Decomposition and Recycling

For the overview of death and decomposition, see Death and Decomposition. For how mortality produces the dead biomass that enters this pathway, see Mortality Mechanisms.

Why Decomposition Sets the Pace of the Whole Ecosystem

Decomposition is the rate-limiting step that controls nutrient availability. Every atom of nitrogen and phosphorus in a dead organism is locked inside organic molecules until decomposition frees it — a process called mineralization. If decomposition is fast, nutrients cycle back to producers within days and the ecosystem runs a tight, efficient loop. If decomposition is slow — because oxygen is low, temperatures are cold, or bacterial populations have been suppressed by grazers — nutrients pile up in detritus and DOM, starving producers of the raw materials they need to photosynthesize and produce oxygen.

This makes decomposition the hidden regulator of ecosystem health. A system that looks stable can be slowly accumulating a debt of undecomposed organic matter. When that debt gets large enough — or when a temperature spike suddenly accelerates decomposition — the oxygen demand from processing the backlog can overwhelm the system's oxygen supply and trigger a crash. Understanding where organic matter is, how fast it is breaking down, and how much oxygen that breakdown costs is essential for predicting whether an ecosystem will remain stable.

Death Products: Where Dead Biomass Goes First

When an organism dies, its carbon, nitrogen, and phosphorus are routed to one or more of these destinations, depending on the species:

Most species (algae, consumers, nitrifiers) route all of their dead biomass to detritus, split between suspended and settled pools. The exact split varies by species:

Species	Suspended	Settled
Daphnia	10%	90%
Copepod	20%	80%
Rotifers	50%	50%
Bladder snail	5%	95%
Green microalgae (unicellular: Scenedesmus, Chlorella, etc.)	30%	70%
Ciliates	70%	30%
Nanoflagellates (HNF)	85%	15%
Nitrifying bacteria	80%	20%

The pattern makes physical sense: large-bodied organisms like Daphnia mostly settle to the bottom when they die, while tiny organisms like nitrifying bacteria and ciliates mostly stay suspended as fine particles.

Heterotrophic bacteria are different. When bacteria die (including from viral lysis), 80% of their biomass goes directly to dissolved organic matter (DOM) rather than detritus. This represents cell lysis, where the contents of the bacterial cell spill out into the water as dissolved molecules. The remaining 20% goes to detritus, split 50% suspended and 50% settled.

Green periphyton (surface-dwelling microalgae) are also different. When periphyton die, 20% of their biomass goes directly to DOM (from cell lysis), and the remaining 80% goes to detritus, split 50/50 between suspended and settled.

The Two Detritus Pools

The simulator tracks dead organic matter in two separate pools:

Suspended detritus consists of fine particles floating in the water column. These are small fragments of dead cells, tiny fecal pellets, and other fine debris that stay suspended in the water rather than sinking. Suspended detritus decomposes faster because it has more surface area exposed to bacteria and oxygen.

Settled detritus consists of larger particles and aggregates that have sunk to the bottom. This includes large fecal pellets, dead filaments, dead animal bodies, and aggregated clumps of smaller particles. Settled detritus decomposes more slowly because it has less surface area and the conditions at the bottom tend to be more oxygen-poor.

Exchange between pools: Material moves between these two pools in both directions:

Aggregation (suspended to settled): Fine suspended particles collide with each other, stick together, form larger clumps, and eventually sink. This happens at a rate of about 1.5% per day.
Resuspension (settled to suspended): Mixing forces (convection from temperature gradients, gas bubbles from photosynthesis, animal movement) stir settled material back up into the water column. This also happens at about 1.5% per day.

The Decomposition Process

Decomposition is the breakdown of detritus into simpler compounds. The rates and controls below determine whether nutrients locked in dead matter return to the living community in days or weeks — and that difference alone can decide whether an ecosystem stays productive or slowly starves.

Decomposition rates: Suspended detritus decomposes (abiotically) at about 12% per day. Settled detritus decomposes abiotically at about 4% per day. Heterotrophic bacteria add roughly another 4% per day of biotic decomposition to settled detritus at typical bacterial densities, bringing the total to about 8% per day under normal conditions. The abiotic/biotic split matters because the biotic fraction scales with bacterial biomass — when bacterivores suppress bacteria, settled detritus decomposes more slowly and sediment accumulates. This is one reason why bacterial population dynamics can have outsized effects on the whole ecosystem. See Microbes for the biotic decomposition pathway.

