Death and Decomposition

Death is not a passive cleanup process — it is the engine that drives nutrient recycling and controls population dynamics. Every organism that dies becomes raw material for the next generation, and the rate at which that dead matter is recycled back into usable nutrients (mineralization) determines whether the ecosystem thrives or slowly starves.

How Organisms Die

Every species in the simulator faces multiple threats to its survival. These threats are calculated independently and added together — an organism dealing with heat stress and low oxygen simultaneously suffers the combined penalty of both. The total mortality rate is capped per species to prevent numerical problems.

The model includes ten distinct mortality mechanisms. Each follows a common pattern: a safe range where no mortality occurs, and a stress-to-lethal ramp (a mortality ramp) where mortality increases linearly with the severity of the insult.

Environmental stressors — four mechanisms that affect most or all species:

Base mortality. A small, constant background death rate (1-5% per day) from aging, disease, and other unavoidable causes. Always active.
Temperature mortality. Each species has a comfort range; outside it, mortality ramps up toward lethal thresholds. Cold-hardy copepods and warm-tolerant bacteria differ widely in their safe zones.
Salinity mortality. Same ramp structure as temperature. Most species are freshwater and very salt-sensitive.
pH mortality. Extreme acidity or alkalinity causes increasing mortality beyond species-specific thresholds.

Chemical stressors — two mechanisms tied to water chemistry:

Ammonia toxicity. The unionized form of ammonia (NH3) is toxic to consumers. The fraction in this toxic form depends on pH and temperature — at high pH, even modest total ammonia concentrations become dangerous. Modeled for all consumer species, not for algae or bacteria.
Hypoxia mortality. Low dissolved oxygen causes stress and death in aerobic organisms. Different species have very different tolerances: heterotrophic bacteria can survive near-anoxic conditions, while Daphnia begin to suffer below about 2 mg/L.

Biotic stressors — four mechanisms that depend on the organism's own population or food supply:

Starvation. Consumers that cannot find enough food to cover their metabolic needs experience increasing mortality. Species with lipid reserves (copepods) survive food scarcity longer than those without (rotifers).
Crowding. At high population densities, Daphnia, rotifers, ostracods, and bladder snails suffer extra mortality from competition, waste buildup, and disease. Water-column species scale with volumetric density; benthic species scale with areal density on crawlable substrate.
Cannibalism. Copepods eat their own young. At high density, this becomes a significant population control mechanism.
Viral lysis. Viruses kill heterotrophic bacteria, nitrifiers, HNF, ciliates, and planktonic phytoplankton (cyanobacteria, green algae, diatoms) in a density-dependent manner. For phytoplankton it is often the primary bloom-termination mechanism — cyanophage outbreaks routinely drive Microcystis crashes faster than grazing or nutrient depletion would. Lysed cytoplasm enters the viral shunt as labile DOM rather than detritus, fuelling rapid bacterial recycling.

All applicable sources stack additively, so an organism under multiple mild stresses can suffer higher total mortality than one under a single severe stress. For the full details — per-species threshold values, the linear ramp formula, Q10 adjustments, and the Michaelis-Menten kinetics of density-dependent mechanisms — see Mortality Mechanisms.

What Happens to Dead Matter

When organisms die, their biomass does not vanish. It enters the decomposition pathway — a multi-step process that eventually recycles the carbon, nitrogen, and phosphorus in dead organisms back into the simple inorganic forms (dissolved CO₂, ammonium, and phosphate) that living organisms can use again.

Death products. Most species route all dead biomass to detritus, split between suspended particles in the water column and settled material on the bottom. The split varies by species — large-bodied organisms like Daphnia mostly settle (90%), while tiny organisms like ciliates mostly stay suspended (70%). Heterotrophic bacteria are different: 80% of their dead biomass goes directly to dissolved organic matter (DOM) through cell lysis, bypassing detritus entirely.

Two detritus pools. Suspended detritus (fine particles in the water column) decomposes faster than settled detritus (material on the bottom), because it has more surface area exposed to oxygen and bacteria. Material moves between the two pools in both directions — aggregation pulls suspended particles down, and mixing forces resuspend settled material.

Decomposition. Detritus breaks down into two products: 70% becomes dissolved organic matter (DOM), and 30% is directly mineralized to inorganic nutrients (DIC, NH4, PO4). Decomposition rate depends on temperature (Q10 = 2.0) and oxygen availability (slows to 15% of the aerobic rate under anoxia). Settled detritus decomposes with reduced oxygen access, modeling the partially anoxic conditions at the bottom.

Dissolved organic matter (DOM). DOM exists as two fractions with very different fates. Labile DOM (fresh, simple molecules from exudation and cell lysis) is consumed rapidly by bacteria with about 28% growth efficiency (BGE). Refractory DOM (humic/fulvic polymers) is consumed at one-tenth the rate by bacteria with only 8% efficiency, but is the preferred substrate for aquatic fungi, which break it down with 15% efficiency and convert a portion to labile DOM through fungal conditioning. Refractory DOM also absorbs light, darkening the water as it accumulates. UV photodegradation provides a secondary, abiotic pathway that mineralizes DOM directly.

The recycling loop. Death → detritus → DOM → bacterial biomass → bacterial death → DOM → and around again. Fungi add a parallel pathway through this loop: they consume refractory DOM, settled detritus, and soil OM directly, converting a fraction to labile DOM (fungal conditioning) that bacteria then exploit. With each pass through the loop, more carbon is respired as CO₂ and more nitrogen and phosphorus are released as NH4 and PO4, eventually returning all nutrients to the inorganic pool for producers to use. The speed of this recycling loop is critical for ecosystem stability — fast recycling keeps nutrients available; slow recycling locks them in dead matter and starves the living community.

For the full details — per-species death product routing tables, decomposition rate controls, the settled detritus O₂ scaling model, DOM fraction sources and sinks, UV photodegradation mechanics, and the complete recycling flow — see Decomposition and Recycling.

Soil Organic Matter and Pore Water

Some scenarios include a buried organic substrate layer -- the Walstad approach for planted aquaria. This substrate acts as a slow-release nutrient reservoir, mineralizing over months to years rather than the days-to-weeks timescale of water-column detritus. The model tracks two soil organic matter fractions: labile soil OM (manure, compost; turnover ~0.24% per day at 20°C) and refractory soil OM (peat, bark; turnover ~0.012% per day -- roughly 20 times slower). Labile material releases meaningful nutrient fluxes in the first weeks to months; refractory material sustains a tank for years.

Unlike water-column decomposition, soil mineralization releases its products into pore water -- the interstitial water trapped between soil particles -- rather than directly into the water column. Pore water nutrients (NH4, NO3, PO4, CO2) reach the water column by two routes: Fickian diffusion through the sand cap and direct root uptake by rooted macrophytes. This separation of soil products from the water column is what makes soil a slow-release reservoir rather than an acute nutrient pulse.

In scenarios without soil substrate, all soil OM and pore water pools remain at zero and have no effect on the simulation.

For the full details -- mineralization rate controls, bacterial stimulation, the Fick's law diffusion formula, per-solute diffusivities, and the comparison table between water-column and soil decomposition -- see Soil Organic Matter and Pore Water Diffusion.

Death and Decomposition

How Organisms Die

What Happens to Dead Matter

Soil Organic Matter and Pore Water

Further Reading