The Nitrogen Cycle

Before we start filling our new aquarium with saltwater and live rock, we first we need to understand the saltwater aquarium cycle, sometimes referred to as the Nitrogen Cycle.

Understanding the nitrogen cycle will give us an insight into the natural processes that take place within a healthy aquarium.

nitrogen cycle

The Nitrogen Cycle keeps this aquarium thriving

Hopefully, it will also drive home the importance of the Nitrogen Cycle, and how it is absolutely vital that both Time and Nature are allowed to run their natural course before we start adding our new marine inhabitants.

So What Is The Nitrogen Cycle?

Marine fish drink the water in their environment constantly and excrete small amounts of very concentrated urine constantly. Combine this concentrated urine with fecal pellets, multiply that by several fish and throw in a good measure of uneaten, decomposing food into the equation, and we get ammonia.

Even 1 ppm (part per million) of ammonia is deadly to fish and corals.

In order for marine fish and corals to survive and thrive in our enclosed aquarium environment, we need to develop and cultivate a healthy population of beneficial bacteria that will neutralize the ammonia.  Breaking down ammonia is necessary for the nitrogen cycle to begin.

Once allowed to multiply, these bacteria will populate the hard substrate in the tank, including the live rock, sandbed, tank walls and even the surfaces of powerheads and pumps. If it’s underwater, these bacteria will colonize it.

The first group of nitrifying bacteria — the aerobic, oxygen-loving Nitrosomonas — break down the ammonia produced by fish waste into nitrite (No2). Nitrite, while not as lethal as ammonia, is still poisonous to aquatic life.

The second group of oxygen-loving bacteria, Nitrobacter, consume the nitrite and convert it to nitrate (No3). Nitrate is far less harmful to fish and is easily tolerated unless it reaches very high concentrations of 200 ppm or more.

But unlike fish, corals do not tolerate nitrate well. It is recommended that not more than 5ppm of nitrate be present in an aquarium stocked with small-polyped stony corals (SPS), with 20ppm being the upper threshold for large-polyped stony corals (LPS).

If the ammonia in our aquariums were to endlessly convert to nitrate, and if the nitrogen cycle were to stop there, we would soon have a nitrate factory, on our hands.

Not so good.

And this is where denitrifying bacteria come to the rescue. This genera of anaerobic bacteria live within the pores of live rock and deep within the sandbed where oxygen is poor. Denitrifying bacteria reduce nitrate to harmless nitrogen gas which escapes from the aquarium water in the form of gas bubbles, in effect completing the nitrogen cycle.

The nitrogen cycle is Nature’s perfect solution for maintaining a healthy saltwater aquarium!

Which finally brings us to…

The Nitrogen Cycle And How To Properly Cycle Your Saltwater Aquarium

If you’ve read this far, Congratulations.

brown diatoms on sandbed

Brown diatoms on sandbed, even after cycling

It is likely that you will also be patient enough when it comes time to sit through your saltwater aquarium cycle.

By now you will have come to realise that the nitrogen cycle is all about the bacteria.

When we cycle a brand new aquarium, all we are doing is giving the different species of bacteria enough time to establish themselves. The aim is to have a large, diverse population of bacteria so that they will be able to complete the nitrogen cycle through all its stages, from ammonia to nitrite and nitrate, and finally, to nitrogen gas.

Starting the Nitrogen Cycle

Now for the bad news. it will take a minimum of 4 weeks to cycle your tank and to establish the nitrogen cycle. And that is only if you are using fully cured live rock.

I usually shoot for a full 6 weeks of cycling when using semi-cured live rock. But in any case, more weeks is always better.

And now for more bad news — no livestock should be in your tank during the cycling process. No fish, corals, shrimp.. nothing.

And please do not use live fish to cycle your saltwater aquarium!  Fishless aquarium cycling is not only humane, but is just as effective.

I started my very first saltwater aquarium in 2005 and cycled it with two yellow-tail damsels. A bad idea. The conventional wisdom at the time, supported with some very bad advice from my local fish shop, was to use a hardy fish or two to start the nitrogen cycle and see it through to completion. If they survived. One of my yellow-tail damsels died within a day. The other damsel, Bluey, I am happy to report is very much alive, plump and happy today, in November 2011.

