Macrophytes

Rooted Macrophytes

Rooted macrophytes are vascular aquatic plants whose roots and rhizomes are embedded in the sediment. They differ from all algae 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. All rooted macrophyte species share the same core mechanics and belong to the "rooted_macrophyte" food-chain category, meaning standard algae grazers do not automatically 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.

Core mechanics

The shared rooted macrophyte mechanics cover:

Two biomass pools (shoot and root). This is distinct from the planktonic-plus-surface layout used by algae.
Photosynthesis using shoot biomass and the light available at the attached substrate surface, following the same Michaelis-Menten kinetics used by all other producers (light limitation, CO2/HCO3 limitation, N and P limitation via Liebig's law of the minimum, carbon storage feedback, and photorespiration).
Dual-source nutrient uptake: rooted macrophytes draw nitrogen and phosphorus from two independent sources -- the water column (via leaves) and pore water (via roots) -- each with its own Michaelis-Menten kinetics. A species-level parameter sets the fraction of uptake capacity allocated to each pathway (the two fractions sum to 1.0). The combined nutrient limitation factor is a weighted sum of the two pathways' Michaelis-Menten terms. The two pathways have separate half-saturation constants reflecting different transporter biology. Leaf uptake from the water column uses lower-affinity constants (half-saturation for N around 10-15 umol/L, for P around 0.3-0.5 umol/L), typical of general-purpose membrane transporters. Root uptake from pore water uses higher-affinity constants roughly 5 times lower (half-saturation for N around 2 umol/L, for P around 0.05-0.1 umol/L), reflecting specialized high-affinity root transporters (system I; Epstein & Hagen 1952; Caffrey & Kemp 1992). This means roots can scavenge nutrients efficiently even from dilute pore water, while leaves require higher water-column concentrations to achieve the same uptake rate. A critical detail: root uptake capacity scales with root biomass, while leaf uptake scales with shoot biomass. A plant with a large root system and small shoots draws most of its nutrients from pore water; a plant with lush shoots but undeveloped roots relies more on the water column. This coupling between biomass allocation and nutrient access creates emergent establishment dynamics (see Establishment proxy below). The actual uptake from each source is demand-limited: the plant computes its total N and P demand from photosynthetic carbon fixation, then draws from water and pore proportional to each pathway's capacity. If total capacity exceeds demand, uptake is scaled down; if demand exceeds capacity, growth is nutrient-limited. In non-soil scenarios where pore water pools are empty, leaf uptake is automatically set to 100% so the plant behaves as a pure water-column feeder. Species vary substantially in their uptake partition: Cryptocoryne is heavily root-dependent (80% root, 20% leaf), reflecting its ecology as a slow-growing, shade-tolerant plant that invests in a dense root system to exploit rich sediment. Vallisneria is more balanced (55% root, 45% leaf), consistent with its faster growth and longer leaves that intercept more water-column nutrients. Both species also draw CO2 from pore water via root aerenchyma (70% for Cryptocoryne, 30% for Vallisneria), bypassing the pH-dependent bulk-water carbonate equilibrium -- this is a major advantage in Walstad-style tanks where soil CO2 concentrations can be 10-70 times higher than the water column.
Carbon allocation to roots: a fixed fraction of gross carbon fixation (typically 25%) is translocated to root biomass each timestep via phloem. Complementary N/P follows the root C:N:P stoichiometry (Lambers et al. 2008).
Root respiration: scales with root biomass, temperature (Q10), and O2 availability.
Shoot mortality with stress multipliers: low O2 triggers a 3x mortality increase; pH outside the tolerable range triggers a 2x increase. Dead shoot biomass becomes settled detritus.
Root turnover: a species-specific fraction of root biomass dies each hour. Dead root biomass enters the labile soil organic matter pool, feeding soil bacteria.

Establishment proxy: root biomass implicitly represents the degree of plant establishment. Pore-water uptake capacity scales linearly with root biomass, so a newly planted crown with a small root system draws less pore-water N and P than an established plant, even in equally rich substrate. As root biomass grows, uptake increases, enabling faster shoot growth -- an emergent sigmoid growth curve matching real tank observations.

