It therefore can deplete the oxygen content of the water if the demand on it is high. Wet/dry and bio-wheels circumvent that problem as the biological filter media is continually exposed to the air where atmospheric oxygen is available. This limits the need for dissolved oxygen in the water column to keep the aerobic bacteria active to remove waste. As a freshwater tank is almost sterile at start-up, some sort of seed (usually a small fish) is added to get the needed bacteria into the tank. Freshwater fish are fairly tolerant of ammonia so usually in a freshwater tank, the fish manages to survive this ordeal.

In the early days of saltwater the same filters were also used and the 'Wet/Dry' was the most common option. Tanks in those days were mainly fish-only and a wet/dry worked well. As invertebrates (such as corals) became popular, a problem arose. The fixed media bio-filters would indeed remove ammonia and other organic materials but they also left behind large quantities of nitrate, a byproduct of ammonia oxidation. This was toxic to invertebrates at far lower levels than it was to fish.

Solutions were forthcoming from both Indonesia and Europe. Lee Chin Eng , an Indonesian, was collecting what he called "Living Stones" from the sea coast and adding these to his tanks. He found this allowed him to keep corals and other invertebrates that before then had been impossible to keep. In Europe, the protein skimmer was introduced to limit the amount of protein that was subject to biological conversion to ammonia. Latter, both methods were married up in what became known as the "Berlin Method." With the advent of this new means of reef keeping, the hobby soon took off.

Living Stones Tend to Rock!

Unless this is the very first article you have read on reef keeping, then one surely knows that modern tanks run on what we call natural filtration. That is, what we call live rock is the basis for a successful marine tank. Even if the hobbyist is only going to keep fish, they usually have live rock in the saltwater tank.

Now, what exactly is live rock? One can ask a hundred reef enthusiasts and get about a hundred different answers. The most basic usually is that it is rock that has purple algae, called coralline, growing on it and it is usually a very porous rock. Well, that is certainly true but neither of these items gives it all the beneficial qualities it exhibits.

It is not just coralline algae that makes live rock 'live.' In fact, considering the slow rate of growth of coralline algae, it would hardly make a dent in the nitrogen cycle in most tanks. Actually, it is the host of bacteria that cling to the rock that make it truly live. In my little tale I started off with this month, I fostered the image that many new hobbyists have that the "good" bacteria we want in our tanks swim merrily about all day long, processing proteins into ammonia while others convert that to nitrite and nitrate. In reality, they are holding on to the rock and substrate for their dear lives. Being swept around the water column is like hanging a sign that says, "Eat Me" on your back. It is far safer to cling together with a great group of relatives and friends than to venture out into the water column.

Just a small number of free swimming bacteria survive in the water column. Not exactly Olympic swimmers, they are easy prey for the various free swimming, ciliated protozoa that live in the tank. Their lives are numbered with these voracious predators swimming in the same pool. Attached to rock and other substrate is a far safer route to survival. Also, it is in the substrate and other attached surfaces that food normally settles. A square inch of live rock surface may contain several times the total number of bacteria swimming around in the water column.

The live rock surface becomes a massive engine to remove ammonia and covert it to nitrite and nitrate. The latter event, caused by very slow growing autotrophs (bacteria that derive energy from chemical reactions, rather than photosythetically or by direct carbon oxidation), are growing rampant upon the surface of good live rock. Do you need to add a fish to add some food? Not on your life; live rock, by its very nature is a nitrogen processing factory from Day One.

Busting a Myth

In nature, live rock is not limited to just a bacterial film. Those free swimming ciliates have cousins that graze across the surface. Grazers like Colpidium, and attached stalked ciliates like Vorticella, grow on the rock's surface. Think of them as pruning sheers keeping the bacteria in check. They, in turn, become food for rotifers, foraminifera (a type of amoeba with a carbonate shell that is important in live rock and live sand formation), sponges, polychaetae (tube worms), and encrusting corals that live on the surface of the rock.

