Macrophytes: Aquatic Plants

For a summary introduction, see producers.md.

Why Macrophytes Play by Different Rules

Macrophytes are the only organisms in the model that bridge two worlds. Their leaves photosynthesize in the water column while their roots mine the sediment for nutrients — tapping pore water pools of nitrogen, phosphorus, and CO₂ that are invisible to every other producer. This dual access fundamentally changes their ecological role. An algal bloom crashes when water-column nutrients run out; a rooted Cryptocoryne barely notices, drawing 80% of its nitrogen from the soil below.

But this advantage comes with a cost. Macrophytes invest heavily in structural carbon — cell walls, vascular tissue, rhizome storage — so their maximum growth rate per unit biomass is 10 to 100 times lower than microalgae. They cannot outcompete algae in a sprint. Instead, they win by persistence: slow, steady growth fueled by a nutrient source that algae cannot reach, combined with shading that suppresses the algae growing above them. In a Walstad-style planted tank, this slow-and-steady strategy is the foundation of long-term stability.

Rooted macrophytes

Rooted aquatic plants (Cryptocoryne, Vallisneria) are fundamentally different from all algae. Three structural differences set them apart.

Two biomass pools instead of one

Every rooted macrophyte tracks shoot biomass (leaves and stems above the substrate) and root biomass (roots and rhizomes buried in the sediment) as separate pools with separate carbon-to-nitrogen-to-phosphorus ratios. Carbon flows from shoot to root via phloem translocation: a fixed fraction of gross carbon fixation (typically 25%) is moved to the root pool each hour (Lambers et al. 2008). Root biomass has its own slower respiration and turnover rate.

This split is ecologically meaningful: roots consume photosynthate to stay alive, and root death returns organic matter directly to the soil as fresh labile root debris rather than to the water column.

Dual nutrient sources

Algae take up all their nitrogen and phosphorus from the overlying water. Rooted macrophytes draw nutrients from two sources simultaneously:

Water column (via leaves): Low-affinity Michaelis-Menten uptake of NH4, NO3, and PO4 from the bulk water. Leaf transporters are not as specialised as root transporters because the water column is generally less concentrated and more uniform.
Pore water (via roots): High-affinity uptake of NH4, NO3, and PO4 from the interstitial water within the sediment. Root transporters (high-affinity system I, Epstein & Hagen 1952) have much lower half-saturation constants -- they are built to extract nutrients from a locally depleted, diffusion-limited environment. This is the dominant pathway for most Walstad-tank species: typically 60-90% of phosphorus and 50-80% of nitrogen comes from sediment pore water (Barko & Smart 1985; Carignan & Kalff 1980).

The split between these two sources is set by species-specific fractions that sum to 1.0. If no soil layer is configured in the scenario, the model automatically falls back to water-column-only uptake.

Much slower growth

Macrophytes invest heavily in structural carbon: cell walls, vascular tissue, and rhizome storage. As a result, their maximum photosynthetic rate per unit biomass is 10 to 100 times lower than microalgae. A healthy Cryptocoryne might double in biomass over several months, whereas green microalgae (Scenedesmus, Chlorella, etc.) can double in less than a day (Chambers & Kalff 1985). This slow growth is also why macrophytes are not a major short-term food source for grazers -- their structural carbon makes them energetically expensive to digest relative to soft algal cells.

Because maximum photosynthesis is so much lower than in algae, maintenance respiration must also be proportionally lower. If maintenance respiration 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.

Establishment dynamics and root biomass as a proxy

The model has no explicit "establishing" vs "established" state flag, but root carbon biomass serves as an implicit proxy for establishment. Pore-water nutrient uptake capacity scales directly with root biomass:

pore uptake capacity = root uptake fraction × maximum nitrogen uptake rate × [nutrient saturation] × root carbon biomass

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 via the root allocation fraction -- a positive feedback loop that produces the characteristic sigmoid growth curve of an establishing macrophyte: slow in the first months, accelerating once roots are established.

