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Thursday, October 15, 2026 · Week 04

Where Are the Corals? Understanding the Nitrogen Cycle

One of the most common questions I’ve been getting since starting this project is, “Where are all the corals?”

And my answer is always the same.

“I’m cycling the tank.”

But I’ve come to realize that, from a non aquarist perspective, I may as well be speaking Chinese. So I figured I’d take some time this week to explain what cycling actually means, why it’s so important, and why I’ve spent the last several weeks staring at test tubes instead of growing corals.

First, What Exactly Is Cycling?

An aquarium isn’t just a container of water with some fish and corals thrown in. It’s an ecosystem, and like any ecosystem, there are biological processes happening constantly that keep its inhabitants alive.

One of the most important is the nitrogen cycle.

Every living organism produces waste. Fish excrete ammonia, uneaten food decomposes, and organic matter breaks down. In the ocean, these waste products are processed by an enormous and incredibly diverse community of microorganisms.

In an aquarium, we’re trying to recreate a small part of that process.

The problem is that when you fill a brand new aquarium with saltwater, the biological filtration system isn’t magically there. You have to establish it.

And unfortunately, the organisms responsible for this process aren’t particularly fast growers.

There are three nitrogen compounds we’re primarily concerned with: Ammonia (NH₃/NH₄⁺), Nitrite (NO₂⁻), and Nitrate (NO₃⁻).

The process of converting ammonia into nitrite and then nitrate is called nitrification.

Ammonia: The First Problem

Ammonia is produced by fish and the decomposition of organic material. It’s also extremely toxic to aquatic life in its uncharged form, NH₃.

Something worth mentioning is that ammonia actually exists in two forms in water: ammonia (NH₃) and ammonium (NH₄⁺). The ratio between them depends on temperature and pH.

This is particularly relevant in saltwater aquariums because the relatively high pH favors a greater proportion of the more toxic NH₃.

So obviously, we don’t want ammonia accumulating in the system.

Fortunately, there are microorganisms that actually use ammonia as an energy source.

One of the better known groups is the bacterial genus Nitrosomonas, which belongs to the phylum Pseudomonadota, formerly known as Proteobacteria.

There are other bacteria capable of oxidizing ammonia, such as Nitrosospira, and even ammonia oxidizing archaea.

Archaea are particularly interesting because, although they look similar to bacteria under a microscope, they’re an entirely separate domain of life.

These organisms oxidize ammonia into nitrite.

Great! Problem solved, right?

Not exactly.

Nitrite: Trading One Problem for Another

Once ammonia is converted, we’re left with nitrite (NO₂⁻).

Nitrite can also be toxic to aquatic organisms, although there’s an interesting distinction between freshwater and saltwater fish.

Marine fish are generally much more resistant to nitrite toxicity because seawater contains an abundance of chloride ions, which interfere with nitrite uptake through the gills.

Still, an accumulation of nitrite tells us that our biological filtration system hasn’t fully established itself.

This is where a second group of bacteria comes into play.

Bacteria responsible for nitrite oxidation, commonly called NOB, convert nitrite into nitrate.

Two genera worth mentioning are Nitrobacter and Nitrospira.

Nitrobacter belongs to the phylum Pseudomonadota, while Nitrospira belongs to the phylum Nitrospirota.

For a long time, aquarium hobbyists were taught that Nitrosomonas converted ammonia into nitrite and Nitrobacter converted nitrite into nitrate.

That’s not necessarily wrong, but it’s an oversimplification.

Research has shown that Nitrospira can be particularly important in biological filtration systems.

Even more interesting, some Nitrospira species can perform both steps of nitrification themselves!

These are known as comammox bacteria, short for complete ammonia oxidizers.

Microbiology is a lot more complicated than the little diagrams on the back of aquarium test kits would have you believe.

Nitrate: Finally, Something Manageable

Once nitrite is oxidized, we’re left with nitrate (NO₃⁻).

Nitrate is generally much less acutely toxic than ammonia, and unlike the other two compounds, it’s something we actually expect to have in a functioning reef aquarium.