Temperature dependence: Decomposition follows a Q10 of 2.0 — for every 10°C increase, the rate roughly doubles. A warm jar recycles nutrients faster, but it also demands more oxygen to do so. This tradeoff is at the heart of why temperature spikes can trigger crashes: decomposition accelerates, oxygen demand surges, and if photosynthesis cannot keep up, the system tips into anoxia.

Oxygen dependence: Decomposition is much more efficient when oxygen is available (aerobic decomposition), but it does not stop completely without oxygen. The relationship follows Michaelis-Menten kinetics (half-saturation K = 1.0 × 10⁻⁵ mol O2/L):

Under fully aerobic conditions, decomposition runs at 100% of its potential rate.
Under completely anoxic (zero oxygen) conditions, decomposition slows to about 15% of the aerobic rate. This represents anaerobic decomposition pathways (fermentation, etc.) that are much less efficient.

For suspended detritus, the O2 factor is applied directly — if water O2 is high, suspended decomposition runs at full speed.

For settled detritus, two additional reduction factors model the fact that detritus on the bottom sits in a partially anoxic microenvironment where oxygen from the overlying water only partially penetrates:

O2 scaling on decomposition rate. The aerobic bonus to the decomposition rate is halved (scaling factor of 0.5) for settled material. Specifically, the settled O2 factor is computed as: anaerobic floor + 0.5 × (water-column O2 factor − anaerobic floor). When water O2 is high and the suspended O2 factor would be 1.0, the settled O2 factor is only 0.575 (= 0.15 + 0.5 × 0.85). This reflects the physical reality that even when the overlying water is well-oxygenated, oxygen only diffuses partway into the settled detritus layer, so the average O2 availability within the layer is lower than at the surface.
O2 access fraction on O2 demand. The oxygen actually consumed from the water column by settled decomposition is reduced to 30% of what would be expected stoichiometrically. The remaining 70% of the carbon oxidation is assumed to occur via anaerobic pathways (fermentation, sulfate reduction, etc.) that do not draw dissolved O2 from the water column. This prevents settled detritus decomposition from creating an unrealistically large O2 sink — in real sediments, much of the mineralization happens anaerobically using alternative electron acceptors.

These two factors serve different purposes: the first controls how fast settled detritus decomposes (a rate effect), while the second controls how much oxygen that decomposition costs (a stoichiometric effect). Together they capture the dual nature of benthic decomposition — it proceeds more slowly than water-column decomposition, and the fraction that does proceed consumes less dissolved O2 per unit of carbon processed.

Decomposition products: When detritus breaks down, the products are split two ways:

70% becomes DOM (dissolved organic matter). These are organic molecules that have been broken free from the solid detritus particles and are now dissolved in the water. Heterotrophic bacteria are the primary consumers of this DOM.
30% is directly mineralized to inorganic compounds: dissolved inorganic carbon (DIC), ammonium (NH4), and phosphate (PO4). This represents fast abiotic breakdown of simple organic compounds that does not require bacterial processing.

Oxygen consumption: Decomposition consumes dissolved oxygen, but only for the fraction that is directly mineralized (the 30% that becomes DIC/NH4/PO4 immediately). The 70% that becomes DOM does not cost O2 at this stage — that O2 cost is paid later when bacteria consume the DOM and respire it. For suspended detritus, O2 demand equals the directly-mineralized carbon scaled by the aerobic fraction. For settled detritus, O2 demand is further reduced by the O2 access fraction (0.3), so settled decomposition draws only about 30% as much O2 from the water column per unit of carbon mineralized as suspended decomposition does.

DOM (Dissolved Organic Matter)

DOM is the invisible fuel of the microbial loop — the dissolved remains of dead organisms, broken free from solid detritus and floating as individual molecules in the water. It is what connects death to new life: bacteria eat DOM, grow, and themselves become food for protists and filter-feeders, returning nutrients to the food web one trophic level at a time. DOM has carbon, nitrogen, and phosphorus pools, and comes from two sources:

Decomposition of detritus (the 70% fraction described above)
Direct cell lysis when certain organisms die (bacteria: 80% to DOM; green periphyton: 20% to DOM)

In addition to these death-related sources, DOM also receives carbon from active DOC excretion by producers during photosynthesis. Algae and periphyton excrete 5-10% of their photosynthetically fixed carbon as dissolved organics (exudation). This is an ongoing source of DOM that fuels the microbial loop even when no organisms are dying.

