Algae Settlement and Surface Dynamics

For a general introduction to producers, see producers.md.

Why It Matters Whether an Alga Is Floating or Stuck

Whether an algal cell is drifting in the water column or anchored to a surface changes almost everything about its life. A planktonic cell competes for light with every other cell above and below it, faces the full force of grazer feeding, and sees only the well-mixed bulk nutrient concentration. The same cell attached to a rough ceramic surface receives a fixed light level determined by the surface's position, gains partial protection from grazers that cannot reach into crevices, and perceives nutrient concentrations enriched by the biofilm boundary layer. The continuous exchange of cells between these two states — settlement onto surfaces and detachment back into the water — is what creates the spatial structure of the producer community and determines how much of the ecosystem's primary production is vulnerable to grazing versus protected in biofilms.

Planktonic vs. surface-attached pools

Because the life of a floating cell is so different from the life of an attached one — different light, different grazing pressure, different nutrient access — the model cannot treat a species as a single lump of biomass. It needs to know how much of each species is floating in the water column and how much is living on each surface, because those populations grow at different rates, face different mortality, and serve different roles in the food web.

Each algae species (except green periphyton) therefore maintains separate biomass pools for its planktonic population and for each surface it can live on. For example, if a scenario has two surfaces (say, "gravel" and "ceramic"), green microalgae would have three biomass pools: one planktonic pool, one gravel pool, and one ceramic pool. Each pool tracks both carbon (C) and nitrogen (N) independently.

These pools are connected by settlement and detachment fluxes, and they grow somewhat independently — a surface pool in dim conditions will photosynthesize more slowly than one in bright light, even though both belong to the same species.

Settlement: planktonic to surface

Planktonic algae settle onto available surfaces at a species-specific base rate (expressed per hour). The total settlement flux is distributed among surfaces based on their area weighted by roughness. Rougher surfaces with more area receive a larger share of settling algae.

The distribution works as follows: each surface's "weight" is its area multiplied by its roughness. The fraction of settling algae that goes to a given surface equals that surface's weight divided by the total weight of all surfaces. This means a large rough surface (like porous ceramic) attracts far more settlers than a small smooth surface (like glass).

Settlement rates vary considerably by species:

Benthic green algae: 0.008/h -- highest settlement via EPS-mediated adhesion
Diatom community: 0.004/h -- strong settlement, heavy frustules and mucilage pads
Green microalgae (Scenedesmus, Chlorella, etc.): 0.001/h -- weak, mostly passive sedimentation (no holdfast structures)

Detachment: surface to planktonic

Attached algae detach from surfaces and return to the planktonic pool. The detachment rate for a given species on a given surface is determined by three factors:

Surface detachment rate: Each surface has its own detachment rate (expressed per day, converted internally to per hour). Smooth surfaces like glass have high detachment rates (0.10/day). Rough surfaces like porous ceramic have low rates (0.02/day). Filamentous algae surfaces are intermediate (0.08-0.10/day).
Species detachment multiplier: A species-specific scaling factor that reflects how well the organism holds on. Values less than 1 mean the species resists detachment; values greater than 1 mean it detaches easily:
- Diatom community: 1.5 -- moderate adhesion via mucilage
- Benthic green algae: 2.0 -- EPS improves adhesion but cells can still be dislodged
- Green microalgae: 3.0 -- easily dislodged, no holdfast structures
Crowding factor: As surface biomass approaches the surface's carrying capacity, detachment increases. The crowding factor is 1 + (biomass N / carrying capacity N), so a surface at half capacity has 1.5x the base detachment rate, and a surface at full capacity has 2x. This is the same density-dependent mechanism used by green periphyton, and it prevents unrealistic biomass accumulation on surfaces.

The actual detachment flux is: surface detachment rate per hour × species detachment multiplier × crowding factor × attached biomass.

Dispersal of new growth

When algae grow on a surface, not all of the new growth stays on that surface. A fraction (the "dispersal fraction") is redistributed to all surfaces proportional to their area. This mechanism is important for ecosystem stability: it allows algae on protected surfaces (refugia) to seed exposed surfaces that have been grazed down.

