Producers

Producers are the photosynthetic organisms -- algae and aquatic plants -- that form the foundation of every aquatic ecosystem in this simulator. They capture light energy and use it to build organic matter from simple dissolved chemicals (CO2 and nutrients), producing oxygen as a byproduct. Everything else in the ecosystem ultimately depends on the organic matter and oxygen that producers create.

The model includes two broad categories of producers: microalgae (fast-growing, microscopic, single-celled or filamentous) and macrophytes (slower-growing vascular plants with roots, fronds, or stems). Microalgae dominate the short-term nutrient cycle and food web; macrophytes dominate the long-term structure and nutrient storage of planted systems.

Two lifestyles: floating vs. attached

Every algae species in the model can exist in one of two states (or both at once):

Planktonic (floating): Algae drifting freely in the water column. They get full exposure to light but are also fully exposed to grazers.
Surface-attached (benthic): Algae living on surfaces like gravel, ceramic, glass, or even the filaments of other algae. They receive less light (since the surface may be shaded) but may be partially protected from grazers.

Algae constantly move between these two states. Planktonic algae settle onto surfaces; attached algae detach and become planktonic. The settlement and detachment rates depend on the species and the surface properties. For more detail on how this works, see producers/attachment.md.

What algae need to grow

Producers need four things to photosynthesize (five for diatoms):

Light: The energy source. Growth increases with light up to a point, then levels off. No light means no photosynthesis (but respiration continues, so algae slowly lose biomass in the dark).
Carbon (CO2): The raw material for building organic molecules. Algae pull dissolved CO2 out of the water. Some species can also use bicarbonate (a related dissolved carbon form that is more abundant at higher pH) through special internal pumps called carbon concentrating mechanisms. Species differ significantly in how well they can use bicarbonate.
Nitrogen (NH4 or NO3): Essential for building proteins, DNA, and chlorophyll. Algae prefer ammonium (NH4) because it is cheaper to use, but they can also take up nitrate (NO3) when ammonium runs low -- though nitrate uptake works better in the light than in the dark.
Phosphorus (PO4): Essential for DNA, RNA, ATP, and cell membranes. Algae take up dissolved orthophosphate (PO4) from the water. Phosphorus limitation follows the same Michaelis-Menten saturation kinetics as nitrogen limitation.
Dissolved silica (DSi) — diatoms only: Diatoms build their cell walls (frustules) from amorphous opal and cannot divide without an adequate supply of dissolved silica from the water. When DSi is exhausted, diatom growth stops even if all other conditions are ideal. No other producer in the model requires silica.
Trace iron (Fe): Every photosynthetic organism needs iron for chlorophyll synthesis, cytochromes, ferredoxins, and nitrate reductase. Demand is small (Fe:C ≈ 2 × 10⁻⁵ mol/mol), but iron availability is equally small — dissolved Fe is in the nanomolar range in oxic freshwater, and Fe²⁺ oxidises within hours to insoluble Fe(III)-oxides that settle onto sediment. Fe limitation slots into the same Liebig co-limit as N and P. Rooted macrophytes bypass the water-column bottleneck by reducing sediment Fe(III) directly in their rhizosphere — one reason planted soils support plant growth that would stall in a bare-glass tank. See Iron Cycle.

Growth is limited by whichever of these resources is scarcest (Liebig's law of the minimum for N, P, and Fe; multiplicative for light, CO2, Si, and other factors). Even if light and carbon are abundant, low nitrogen, phosphorus, silica, or iron will slow growth. Conversely, even with plenty of nutrients, growth stops in the dark.

The daily cycle: photosynthesis and respiration

During the day (when lights are on): Algae photosynthesize, fixing CO2 into organic carbon, taking up nitrogen from the water, and releasing oxygen. At the same time, they also respire (burn some of their own carbon for maintenance energy), consuming some oxygen and releasing CO2.

