We’re Cycling Aquariums for Failure

The Glass Box Paradox

Modern planted aquariums look like underwater art, but under the hood most of us are still running a 50‑year‑old wastewater playbook. Classic books and beginner guides treated the tank like a tiny sewage plant: vacuum everything, fear mulm, and chase zeros on the test kit as if that number alone equals fish happiness.

That industrial mindset has side effects. It demonizes organic matter, pushes constant “sterilize and reset” maintenance, and has created an entire market of cycling products that select for bacteria adapted to a sewer, not to a low‑nutrient planted tank. We end up training sprinters for a marathon, then act surprised when the system crashes a few months in.

The Industrial Hangover

The traditional nitrogen cycle diagram every hobbyist sees comes straight from sanitary engineering. It assumes a two‑step oxidation assembly line: Nitrosomonas eat ammonia and make nitrite, then Nitrobacter eat nitrite and make nitrate, all under relatively high ammonia conditions like you would find in wastewater treatment.

A planted aquarium is not a sewer. It is, by definition, oligotrophic in inorganic nitrogen: plant‑available nitrogen in the water column is usually low because plants and microbes are constantly stripping it out. So the real environment inside a healthy planted tank is low‑ammonia, plant‑dominated, and resource‑limited, not a high‑load waste stream.

Comammox Nitrospira

For years, Nitrospira were treated as nitrite‑only cleanup crew. The discovery of Comammox Nitrospira (Complete Ammonia Oxidizers) flipped that story: a single Nitrospira cell can take ammonia all the way to nitrate by itself. Think of them as the swiss‑knife nitrifiers.

Ecologically, Comammox Nitrospira behaves as K‑strategists. They are adapted to stable, resource‑limited environments, grow slowly, and use high‑affinity enzymes to grab ammonia at concentrations the classic beneficial bacteria barely notice.

A 2024 study by McKnight and Neufeld on freshwater aquarium biofilters found Comammox Nitrospira to be ubiquitous and often dominant among ammonia oxidizers, not just background noise. In other words, the organisms that actually run nitrification in many mature aquarium filters are not the stars of the cycling charts hobbyists obsess over.

Rethinking what “stable” means

None of this is an excuse to toss fish into raw tap water and hope for the best. These organisms are not toys. It is an argument to change what we aim for. Instead of worshipping fast conversion to nitrate under heavy dosing, a planted‑tank mindset cares more about:

• How quickly plants and biofilms can mop up ammonium before it spikes
• How effectively the system processes detritus into reusable nutrients
• How boringly stable the tank is across months and years, not how fast it hits “zero”

Mulm becomes a resource and a habitat, not something to fear. The filter stops being a standalone waste machine and becomes just one organ in a bigger body that includes substrate, plants, biofilms, and microfauna.

From Nitrogen Cycle to Aquarium Cycle

The old nitrogen cycle diagram is basically a postcard from industrial engineering. A more honest “aquarium cycle” for planted tanks looks like a loop:

Food and plant litter enter and become detritus. Microbes and detritivores break detritus into dissolved organics, then inorganic nutrients. High‑affinity nitrifiers (including Comammox) and plant roots capture reduced nitrogen at low concentrations.

Once you see your tank as this loop, the standard cycling routine feels less like a goal and more like a clumsy boot sequence. The fun question becomes: how do you design your substrate and food web to support this loop from day one?

That is where SLESS comes in.