Bacteria & plants do the work — nitrification and uptake

The two-step nitrification reaction

Step 2a (AOB, e.g. Nitrosomonas): NH₄⁺ + 1.5 O₂ → NO₂⁻ + 2 H⁺ + H₂O. Step 2b (NOB, e.g. Nitrobacter, Nitrospira): NO₂⁻ + 0.5 O₂ → NO₃⁻. Each gram of ammonia oxidised consumes about 4.6 g of dissolved oxygen and 7.1 g of alkalinity (as CaCO₃) — which is why alkalinity buffering is part of every well-run system.

Modern microbiology: it's not just Nitrobacter

Older texts attribute nitrite oxidation to Nitrobacter; molecular studies in the last two decades have shown that in low-ammonia, biofilm-dominated systems (which aquaponics is) Nitrospira is usually the more abundant NOB. Some systems are even dominated by complete-ammonia-oxidising 'comammox' Nitrospira that perform both steps in one cell.

What plants actually take up — and why aquaponic produce is competitive

Most leafy and fruiting crops absorb nitrogen primarily as NO₃⁻, with smaller uptake of NH₄⁺. Aquaponic effluent typically supplies adequate N, P, K and S but can run low in Fe, Mn, K and Ca relative to standard hydroponic recipes — which is why mature commercial aquaponics supplements micronutrients (chelated Fe is the most common addition).

Comparative trials have repeatedly shown that, once nutrient levels are matched, aquaponic and hydroponic lettuce yields are statistically equivalent — and aquaponic lettuce often shows a higher root mass and better post-harvest shelf life.

Operating conditions a healthy biofilter needs

• pH 6.8–7.2 — a working compromise between fish (prefer 7.0–8.0), bacteria (prefer 7.5–8.5) and plant uptake (prefer 5.5–6.5).
• Temperature 25–30 °C — nitrification roughly halves for every 10 °C drop below the optimum.
• Dissolved oxygen ≥ 4–5 mg/L in the biofilter — nitrification is strongly aerobic.
• Alkalinity buffering with KHCO₃ or Ca(OH)₂ — both add nutrients while holding pH up.

“Approximately 4.6 g of oxygen and 7.1 g of alkalinity (as CaCO₃) are consumed for every gram of ammonia-nitrogen oxidised to nitrate. Failure to plan for this is the single most common cause of aquaponic system crashes.”

— Timmons & Ebeling, 2013