Cycling and System Maturation

A system is cycled when its nitrifiers can turn the ammonia it gets now into nitrate, with ammonia and nitrite at zero (Module 8). That's enough for a few hardy animals. It isn't enough for everything.

A mature system has more than nitrifiers. It has a varied, settled community of microbes, tiny animals on the rock and sand, and algae that have found their balance. Its numbers hold steady week after week, and it handles a missed feeding or a hot day without big swings. A mature system has more ways to absorb a problem.

Most of this module is about the time between cycled and mature: what to add, when, and what can go wrong on the way.

A system built with dry rock and dry sand starts with almost no bacteria. It needs a full cycle before animals go in.

A system built with established rock or sand from a healthy system, or with new live rock, may already have enough helpful bacteria to skip the cycle. Test ammonia and nitrite before and after the first animals go in to confirm it. New live rock has a catch: if a lot of the life on it dies off, the rot can cause water quality problems (section 5).

In the experience of Michael Maddox, President of IMARCS, starting a reef system from dry rock is a mistake; he starts reef systems with high-quality live rock from the ocean, and uses dry rock only for systems such as breeding or holding fish. Module 36 sets out his approach.

Seeded media from a healthy system speeds things up. Anything from another system can carry pests and disease, so the biosecurity rules from Module 2 apply to rock, sand, media and water alike.

The bacteria need ammonia to grow. In a fishless cycle, it comes from an ammonia source added on purpose. One common product, ammonium chloride made for cycling, is dosed to bring ammonia to about 2 ppm, and its maker warns never to go above 5 ppm. Rotting food or a dead shrimp also make ammonia, but they add the leftovers of decay too, and the amount is hard to control. A measured ammonia source makes the cycle easier to read.

Test ammonia and nitrite often, and top the ammonia back up as the bacteria use it, so they keep growing. Turn off UV sterilizers and ozone during the first cycle. The system is cycled when ammonia and nitrite read zero and nitrate is being made (Module 8).

Bacteria that go without ammonia shrink (Module 8). If animals don't go in soon after the cycle finishes, keep feeding the bacteria until they do.

Live rock loses some of its life in shipping. When it goes back in water, that dead life rots and can spike ammonia and phosphate and release organics. Dry rock can carry dead marine life too, dried in place, and it can leach nutrients and organics as it decays. Some dry rock products are sold as needing only a rinse; check what the maker says.

Cure rock in warm, moving water (about 26 C, 78 to 80 F) with a skimmer running, in a separate container or in the new system before any animals or sand go in. Keep the light short to limit nuisance algae. Change water often, siphon out dead material and remove anything clearly dead. Watch for hitchhikers, like crabs or mantis shrimp, and remove them before the rock is placed.

Test ammonia. Rock is cured when ammonia stays at zero and there's no rotten-egg smell. That can take a couple of weeks, or months for rock carrying a lot of dead material.

Not all live rock is cured. In the approach of Michael Maddox, President of IMARCS (Module 36), high-quality live rock is shipped in water, arrives within about 24 hours of being shipped, and goes into the system quickly without curing. Test and watch for die-off all the same (section 5).

Die-off happens when rock or sand life is shipped, dried, moved or cut off from flow, or when a lot of animals die at once. Decomposers break the dead material down, releasing ammonia, phosphate and organics (Module 8). Signs include a rotten-egg smell, extra foam from the skimmer, cloudy water and rising ammonia.

That's why new live rock that hasn't been cured, or established rock that sat out of water too long, can push ammonia up even in a system that cycled. Remove what's dead, test ammonia and nitrite, do matched water changes, and report it. Hold off on new animals until the numbers settle.

Microfauna are the tiny animals in a system, like copepods, small crustaceans often called pods. Copepods eat small amounts of detritus, leftover food and film algae. In turn, they're food for fish that hunt tiny live prey across the rock and sand, such as mandarins, wrasses and small gobies.

Live rock brings these animals in. A system built from dry rock starts without them. They can be added from a culture, ideally soon after the cycle, before fish start hunting them: add them with the lights off and pumps paused, near cover like rock or a refugium, so they can settle. More kinds of life make it harder for pests and nuisance organisms to take hold.

Fish that hunt pods, like mandarins, find little to eat in a new system that has few of them. Those fish belong in mature systems with plenty of pods.

Before the first animals go in, three things should be true. The system is cycled: ammonia and nitrite at zero and nitrate being made. Salinity and temperature are steady. And after a feeding or an ammonia dose, ammonia and nitrite stay at zero, so the bacteria can handle a load.

If the system was started with established rock or new live rock, confirm the same things by testing, even if it never showed a cycle. A system that skipped the cycle still has to prove it can handle animals.

Add animals one at a time, with time between them. Space fish at least a week apart so the bacteria can catch up with each new load. Test ammonia and nitrite after each addition.

Start with hardy animals that add little load. Hardy corals add far less load than fish, because fish give off ammonia through their gills. Clean-up animals like snails go in to match the food that's there for them; added early with nothing to eat, they starve and add to the load when they die. Add fish from least to most aggressive. After the last addition, let the system settle; every change in load is another source of instability.

Every new animal is also a biosecurity risk. New arrivals go through quarantine before they join a system (covered in the quarantine module).

Calcifiers that are sensitive to swings need alkalinity, calcium and magnesium to stay steady and inside their normal ranges (Module 6). They need nutrients that are detectable, not zero and not too high. And they need a system that isn't still going through its ugly stage (Module 8).

There's no fixed number of weeks or months. The log decides: weeks of stable readings, no drift and no swings, with the dosing and testing routine settled. A system that still needs constant fixes isn't ready for animals that can't handle change.

First, stop the cause, if it's still happening: restore power and flow, fix the heater, stop the dosing. Remove anything dead. Do matched water changes to bring ammonia and nitrite down while the bacteria recover (Module 8). If the numbers are high or keep coming back, make them large and repeat them as often as needed (Module 5 covers making and matching new salt water). Put in fresh activated carbon (Module 6) and add a poly filter, a chemical filter pad made to pull contaminants out of the water. Adding a bottled beneficial bacteria product may help, as long as there isn't already a bacterial bloom (Module 8). Feed lightly, because every feeding adds load, and test ammonia and nitrite daily. Report it, with what you saw and what you did.

The bacteria that were lost grow back slowly. Until the numbers hold steady again, don't add animals or make other big changes. A crash can also set off nuisance blooms as the community rebuilds; treat them as you would in a new system, with the basics and patience.

Rushing	What it causes
Adding animals before the system is cycled	Ammonia and nitrite spikes. Animals suffer or die.
Adding many animals at once	The bacteria fall behind. Ammonia rises.
Treating every nuisance bloom	Bigger swings. The ugly stage lasts longer.
Chasing numbers every day	A new number every day for the animals (Module 6).
Sensitive animals in a new system	They can't handle the swings a new system still has.
Skipping the tests because the water looks clear	Clear water doesn't show ammonia or nitrite.

The cure for each is the same: test, wait, add slowly, and let the log show when the system is ready.