The system is up, fish emulsion added, bacteria are "doing everything themselves." Three weeks later: pH 4.8, the solution smells of ammonia, roots are brown. Bacteria do not work on their own — they are the most demanding organisms in the system: they require constant oxygen, a narrow pH and temperature range, and are killed by most disinfectants. Without actively maintaining conditions, the nitrification cycle stalls and the system becomes an organic broth.
Quick Glossary
- Nitrification — a two-stage microbial oxidation process: first ammonium (NH₄⁺) → nitrite (NO₂⁻) via Nitrosomonas, then nitrite (NO₂⁻) → nitrate (NO₃⁻) via Nitrobacter; nitrate is the primary form of nitrogen taken up by plants
- DO (Dissolved Oxygen) — oxygen concentration in solution in mg/L; nitrifying bacteria are strictly aerobic and nitrification stops below DO 2 mg/L
- pH — solution acidity; nitrification acidifies the solution (alkalinity is consumed) and below pH 6.0 Nitrobacter is virtually inactive
The Nitrification Cycle: Two Stages, Two Problems
Nitrification is not one process but two sequential ones, carried out by different bacteria with different requirements:
Stage 1: ammonification → nitrite (Nitrosomonas) — ammonium is oxidised to nitrite. The reaction consumes oxygen and releases H⁺ ions — acidifying the solution. Nitrosomonas is relatively tolerant of lower pH (active down to 6.0) and less sensitive to temperature fluctuations.
Stage 2: nitrite → nitrate (Nitrobacter) — nitrite is oxidised to nitrate. Also consumes oxygen. Nitrobacter is strictly pH-sensitive: below 6.5 activity drops significantly; below 6.0 it virtually stops. Higher temperature requirements: optimum 25–30°C.
The typical cascade failure: the system acidifies from nitrification, pH drops to 6.0–6.2 → Nitrobacter is suppressed → nitrite accumulates → nitrite is toxic to plants and to the bacteria themselves → the system degrades further. Without pH buffering, the cycle breaks itself.
Why DO Is the Most Critical Parameter
Both stages of nitrification are aerobic. For every mole of ammonium oxidised to nitrate, 2 moles of O₂ are consumed. Under active nitrification and organic load, oxygen demand is significant — and if aeration cannot replenish DO fast enough, concentration falls.
DO thresholds:
- DO above 6 mg/L — nitrification is active
- DO 4–6 mg/L — nitrification is slowed
- DO below 2–3 mg/L — nitrification has effectively stopped; anaerobic fermentation begins
Solution temperature is critical: at 20°C water can hold up to 9.1 mg/L O₂ at saturation; at 28°C only 7.8 mg/L. In a warm system, saturation is harder to reach and the margin to the critical threshold is smaller.
In practice: measure DO regularly — at least as often as pH. Aeration (pumps, air stones, Venturi injectors) in a bioponic system should be generous, not minimally sufficient.
pH Buffering: What Maintains Alkalinity During Nitrification
Nitrification consumes alkalinity (carbonates and bicarbonates) and acidifies the solution. In a low-buffer system, pH can fall from 7.0 to 5.5 within days under active nitrification.
Carbonate alkalinity (KH) is the natural buffer. In conventional hydroponics, low KH is often preferred for easier pH control. In bioponics — the opposite: KH 4–8°dKH (70–140 mg/L CaCO₃) gives the system a buffer that prevents catastrophic pH drops. Add as calcium carbonate (limestone) or potassium bicarbonate.
Control: measure KH regularly when organic load changes. As fish emulsion dose increases, nitrification accelerates and alkalinity is consumed faster.
How to Start Nitrification: Steps Before the First Plant
Nitrifying bacteria grow slowly — population doubling takes 8–24 hours compared to 20 minutes for ordinary bacteria. Starting a system from scratch takes 3–6 weeks.
Step 1 — Seed culture. Starting microbiology: a commercial nitrifying bacteria concentrate, water from an active living system with established nitrification, or substrate from an existing system.
Step 2 — Ammonium source for "feeding." Without ammonium the bacteria have nothing to oxidise — they will not grow. Small doses of fish emulsion or ammonium chloride to sustain nutrition during start-up.
Step 3 — Parameter control during start-up. pH 7.0–7.5 initially (before nitrification begins acidifying), DO above 6 mg/L continuously, temperature 22–26°C, no disinfectants or antibiotics in the water.
Step 4 — Track the indicators. Ammonium rises first, then falls — a sign that Nitrosomonas is active. Nitrite rises, then falls while nitrates increase — a sign that Nitrobacter has joined. The system is ready when both ammonium and nitrite hold at low levels and nitrates are climbing.
Three Mistakes That Cost the Most
Adding the maximum organic dose immediately at start-up. Excess ammonium with a weak microbial colony produces toxic concentrations of free ammonia (NH₃) that kills the nitrifiers themselves. Start with a minimum dose and increase gradually as the colony grows.
Ignoring DO and relying only on pH. pH may look acceptable while DO is already below the critical threshold and nitrification has stopped. In warm water with organic load, DO drops faster than pH responds. Measure DO as regularly as pH.
Disinfecting the system between cycles with aggressive agents. Hydrogen peroxide, chlorine, ozone — all completely destroy the nitrifying colony. After such treatment: a new starting point and 3–6 weeks before the next plant. Sanitation in bioponics requires methods that preserve the nitrifiers.
How to Know Nitrification Is Stable
- Test kit or drop test: ammonium below 1 mg/L, nitrite below 0.5 mg/L, nitrates rising
- DO above 5 mg/L at operating temperature
- pH holds in the 6.5–7.2 range without sharp daily swings of more than 0.5 pH units
- Plants are actively growing with no signs of nitrogen starvation