Maintenance-to-photosynthesis ratio. All macrophytes follow a fundamental scaling rule: the maintenance respiration rate must be a fixed fraction of the maximum photosynthesis rate, typically 10-15%. This ratio ensures that a species can achieve net positive carbon balance under realistic light conditions. If maintenance is too high relative to the maximum photosynthesis rate, the plant cannot photosynthesize fast enough to cover its respiratory costs and slowly starves even in good light. If maintenance is too low, the plant accumulates unrealistic biomass because respiratory losses are negligible. Across all macrophyte species, this ratio is tightly constrained: Cryptocoryne and Vallisneria use 12.5%, Salvinia, duckweed, and hornwort use 10%, and the floating macrophyte default is 15%.

Retranslocation gap: carbon flows only from shoot to root (phloem). The reverse pathway -- mobilising rhizome carbohydrate reserves to support shoot growth during low-light periods or after trimming -- is not modelled. This means the model represents the "establishing, no reserves" condition. To approximate an established plant with substantial rhizome reserves, seed the simulation with more initial biomass in roots relative to shoots, or pre-run the simulation for several months.

Key literature:

Barko, J.W. & Smart, R.M. (1985). Ecol. Monogr., 55, 63-78. [sediment nutrient dominance; root biomass scales uptake]
Barko, J.W., Gunnison, D. & Carpenter, S.R. (1991). Aquat. Bot., 41, 41-65. [sediment-macrophyte review]
Carignan, R. & Kalff, J. (1980). Science, 207, 987-989. [60-90% P from sediment]
Caffrey, J.M. & Kemp, W.M. (1992). Limnol. Oceanogr., 37, 1483-1495. [root N uptake kinetics]
Chambers, P.A. & Kalff, J. (1985). Can. J. Fish. Aquat. Sci., 42, 701-709. [growth rates vs. algae]
Epstein, E. & Hagen, C.E. (1952). Plant Physiol., 27, 457-474. [high-affinity root transporters]
Lambers, H., Chapin, F.S. & Pons, T.L. (2008). Plant Physiological Ecology, 2nd ed. Springer.

Rooted species

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. All floating macrophytes belong to the "floating macrophyte" species category, meaning standard algae grazers do not consume them.

Core mechanics

The shared floating macrophyte mechanics cover:

Canopy light: floating plants receive pre-canopy schedule light (before any submerged attenuation) and compute Beer-Lambert self-shading using their own frond biomass and the tank surface area. This is independent of the submerged light pipeline (see environment/light_and_temperature.md).
Canopy transmittance: the combined optical depth across all floating species determines how much light reaches submerged organisms. This is automatic -- submerged species are shaded without any special configuration.
Surface coverage limit: a maximum fractional surface coverage parameter controls density-dependent growth suppression. As coverage approaches the maximum, the carbon available for new frond growth is linearly suppressed; blocked carbon is excreted as labile DOM. Default is unlimited; Salvinia overrides to 95%.
Nutrient uptake: water-column NH4, NO3, and PO4 only, via Michaelis-Menten with high-affinity constants (half-saturation for N around 4 umol/L, matching values from Cedergreen & Madsen 2002 for Lemna minor).
Mortality routing: 90% settled detritus, 10% suspended detritus (dead fronds sink).

Floating species

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.

Shared mechanics:

Biomass pool: a single stem pool (tracking carbon, nitrogen, and phosphorus).
Light: Beer-Lambert attenuation to the stem depth, including planktonic algae, submerged stem biomass, refractory DOM, and background attenuation.
Water-column shading: submerged stem biomass contributes to Beer-Lambert attenuation for all deeper organisms each timestep.
Nutrient uptake: NH4, NO3, PO4 from water column only; Michaelis-Menten kinetics with half-saturation for N around 5 umol/L.
Mortality routing: 30% suspended detritus, 70% settled detritus.

Submerged species

Hornwort (Ceratophyllum demersum)