Phosphorus Cycle

For a high-level tour of how every element moves through the tank, start with Nutrient Cycling. Phosphorus is the quiet limiter — the nutrient that never leaves the tank, and the one that, in the long run, sets the ceiling on how much life the water can carry.

Why phosphorus is the quiet limiter

Phosphorus is the element that never leaves. Unlike nitrogen, which bleeds away as nitrogen gas through denitrification, and carbon, which trades freely with the atmosphere as CO₂, phosphorus has no gaseous form and no escape route. Every atom present at the start of a simulation is still in the system at the end — locked in biomass, dissolved in the water, buried in soil, or sitting in detritus, but always accounted for. Total phosphorus is strictly conserved (see mass balance).

That permanence is what makes phosphorus the ultimate long-run limiting nutrient. In a closed system nitrogen drains away over time as denitrification works, and cyanobacteria can patch the loss by fixing atmospheric nitrogen — but nitrogen fixation itself runs on phosphorus, for ribosomes, for ATP, for the energy-hungry nitrogenase enzyme. If phosphorus is scarce, cyanobacteria cannot fix nitrogen, and the system has no way to replace what denitrification removes. Phosphorus therefore acts as the master control on total productivity: it sets a ceiling that no amount of nitrogen fixation can break through.

The model enforces this through Liebig's law of the minimum — growth is set by whichever nutrient is scarcest at any moment. Most simulations start nitrogen-limited, with phosphorus in comfortable excess. But as a system ages and nitrogen is topped up by fixation while phosphorus is topped up by nothing, the balance can tip toward phosphorus limitation — slowly, quietly, and irreversibly.

The one dissolved form

Phosphorus has a simple inorganic chemistry: a single biologically available form, orthophosphate, which every producer takes up directly. There is no equivalent of the ammonium/nitrate distinction that exists for nitrogen, and no gaseous form at all. Even in an open tank with a leaky lid, the gases that escape — oxygen, CO₂, ammonia — carry no phosphorus with them. Total phosphorus is conserved in open and closed systems alike, which makes its dynamics fundamentally different from nitrogen's.

What returns phosphorus to the water

Phosphorus comes back to the dissolved pool through several pathways, all ultimately driven by death and digestion.

The largest biological source is consumer excretion. Grazers, shrimp, and other animals hold fixed body N:P ratios — Daphnia are P-rich at an N:P near 12 and retain more of their phosphorus, copepods are N-rich at around 22 and excrete more, with rotifers, ciliates, and flagellates near the Redfield ratio of 16 and shrimp, snails, and ostracods near 20. When an animal eats food richer in phosphorus than its body needs, it excretes the surplus as phosphate. This stoichiometric homeostasis means the consumer community's makeup directly shapes how fast phosphorus recycles — a Daphnia-dominated tank recycles it more slowly than a copepod-dominated one. Consumers also assimilate phosphorus a little more efficiently than carbon, reflecting how bioavailable organic phosphorus is.

Decomposition is the other major source. When detritus breaks down, part of its phosphorus is released straight to phosphate — the fast abiotic fraction — while the rest enters the DOM pool for bacteria to process. Heterotrophic bacteria are the most phosphorus-rich organisms in the model, holding a body N:P near 10, so they keep most of the phosphorus they absorb and release only the surplus; when oxygen limits their growth, the phosphorus they cannot use is remineralized too.

UV photodegradation is a parallel abiotic route: sunlight breaks dissolved organic molecules apart, releasing their phosphorus as phosphate alongside carbon and nitrogen, with refractory humics breaking down faster than labile material because they absorb more UV.

In anoxic sediments, denitrification and DNRA both consume settled detritus as an electron donor and release its organic phosphorus as phosphate — a significant source in organic-rich sediments. And in tanks with a buried organic substrate, soil organic matter mineralization releases phosphate into the pore water, slowly but relentlessly, preserving the soil's carbon-to-nitrogen-to-phosphorus balance as it depletes. That pore phosphate then reaches the water column through root uptake and Fickian diffusion. The exact mineralization rates and their temperature and oxygen modifiers are tabulated in the Parameter Reference; see also Soil and Pore Water.