With new tanks I fill them up with pure reverse osmosis (RO) or de-ionized (DI) water and add salt right into the aquarium to a Specific Gravity of between 1.022 to 1.025. The powerheads will dissolve the salt which will take anywhere from a few hours to a full day depending on the size of your tank.

Some aquarists use dechlorinated tap water for the cycling phase. I disagree, as nitrates and phosphates present in tap water, will lead to serious algae bloom problems during cycling.

After the salt has dissolved fully, add the sandbed. If you can get a handful of ‘live sand’ from a disease-free, well-established saltwater aquarium, so much the better. Scatter this live sand over your new, ‘not-yet-live’ sandbed and you’ve just helped with a population explosion of beneficial bacteria and miscellaneous microorganisms. Always a good thing!

There’s a full article on types of sand and how to add a sandbed to your saltwater aquarium here.

After we’ve added the sand — and once the dust has more or less settled — we can go ahead and add the live rock and try our hand at aquascaping.

Let Live Rock Do Its Thing!

I’ve always cycled my aquariums with cured or semi-cured live rock. Dead rock, which has been left out of water for many weeks and left to dry out completely, will take a very long time to become ‘live’, and will drag the cycling process on longer than it needs to.

With semi-cured live rock, some organisms on and within the rock will die-off producing ammonia. This is good as it kick-starts the beginning of the nitrogen cycle.

Nitrifying bacteria will start to populate every inch of the tank, while denitrifying bacteria will multiply within the pores of the live rock and spread into the sandbed.

Using Bottled Bacteria Starters To Kick-Start The Nitrogen Cycle

There are a number of commercially available bacteria starter formulations to help establish the initial population of available nitrifying and denitrifying bacteria, especially if live sand and live rock are not available.  These formulations are also useful for adding to the diversity of the bacterial populations in established aquariums.

The First Week

With the live rock, sand and saltwater in the tank, your Nitrogen Cycle will have officially begun. A small amount of ammonia can be introduced to the tank at this time, although this is really optional, given the natural die-off from the live rock.

Most aquarists get a small shrimp from the fishmongers and throw into the tank. The ammonia produced by the decomposing shrimp will kick-start the nitrogen cycle in a big way.

A few aquarists have even been known to use their own urine as an ammonia source. Having never done this myself, I cannot give you the exact quantity to use, relative to the size of your tank! I would stick with the shrimp to start the nitrogen cycle.

Let the tank run with all return pumps, powerheads and protein skimmer on. The skimmer may or may not produce skimmate during this time. My experience with some models is that they will skim off fine sand particles floating in the water column after the sandbed was laid. It may also start skimming dark skimmate, depending on the amount of die-off from the semi-cured live rock.

If you spot any unwanted hitchikers emerging from your live rock — mantis shrimp, large bristle worms or fireworms, you might want to trap and remove them. They could pose a problem later on, eating your coral or attacking your fish! But let friendly hitchhikers such as tiny worms or starfish be. If they survive the nitrogen cycle they will add interesting bio-diversity to your tank.

Aquarium lights should be turned off during cycling. Different species of diatom algae will bloom and recede during the cycling process, with one superceding the next. Turning on the aquarium lights at this time will encourage photosynthesis, intensifying each algae bloom.

We also don’t want to kill off our friendly bacteria with cold or excess heat while they are trying to gain a foothold. You can leave the chiller off but make sure the temperature doesn’t rise above 30 degrees Celsius. You will need to turn the aquarium heater on if the temperature tends to drop below 24 degrees Celsius.

By Day 3 of the first week you should be seeing measurable amounts of ammonia when you test, a clear signal that the nitrogen cycle has begun.

The Second Week

Ammonia will continue to rise in the second week and peak at around Day 10, after which it will slowly start to decline. By this time, the water may take on a slightly cloudy appearance and an unpleasant smell may also be detected.

At the start of the second week, nitrite should be measurable and will start to climb. This is a good sign as it shows that the bacteria are doing their job and the nitrogen cycle is progressing.

If you’re using fully cured live rock, there is a possibility that you will not see get any ammonia readings at all. Lots of cured live rock can form an instant living biofilter and all you might measure is a small amount of nitrite at the start of the second week. But again every tank is different and you should be testing for ammonia and nitrite every two or three days during the second week.

