Nitrification in Aquarium 2 (Report)

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This is the summarized report of the Nitrification in Aquarium 2 experiment. For more details, please refer to the detailed lab journal of this experiment.


As stated on the main project page, our second “Nitrification in Aquarium” experiment (NA2) is an adaptation of the first “cycling” step of aquaponics. We will start from an aquarium, an air pump and drippers and some pond water. We will feed the system with urine everyday, as they do with ammonium in this protocol [1]. This is supposed to lead to the build up of a strong culture of nitrifyers, which will convert urine into nitrate.

This second experiment is a variation of the first one (NA1) we conducted. We started from the same culture as NA1, but reduced the reaction volume to 15 l (instead of 40 l for NA1), while keeping the same aeration rate, to have a better oxygenation of the system. This NA2 experiment will be fed with relatively low amounts of urine everyday, to make sure that we do not produce large amounts of nitrite which might poison nitrifyers I & II. It is thereby intended as a backup for NA3.

Material & Methods

Experimental setup


We started the culture for NA2 on August 12th, 2015, from 15 l of the mix from NA1. The bucket was covered with a piece of cardboard cut in a pizza box, to avoid light to get in the bioreactor.

Recalling the main concentrations for NA1 culture at 7 pm :

  • pH = 7.4
  • Ammonium concentration = 1.5 mgN/l
  • Nitrate concentration = 20 mgN/l
  • Nitrite concentration = 0.8 mgN/l

However, we measured different values when measuring in our new “bioreactor”

  • pH = 7.4 (stable)
  • Ammonium concentration = 3 mgN/l
  • Nitrate concentration = 10 mgN/l
  • Nitrite concentration = 0.8 mgN/l

(We took out 30 ml of culture for analysis purposes.)

This difference in our measurements most probably comes from the inaccuracy of our analysis kits.

We fed the culture with 25 ml of urine, from the batch started on August 12th.

The pH of urine slightly increased to 7.2, urea hydroloysis has probably not happened yet.


This culture was poured in a 20 L opaque bucket , in which a pump (the one used for NA1) was dripping 380l/h of air through two diffusers.

Concentrations measurement

We used aquariophilic measurement kits for ammonium [2], nitrite [3] & nitrate [4] from JBL. A manual on how to use the kit for concentration monitoring is included in each kit.

When concentrations were high, we sometimes used preliminary urine dilutions to get a better precision in our measurements.

We also used pH-measuring paper strips. Instructions are also included when you buy them.

All these color-based indicators were not very precise, inducing quite strong uncertainty in our measurements.


We terminated the experiment on August 21st, 2015, after 9 days.

We obtained a quite satisfying nitrate concentration (160 mgN/l) at the end of the experiment. This concentration is in the range of those used in aquaponics/hydroponics to feed plants.

Discussion & Conclusion

Comparing NA1, NA2 and NA3, it is difficult to understand why N2 led to a satisfying ammonium concentration while NA1 and NA3 did not.

The most probable explanation seems to be a good coordination between processes at stake, which failed to happen in the previous experiments. Potential contamination by competing bacteria in NA1 and NA3, which would have failed to develop in NA2 may also be an explanation.

The rise to a nitrate concentration of 80 mgN/l, and then to 160 mgN/l did not follow any specific change in the conditions, neither in the urine fed to the system nor in the culture pH, light or aeration conditions.

Further investigation should be performed to understand better the dynamics at stake.