What removes phosphorus from the water

Every producer takes up phosphate, but they differ in affinity, demand, and access.

Microalgae are the primary consumers. Every algal class — green, diatom, and cyanobacterium — takes up phosphate by luxury Droop uptake, banking it in an internal polyphosphate reserve that is decoupled from carbon fixation. Their uptake affinity is so high that cells keep scavenging phosphate down to trace levels long after dissolved phosphorus has fallen below the usual detection limit — which is the mechanistic explanation for the empty-looking water column of a post-bloom tank or lake: the phosphorus is in the cells, not the water. True growth limitation only sets in once a cell's own internal reserve runs down toward empty, which can take days after the water has been stripped. Cyanobacteria add a twist: their nitrogen-fixation rate is co-limited by the same phosphorus reserve that governs ordinary growth, so phosphorus scarcity can shut down the ecosystem's only route to replacing lost nitrogen — and because cyanobacteria carry the largest polyphosphate reserves of any algal class, they can keep fixing nitrogen for several days into a phosphorus-depleted phase.

Macrophytes span a wide range of strategies but share the same luxury-reserve trick. Floating plants like Salvinia and duckweed carry the same vacuolar polyphosphate reserve microalgae use — Lemna's phosphorus content ranges across nearly a sixfold span between its minimum and maximum cell quota (Skillicorn et al. 1993; Cedergreen & Madsen 2002) — and scavenge phosphate from the surface with high-affinity transporters that ramp up under phosphorus deprivation (Paterson et al. 2020). Rootless submerged plants like hornwort do the same across their whole stem surface, with slightly leaner reserves reflecting their more cellulose-rich tissue (Madsen & Cedergreen 2002; Pedersen et al. 2013). Both keep taking up phosphorus well after the bulk water has crashed, growing on stored reserves for several days.

Rooted plants are the most interesting case, because they feed from two sources at once. Their roots absorb pore-water phosphate with very high affinity while their shoots take it from the water column with lower affinity, and each end fills its own internal reserve (Carignan & Kalff 1980; Barko et al. 1991). The plant grows on whichever reserve is richer — so a phosphorus-rich substrate keeps it going when the water is drained, and vice versa. Stored phosphate moves between the two reserves through the plant's phloem on a roughly three-day timescale, the richer end donating to the leaner (Marschner 1995). Under the realistic Walstad case — rich pore water, poor open water — pore phosphate fills the root reserve and the phloem slowly leaks it up to keep the leaves growing while the bulk water stays drawn down. Rooted plants need relatively little phosphorus per unit of tissue but draw most of it from the sediment, acting as a short-circuit between soil mineralization and the water-column food web. The exact cell-quota limits, uptake affinities, and transport rate are in the Parameter Reference.

Bacteria round out the sinks. Heterotrophs take up phosphorus from their DOM and detritus food, keep what they need at their phosphorus-rich body composition, and release the rest. Nitrifiers assimilate a little phosphate for growth — a minor sink next to algae and plants.

The organic phosphorus pools

Phosphorus exists in organic form across several pools, tracked in parallel with carbon and nitrogen:

Living biomass — every species carries a phosphorus pool, its content set by the species' N:P ratio.
Detritus — dead organic matter in suspended and settled sub-pools, each tracking phosphorus alongside carbon and nitrogen.
Dissolved organic matter — split into labile and refractory fractions, each tracking phosphorus independently.
Soil organic matter (buried-substrate scenarios only) — labile and refractory fractions, each with a phosphorus pool.
Pore-water phosphate (buried-substrate scenarios only) — the phosphate in the soil's interstitial water, the product of soil mineralization and the source for root uptake and diffusion.

How phosphorus moves between the pools

Uptake into producers. Algae, macrophytes, and cyanobacteria take up phosphate at a rate tied to their carbon fixation and body N:P. A small share is re-excreted as dissolved organic phosphorus into the labile pool, paralleling the carbon and nitrogen excretion pathways.