The exact makeup of what is on any piece of rock depends on the rock's origin and the amount of damage that occurred in transit to your tank.

Now the true live rock you buy, online or otherwise, has undergone a perilous journey on its way to your door. It goes like this…

Natives, armed only with canoes, dive down and collect live rock off the reef. After harvesting the rock and several days' journey, they reach the abode of the "Great Live Rock Hunter." After paying off the natives with plastic beads and some Gummy Bears, he places the rock on the slow boat to San Francisco where, upon your placing an order, it is shipped overnight air (you're paying the freight now) to your home.

There are also named varieties of live rock (based on where it comes from); we have Fiji, Tonga, Marshall, Caribbean; and even one called Kaelini, named after a "Great White Rock Hunter's" daughter ( she was impressed). The major difference here is porosity.

One of the live rock fables centers around how porous the live rock is. A completely smooth rock with no nooks and crannies does a fine job of converting ammonia to nitrite and nitrate. The problem is most invertebrates do not tolerate high levels of these two bi-products very well. However, there is some salvation if one can reduce oxygen levels to near zero. Many bacteria can then use the oxygen in nitrate (NO3) to provide the oxygen needed to metabolize food. This converts nitrate to harmless nitrogen gas that bubbles out of the tank. As Martha Stewart would say, "This is a good thing."

Rock with a pore structure allows depleted oxygen zones (termed anoxic) to form in those pores and thereby convert nitrate to nitrogen. Porous is therefore good.

This is why the "Berlin System" works. In a marine tank with a protein skimmer to reduce overall protein contributions, and some live rock to handle the rest of the nitrogen, we have a very efficient marine tank. Nitrate levels are controlled and corals can thrive.

Enter the HOBBYIST. While the good folks in Germany were content to keep a few fish and corals in their tanks, those across the pond were accustomed to tanks filled with tons of freshwater, tropical fish. When they tried the same thing in the marine environment using the "Berlin Method," things went well at first and then started to go rapidly down hill. The reason -- live rock has only so many pores. The surface of live rock is covered with a biological film. So are the interior of the pores. The only problem we have is that, over time, the bacteria in the pores become so numerous that they effectively seal off the pore structure. The interior of the pore becomes completely anaerobic and things like sulfates are also sacrificed to provide oxygen. This produces hazardous gasses like hydrogen sulfide and shuts down the ability of beneficial bacteria to effectively convert nitrate to nitrogen. A heavily stocked tank with only a skimmer and live rock is asking for trouble over time. There are only so many pore spaces to accumulate waste, and the bacteria that render that waste harmless tend to fill them up, so that eventually the system shuts down and nitrate levels rise.

For the past several years, there has been a return to the Berlin System in what is now called the "Bare Bottom" approach. Basically, it is the original Berlin System with a few bells and whistles. The early advocates promoting this approach were some very experienced reef keepers. They, like those using the Berlin Method several decades earlier, were content to not overtax the tank's bio-load and let the live rock itself handle the nitrogen cycle on the tank. Some of these tanks have been running fine for over five years without problems.

Once again, we get those that feel that a marine tank can be stocked just like a freshwater tank. Most tanks were using not only live rock but also a deep sand bed to control nitrogen, and thus could be heavily stocked. When they tried to keep this same heavy bio-load with a bare bottom (no substrate) tank, they learned that problems can arise in such a system. The pore structure in the rock would soon clog with bacteria and mineralization products and nitrate levels would rise as stocking levels increased. Sometimes the result was losing an entire tank full of livestock.

Faced with these drawbacks, some reef keepers proposed what they termed "Cooking the Rock" where they took poorly functioning rock and placed it in dark bins without food or much in the way of water changes. The reported benefit was that the rock would undergo endogenous respiration, a theory where cells feed off themselves until they actually consume themselves and disappear while waste is shed at the same time, thereby renewing the rock. A dubious undertaking at best since having two tanks' worth of rock, one for the tank and one "cooking," is pretty darn expensive. Actually, "cooking" rock is like killing it off, re-curing it and then waiting for it to become "like new" again. One of the benefits of getting good live rock is that it has great biological diversity. Periodically killing everything on the rock is not a good method to encourage a diverse population that took decades to form in the rock's natural reef setting.