During the night (when lights are off): Photosynthesis stops entirely, but respiration continues. Algae are net consumers of oxygen in the dark. This creates the daily oxygen swings you see in simulation results -- oxygen rises during the day and falls at night.

For details on how all the limiting factors interact and how the model calculates photosynthesis rates, see producers/photosynthesis.md.

Types of algae

The simulator includes several types of algae that differ in size, growth strategy, and environmental preferences:

Siliceous algae (diatoms)

Diatoms are split into two functional subcommunities that share silicon physiology but diverge in growth strategy and habitat. Both require dissolved silica (DSi) for frustule synthesis — their glass cell walls — making silica availability a fifth co-limiting factor on growth alongside light, CO2, N, and P.

Centric diatoms (Cyclotella, Asterionella, Fragilaria, Synedra) are the fast-growing planktonic "spring bloom" specialists. Cool-adapted (photosynthetic optimum 16°C), r-strategists with a growth rate of ~2.0 doublings/day, and predominantly free-floating (~90% planktonic). They drive the classic DSi drawdown curve and crash quickly when silica runs out.
Pennate diatoms (Navicula, Nitzschia, Gomphonema, Cymbella, Achnanthes) are the slow-growing biofilm dwellers — the "brown algae" coating of new aquaria. Shade-tolerant (half-saturation for light at 12 µmol/m²/s), temperate (optimum 22°C), K-strategists with heavy mucilage investment that glues them to glass, sand, and ceramic. Roughly 85% of their biomass lives attached to surfaces, and they scavenge dilute residual Si more efficiently than centrics.

Together, centric and pennate diatoms bloom characteristically in new aquaria (weeks 1–8) while DSi from tap water and substrate is available, then decline as DSi is exhausted, giving way to Si-independent periphyton — an example of ecological succession. See Species Catalog for full parameterization.

Planktonic green algae

The mixed community of small unicellular green algae that dominates the water column in temperate freshwater systems — Scenedesmus, Ankistrodesmus, Desmodesmus, Chlorella, Monoraphidium, Pediastrum. Fast-growing (~1.9 doublings/day at 28°C optimum) and excellent food for filter-feeding zooplankton. Has moderate bicarbonate-use capability (carbon concentrating mechanism). Warm-adapted (optimum 28°C); less competitive in cool new-tank conditions where centric diatoms dominate.

Cyanobacteria

Cyanobacteria are split into two functional subcommunities that share N₂-fixation physiology but diverge in growth strategy and habitat. Both use a potent carboxysome-based carbon concentrating mechanism (~60% bicarbonate-based carbon uptake) and are capable of N₂ fixation under nitrogen-limited conditions. This makes cyanobacteria the only organisms in the model that can increase total system nitrogen. Fixation is regulated by light, dissolved inorganic nitrogen availability, dissolved oxygen (nitrogenase is inactivated by O₂), and phosphorus co-limitation. It is energetically expensive — about 25% extra carbon is respired per unit of nitrogen fixed.

Planktonic cyanobacteria (Microcystis, Dolichospermum, Aphanizomenon, Cylindrospermopsis) are the fast-growing bloom formers of eutrophic lakes and summer reservoirs. Warm-adapted (optimum 26°C), high-light (K_light = 35 µmol/m²/s), r-strategists with ~1.6 doublings/day. Heterocystous forms have the most efficient N₂-fixing machinery but strict O₂-sensitivity. They drive the cyanotoxin blooms responsible for most freshwater harmful algal events; weakly surface-attached (~90% planktonic).
Benthic cyanobacteria (Oscillatoria, Phormidium, Lyngbya, Nostoc) are the slow-growing mat formers — the dreaded "BGA" pest of planted aquaria. Shade-adapted (K_light = 12 µmol/m²/s), temperate (optimum 22°C), K-strategists with very high EPS investment (DOC excretion 0.22) that builds a cohesive, grazer-resistant scaffold. Most are non-heterocystous but fix N₂ anyway via microaerobic mat interiors. Roughly 90% of biomass lives attached to substrate and is very hard to dislodge.