Root biomass also controls a second, indirect mechanism: rhizosphere interception of nutrients diffusing upward through the substrate. Root tissue physically obstructs diffusion pathways, root-released O₂ drives coupled nitrification-denitrification in the surrounding soil, and root exudates stimulate microbial immobilisation of dissolved nutrients. Together, these processes can intercept up to ~50% of the raw Fickian flux at saturating root density (Caffrey & Kemp 1992; Wigand et al. 1997). This means an established root system not only feeds the plant directly but also starves the water column of pore-derived nutrients that would otherwise fuel algal growth. See Soil and Pore Water: Rhizosphere Interception for the full model.

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. This is biologically correct and is captured correctly by the model.

What the model does not capture: carbon retranslocation from root to shoot. An established macrophyte can mobilise carbohydrate reserves stored in its rhizome to push out new leaves during low-light periods, after trimming, or during stress recovery. The model only allows carbon to flow shoot → root, never the reverse. As a result, the model always represents the "no reserves" condition. To simulate a more established plant, seed with a larger initial root biomass or pre-run the scenario for 6-12 months.

Pore water CO2 access

In soil-substrate scenarios, aerobic decomposition of organic matter produces CO2 that accumulates in sediment pore water. This pore CO2 reservoir can reach 200–1000 µmol/L — an order of magnitude above the bulk water column (~14 µmol/L at atmospheric equilibrium in an open tank). For rooted macrophytes that rely on dissolved CO2 (rather than bicarbonate), this difference is critical: at pH 8, roughly two-thirds of bulk-water DIC is bicarbonate, making free CO2 scarce for species without a carbon-concentrating mechanism.

The model handles this through three steps:

Soil mineralization produces CO2 that goes into the pore water pool rather than directly into the water column — reflecting the reality that CO2 is generated in the sediment, not at the water surface.
Fickian diffusion transports pore CO2 to the bulk water column along the concentration gradient, passing through the soil matrix and sand cap in series. CO2 diffuses ~2.8× faster than NH4 in free water (Jähne et al. 1987), so back-diffusion carries excess pore CO2 upward continuously.
Macrophyte direct uptake: each rooted macrophyte species draws a species-specific fraction (the root CO₂ uptake fraction) of its photosynthetic CO2 directly from pore water via root aerenchyma, bypassing the substrate diffusion path entirely. The effective CO2 available for photosynthesis is a weighted blend of bulk-water and pore-water CO2.

In scenarios without soil substrate, the pore CO2 pool stays at zero and macrophytes automatically fall back to bulk-water CO2 only.

References: Walstad (1999); Smits et al. (1990); Jähne et al. (1987).

Light and canopy depth

Photosynthesis uses the light available at the plant's attached substrate surface (the same calculation used for green periphyton). For sand or gravel surfaces, this is computed at the surface depth, which represents the bottom of the tank.

For rosette plants like Cryptocoryne, whose leaves reach up through the water column, the effective canopy intercepts light at mid-column depth, not at substrate depth. In scenarios with tall water columns, the surface depth should be set to the approximate midpoint of the leaf canopy (e.g. ~10 cm for a Crypt with 10 cm leaves in a 25 cm column), not to the tank floor. The light fraction can also be increased slightly to reflect that leaves project outward from the substrate rather than lying flat against it.

Water-column shading

Tall rooted macrophytes do not just receive light -- they also block it. A dense Vallisneria bed, with strap-shaped leaves extending from substrate to surface, intercepts a significant fraction of incoming light before it can reach planktonic algae or benthic surfaces below. Short rosette plants like Cryptocoryne, whose leaves stay near the substrate, have no meaningful shading effect and are excluded from this calculation.

The model captures this through two complementary mechanisms (see Light and Temperature: Rooted Macrophyte Canopy Shading for the full light-model perspective):

Canopy transmittance shades planktonic organisms. Each tall species contributes a leaf area index (LAI) based on its shoot carbon per unit of tank surface area. Light transmittance through the canopy follows Beer-Lambert: transmittance = exp(-k_canopy × shoot_C / tank_area). This is the same approach used by floating macrophytes, and the two canopy layers stack multiplicatively -- a tank with Salvinia on the surface and Vallisneria below will shade planktonic algae from both directions.