Grazing. Consumers eat producers and assimilate phosphorus with slightly enhanced efficiency. Any phosphorus beyond their body's needs is excreted as phosphate; the undigested remainder is egested as fecal pellets that become detritus, with a "sloppy" fraction released as DOM during messy feeding.

Death. When organisms die their phosphorus enters the detritus pools, split between suspended and settled by organism type. Bacteria are the exception — most of their phosphorus goes to labile DOM, because their cells lyse and spill their contents. Rooted-plant roots are another special case: dead root phosphorus enters the soil organic-matter pool rather than water-column detritus, enriching the substrate, while dead shoots fall to the bottom as settled detritus.

Decomposition. Of the detritus phosphorus that breaks down, most becomes DOM and the rest is mineralized straight to phosphate, with the DOM share divided between labile and refractory fractions. This routing is identical for carbon, nitrogen, and phosphorus, so the source detritus's stoichiometry is preserved in the products.

The microbial loop. Heterotrophic bacteria consume DOM, assimilate the phosphorus they need, and release the rest as phosphate — more so when oxygen limits their growth. Sunlight mineralizes a parallel share directly through photodegradation.

Detritus exchange. Suspended and settled detritus trade slowly through aggregation and resuspension, carrying phosphorus along with carbon and nitrogen.

Soil to pore water, and pore water to the column. Soil organic matter decomposes and releases phosphate into the pore water, where it is either taken by roots or diffuses upward. Phosphate diffuses slowly through the substrate — more slowly than ammonium and far more slowly than CO₂ (Li & Gregory 1974), each layer of soil and sand cutting the rate further — so it tends to accumulate in the pore water rather than reaching the producers above. Diffusion is bidirectional, and reverses to recharge the pore water if the column ever holds more phosphate, though that is rare. When rooted plants are present, two extra rhizosphere effects act on pore phosphate: a physical root-mat barrier that slows diffusion, and an iron-phosphate plaque sink that scavenges phosphate onto fresh ferric oxide as the roots' radial oxygen loss oxidizes pore iron. Running in the opposite direction, rhizosphere iron reduction releases iron-bound phosphate back to the pore water — the rice-paddy pattern — so the rooted plant cycles phosphorus between mineral-locked and biologically available forms at the same time. The chemistry of that iron-phosphate coupling is detailed in the Iron Cycle.

Pore water to roots. Rooted plants draw phosphate directly from the pore water with high-affinity transporters, short-circuiting the slow diffusion path and making them the dominant conduit for soil-derived phosphorus into the water-column food web.

Conservation

Phosphorus has no loss pathway in the model. Unlike nitrogen, which can leave as nitrogen gas or ammonia, and carbon, which trades freely as CO₂, phosphorus is strictly conserved — total phosphorus across phosphate, all living biomass, detritus, DOM, soil organic matter, and pore water stays constant for the whole run. This makes phosphorus the most reliable element for mass-balance checks: if total phosphorus drifts during a run, it points to a bug. Phosphorus cycling also has no effect on alkalinity, because the model treats phosphate as a single species rather than tracking its pH-dependent acid–base forms — a simplification with no ecological cost, since phosphorus concentrations in these systems are far too low to measurably move pH.

When phosphorus limits growth

Phosphorus limitation sets in when the phosphate limitation factor falls below the combined nitrogen limitation factor — typically when starting phosphate is very low, when dense rooted plantings draw down pore phosphate faster than soil mineralization replenishes it, when a heavy algal bloom strips the water column faster than recycling refills it, or when a bacterial bloom temporarily immobilizes significant phosphorus (bacteria, being phosphorus-rich, are strong competitors for it). Because all microalgae share roughly the same phosphate affinity, phosphorus limitation does not differentially select between algal species the way silica limitation selects against diatoms — when phosphorus limits growth, all producers are throttled together.

