EcoSym

Species Catalog

This is a reference listing of every species currently modeled in the simulator. Each entry describes what the organism is, what role it plays in the ecosystem, and what key behaviors the model tracks for it.

Algae

Algae are the primary producers -- they use light to convert CO2 and dissolved nutrients into living biomass and oxygen. All algae in the model share the same core photosynthesis mechanics (light limitation, nitrogen and phosphorus limitation via Liebig's law of the minimum, CO2 limitation, carbon storage, and photorespiration) but differ in growth rate, surface attachment, grazer vulnerability, and environmental tolerances. Every algae species can exist in both a free-floating (planktonic) form and attached to surfaces. They settle onto surfaces at species-specific rates weighted by surface area and roughness, and detach back into the water column. When nitrogen is scarce, algae reduce their photosynthesis rate but can still fix carbon into storage compounds (like starch or lipids), which increases their carbon-to-nitrogen ratio up to a species-specific maximum. All algae species can use dissolved CO2 for photosynthesis, and most can also use bicarbonate to varying degrees through carbon concentrating mechanisms. At high oxygen-to-CO2 ratios, photorespiration kicks in -- the photosynthetic enzyme RuBisCO mistakenly grabs oxygen instead of CO2, reducing net carbon fixation and oxygen production.

Diatoms have an additional requirement: dissolved silica (DSi). Their cell walls (frustules) are made of amorphous opal (SiO2*nH2O), and they cannot divide without a supply of silicic acid from the water. This makes silica availability an independent co-limiting factor on diatom growth, beyond the standard light/N/P/CO2 suite that applies to all other algae.

Species:

Consumers

Consumers are animals and protists that eat other organisms. They cannot make their own food from light and must eat to survive. All consumers in the model share mechanics for activity modulation by oxygen and salinity, stoichiometric homeostasis (maintaining fixed body C:N and N:P ratios by excreting excess nitrogen as NH4 and excess phosphorus as PO4), starvation mortality when food intake is insufficient, ammonia toxicity from high NH3 levels, and respiration that consumes oxygen and produces CO2. Feeding follows a saturating functional response: intake rate increases with food availability but hits a maximum. Consumers have reduced activity at night and when oxygen is low. Undigested food is egested as fecal pellets that become detritus.

Grazers

Animals ranging from microscopic rotifers to cherry shrimp at 1.5-3 cm, each with a different feeding strategy -- filter feeding, raptorial hunting, or benthic scraping.

Microzooplankton

Single-celled protists that occupy the microbial loop, linking bacteria and dissolved organic matter to larger consumers.

Fish

Fish are modeled as a boundary condition on the ecosystem rather than a closed-mass-balance member: their biomass is a user-set stocking level held fixed (no growth or reproduction in V1; only death removes it), and the model instead tracks the bioload they impose (an oxygen sink and an ammonia/CO₂/phosphate source, fed by an external feeding subsystem) and their health ∈ [0, 1]. The fragile ↔ hardy spread across the roster emerges from per-species tolerance thresholds calibrated against the toxicology literature. See the Fish catalog and the conceptual page Fish & Feeding.

Macrophytes

Rooted Macrophytes

Rooted macrophytes are vascular aquatic plants whose roots and rhizomes are embedded in the sediment. They differ from all algae in the model by having two separate biomass pools (shoot and root), two nutrient sources (water column and pore water), and 10 to 100 times slower growth rates. Standard algae grazers do not eat them. They are photosynthetically active (C3 plants), low-light adapted, and primarily suited to Walstad-style planted tanks where a nutrient-rich buried substrate provides their nitrogen and phosphorus through root uptake.

Floating Macrophytes

Floating macrophytes are vascular plants that live at the air-water interface. Unlike rooted macrophytes, they have no sediment attachment -- their entire biomass is tracked as a single frond pool. They absorb all nutrients from the water column through dense root-hair-like filaments on their frond undersides, using high-affinity transporters (half-saturation for N around 4 umol/L) to scavenge dilute NH4. Their primary ecological role is early NH4 spike control in Walstad-style scenarios: a small starter cluster introduced on day 3 can grow to full surface coverage within 60 days, reducing water-column NH4 by up to 3x. Standard algae grazers do not consume them.

Submerged Macrophytes

Submerged macrophytes are rootless vascular plants fully immersed in the water column. They differ from rooted macrophytes (no roots, no pore-water access) and from floating macrophytes (no surface canopy, no atmospheric CO2 boundary layer). All nutrients come from the water column. Light is computed at the plant's actual depth via Beer-Lambert, not at the surface. Standard algae grazers do not eat them.

Rooted species:

Floating species:

Submerged species:

Fungi

Aquatic fungi are the specialists of refractory decomposition -- they break down tough, humic-like substrates that bacteria handle poorly, using extracellular enzyme systems (cellulases, laccases, peroxidases). Their key ecological function is fungal conditioning: converting refractory carbon into labile DOM that bacteria can then exploit, driving the fungal-to-bacterial decomposition succession. They grow far more slowly than bacteria (~7 day doubling time vs ~4 hours) but persistently colonize solid substrates via hyphal networks. In Walstad-style scenarios, they are responsible for the weeks 2-8 substrate conditioning phase that converts raw soil into productive habitat. Their chytrid zoospore fraction is grazeable by ciliates and nanoflagellates.

Species:

Bacteria

Species:

Last updated: 6/7/2026