If you’re a very detailed person and you care to test every day, you might get hold of some graph paper and do a chart with a timeline and ammonia and nitrite readings in ppm over the course of 30 days.

fully cycled and maturing marine aquarium

6-month old aquarium, fully cycled and maturing

The Third Week

By Day 21, ammonia would have tapered off to nearly zero. Nitrite will peak by Day 26 and at the end of the third week and will have started its gradual decline.

The third week is when the patience of most people is truly tested. You have been looking at an empty tank filled with nothing but saltwater and rocks. But I must ask you to resist the urge to go out and buy a couple of fish at this point.

Remember, although our ammonia levels have dropped, nitrite is deadly to fish and other livestock!

The Fourth Week

Nitrates will be measurable by Day 28 of the cycling process. You’re also likely to get a bloom of brown diatom algae, fueled by the nitrates and the ambient light from outside the tank! No reason to panic, as this diatom bloom usually fades away after a week of appearing.

The Fifth Week

By Day 35, nitrite concentrations would have become unmeasurable on your test kit. Nitrates will continue to rise but to low levels of 2 – 5 ppm.

You might want to do a 25% water change once nitrate is detectable and ammonia and nitrite are both zero.

It is only at this point, and after you’ve done one final check for ammonia and nitrite, that you can start stocking your tank slowly.

And if you happen notice brand-new specks of pink coralline algae on you aquarium glass, this is an excellent indicator that your tank has fully cycled and is ready to receive its first few aquarium inhabitants. Now would be a good time to add your reef cleanup crew — hermit crabs, shrimp and snails.

But go easy on adding fish at first. It’s a good idea to add just two fish as a start and see how everything goes for one week. Feed as normal, but be careful not to overfeed. Your first few fish will add to the bioload in your new tank and increase the population of bacteria further, as they try to cope with the increased amount of waste.

Adding too many fish too soon will overwhelm the bacteria and what they can digest, creating a recurrence in ammonia — an ammonia spike — and you will be back to square one of cycling your tank. Although we have a good population of bacteria already, we need to allow them to multiply even further to meet the biological demands of our new fish.

Some aquarists also add some corals at this time. If nitrate is low enough, you can even start stocking large-polyp stony (LPS) corals, or even the more demanding small-polyped stony (SPS) corals at this time.

It should be noted that both corals and invertebrates do not contribute to the bioload as much as fish, as far producing waste. But proceed stocking them with care in any case.

Add two fish per week over the next few weeks, or until your ideal fish population is reached.

A Word About ‘Instantly Cycled’ Saltwater Aquariums

I have started ‘instantly cycled’ saltwater aquariums before, using saltwater, live rock, live sand and filter sponges, all from another established tank. It requires that less than an hour elapses between the time the biological filter leaves the established aquarium, is transported in the same tank water, and gets placed into the new aquarium. It also requires that most of the water, about 30% of it, is from an established aquarium and is not entirely newly mixed saltwater.

This method establishes the biological filter and the nitrogen cycle immediately but is more suited to an experienced aquarist, or someone who will be able to transfer his livestock back into another established aquarium should trouble arise.

Using Phosphate Remover During Cycling

Placing phosphate remover in a bag placed in an area of moderate water flow, or running a phosphate reactor during cycling is a very good idea and something that should be done by more saltwater aquarium keepers.

As small organisms die off within your cured or semi-cured live rock during the cycling process, phosphates are released into the water.

Along with nitrates, phosphates are a huge culprit as far as algae blooms. In fact, phosphates are the leading cause of sudden algae blooms in established tanks, especially the unsightly and difficult-to-remove variety of algae that covers all your live rock in a layer of vivid green.

Using a phosphate remover during the cycle, and on a permanent basis thereafter, ensures that no unexpected algae blooms will ever occur in your saltwater aquarium.

One Final Word

Once again, if you are going to have any success in this hobby, and for the sake of your aquarium inhabitants, please take the time to cycle your aquarium.  I cannot emphasize enough that patience, and the help of our all-important ally the nitrogen cycle, is the key to establishing a beautiful saltwater aquarium.

Read more about:

Nitrogen Cycle Not Starting?

Ammonia And Nitrite

Nitrate In The Aquarium

New Tank Syndrome

New Tank Syndrome | Don’t Let It Happen To You

Water Parameters – Danger Levels

Mixing Saltwater

What To Look For In An Aquarium Salt 

Natural Seawater

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