Key ecological dynamics

Phosphorus limitation cascades differently than nitrogen limitation

When nitrogen runs low, cyanobacteria can fix atmospheric nitrogen to compensate — the ecosystem has a built-in recovery mechanism. When phosphorus runs low, there is no equivalent. No organism in the model can conjure phosphorus from thin air, so phosphorus limitation is more absolute: once phosphate is depleted and the cells' internal reserves have drained, the only way to restart the system is to wait for organisms to die and decompose, releasing the phosphorus locked in their biomass. This makes phosphorus-limited ecosystems sluggish recyclers — every atom has to pass through the full death-and-decomposition pathway before it is available again.

In practice, phosphorus limitation suppresses the whole community roughly equally, because all microalgae share similar minimum quotas and uptake affinities. But it acts on a time-shifted basis: cyanobacteria, with their large reserves, can keep growing for several days into a phosphorus-depleted column on internal stores, while greens drop out within a few days as their smaller reserves run dry.

Luxury uptake and bloom crashes

The Droop quota architecture produces dynamics that older single-step schemes cannot, in three regimes. In a replete column, cells fill their polyphosphate reserves and growth tracks the filling reserve, drawing dissolved phosphate down rapidly. In a crashing column, once phosphate drops below the uptake threshold the luxury uptake collapses — but growth continues on stored reserves at near-full rate for one to four days while the internal store drains. This is the post-bloom overshoot: biomass keeps rising even though dissolved phosphorus is already gone. Finally, in empty cells, the reserve approaches its minimum, growth halts, and biomass declines smoothly over the following week as mortality and maintenance take over.

This decoupling of fast uptake from slow growth is what produces the "post-bloom water clarity" effect: an aquarium that turned green in three days clears over the following week, even though dissolved phosphorus had been near zero for the whole crash. Hobbyists report it as "my green water cleared overnight," but the real decline runs three to seven days from peak biomass.

The phosphorus–fixation bottleneck

The most consequential phosphorus dynamic in long-running closed systems is its interaction with cyanobacterial nitrogen fixation. Fixation needs phosphorus for ribosomes and to power the nitrogenase enzyme, and its rate is co-limited by the same phosphate limitation factor that governs ordinary cyanobacterial growth. When phosphate falls far enough, fixation slows dramatically — even if nitrogen is fully depleted and the machinery is switched on.

This can strand a system: nitrogen limits growth, cyanobacteria have the genetic capacity to fix it, but phosphorus scarcity stops them. The tank is simultaneously nitrogen-limited (too little for most producers) and phosphorus-limited (too little for the one organism that could solve the nitrogen problem), and total productivity drifts down as denitrification keeps draining nitrogen that fixation cannot replace.

Iron-bound phosphorus and internal P-loading

In tanks with a soil substrate, the single largest phosphorus reservoir is usually not pore-water phosphate but iron-bound phosphorus — phosphate scavenged onto ferrihydrite surfaces and held in the soil. Different soils hold very different iron-bound fractions, from acidic peat at one extreme to iron-rich volcanic clay at the other.

When the sediment goes anoxic — under heavy detritus, long dark periods in a sealed tank, or the deep-sediment stratification of an aged substrate — the ferric iron is reduced and its phosphorus is released into the pore water. This is the classic internal P-loading mechanism (Mortimer 1941; Gächter & Müller 2003), a delayed phosphorus pulse that can fuel algal and plant growth months after setup with no external input. In oxic water the iron re-oxidizes and re-scavenges phosphate, locking it back into the sediment — so iron redox state acts as a switch on sediment phosphorus availability. Rooted plants tap this reservoir faster still: their root chemistry drives iron reduction directly, liberating iron-bound phosphorus right where the roots can absorb it. See the Iron Cycle for the full coupling.