Think of dispersal as fragments, daughter cells, or spores that drift away from where they were produced and land on other surfaces. The dispersal fraction varies by species based on their physical form:

Green microalgae: 25% -- unicellular, easily disperses
Green periphyton (benthic green algae): 15% -- EPS-mediated surface-to-surface spreading

The remaining growth (100% minus the dispersal fraction) stays on the surface where it was produced.

Carrying capacity

Each surface has a maximum density of algae it can support, measured in micrograms of nitrogen per square centimeter. This sets a ceiling on how much biofilm can accumulate on that surface.

Typical maximum densities from the model's surface presets:

Porous ceramic: 10 ug N/cm2 -- highest, because protected pores allow dense growth
Smooth ceramic: 8 ug N/cm2
Gravel: 7 ug N/cm2
Sand: 5 ug N/cm2 -- grain shifting limits accumulation
Glass: 4 ug N/cm2 -- smooth surface, low density

For green periphyton, carrying capacity directly limits growth. The model computes a "space factor" for each surface:

space factor = 1 - (current periphyton N / carrying capacity N)

When a surface is empty, space_factor is 1 (full growth). As periphyton biomass approaches carrying capacity, space_factor drops toward 0, throttling growth. This means periphyton on a crowded surface essentially stop growing until some biomass is removed (by grazing, detachment, or mortality).

For the non-periphyton algae species (green microalgae, diatoms, etc.), carrying capacity does not directly limit their growth rate, but it does affect detachment. As surface biomass approaches carrying capacity, the density-dependent crowding factor increases detachment, providing an indirect limit on surface biomass accumulation. Growth itself is primarily limited by nutrients and light.

How macrophytes differ from algae

Rooted and floating macrophytes do not participate in the settlement/detachment cycle described above — they are permanently fixed in place and have their own growth and nutrient mechanics. See Macrophytes for the full treatment.

That said, macrophyte leaves are themselves a colonizable substrate for everything else. As Hornwort or Vallisneria grow, their leaves provide an increasing area of soft, well-lit habitat for epiphytic periphyton, nitrifiers, and biofilm bacteria. The model captures this through an aggregated dynamic surface called macrophyte_leaf_surface, whose area = Σ (SLA_cm2_per_mg_C × shoot/stem/frond C) summed across every macrophyte in the scenario. In a dense planted tank this dynamic surface can easily exceed the area of the jar walls and substrate combined by an order of magnitude — see Surfaces for the per-species SLA values, the canopy self-shading machinery, and the list of species that colonize the leaf surface.

Green periphyton: surface-only organisms

Green periphyton are a special case. Unlike all other algae, they have no planktonic pool — they exist only on surfaces.

This means there is no settlement/detachment cycle for green periphyton. Instead, they colonize surfaces through their dispersal mechanism: growth on one surface sends a fraction of new biomass to all other surfaces proportional to area. This is how they spread from surface to surface.

Green periphyton also have a surface-specific detachment/sloughing rate that acts as additional mortality. This rate increases with crowding -- when a surface is densely colonized, more biofilm sloughs off. The crowding effect is modeled as:

detachment mortality = surface detachment rate x (1 + periphyton N / carrying capacity N)

So a surface at half its carrying capacity has 1.5x the base detachment rate, and a surface at full capacity has 2x.

Green periphyton represent the primary food source for grazers. The grazer_access property on each surface determines what fraction of the periphyton there are available to grazers, creating a natural refugia system where some surfaces protect periphyton from being completely consumed.

Surface types and presets

The model provides preset configurations for common substrate types — porous ceramic, smooth ceramic, gravel, sand, glass. Each preset defines roughness, grazer access, detachment rate, and carrying capacity values tuned to the physical characteristics of that substrate. For the full preset tables and property definitions, see Surfaces.

Mortality and detritus routing

When attached algae die, the dead biomass is routed to the detritus pools. The split between suspended detritus (fine particles floating in the water) and settled detritus (debris on the bottom) depends on whether the dead algae were planktonic or surface-attached:

Planktonic mortality uses the species' death_to_suspended_frac parameter (ranging from 10% to 50% suspended depending on species)
Surface mortality sends most dead biomass to settled detritus, since biofilm that sloughs off tends to sink. The exact split varies: green microalgae surface mortality is 20% suspended / 80% settled, and green periphyton are 50/50.

For green periphyton specifically, a fraction of dead biomass (20%) also becomes dissolved organic matter (DOM) from cell lysis, in addition to the detritus fractions.