Biofilm Nutrient Enrichment

For the physical properties of surfaces (roughness, carrying capacity, grazer access), see Surfaces. For how organisms move between planktonic and surface-attached states, see Algae Settlement and Surface Dynamics. For a general introduction to the physical environment, see The Environment.

Why Surface Organisms Live in a Different Chemical World

A diatom stuck to a grain of sand does not experience the same water as a diatom floating in the open column. In any real aquatic system, a thin layer of slow-moving water clings to every submerged surface — the diffusion boundary layer (DBL), typically tens to hundreds of micrometres thick. Nutrients released within this layer — from decomposing detritus below, from bacterial activity in the biofilm, from pore water seeping upward through the sediment — do not instantly mix into the bulk water. They linger long enough for attached organisms to intercept them before dilution carries them away. A planktonic alga floating past the same spot sees only the well-mixed bulk concentration. The result is that surface-attached organisms can perceive nitrogen concentrations 5 to 50 times higher than what a probe measuring the open water would report.

This enrichment effect is why biofilms dominate nutrient-poor systems. It explains why diatoms bloom on surfaces weeks before planktonic algae take off, why periphyton can sustain dense growth even when water-column nitrogen is nearly undetectable, and why the classic diatom-to-periphyton succession unfolds on surfaces rather than in open water. Without modeling this enrichment, surface-attached growth would be chronically underestimated.

The model captures this asymmetry explicitly. Every surface in the simulation has an enrichment value — an extra nitrogen concentration that surface-attached organisms "perceive" on top of the bulk water nitrogen. The enrichment comes from three distinct sources, each representing a real physical mechanism.

How the Model Handles Enrichment

The model uses a perceived concentration approach. Enrichment increases the effective nitrogen concentration that surface-attached organisms use when calculating their growth limitation (the Monod saturation factor), but it does not change where the actual nitrogen comes from. When a surface diatom grows faster because of enrichment, the nitrogen it incorporates still comes out of the bulk water pools (NH4 and NO3 in the water column). No separate "enriched nitrogen pool" exists in the state vector.

This preserves mass balance by construction: the total nitrogen in the system is unaffected by enrichment. What enrichment changes is growth rate, not mass. It models the ecological reality that surface organisms grow faster because they sit in a nutrient-rich microenvironment, while the ultimate source of those nutrients is still the same dissolved pool that the ODE integrator tracks.

The enrichment for each surface is computed once per timestep, before any species calculates its growth, so all organisms on a given surface see the same enrichment value for that step.

Three Sources of Enrichment

Each surface's total enrichment is the sum of three independent sources. Not every source contributes to every surface -- pore water enrichment only matters for benthic surfaces over soil, for instance. The sources add linearly.

Source A: Settled Detritus Mineralization

Dead organic matter that settles on the bottom decomposes, releasing ammonium into the surrounding water. In the DBL, this locally released ammonium has not yet diffused away, so organisms on nearby surfaces experience elevated nitrogen.

The enrichment from this source depends on two things: how much settled detritus is present (more detritus means more mineralization), and how active the heterotrophic bacteria are (bacteria drive decomposition, so low bacterial biomass means slow mineralization regardless of how much detritus is available).

Bacterial activity follows Monod saturation with a half-saturation constant of about 0.01 mmol C/L. Below this concentration, enrichment from detritus mineralization is weak; above it, enrichment saturates and further bacterial growth adds little. The scaling factor converting detritus nitrogen density into enrichment concentration is 8.0.

Only surfaces with a benthic component benefit from this source -- a vertical glass wall far from the substrate receives no detritus mineralization enrichment, while a horizontal sand bed receives the full amount.

Source B: Pore Water Proximity

In scenarios with a soil substrate, the pore water trapped between soil particles is much richer in dissolved nitrogen than the overlying water column. Pore water ammonium and nitrate concentrations can be ten or more times higher than bulk water values, because soil organic matter continuously mineralizes within the sediment.

