Aquaponics · Microbiology and water treatment
Bacterial conversion and biofilters
Nitrifying microorganisms protect the fish from accumulation of total ammonium and nitrite. However, a resilient biofilter is not created by “good bacteria” alone, but rather by sufficient surface area, oxygen, flow, alkalinity and a design that matches the feed load.
Correctly classify system functions
1. What bacterial conversion does in aquaponics
Fish release nitrogen-containing metabolic products primarily through their gills; In addition, dissolved nitrogen compounds are formed when feed residues and solids are broken down. Measurements are carried out frequently TAN – Total Ammonia Nitrogen, i.e. the sum of ionized ammonium and non-ionized ammonia. The proportion of NH₃, which is particularly toxic to fish, increases with pH and temperature.
Fish protection
Nitrification lowers TAN and nitrite. It does not replace ventilation, solids separation or regular measurements.
plant nutrient
Nitrate is an important nitrogen carrier, but not a complete nutrient solution. Potassium, calcium, iron and other elements may be missing.
Process stability
The biofilter performance must match the daily feed quantity, the type of fish, the temperature and the actual water chemistry.
Distinguish forms of nitrogen
2. TAN, ammonium and ammonia
| Measuring or fabric size | Meaning | Operational consequence |
|---|---|---|
| TAN | Total ammonia/ammonium nitrogen. Note the spelling of the test procedure. | Do not evaluate without pH and temperature. |
| NH₄⁺ | Ionized form; with usual aquaponics pH values often the larger proportion. | Substrate for ammonium oxidizers and partly directly available to plants. |
| NH₃ | Non-ionized form with significantly higher toxicity to fish. | Particularly critical at high pH and high temperatures. |
| NO₂⁻ | intermediate product of nitrification; can affect oxygen transport in fish. | Limit stocking and feeding, eliminate cause; Chloride management only species-specific and professionally. |
| NO₃⁻ | End product of aerobic nitrification and important nitrogen carrier. | Balance through plant intake, water changes or further treatment. |
Microbial process network
3. Nitrification is more than Nitrosomonas and Nitrobacter
The classic dichotomy remains useful as a process model, but is microbiologically shortened. Depending on the system, ammonia-oxidizing bacteria and archaea, nitrite-oxidizing Nitrospira as well as complete ammonia oxidizers (Comammox). An aquaponics study showed comammoxNitrospira at low, stable ammonium concentrations. That's why the function of the biofilm is monitored - not a supposedly fixed list of species.
Plan for chemical side effects
4. Oxygen and alkalinity requirements
Oxygen
Nitrification is aerobic. If dissolved oxygen decreases or the surface becomes overloaded with organic material, fast-growing heterotrophic microorganisms compete with the slower nitrifiers.
alkalinity
Oxidation produces hydrogen ions; the buffer capacity is used up and the pH can fall. Alkalinity and pH must therefore be monitored together and corrected in a way that is compatible with the species and plants.
Function before container shape
5. Where the biofilm actually works
Nitrifying communities colonize wetted surfaces in biofilter media, plant modules, pipelines and containers. Whether a separate biofilter is required depends on the system architecture, available surface area, solids load and safety margin. Media beds can take over some of the biofiltration; More heavily populated NFT or DWC assets typically require a clearly measured biological level.
fixed bed
High specific surface area, but pay attention to even flow and risk of clogging.
Moving bed
Carrier material is moved in a ventilated manner; Ensure hydraulic retention and discharge of the medium.
Integrated interface
Beds, roots and plant areas can contribute, but are more difficult to account for as defined reactor stages.
Load-oriented instead of container volume
6. Lay out the biofilter
The measurement begins with fish species, biomass, feed composition and daily feed amount. The expected TAN load is estimated from this. Only then are the permissible surface loading of the selected medium, temperature correction, oxygen supply, hydraulic throughput and safety reserve applied.
- Determine the maximum daily feed amount and raw protein content.
- Calculate TAN production with comprehensible assumptions that match the fish species.
- Use rated performance of the biofilter medium under real operating conditions.
