Surfaces

For a general introduction to the physical environment, see The Environment. Surfaces are what turn a jar of water into a habitat — the rough ceramic, gravel, and leaves that decide who gets to settle, who can hide, and how much life the tank can hold.

Why Surfaces Transform the Ecosystem

A jar of open water supports only planktonic life — free-floating algae, bacteria, and grazers drifting through a homogeneous volume. Add a rough ceramic stick or a bed of gravel, and the ecosystem changes fundamentally. Surfaces create real estate for biofilms, refugia where prey can hide from grazers, and nutrient-enriched boundary layers where attached organisms access concentrations far higher than the open water. The physical structure of the habitat matters as much as its chemistry.

In the model, every surface is a distinct microhabitat. Algae growing on porous ceramic receive different light, face different grazing pressure, and perceive different nutrient concentrations than algae on smooth glass — even though both surfaces sit in the same water. The number, type, and roughness of surfaces in a scenario directly control which species can persist, how much biomass the system supports, and whether grazers can drive their prey to extinction or are held in check by physical refugia.

Static and Dynamic Surfaces

There are two kinds of surface. Static surfaces — ceramic, gravel, sand, glass — have a fixed area: a piece of ceramic or a glass wall is the same size regardless of what grows on it. Dynamic surfaces have an area that grows along with the organisms that create them. The one dynamic surface in the model today is the living leaf surface of the plants: every macrophyte adds leaf area for epiphytes to colonize, so a dense hornwort thicket or a Vallisneria forest can multiply the colonizable area many times over what the jar walls and substrate alone provide.

A scenario can include up to three different static surfaces — typically glass, sand, and perhaps gravel or ceramic — plus the living leaf surface. The algae growing on each surface are tracked separately, because each is a genuinely different place to live.

Surface Properties

Every surface is defined by a handful of properties that together determine what kind of microhabitat it provides. The most intuitive is area. But area alone does not determine how much life a surface supports; that depends on light, texture, and exposure.

Light reaches a surface through two filters. The first is geometry — orientation and obstruction. A surface tucked behind a rock or facing away from the lamp receives only a fraction of the incident light. The second is Beer-Lambert attenuation through the water column above the surface, which depends on the surface's depth below the water line and the density of planktonic algae overhead. Deeper surfaces receive less light, and this effect strengthens as plankton grow denser. Both the growth rate and the maximum biofilm density scale with the light that actually arrives.

Roughness controls how easily algae colonize the surface. Microscopic pits and ridges give cells something to grip, so a rough surface like porous ceramic accumulates biofilm much faster than smooth glass. The boost is steep at first and then levels off — even moderate roughness gives cells a meaningful foothold, and there is little extra gain from making an already-rough surface rougher.

Grazer access determines how much of the biofilm grazers can actually reach. A flat glass wall leaves periphyton fully exposed to copepods and Daphnia, while porous ceramic, or a deliberately protected refuge, hides some fraction away. This is the mechanism that creates refugia — see Refugia for the full story.

Detachment is how fast biofilm naturally sloughs off and re-enters the water column. Smooth surfaces shed biofilm readily; rough ones hold onto it.

Finally, carrying capacity sets the ceiling on biofilm density — the maximum a given surface can support per unit area. Porous ceramic can hold more than twice the film of bare glass, and the effective ceiling also scales with light: a surface in the dark cannot support as much growth as one in full light.

Biofilm maturity tracks the structural complexity of the biofilm on each surface as the tank ages. A freshly submerged surface starts bare and matures over months as bacteria, fungi, and nitrifiers build an EPS scaffold. Maturity determines habitat quality for benthic consumers, the degree of predation protection and light shielding for embedded nitrifiers, and how much shelter the surface provides beyond its bare texture. Grazer scraping partially damages the scaffold and slows maturation. Different surfaces mature at different rates, because detritus accumulation and nitrifier colonization vary from one surface to another. See Biofilm Maturity for the full mechanics.

