Biological Nutrient Removal: The Microbiology of N and P

Why do we remove nitrogen and phosphorus biologically?

Discharging reactive nitrogen and phosphorus drives eutrophication: algal blooms, hypoxia and loss of aquatic life. Chemical routes exist (breakpoint chlorination for ammonia, metal-salt precipitation for phosphate), but they are reagent-hungry and generate chemical sludge. Biological nutrient removal instead exploits the metabolism of specific microbial guilds, converting nitrogen to inert dinitrogen gas and concentrating phosphorus into a wasted, potentially recoverable, biomass.

BNR is layered onto conventional activated sludge, so it inherits that framework. If you are new to the base process, start with our primer on the activated sludge process design, then read this as the nutrient-focused extension. The consent limits that make BNR necessary are set out in the UK effluent discharge standards.

How does nitrification work, and why is it the bottleneck?

Nitrification is a two-step autotrophic oxidation carried out by chemolithotrophs that fix CO₂ for carbon and derive energy from oxidising inorganic nitrogen. Ammonia-oxidising bacteria (AOB, e.g. Nitrosomonas) run the first step; nitrite-oxidising bacteria (NOB, e.g. Nitrobacter, Nitrospira) run the second:

Autotrophs grow slowly: maximum specific growth rate μ_max ≈ 0.5–0.9 d⁻¹ at 20 °C, roughly a fifth of heterotrophs, and it halves with each ~10 °C drop. Because washout occurs when the solids retention time (SRT) falls below 1/μ, nitrifiers set the minimum aerobic SRT — typically 8–15 days with a safety factor, longer in cold climates. Ammonia oxidation follows Monod kinetics with a low half-saturation constant (K_N ≈ 0.5–1 mg N/L), so the reaction is near zero-order until ammonia is almost exhausted, then falls sharply. Dissolved oxygen must stay above ~2 mg/L, since oxygen is itself a Monod substrate for AOB.

How does denitrification recover alkalinity and remove nitrogen?

Nitrification only converts ammonia to nitrate; it does not remove nitrogen from the water. Removal happens in the anoxic zone, where facultative heterotrophs use nitrate as the terminal electron acceptor in place of oxygen, reducing it stepwise to dinitrogen gas:

Two conditions are essential: the absence of dissolved oxygen (which is energetically preferred and represses the denitrifying enzymes) and a supply of readily biodegradable carbon. Where the incoming wastewater carries enough BOD — a COD:N ratio above roughly 4–5 — the influent itself is the donor, which is why pre-anoxic (upstream) configurations are efficient. When carbon is short, a supplemental donor such as methanol, acetate or glycerol is dosed. Denitrification returns about half the alkalinity that nitrification destroyed, which is why combined nitrification–denitrification plants are far more pH-stable than nitrification alone.

How does enhanced biological phosphorus removal (EBPR) work?

EBPR relies on polyphosphate-accumulating organisms (PAOs), chiefly Candidatus Accumulibacter, that store phosphorus far in excess of normal growth needs. The trick is to cycle them between anaerobic and aerobic conditions so they out-compete ordinary heterotrophs.

• Anaerobic zone (no O₂, no NO₃): PAOs take up volatile fatty acids (VFAs) such as acetate and store them as poly-β-hydroxyalkanoates (PHA). They fund this uptake by hydrolysing intracellular polyphosphate and glycogen, releasing orthophosphate to the liquid — phosphate goes up here.
• Aerobic zone: PAOs oxidise the stored PHA for energy and growth, and use that energy to take up phosphate in excess, rebuilding poly-P granules. Bulk phosphate falls to low residuals.

Net phosphorus removal happens when the P-rich biomass is wasted as sludge. The anaerobic contact stage must be genuinely free of nitrate and oxygen; if nitrate leaks in, ordinary denitrifiers consume the VFAs and PAOs are starved. Glycogen-accumulating organisms (GAOs) compete for the same VFAs without removing phosphorus, and are favoured at high temperature and low pH — a key operational risk. Because EBPR concentrates phosphorus into a defined solids stream, it also opens the door to struvite recovery.

What are the main BNR process configurations?

BNR schemes differ in how they sequence anaerobic, anoxic and aerobic zones and how they recycle nitrate-rich mixed liquor. The workhorses are compared below.

Anammox bacteria oxidise ammonium directly with nitrite as acceptor (NH₄⁺ + NO₂⁻ → N₂ + 2 H₂O), bypassing the full nitrate cycle. Because it needs no organic carbon and far less oxygen, deammonification is the standard for treating ammonia-rich sidestreams from sludge dewatering. Selecting and hydraulically sizing these reactors is a specialist task; our engineers can support nutrient-removal process design for industrial effluent from mass balance through to commissioning.

Worked example: supplemental carbon and alkalinity for a nitrogen load

A plant treats 2,000 m³/d of wastewater. Total Kjeldahl nitrogen to be nitrified is 40 mg N/L; the influent supplies only 20 mg N/L of readily biodegradable COD equivalent for denitrification, and the consent requires the effluent nitrate to reach 8 mg N/L. Assume ~1 mg N/L is assimilated into biomass. We size the methanol dose and check alkalinity.

• Nitrogen mass load: 40 g/m³ × 2,000 m³/d = 80 kg N/d to nitrify.
• Nitrate to denitrify: (40 − 8 − 1) = 31 mg N/L × 2,000 = 62 kg N/d must be reduced to N₂.
• Carbon from influent: covers ~20 mg N/L × 2,000 = 40 kg N/d. Shortfall = 62 − 40 = 22 kg N/d needs supplemental carbon.
• Methanol dose: the accepted stoichiometric requirement is ~2.86 g COD per g NO₃-N, and methanol is 1.5 g COD/g. Allowing for cell synthesis, a practical figure is ~3.0 g methanol per g N. Dose = 22 kg N/d × 3.0 = 66 kg methanol/d (≈ 83 L/d at 0.79 kg/L).
• Oxygen for nitrification: 80 kg N/d × 4.57 = 366 kg O₂/d for the nitrogen alone (carbonaceous BOD demand is additional).
• Alkalinity balance: nitrification destroys 80 × 7.14 = 571 kg CaCO₃/d; denitrification of 62 kg N/d recovers 62 × 3.57 = 221 kg/d. Net loss ≈ 350 kg CaCO₃/d, or 175 mg/L — enough to depress pH unless influent alkalinity or dosing covers it.

The result: dose roughly 66 kg/d of methanol, supply ~366 kg/d of oxygen for nitrification, and confirm at least ~175 mg/L of alkalinity is available (from the influent or by caustic/lime dosing) to hold pH near 7. Every figure would be refined with site COD fractionation and temperature-corrected kinetics before detailed reactor sizing and aeration design.

What are the common operational pitfalls in BNR?

• Nitrifier washout. Cutting SRT below the temperature-corrected minimum (or a cold snap) loses the slow-growing autotrophs first — ammonia breaks through before anything else.
• Alkalinity crash. Nitrification acidifies; a low-alkalinity influent can drop pH below 6.5 and stall the AOB. Recover alkalinity via denitrification or supplement it.
• Nitrate in the anaerobic zone. Recycle or poor separation feeds nitrate to the EBPR selector, letting denitrifiers steal the VFAs and collapsing phosphorus removal.
• GAO takeover. Warm, low-pH, VFA-limited conditions favour glycogen accumulators that mimic PAOs without removing phosphorus.
• Over- or under-aeration. Too little DO stalls nitrification; too much carries dissolved oxygen into the anoxic zone and suppresses denitrification. Cascade DO control is essential.