Rooted plants as phosphorus conduits

In soil scenarios, rooted plants fundamentally change phosphorus dynamics by bypassing the slow diffusion path. Soil organic matter mineralizes phosphate into the pore water between grains, and without plants that phosphate must diffuse slowly up through the sand cap to reach the column — so it accumulates below rather than reaching the producers that need it. Rooted plants short-circuit the bottleneck entirely: their roots absorb pore phosphate directly and build it into shoot tissue, and when grazers eat the shoots or the shoots die and decompose, the phosphorus enters the water-column food web. The plants act as a living pump, moving phosphorus from the inaccessible sediment into the active water far faster than diffusion alone could.

How phosphorus interacts with the other cycles

Iron — the headline coupling in a soil tank. Iron scavenges phosphate when it oxidizes and releases it when it reduces, so the substrate's redox state governs the long-run phosphorus supply and drives the internal-P-loading pulses of an aging tank. See Iron Cycle.
Nitrogen — the two share the Liebig co-limitation that sets producer growth, and phosphorus gates the cyanobacterial fixation that is nitrogen's only recovery route. See Nitrogen Cycle.
Carbon — phosphorus availability sets how much primary production, and therefore how much carbon fixation, the system can sustain; the two move together through the food web and decomposition.
Silicon — when silica starves the diatoms, the phosphorus they would have taken up is left for silicon-independent algae instead. See Silicon Cycle.

How phosphorus differs from nitrogen

Property	Nitrogen	Phosphorus
Dissolved inorganic forms	Two (ammonium, nitrate)	One (phosphate)
Gaseous loss pathway	Yes (nitrogen gas, ammonia)	None
Conservation	Approximate (gas losses)	Strictly conserved
Two-step oxidation	Yes (nitrification)	No equivalent
Preferential uptake	Yes (ammonium over nitrate)	N/A (one form)
Light-dependent uptake	Yes (nitrate reduction needs light)	No
Alkalinity effects	Yes (multiple pathways)	None
Soil pathways	Ammonium to pore water, with coupled nitrification–denitrification	Phosphate to pore water (simpler)

Key references

Barko, J.W., Gunnison, D. & Carpenter, S.R. (1991). Sediment interactions with submersed macrophyte growth and community dynamics. Aquatic Botany 41, 41–65.
Carignan, R. & Kalff, J. (1980). Phosphorus sources for aquatic weeds: water or sediments? Science 207, 987–989.
Cedergreen, N. & Madsen, T.V. (2002). Nitrogen uptake by the floating macrophyte Lemna minor. New Phytologist 155, 285–292.
Elser, J.J., Fagan, W.F., Denno, R.F., et al. (2000). Nutritional constraints in terrestrial and freshwater food webs. Nature 408, 578–580.
Gächter, R. & Müller, B. (2003). Why the phosphorus retention of lakes does not necessarily depend on the oxygen supply to their sediment surface. Limnology and Oceanography 48, 929–933.
Li, Y.H. & Gregory, S. (1974). Diffusion of ions in sea water and in deep-sea sediments. Geochimica et Cosmochimica Acta 38, 703–714.
Marschner, H. (1995). Mineral Nutrition of Higher Plants, 2nd ed. Academic Press.
Mortimer, C.H. (1941). The exchange of dissolved substances between mud and water in lakes. Journal of Ecology 29, 280–329.
Paterson, M.J. et al. (2020). Phosphate transporters and their regulation in aquatic plants. Food and Energy Security 9, e208.
Pedersen, O., Colmer, T.D. & Sand-Jensen, K. (2013). Underwater photosynthesis of submerged plants. Frontiers in Plant Science 4, 140.
Redfield, A.C. (1958). The biological control of chemical factors in the environment. American Scientist 46, 205–221.
Reynolds, C.S. (2006). The Ecology of Phytoplankton. Cambridge University Press.
Skillicorn, P., Spira, W. & Journey, W. (1993). Duckweed Aquaculture: A New Aquatic Farming System for Developing Countries. World Bank.
Sterner, R.W. & Elser, J.J. (2002). Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere. Princeton University Press.
Madsen, T.V. & Cedergreen, N. (2002). Sources of nutrients to rooted submerged macrophytes growing in a nutrient-rich stream. Freshwater Biology 47, 283–291.