Corals and their symbiotic algae need nitrogen for growth. The goal isn’t necessarily to have absolutely zero nitrate.

But too much nitrate can become a problem, contributing to nutrient imbalances and potentially encouraging unwanted algae growth.

Unlike ammonia and nitrite, nitrate isn’t automatically converted into another compound by the same aerobic nitrification process.

It can be removed through water changes, taken up by algae and other organisms, or converted into nitrogen gas by denitrifying microorganisms under conditions where oxygen availability is low.

This is why nutrient management remains important even after an aquarium has finished cycling.

Why Is This Taking So Damn Long?

This is probably the part that’s been frustrating me the most.

Nitrifying microorganisms are relatively slow growers.

Under favorable conditions, some bacteria responsible for ammonia oxidation can double their populations in approximately 8 to 24 hours. Many organisms responsible for nitrite oxidation may require a day or several days, depending on the species and environmental conditions.

For comparison, E. coli can double approximately every 20 minutes under ideal laboratory conditions.

That’s a pretty ridiculous difference.

And these organisms aren’t just floating around in the water waiting to get to work. They establish themselves on submerged surfaces, forming microbial communities known as biofilms.

They’re colonizing the plumbing, the sump, the tank walls, and just about every other available surface.

You can add bottled nitrifying bacteria to help kickstart the process, which I’ve done, but that doesn’t necessarily mean you’ve instantly established a mature biological filter.

The bacteria still need time to colonize the system and reproduce in sufficient numbers to process the waste being produced.

A conventional aquarium cycle can take anywhere from 4 to 8 weeks, sometimes longer. Systems with established biological media can cycle considerably faster.

There’s no magic number of days where an aquarium suddenly becomes safe.

You have to actually test the water.

So Where Am I in This Process?

Well, after several weeks of testing, water changes, bacterial additions, and more testing, I’ve finally started seeing some meaningful progress.

My ammonia has reached 0 ppm!

This is a pretty significant milestone considering I was previously measuring ammonia concentrations around 1 to 2 ppm.

But here’s the catch.

My nitrite has climbed to 2.0 ppm or higher, which is at the upper end of what my test kit can measure.

This suggests that the microbial community responsible for ammonia oxidation is doing its job, but the organisms responsible for nitrite oxidation haven’t quite caught up yet.

I’ve also measured substantial nitrate concentrations, although nitrate tests can sometimes be affected by elevated nitrite, so I’m being careful about how I interpret those results.

Essentially, I’m watching the microbial ecosystem establish itself in real time.

It’s actually pretty fascinating, even if it means my expensive coral farm currently looks like a glorified saltwater bathtub.

So Why Haven’t I Added Corals?

Technically, some hardy corals might tolerate the conditions in a young aquarium, and nitrite itself is generally much less concerning in seawater than in freshwater.

But that’s not really the point.

I’m not building this system just to keep a few corals alive.

I want to grow them, propagate them, and eventually turn this into a functioning coral production system.

That means I need consistency.

Ammonia needs to remain undetectable under the expected biological load. The nitrifying community needs to be established. Temperature, salinity, alkalinity, calcium, magnesium, lighting, and water movement all need to be appropriate.

And just because a tank is technically cycled doesn’t mean it’s mature.

A reef aquarium can continue developing biologically for months after the initial nitrogen cycle is complete.

I could go out tomorrow, buy a bunch of coral frags, throw them on the racks, and finally have something colorful to show everyone.

But I’d rather do this correctly.

For now, the frag racks are empty, the test kits are getting plenty of use, and billions of microscopic organisms are doing the actual work.

Not exactly the most exciting thing to photograph.

But hopefully, in a few weeks, I’ll finally have something a little more interesting to show you.

Monday, October 12, 2026 · Week 04

The Blog Has Comments Now!

I've added a comment section to the blog. Visitors can now leave comments without having to create an account, and they can reply directly to each other in threads.

I wanted to make the blog a little more interactive rather than just having people read along. Now anyone following the progress of Alquatics can ask questions, share advice, or just leave their thoughts.

It's a small addition, but one I'm pretty excited about. I'm curious to see if anyone actually uses it!