Depth attenuation shades benthic organisms. Shoot tissue in the water column also attenuates light reaching surfaces at depth (periphyton, benthic diatoms). The model converts shoot carbon to an equivalent planktonic algae concentration based on the ratio of the species' shoot attenuation coefficient to the phytoplankton attenuation coefficient, then includes it in the standard Beer-Lambert depth calculation used by surface_light().

Neither mechanism affects the macrophyte's own light -- the plant receives light at its configured surface depth via the normal surface light calculation, avoiding self-shading artifacts.

Species-specific parameters:

Species	k_canopy (m²/mol C)	k_shoot_atten (per mol C/L)	Shading role
Vallisneria	0.45	40.0	Tall canopy-former; shades planktonic and benthic algae
Cryptocoryne	0.0	0.0	Short rosette; no water-column shading

Vallisneria's canopy coefficient is derived from a specific leaf area of ~0.9 m² per mol C and a canopy extinction of ~0.5 per unit LAI (Titus & Adams 1979; Sand-Jensen 1998). The depth attenuation coefficient (40.0) is about 13% of the phytoplankton value (300), reflecting that strap-shaped leaves are less optically dense per unit carbon than a suspension of unicellular algae.

This shading is a key mechanism in the transition from algae-dominated to plant-dominated conditions. As a Vallisneria bed establishes and shoot biomass accumulates, the canopy progressively reduces the light available to competing algae -- both in the water column and on surfaces. Combined with root-mediated nutrient interception from pore water, this produces the "clear water" stable state characteristic of healthy planted aquaria (Scheffer et al. 1993; Walstad 1999).

Mortality routing

Shoot mortality (senescence, stress) → settled detritus (leaf litter on the substrate)
Root turnover → soil organic matter labile pool. Dead fine roots are a labile organic matter input that feeds soil bacteria -- a key component of the Walstad nutrient cycle.

Stress responses

Hypoxia (O2 below ~2 mg/L): shoot mortality increases 3×
Extreme pH (outside species-specific stress range): shoot mortality increases 2×

Implemented species

Cryptocoryne wendtii -- slow-growing, shade-tolerant, relies entirely on dissolved CO2 (no bicarbonate use), and strongly substrate-dependent (80% of nutrient uptake from roots). The primary beneficiary of pore CO2: about 70% of its photosynthetic carbon comes from sediment pore water in Walstad scenarios, which dramatically improves CO2 availability compared to relying on the bulk water column alone. See Species Catalog.
Vallisneria spiralis -- fast-growing (about 3× Cryptocoryne's growth rate), light-demanding, and an active bicarbonate user (about 40% of carbon uptake can come from bicarbonate). More balanced between water-column and root uptake (55% from roots). Tolerates alkaline water well. Forms a tall leaf canopy that shades the water column as it establishes (see Water-column shading above). See Species Catalog.