Well, I'm getting ahead of myself here. I'll be talking about deep sand beds next month which, at least in my opinion, is the best way for a new reef keeper to set up their first tank.

Choosing Rock and Finding a Cure

I've mentioned that there are many varieties of live rock that one may purchase. Much natural rock is from the Pacific Reef islands. The main difference is some are more porous while others are fairly dense. Some live rock is also harvested from the Caribbean. Finally, there is man-made live rock which is aqua-cultured. All are fine to use but do check out the aqua-cultured rock as in some cases it is almost as good as natural. The main difference is that it may not be quite as diverse as natural rock, and it usually requires far less curing.

You can also use base rock, dead rock if you will, and seed it with live rock. Be warned, the aqua-culture of rock at home is a long, drawn-out process. Use this method only if you are very patient and can wait months to stock your tank.

As I have indicated, there is no cycle, per say, if live rock is used in a tank. All the bacteria needed are on the rock itself. What we do face is a curing period. That is the period when dead material on the rock is consumed and toxic organic production from the rock itself is brought into check. If you get a shipment of live rock, it is normally only wrapped in wet newspaper. When you open the shipping box, your nose knows that something isn't right. Usually the shipment stinks. This is because much of what lives on the rock does not survive the journey from the ocean to your door. Usually, the major culprits are the encrusting sponges that normally cover live rock. Once exposed to air, they quickly die and often appear as a black, slimy coating on the rock. Somewhat like wet shoe leather. If such black gunk is covering your rock, peel off as much as you can. It will speed along further curing steps.

Many people just place the rock in their nice new aquarium filled with saltwater and wait things out. While this works, it may come back to bite you when algae starts to grow. All that decomposing organic matter is leaking all sorts of nutrients into the water. After the rock reaches the stage where heavy ammonia production ceases, algae goes on a feast with all the goodies in the water that can last a few months. Huge water changes help, but even so, it is hard to remove all this material.

I always recommend setting up a rock curing line. All you need are some shallow plastic trays; you can usually pick up ones that hold five to ten gallons at a thrift store for about $5 each. You then pretty much fill them with the new live rock and cover that completely with water. If the room temp is around 72-75 degrees, heating is not needed. If one wishes to avoid the stink, then do this in the garage and buy those heating mats used under plant seedlings to warm the trays. Warmer water temperature means faster curing times, but keep it under 85º F.

Now here is a point I wish to make—Do Large Daily Water Changes on the Curing Vats. One of the most common Newbie misconceptions in that not changing water will speed up the curing process. It is the other way around. With less nasty junk in the water column, the bacteria will be able to digest the dead stuff on the rock. It also helps get rid of toxic ammonia, keeping it from killing some of the live things that the rock contains. There is no reason why one should not do 100% water changes on curing rock. It will pay off with a better quality finished product that is ready in far less time. I also like to move or rotate the rock every couple of days. This ensures that the rock is not touching other rocks at the same points which fosters dead spots on the rock.

This is also the time for one to flex their chemistry wings. Once the smell starts to lessen, it is time to do ammonia testing. You want to perform this test daily until the ammonia level stays at zero for a couple of days. Once that happens the curing period is over and the rock can be rinsed and placed in the display.

Well, they tell me I need to crawl back into my dark cave where they give me no food and very limited water changes. They tell me that soon I'll be renewed and my pores will open up. I guess we'll get back to working with rock next month and also explore deep sand beds.

Until then.

If you have any questions or comments about this article, please visit this thread in the New to the Hobby forum on Reef Central.

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Reefkeeping 101 - Completing the Initial Set-up by Tom Murphy (aka WaterKeeper) -