In a sealed, N-depleted aquarium, simulations show about +0.36% N gain over 60 days from N₂ fixation, consistent with measured field rates (Howarth et al. 1988). Cyanobacteria have lower grazer palatability than green algae — Daphnia and copepods both prefer green algae roughly 2× more. Mucilage sheaths, large colony size, and mat cohesion reduce access for most consumers.

Iron limitation on N₂ fixation. The nitrogenase enzyme that catalyses N₂ fixation carries an Fe-Mo cofactor that makes diazotrophs among the most iron-demanding organisms known — roughly an order of magnitude more Fe-hungry than typical phytoplankton. The model applies a dedicated half-saturation constant (K_Fe_nif ≈ 50 nM) to the fixation rate on top of the baseline Fe co-limitation on growth. In low-Fe water — RO-based aquaria without Fe supplementation, or alkaline water where Fe precipitates rapidly — N₂ fixation can collapse well before light, N-repression, or P limitation would otherwise throttle it (Berman-Frank et al. 2001; Kustka et al. 2003). Benthic cyanobacterial mats partially sidestep this by sitting directly on the sediment, where the Fe(III)-oxide reservoir is their access point to pore-water Fe²⁺.

References: Howarth et al. (1988); Paerl & Huisman (2008); Paerl & Bebout (1988); Gliwicz (1990); Fay (1992).

Benthic green algae (surface biofilm)

The mature epilithic green algal community that colonizes submerged surfaces — Stigeoclonium, Ulothrix, epilithic Chlorococcales, Oocystis, Chaetophora. Produces an exopolysaccharide (EPS) matrix that anchors cells and forms stratified biofilms. Growth rate ~1.56 doublings/day at 22°C, intentionally close to diatoms (~1.7/day) so that early-succession diatom dominance is driven by better adhesion, Si availability, and shade tolerance rather than a large growth-rate gap. More light-dependent than shade-adapted diatoms (half-saturation at 40 µmol/m²/s vs 20).

Benthic green algae have a small planktonic dispersal pool — cells detach from surfaces, drift in the water column, and settle onto new surfaces. At equilibrium, about 85% of biomass is on surfaces and 15% is planktonic. Filter feeders (Daphnia, rotifers) can consume the planktonic dispersal cells. Surface-to-surface lateral dispersal also occurs via EPS-mediated spreading.

References: Biggs (1996); Stevenson (1996); Hoagland et al. (1982); Fogg (1983).

Macrophytes: aquatic plants

Beyond microalgae, the model includes vascular aquatic plants that grow 10 to 100 times more slowly than microalgae but play fundamentally different ecological roles. They invest heavily in structural carbon (cell walls, vascular tissue, rhizome storage), which makes them long-lived, resistant to grazing, and important for long-term nutrient storage. Standard algae grazers do not consume macrophytes.

Because maximum photosynthesis is so much lower than in algae, maintenance respiration must also be proportionally lower. If maintenance costs exceed what the plant can fix during its daily light period, it cannot achieve positive net growth at any light level. In the model, the maintenance-to-maximum-photosynthesis ratio is tightly constrained at roughly 10-15% across all macrophyte species.

The model includes three categories of macrophytes, each with a distinct growth strategy and ecological niche.

Rooted macrophytes

Rooted macrophytes (Cryptocoryne, Vallisneria) anchor to the sediment and draw nutrients from two sources simultaneously: the water column through their leaves and the sediment pore water through their roots. Each plant tracks separate shoot and root biomass pools. Carbon flows from shoot to root via phloem translocation (typically 25% of gross fixation), and root death returns organic matter directly to the soil rather than the water column.