References

Barko, J.W. & Smart, R.M. (1985). Laboratory study of sediment-related factors affecting aquatic plant development. Ecol. Monogr., 55, 63-78.
Caffrey, J.M. & Kemp, W.M. (1992). Influence of the submersed plant Potamogeton perfoliatus on nitrogen cycling in estuarine sediments. Limnol. Oceanogr., 37, 1483-1495. [rhizosphere interception of pore-water NH4]
Carignan, R. & Kalff, J. (1980). Phosphorus sources for aquatic weeds: water or sediments? Science, 207, 987-989.
Chambers, P.A. & Kalff, J. (1985). Depth distribution and biomass of submersed macrophyte communities. Can. J. Fish. Aquat. Sci., 42, 701-709.
Epstein, E. & Hagen, C.E. (1952). A kinetic study of absorption of alkali cations by barley roots. Plant Physiol., 27, 457-474.
Jähne, B. et al. (1987). On the parameters influencing air-water gas exchange. J. Geophys. Res., 92, 1937-1949. [CO2(aq) diffusion coefficient]
Lambers, H., Chapin, F.S. & Pons, T.L. (2008). Plant Physiological Ecology, 2nd ed. Springer.
Sand-Jensen, K. (1998). Influence of submerged macrophytes on sediment composition and near-bed flow in lowland streams. Freshw. Biol., 39, 663–679. [SLA and light attenuation by submerged leaf canopies]
Scheffer, M., Hosper, S.H., Meijer, M.-L., Moss, B. & Jeppesen, E. (1993). Alternative equilibria in shallow lakes. Trends Ecol. Evol., 8, 275–279. [macrophyte-dominated clear-water stable state]
Smits, A.J.M., van Avesaath, P.H. & van der Velde, G. (1990). Carbonate chemistry and the availability of CO2 and HCO3 for Potamogeton pectinatus in sediments. Aquat. Bot., 38, 345-362. [pore CO2 as macrophyte C source]
Titus, J.E. & Adams, M.S. (1979). Coexistence and the comparative light relations of the submersed macrophytes Myriophyllum spicatum L. and Vallisneria americana Michx. Oecologia, 40, 273–286. [canopy extinction for Vallisneria beds]
Walstad, D.L. (1999). Ecology of the Planted Aquarium. Echinodorus Publishing. [pore CO2 mechanism in low-tech planted tanks]
Wigand, C., Stevenson, J.C. & Cornwell, J.C. (1997). Effects of different submersed macrophytes on sediment biogeochemistry. Aquat. Bot., 56, 233-244. [root exudate-driven microbial immobilisation of pore-water N]

Floating macrophytes

Floating macrophytes are vascular plants that live at the air-water interface. Unlike algae (which float in the water or attach to surfaces) and rooted macrophytes (which anchor to the substrate), floating plants rest on the water surface and draw all their nutrients from the overlying water column. Standard algae grazers do not consume them.

Single biomass pool

Each floating macrophyte tracks a single frond biomass pool (carbon, nitrogen, phosphorus) that lives at the water surface. There is no shoot/root split and no sediment access.

Water-column-only nutrient uptake

Nutrients are absorbed from the water through frond undersides and root-hair-like filaments. Floating plants have high maximum uptake rates and very low half-saturation constants (~4 µmol N/L), resembling the high-affinity transport system characterised for small floating aquatics (Cedergreen & Madsen 2002). This gives floating plants a strong advantage in scavenging dilute NH4 pulses from spiked substrates.

Canopy shading

Floating macrophytes intercept light at the water surface before it enters the water column. As frond biomass accumulates, the mat becomes progressively more opaque following Beer-Lambert attenuation. The model computes the average light across the mat depth — fronds near the top intercept the most light, while fronds deeper in the mat get progressively less. As the mat thickens, the average light per frond decreases toward zero, slowing growth. This is the same Beer-Lambert layer-averaging used for dense surface mats of filamentous algae (see photosynthesis.md).

Simultaneously, the floating canopy reduces light reaching all submerged organisms. The model sums the optical depths of all floating plant species, computes a single canopy transmittance, and applies it to the light before it reaches any submerged species. Adding Salvinia to a scenario will shade Cryptocoryne and Vallisneria — exactly what happens in a real tank where floating plants compete with submerged plants for light.

Surface coverage limit

Beer-Lambert self-shading slows but does not fully stop growth at high density. A separate spatial carrying capacity provides a hard cap: as surface coverage approaches a species-specific maximum (Salvinia: 95%, duckweed: 90%), new frond growth is suppressed to zero and excess fixed carbon is excreted as dissolved organic matter. Maintenance respiration and mortality continue unaffected at full cover, so the mat biomass declines slowly if it reaches the cap.

How each species interacts with the spatial cap differs. Some species (like Salvinia) compete for space based on the combined coverage of all floating plants. Others (like duckweed) count only their own coverage, reflecting the biology of small-frond species that can grow in the interstices between larger floating fronds.

