Chapter 2: Phenomenal Cosmic Power; Itty Bitty Living Space

The first thing you learn in chemistry is that elements never really disappear. During a chemical reaction, atoms simply rearrange themselves into new compounds. In biology, the same principle holds true — essential elements like carbon, nitrogen, and phosphorus cycle endlessly through different forms. One of the most familiar examples is the water cycle.

Because of water’s chemical stability, it tends to stay as water rather than breaking apart into other molecules. Let’s start with rain. As water condenses in the atmosphere and falls to the ground, it collects in rivers, lakes, or even a simple puddle. When the sun returns, that puddle begins to evaporate, rejoining the clouds to fall again as rain. The details get more complex once biology enters the picture, but the principle remains: water moves in a closed system, continuously recycled through different states.

Each organism, however, functions as an open system — matter flows in and out. You eat and excrete. You drink and exhale. What goes in eventually leaves. Closed systems don’t have that luxury. Just as the total amount of water on Earth doesn’t change, only its form and location, everything within a closed environment must be transformed, not removed.

An aquarium is exactly that — a closed ecosystem (more or less). Everything that enters an aquarium stays there, aside from some evaporation. To put it simply: if you drop a pinch of fish food into a glass box, where does it go? Now add fish and water to that box — the same question applies. Nothing truly leaves; it only changes form.

While carbon and phosphorus play their own important roles in aquariums, it’s nitrogen that decides the fate of your ecosystem. It’s the element that can either sustain life or quietly destroy it.

The Nitrogen Cycle

Nitrogen is fundamental to life. Every amino acid — the building block of proteins — contains nitrogen, and proteins make up nearly everything alive. Fish, being omnivores or carnivores, consume large amounts of protein, usually from animal sources. Prepared fish foods are often 40% or more protein by weight, meaning every feeding adds a significant nitrogen load to your aquarium’s closed system.

When proteins are metabolized, they release ammonia (NH₃) as waste — whether through fish respiration, excretion, or the decay of uneaten food. Dead organisms and excess food decompose into additional ammonia. No matter the source, all protein metabolism leads to the same result: ammonia entering your water.

Ammonia is paradoxical — both a nutrient and a toxin. Plants and microorganisms can use it as a nitrogen source for growth, but most aquariums are too heavily stocked for plant uptake alone to keep levels safe. Without another process to handle it, ammonia quickly becomes lethal to fish.

That process is nitrification, the biological oxidation of ammonia. Specialized autotrophic bacteria convert ammonia into nitrite (NO₂⁻) and then into nitrate (NO₃⁻). Nitrite is still toxic, though less so than ammonia, while nitrate is far less harmful. To put it in human terms, ammonia is as dangerous to fish as chlorine gas is to us, nitrite compares to carbon monoxide, and nitrate sits somewhere around the toxicity of carbon dioxide — tolerable in small amounts, deadly in excess.

Establishing the Cycle

As an aquarium matures from sterile water to a thriving ecosystem, it goes through predictable stages of microbial colonization. Only rarely does a tank skip directly to nitrate production; most follow a clear two-step pattern known as the aquarium nitrogen cycle.

Stage one: ammonia begins to drop as the first wave of bacteria colonize the filter media and surfaces. These bacteria oxidize ammonia into nitrite. With a simple test kit, you’ll see ammonia levels decline while nitrite levels rise. This usually takes a week or two. The key here is patience — letting nature take its course. You can speed the process by seeding your tank with bacteria from an established system, commercial bacterial starters, or even my favorite source: dirt. Nitrifying bacteria already exist everywhere in nature, supporting plants and aquatic life long before aquariums existed.

Stage two: nitrite begins to fall as a second group of bacteria colonize the system, converting nitrite into nitrate. This stage often takes the longest — four to five weeks — because these bacteria reproduce slowly and are sensitive to high oxygen levels and ammonia concentrations. Once this second population stabilizes, your tank becomes self-sustaining, with ammonia and nitrite held near zero and nitrate accumulating slowly over time.

Bioload Considerations

Once established, these bacterial communities are remarkably resilient — but even they can be overwhelmed. The total amount of waste produced by your aquarium’s inhabitants is known as the bioload. It’s not something you measure directly, but rather understand as light, moderate, or heavy based on the volume and type of life inside your system.

A higher bioload means more waste, more ammonia, and more strain on your ecosystem. Overfeeding, crowded tanks, and decomposing matter all push that load upward. While the concept of bioload will be explored in depth later, it’s worth remembering here: in a closed system, nothing disappears. Every gram of food, every breath from a fish, adds to the system’s demand for balance.

Chapter Summary

A fundamental rule of nature — and of aquariums — is that matter cannot be created or destroyed. In a closed aquatic system, everything added stays within the cycle. Proteins become ammonia, ammonia becomes nitrite, and nitrite becomes nitrate. The nitrogen cycle is the biological engine that keeps this world alive, and bioload is the force that drives it. Together, they form the heartbeat of every successful aquarium.