Two fractions of DOM. Not all dissolved organic matter is created equal. The model tracks two distinct DOM pools:

Labile DOM is fresh, simple molecules -- amino acids, sugars, organic acids -- released by algal exudation and cell lysis. Bacteria consume it rapidly because these small molecules are easy to absorb and metabolize.
Refractory DOM is older, more complex material -- humic and fulvic compounds with tangled aromatic structures. Bacteria can still consume it, but at roughly one-tenth the rate of labile DOM and with much lower growth efficiency. Refractory DOM also absorbs light, darkening the water column as it accumulates (the "tea-staining" effect familiar to anyone who has kept an aquarium with driftwood or decaying leaves).

Where does each fraction come from? Fresh sources like algal exudation and cell lysis produce almost entirely labile DOM. Decomposition of detritus produces a mix: suspended detritus yields about 70% labile and 30% refractory, while settled detritus yields about 55% labile and 45% refractory (settled material has already undergone more processing, so a larger share becomes resistant humic compounds).

DOM is removed from the water by two pathways:

Bacterial consumption (primary pathway): Heterotrophic bacteria are the main consumers of DOM. They absorb dissolved organic molecules, use some for building new bacterial biomass, and respire the rest as CO2. Growth efficiency differs sharply between the two fractions: bacteria convert about 28% of labile DOM into new biomass (a bacterial growth efficiency of 0.28), but only about 8% of refractory DOM (the complex molecules cost more energy to break apart). This is the heart of the "microbial loop" -- the process by which dissolved dead matter gets converted back into living biomass that larger organisms can eat.

UV photodegradation (secondary pathway): Sunlight, particularly ultraviolet light, can break down DOM through purely chemical (non-biological) reactions. This process:

Only operates during daylight hours
Scales with light intensity, following a Michaelis-Menten saturation curve (half-saturation at 150 micromoles of photons per square meter per second)
Has a maximum rate of about 3% per day at saturating light levels
At typical indoor light levels (around 55 micromoles per square meter per second), the effective rate is only about 0.8% per day
Refractory DOM photodegrades 1.5× faster than labile DOM, because humic and fulvic aromatic structures are stronger UV absorbers (Zepp & Schlotzhauer 1981; Bertilsson & Tranvik 2000)
Has weak temperature dependence (Q10 of 1.3, compared to 2.0 for most biological processes)

What UV photodegradation actually does. In real aquatic systems, UV photodegradation does two things to DOM: it fully mineralizes some fraction to CO2, NH4, and PO4, and it partially breaks down the rest into smaller, more bioavailable molecules (Moran & Zepp 1997). About 40% of photodegraded DOM is fully mineralized (Bertilsson & Tranvik 2000; Cory et al. 2014). The remaining 60% becomes low-molecular-weight compounds more accessible to bacteria, but these partially degraded molecules are not tracked separately from the original DOM pool.

The practical consequence is that the effective DOM mineralization rate from UV is about 1.2%/day at saturating light (3%/day base rate × 40% fully mineralized), with the remaining 60% of photochemical transformation left implicitly in the DOM pool. This makes UV photodegradation appear to be a slower DOM removal pathway than it physically is — but it correctly accounts for the fraction that actually returns nutrients to the dissolved inorganic pool.

The Recycling Loop

All of these processes together form a closed recycling loop. Here is the complete cycle:

An organism dies. Its biomass (carbon, nitrogen, and phosphorus) is routed to detritus and/or DOM, depending on the species.
Detritus decomposes. Solid dead matter is broken down into DOM (70%) and directly mineralized to DIC + NH4 (30%).
Bacteria consume DOM. Heterotrophic bacteria absorb the dissolved organic matter. They convert about 28% of labile DOM and 8% of refractory DOM into new biomass; the rest is respired as CO2, and excess nitrogen and phosphorus are excreted as NH4 and PO4.
Bacteria die. When bacteria die (from base mortality, viral lysis, or environmental stress), 80% of their biomass becomes DOM again, and 20% becomes detritus.
The cycle repeats. The DOM from dead bacteria feeds living bacteria; the detritus decomposes into more DOM. With each pass through the loop, more carbon is respired away as CO2, more nitrogen is released as NH4, and more phosphorus is released as PO4.
Eventually, everything is mineralized. After enough cycles, all the carbon from the original dead organism has been respired to DIC, all the nitrogen has been released as NH4, and all the phosphorus has been released as PO4. These inorganic nutrients are now available for algae and other primary producers to use for new growth, completing the circle of life in the ecosystem.

UV photodegradation provides a parallel pathway that bypasses the bacteria, directly converting some DOM to DIC, NH4, and PO4, which is particularly important when bacterial populations are small or limited by other factors.

The speed of this recycling loop matters enormously for ecosystem stability. If decomposition and recycling are fast, nutrients are quickly returned to the producers. If they are slow, nutrients can get locked up in dead matter, starving the living organisms of essential resources.