Interspecific competition

When multiple floating species co-occur at high combined coverage, slower-growing species are displaced by faster-growing competitors. The faster-growing species pushes slower-growing fronds under the mat, where they die from lack of light — a mechanism observed in field and aquarium comparisons of Lemna versus Salvinia (Landolt 1986; Skillicorn et al. 1993). The fastest-growing species receives no displacement pressure.

Air-water gas exchange suppression

A floating mat is also a physical lid on the water surface. The wind-driven and convective surface-renewal turbulence that drives air-water gas exchange is suppressed under the mat — fronds break the wave structure, hold a static boundary layer, and (for tightly-contacting species like Lemna) directly cover the meniscus. The model captures this by multiplying the liquid-side kLa for every air-water gas channel (O₂, CO₂, NH₃, H₂S, CH₄) by a community-wide blocking factor that depends on the cover fraction and on each species' physical mat structure.

Each floating species declares a kLa_block_at_full_cover parameter — the local fraction by which a fully-occupied square metre of its mat reduces surface-renewal kLa. Defaults reflect mat geometry: Salvinia is set to 0.70 (hydrophobic trichomes lift the fronds slightly clear of the meniscus and the mat is more porous), and duckweed (Lemna) is set to 0.92 (small flat fronds in tight contact with the water form a near-continuous lid). Field studies of choked tanks report O₂ transfer at ~25–40% of open-water values under a Salvinia mat (Janes 1998; Mitchell & Tur 1975) and ~5–15% under a dense Lemna mat (Pokorný & Rejmánková 1983; Morris & Barker 1977).

When multiple floating species co-occur, the community-wide kLa multiplier weights each species' blocking efficacy by its share of the combined optical depth. The result is that a half-Salvinia / half-duckweed mat at 80% cover gas-blocks more than the same Salvinia density alone, and less than the same duckweed density alone — proportional to which species is contributing more frond cover. The same multiplier is applied to all five gas channels because they all depend on the same underlying surface-renewal rate.

This is what makes a "duckweed taking over my tank" scenario actually suffocate at night: photosynthetic O₂ at the surface is being released to the atmosphere via aerial frond surfaces (not into the water), and the dominant night-time resupply path — atmospheric exchange across the meniscus — is now choked. CO₂ produced by respiration also accumulates in the water rather than venting, dropping pH; NH₃ venting is similarly suppressed, although the pH drop usually pulls dissolved NH₃ down at the same time, so net NH₃ exposure can move in either direction depending on which effect dominates.

Ecological role: early NH4 spike control

In Walstad-style planted aquarium scenarios, labile soil organic matter mineralises rapidly in the first 3–6 months, releasing ammonium faster than slow-growing rooted macrophytes can absorb it. Floating plants — introduced as a small starter cluster on day 3 — grow at ~4–5 day doubling times and scavenge water-column NH4 aggressively. In simulation tests, introducing Salvinia at 0.5 mg N on day 3 reduced water-column NH4 by 3× (1.80 → 0.61 mg N/L at day 180). This matches the approach described by Walstad (1999, ch. 5) and the practical experience of the planted aquarium community.

Mortality routing

Dead fronds mostly sink: about 10% becomes suspended detritus and 90% settles, reflecting the size and density of floating fronds.