Surface Types at a Glance

The simulator ships with realistic defaults for the common surface types, which you can override individually. They differ mainly in texture, how much shelter they give prey, and how tenaciously they hold a biofilm:

Surface	Texture	Grazer exposure	Biofilm tenacity	Typical role
Porous ceramic	very rough	mostly exposed, some shelter	sheds slowly, holds a dense film	dense, well-attached biofilms
Smooth ceramic	moderately rough	mostly exposed	moderate	moderate biofilms
Gravel	rough	fairly exposed	moderate	natural substrate
Sand	smooth, shifting	exposed	shifting grains limit growth	thin films
Glass (jar walls)	very smooth	fully exposed	sheds readily	poor colonization
Protected refuge	—	fully sheltered	—	a fully grazer-safe zone

The protected refuge is a special case — biofilm there is completely safe from grazers. It exists for older scenarios built around a simple "some algae are always safe" idea, before surface-by-surface grazer access made refugia an emergent property of texture and maturity.

The exact roughness, detachment, and carrying-capacity values behind each of these are tabulated in the Parameter Reference.

The Living Leaf Surface

The leaf surface behaves differently from the static surfaces because it grows. Its area is the sum of the leaf area contributed by every plant in the tank, so it expands as the plants grow and shrinks as they die back. Plants differ enormously in how much leaf area they offer per unit of mass: feathery, finely-dissected hornwort presents far more colonizable surface than strap-leaved Vallisneria or broad-leaved Cryptocoryne, while floating plants like Salvinia and duckweed offer only their small submerged rhizoids, since their upper surfaces sit in the air. At peak biomass a well-planted tank's leaves can dwarf the jar walls and substrate as living space for epiphytes. The per-plant leaf-area figures live in the Parameter Reference.

Which grazers can reach leaf biofilm. A film growing on a leaf is only as safe as the grazers' ability to climb up and scrape it, and that depends on how each animal feeds. Snails, dwarf shrimp, and amphipods are documented leaf foragers — radula scrapers and pickers that graze epiphytes efficiently (Brönmark 1985; Jones & Sayer 2003; Wallace & Webster 1996). Filter-feeding Daphnia and raptorial, water-column copepods cannot scrape a surface at all and reach only the cells that slough off into the water (Porter et al. 1983; Biggs 1996; Williamson 1980; Williamson & Reid 2009; Lampert 2006). Ostracods fall in between but are primarily sediment dwellers and weak climbers (Smith & Horne 2002; McGregor 1969). The result is that leaf periphyton enjoys real protection from exactly the grazers that dominate the open water:

Grazer	Feeding mode	Reach onto leaf biofilm
Bladder snail	radula scraper	efficient
Cherry shrimp	picker / scraper	good
Amphipod (scuds)	shredder / scraper	good
Ostracod	benthic crawler	limited
Copepod	raptorial, water-column	minimal
Daphnia	filter feeder	minimal — only sloughed cells

Canopy self-shading. A dense planted canopy shades its own leaves. The model reuses each plant's existing self-shading to dim the light reaching its leaf biofilm: with no plants there is no effect, but as the canopy thickens, interior leaves receive much less light than the ones at the top — exactly as in the plant's own photosynthesis. The shade cast from above by floating plants is handled separately, in the surface light that feeds into this calculation, so it is not double-counted.

Which species colonize leaves. Most biofilm-forming organisms will settle on the living leaf surface by default. Two groups are held back because they are water-column specialists, not epiphytes: centric diatoms (the spring-bloom plankton, whose small attached fraction goes to sand and glass instead) and the bloom-forming planktonic cyanobacteria. Mat-forming benthic cyanobacteria still colonize leaves freely — they are the dreaded "blue-green algae on plants" that hobbyists fight.

How Surfaces Interact with the Ecosystem

These properties do not act in isolation — they combine to create a dynamic equilibrium between planktonic and surface-attached life. Roughness controls how fast algae settle onto surfaces; detachment and crowding determine how fast they leave; grazer access decides how much of the biofilm is vulnerable to predation; light and carrying capacity set the ceiling on how much can accumulate; and biofilm maturity adds a temporal dimension — the age of a surface shapes habitat quality, refugia strength, and nitrifier protection in ways the static properties alone cannot capture. The interplay of these forces is what creates the spatial structure of the producer community. For the full mechanics of settlement, detachment, and dispersal, see Algae Settlement and Surface Dynamics.