Organisms on benthic surfaces intercept some of this nitrogen as it diffuses upward through the substrate. The model treats this as a blending: the surface organism perceives 20% of the difference between pore water nitrogen and bulk water nitrogen (alpha = 0.20), scaled by the surface's benthic fraction. If pore water nitrogen is lower than bulk water nitrogen (rare, but possible early in a simulation), this source contributes nothing.

This source is only active when the scenario includes a soil substrate with pore water. In non-soil scenarios (bare glass jars, gravel-only setups), Source B is always zero.

Source C: Local Nitrification

Nitrifying bacteria that live on surfaces oxidize ammonium to nitrate as part of their metabolism. Some of the nitrate they produce lingers in the DBL before diffusing into the bulk water, effectively enriching the local nitrogen pool for any algae growing on the same surface.

The model estimates the local nitrification rate from the surface-attached nitrifier biomass, the bulk ammonium concentration (with a half-saturation of 0.025 mmol N/L), and the dissolved oxygen concentration (half-saturation 0.03 mmol O2/L). A retention factor of 5.0 converts the nitrification rate into a local enrichment concentration -- this represents the fraction of produced nitrate that is "trapped" in the DBL long enough for co-located algae to benefit.

This creates an ecologically important positive feedback: nitrifiers colonize a surface, their activity enriches the local nitrogen environment, which helps algae grow faster on that surface, which produces more organic matter when those algae die, which feeds the nitrifiers. The feedback is self-limiting because the nitrifiers' own growth is capped by ammonium and oxygen supply.

Enrichment Cap

To prevent unrealistic runaway during early transients (when bulk water nitrogen might be very low but some enrichment sources are already active), total enrichment on any surface is capped at 50 times the bulk water nitrogen concentration. In practice this cap rarely binds -- it serves as a safety valve during the first hours of a simulation before nutrient pools have equilibrated.

Which Organisms Benefit

Three types of surface-attached organisms use enrichment in their growth calculations:

Diatoms compute enrichment independently for each surface they occupy. On a nutrient-rich sand surface, diatom growth may be barely nitrogen-limited, while on a glass wall far from the substrate, the same diatom community can be strongly nitrogen-limited. Planktonic diatoms (floating in the water column) receive no enrichment.

Benthic green algae (periphyton) use the same approach -- each surface's enrichment modifies the Monod nitrogen factor for the local periphyton population. Like diatoms, planktonic green algae receive no enrichment.

Surface-attached nitrifiers use enrichment to boost their effective ammonium substrate concentration. This is both input and output for Source C: nitrifiers produce local nitrate enrichment, and they also benefit from any local ammonium enrichment (from Sources A and B). This bidirectional interaction is one reason nitrifiers preferentially establish on surfaces rather than in the water column.

All planktonic organisms -- whether algae, bacteria, or consumers -- see only the bulk water nutrient concentrations and are unaffected by surface enrichment.

Ecological Consequences

Biofilm enrichment has several important effects on ecosystem dynamics:

Surface heterogeneity. Different surfaces in the same scenario can have very different enrichment levels. A sand bed over active soil may be heavily enriched from all three sources, while a vertical glass wall far from the substrate receives only Source C (and only if nitrifiers have colonized it). This drives spatial structure in the biofilm community.

Diatom-to-periphyton succession. In scenarios with both diatoms and benthic green algae, enrichment helps sustain a large early diatom bloom on surfaces by relaxing nitrogen limitation. The diatoms grow fast, consume dissolved silica, and eventually crash from silica depletion. The periphyton, which do not need silica, then fill the vacant surface space. Without enrichment, the initial diatom bloom would be smaller and the succession less dramatic. See Silicon Cycle for details on silica limitation.

Nitrifier establishment. Biofilm enrichment (combined with reduced predation and light on surfaces) helps explain why nitrifying bacteria in aquaria are overwhelmingly surface organisms. The model reproduces the real-world pattern: planktonic nitrifiers decline during the first weeks as predation and photoinhibition suppress them, while surface populations slowly build on glass, sand, and ceramic until the biological filter is established.