The dual nutrient source gives rooted macrophytes access to nutrients that are unavailable to algae and floating plants. In Walstad-style scenarios with nutrient-rich buried substrates, 50-90% of nitrogen and phosphorus uptake comes through the roots. Rooted macrophytes are also the only producers that can access pore water CO2, which can be an order of magnitude more concentrated than CO2 in the water column — a critical advantage for species without a carbon concentrating mechanism.

A newly planted crown with a small root system has limited pore-water access regardless of how nutrient-rich the substrate is. As root biomass grows, uptake capacity increases, enabling faster shoot growth, which in turn sends more carbon to roots — a positive feedback loop that produces the characteristic sigmoid growth curve. In practice, a freshly planted Cryptocoryne may show almost no visible leaf production in the first 8-12 weeks while investing most of its photosynthate in root development.

Implemented species:

Cryptocoryne wendtii — slow-growing, shade-tolerant rosette plant, relies entirely on dissolved CO2 (no bicarbonate use), strongly substrate-dependent (80% of nutrients from roots). About 70% of its photosynthetic carbon comes from sediment pore water in Walstad scenarios.
Vallisneria spiralis — faster-growing (~3× Cryptocoryne), light-demanding, active bicarbonate user (~40% of carbon from bicarbonate), more balanced between water-column and root uptake (55% from roots).

Floating macrophytes

Floating macrophytes (Salvinia, duckweed) live at the air-water interface. Each plant tracks a single frond biomass pool. They have no roots into the sediment and draw all their nutrients from the water column through frond undersides and root-hair-like filaments, using high-affinity transporters that make them effective at scavenging low nutrient concentrations.

Their primary ecological impact is canopy shading. As frond biomass accumulates, the floating mat intercepts an increasing fraction of incident light before it reaches the water column. At full surface coverage, floating plants can block over 95% of light (self-shading), shading all submerged organisms. Growth is self-limiting: as the mat thickens, fronds deeper in the mat receive less light, and a spatial carrying capacity provides a hard cap on surface coverage.

When multiple floating species co-occur at high combined coverage, slower-growing species are displaced by faster-growing competitors — a form of competitive exclusion. The faster-growing species pushes slower fronds under the mat, where they die from lack of light.

In Walstad-style planted aquarium scenarios, floating plants serve as early NH4 spike controllers. A small starter cluster introduced on day 3 can grow to full surface coverage within 60 days, scavenging water-column ammonium aggressively and reducing NH4 by up to 3× compared to scenarios without floating plants.

Implemented species:

Salvinia natans/minima — fast-growing floating fern.
Lemna minor (duckweed) — common duckweed; fastest-growing floating vascular plant; competitively displaces Salvinia over weeks to months.

Submerged macrophytes

Submerged macrophytes (hornwort) are rootless vascular plants that live fully inside the water column. Each plant tracks a single stem biomass pool. They have no sediment attachment and absorb all nutrients from the surrounding water. Unlike planktonic algae (which see a depth-averaged light), submerged macrophytes receive light computed at their actual depth via Beer-Lambert attenuation. Their stems scatter and absorb light within the water column, shading organisms below them.

Many submerged macrophytes possess a strong carbon concentrating mechanism, giving them access to the large bicarbonate pool in the water. Hornwort can obtain ~45% of its carbon from bicarbonate, consistent with measurements by Prins & Elzenga (1989).

Implemented species:

Hornwort (Ceratophyllum demersum) — rootless, shade-tolerant, strong bicarbonate user, temperate-hardy. Produces allelopathic phenolic exudates.

For the full details on macrophyte mechanics — establishment dynamics, pore water CO2 access, canopy optics, interspecific competition, and mortality routing — see Macrophytes.

Settlement and detachment

Algae constantly exchange between the water column and surfaces. Planktonic cells settle onto surfaces; attached cells detach back into the water. The balance between these processes depends on the species (unicellular algae detach easily; filamentous species hold on tight) and the surface properties (rough surfaces promote attachment; smooth surfaces promote detachment). See producers/attachment.md for the full details.