- Take solids pretreatment and organic surface loading into account.
- Provide reserve for feed peaks, cleaning, pump failure and temperature changes.
- Verify design through TAN and nitrite progression during operation.
Control organic stress
7. Separate solids and mineralization
Heterotrophic microorganisms break down organic substances. This can mobilize bound nutrients, but at the same time increases oxygen demand, turbidity and biofilm growth. Raw sludge therefore does not belong in biofilters or sensitive root zones without being checked. Separation, controlled mineralization and a defined return of suitable fractions are separate process steps.
| Process | Main goal | Important risk |
|---|---|---|
| Solid separation | Remove settleable and suspended load from the fish circuit. | Inadequate cleaning, anaerobic zones and redissolution. |
| Nitrification | TAN and nitrite oxidize aerobically. | Lack of oxygen, buffer or surface area. |
| Mineralization | Organically bound substances are broken down in a controlled manner. | Inappropriate recirculation, hygiene, salt or pollutant accumulation. |
Start new system safely
8. Cycling and maturation
When running in, a resilient nitrification capacity is built up. A mere waiting time does not prove this capacity. It is crucial that a defined nitrogen addition is implemented repeatedly within the intended time window without critical TAN or nitrite residues.
Fishless cycling
Allows a controlled source of ammonium without exposing fish to typical starting spikes. Document the dosage, origin and purity of the source.
Cycling with fish
Only with very careful stocking and feeding regime, frequent measurements and clear control limits. Animal protection and species-specific limits have priority.
Interpret measured values together
9. Monitoring during ongoing operations
| Measurand | Why it is important | Check if there is a deviation |
|---|---|---|
| TAN, pH, temperature | Determine the NH₃ risk together. | Feed, stock, biofilter, ventilation, measuring method. |
| Nitrite | Indicates an incomplete second oxidation state or load peak. | Maturation, oxygen, flow, sudden change in load. |
| Nitrate | Part of the nitrogen balance, but not the sole proof of performance. | Plant intake, water changes, denitrification, sampling. |
| Dissolved oxygen | Limits fish and biofilter performance. | Aerators, pumps, organic load, daily cycle, temperature. |
| Alkalinity and pH | Show buffer consumption and risk of acidification. | Make-up water, nitrification load, corrective agents and dosage. |
From symptom to cause
10. Typical disorders
TAN increases
Check feeding peak, biofilter still immature, lack of oxygen, flow errors, toxic inputs or insufficient active surface.
Nitrite increases
Second oxidation stage may lag after start, cleaning, salt/pH change or load jump.
pH falls quickly
Check alkalinity, nitrification load, make-up water and dosing strategy. Don't blindly correct with strong bases.
Think about failures beforehand
11. Redundancy, cleaning and biosecurity
- Secure ventilation and water pumping with alarms and a replacement strategy.
- Do not completely clean or replace biofilter media at the same time.
- Plan cleaning with system water and without biofilm-toxic agents.
- Provide bypass, shut-off, sampling and controlled emptying.
- Document changes to feeding, stocking, temperature and disinfection.
- Do not treat untested microbial mixtures as a substitute for measurement and proof of maturation.
Decision support
12. When it makes sense to have your own biofilter
A defined biofilter is particularly useful when there are high or fluctuating feed loads, small safety margins, sensitive fish species, NFT/DWC plant modules or separately controllable circuits. In extensive media beds, the existing surface can be sufficient - however, proof is provided via load calculation and measurement data, not via the design designation.
Comprehensible technical basis
13. Specialist sources
- Somerville, C. et al. (2014): Small-scale aquaponic food production, FAO Fisheries and Aquaculture Technical Paper 589.
- Heise, J. et al. (2021): Ammonium Removal in Aquaponics Indicates Participation of Comammox Nitrospira, Current Microbiology.
- McKnight, M.M. et al. (2024): Comammox Nitrospira among dominant ammonia oxidizers in freshwater aquarium biofilters, Applied and Environmental Microbiology.
- Wongkiew, S. (2018): Nitrogen Cycle in Floating Raft Aquaponic Systems, University of Hawaii.