Implemented species

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

References

Cedergreen, N. & Madsen, T.V. (2002). Nitrogen uptake by the floating macrophyte Lemna minor. New Phytol., 155, 285-292.
Hillman, W.S. (1961). The Lemnaceae, or duckweeds. Bot. Rev., 27, 221–287.
Landolt, E. (1986). The family of Lemnaceae — a monographic study. Veröff. Geobot. Inst. ETH, Zürich, 71, 1–566.
Lemon, G.D. & Posluszny, U. (2000). Comparative shoot development and evolution in the Lemnaceae. Int. J. Plant Sci., 161, 733-748.
Skillicorn, P., Spira, W. & Journey, W. (1993). Duckweed Aquaculture. World Bank Technical Paper No. 239.
Walstad, D.L. (1999). Ecology of the Planted Aquarium. Echinodorus Publishing.
Janes, R. (1998). Growth and survival of Azolla filiculoides in Britain. New Phytol., 138, 367–375.
Mitchell, D.S. & Tur, N.M. (1975). The rate of growth of Salvinia molesta (S. auriculata Auct.) in laboratory and natural conditions. J. Appl. Ecol., 12, 213–225.
Pokorný, J. & Rejmánková, E. (1983). Oxygen regime in a fishpond with duckweeds (Lemnaceae) and Ceratophyllum. Aquat. Bot., 17, 125–137.
Morris, P.F. & Barker, W.G. (1977). Oxygen transport rates through mats of Lemna minor and Wolffia sp. and oxygen tension within and below the mat. Can. J. Bot., 55, 1926–1932.

Submerged macrophytes

Submerged macrophytes are vascular plants that live fully inside the water column — neither rooted in sediment (no pore-water access) nor floating at the surface (no canopy mechanics). Standard algae grazers do not consume them.

Single biomass pool

Each submerged macrophyte tracks a single stem biomass pool (carbon, nitrogen, phosphorus). There is no shoot/root split, no pore-water access, and no surface canopy.

Depth-specific light

Unlike planktonic algae (which see a depth-averaged light) and floating plants (which intercept light at the surface), submerged macrophytes receive light computed via Beer-Lambert attenuation at their actual depth in the water column. The light reaching a stem depends on the post-canopy surface light, the planktonic algae concentration above it, any co-occurring submerged macrophyte stems (see Water-column shading below), refractory DOM concentration, and the stem's depth. A stem positioned at 10 cm depth in a turbid or algae-laden tank receives substantially less light than one at 5 cm.

Water-column-only nutrient uptake

Submerged macrophytes absorb NH4, NO3, and PO4 exclusively from the water column via Michaelis-Menten kinetics with low half-saturation constants (~5 µmol N/L). Pore water is never accessed, consistent with the absence of true roots (Nichols & Shaw 1986; Barko & Smart 1981).

Bicarbonate use (CCM)

Many submerged macrophytes possess a strong carbon concentrating mechanism that allows them to strip dissolved bicarbonate (HCO3⁻) from the water, raising pH and consuming alkalinity in the process. Hornwort has one of the highest bicarbonate-use efficiencies among freshwater macrophytes (~45% of its carbon uptake can come from bicarbonate), consistent with measurements by Prins & Elzenga (1989) and Van Ginkel et al. (2001).

Water-column shading

Unlike rooted or floating plants, submerged macrophyte stems scatter and absorb light within the water column itself — shading periphyton on surfaces and organisms below them. The model converts stem biomass into an equivalent planktonic-algae concentration that produces the same light attenuation per metre, then adds this to the Beer-Lambert calculation. This automatically shades surfaces at depth and co-occurring submerged stems below the species' own position.

Hornwort's stem-specific light attenuation is approximately 40% of the phytoplankton coefficient per unit carbon, reflecting that branching stems intercept light less efficiently than dense unicellular suspensions (Vestergaard & Sand-Jensen 2000; Spence 1975).

Mortality routing

Dead stem material splits into about 30% suspended detritus and 70% settled detritus. This is intermediate between planktonic algae (which disperse widely in the water column) and floating plants (which mostly sink directly). Hornwort fragments are well-known vegetative propagules; the suspended fraction models this dispersal capacity (Best 1977; Nichols & Shaw 1986).

Stress responses

The same temperature, salinity, pH, and O2 stress responses as other producers apply. As with rooted macrophytes, maintenance respiration must be proportional to the maximum photosynthesis rate (roughly 10-15% of it), otherwise the plant cannot achieve positive net growth.

Implemented species

Hornwort (Ceratophyllum demersum) — rootless submerged freshwater plant; shade-tolerant; strong bicarbonate user; temperate-hardy. See Species Catalog.