Parameter Reference

A consolidated reference for every rate constant, half-saturation, stoichiometric ratio, tolerance threshold, and calibrated coefficient used in the EcoSym simulator.

For each parameter the table gives one of:

a literature citation (verbatim author-year string, taken from the rationale comment next to the parameter in the source code), or
a category citation ("Redfield ratio", "universal phytoplankton anchor", "ASM2d default", "wastewater nitrifier literature range"), or
a relative-to-species rationale ("2× greens because diatoms are Zn-hungrier"), or
an explicit "no direct source" along with how the value was derived — hand-tuned for a calibration target, estimated by analogy to a similar species, or carried forward from an earlier version of the model.

Long rationale comments in the code have been compressed to roughly one sentence per row. The authoritative explanation for any number is the inline comment next to the parameter in the corresponding species/*.py or processes/*.py file — this page is an index, not a replacement.

Per-section symbol glossaries spell out the local conventions. Across the doc, subscripted forms like Q_N,max or K_NH4 read as in the literature with commas replacing the conventional subscript for plain-text readability; ratios like "Fe:C" are mol/mol. Where a parameter has no canonical literature symbol — internal calibration knobs like "Nocturnal feeding fraction", "Feces → suspended fraction", "Dispersal fraction" — the row uses a short English label instead.

How this page is kept in sync with the code

This doc is intentionally not auto-generated. It is filled in by hand after reading each species/*.py and processes/*.py file. The trade-off is that auto-generation would lose the literature attribution that lives in comments, and the rationale string for every "hand-tuned" value would have to be machine-readable, which is far more invasive than necessary.

When a parameter is added, removed, or changed in species/ or processes/, the relevant row in this page should be added / removed / updated as part of the same change. This is called out in the project CLAUDE.md. The convention is: if a code change touches a numeric parameter and you can describe why the new value is what it is, update this page; the explanation belongs next to the number, not buried in a commit message.

Producers — green algae, diatoms, cyanobacteria
Macrophytes — floating, submerged, rooted
Consumers — rotifers, daphnia, copepods, ostracods, ciliates, nanoflagellates, amphipods, snails, shrimp, hydra
Microbes — nitrifiers, heterotrophs, sediment anaerobes (denitrifier, DNRA, Fe-reducer, sulfate reducer, methanogen), fungi
Biogeochemical & Physical Processes — soil/sediment chemistry, water-column redox, gas exchange, allelopathy decay, biofilm maturity, bioturbation

Producers

Producers — green algae, diatoms, and cyanobacteria — share a common kinetic skeleton: light- and temperature-modulated photosynthesis, Monod uptake on dissolved nutrients, Droop-style internal storage of N and P, trace-metal Liebig gates, and stress/lethal envelopes on temperature, pH, and salinity. The conventions below recur across every producer table; subsequent species sections only spell out the rationale, not the formalism.

Producer symbol glossary

Symbol	Meaning
P_max	Maximum specific photosynthetic rate at T_ref, saturating light, no nutrient limitation. Equivalent to μ_max in most texts.
I_K	Light half-saturation irradiance for photosynthesis (µmol photons m⁻² s⁻¹)
K_X	Monod half-saturation for substrate X (CO₂, HCO₃⁻, NH₄⁺, NO₃⁻, PO₄, DSi, trace metals, allelochemicals)
V_X,max	Maximum cellular uptake rate of X per unit cellular C (luxury-uptake ceiling)
Q_X,min / Q_X,max	Minimum and maximum cellular X:C quota (Droop internal-store kinetics)
Fe:C, Mo:C, ..., C:N, N:P, Si:N	Cellular stoichiometric ratios (mol/mol)
Sc/o	RuBisCO CO₂-vs-O₂ specificity factor (dimensionless)
PQ	Photosynthetic quotient — mol O₂ evolved per mol C fixed
CCM efficiency	Fraction of inorganic C drawn from HCO₃⁻ via the carbon-concentrating mechanism, vs free CO₂
Q10	Multiplicative rate increase per 10 °C; subscripted by process (photo, resp, mort, uptake)
T_opt	Thermal optimum for photosynthesis (°C)
T_stress (low / high)	Onset of thermal stress; mortality begins ramping (°C)
T_lethal (low / high)	Acute thermal lethal threshold (°C)
T_lethal,photo	Temperature above which photosynthesis ceases (°C)
S_opt, σ_S	Salinity optimum and Gaussian tolerance breadth (PSU)
R_maint	Maintenance respiration rate (mol O₂ per mol cellular C per hour)
m_base	Baseline (non-stress) mortality rate (per hour)
m_X,max	Maximum mortality rate from stressor X (thermal, pH, salinity, viral, hypoxia) per hour
DOC excretion fraction	Fraction of fixed C excreted as labile DOM (Fogg 1983 healthy-cell range 5–30%)
Allelo release fraction	Fraction of net production released as polyphenol or cyanotoxin allelochemical
Mat self-shading coefficient	Beer-Lambert attenuation through dense filamentous biomass (m² per mol biomass C)

Notation: subscripted forms (Q_N,max, K_NH4) read as in the literature, with commas replacing the conventional subscript for plain-text readability. Ratios like "Fe:C" are mol/mol. Where a parameter has no canonical literature symbol — EcoSym-internal calibration knobs like NO₃-uptake dark/light preference, biofilm detachment multiplier, or lysis-product routing fractions — the row uses a short English label.

Shared producer base

Anchors universal to every photoautotroph in the model — concrete species override individual rows where they are known to deviate from the anchor.

Trace metal:C anchors

Symbol	Value	Units	Source / Rationale
Fe:C	2.0e-5	mol Fe / mol C	Quigg et al. 2003 — universal detritus anchor for eukaryotic phytoplankton
Mo:C	1.0e-8	mol Mo / mol C	Catalytic anchor; three orders below Fe — one atom per nitrate reductase / nitrogenase α₂β₂ core
Zn:C	4.0e-7	mol Zn / mol C	Quigg 2003, Sunda & Huntsman 1995 — universal anchor (~0.4 µmol/mol); carbonic anhydrase
Cu:C	5.0e-8	mol Cu / mol C	Quigg 2003, Sunda & Huntsman 1995 — plastocyanin / cyt c oxidase anchor
K:C	2.5e-2	mol K / mol C	Sterner & Elser 2002, Karley & White 2009 — dominant intracellular cation
Ni:C	1.0e-7	mol Ni / mol C	Quigg 2003, Sunda & Huntsman 1995 — urease cofactor anchor
Co:C	5.0e-9	mol Co / mol C	Quigg 2003, Sunda & Huntsman 1995 — vitamin B12 anchor (rarest tracked trace metal)
B:C	5.0e-6	mol B / mol C	Reynolds 2006, Bowen 1979 — structural cell-wall / frustule / heterocyst-envelope B
S:C	5.0e-3	mol S / mol C	Sterner & Elser 2002, Redfield-extended — protein / glutathione / Fe-S clusters

Trace-metal Monod half-saturations

Symbol	Value	Units	Source / Rationale
K_Fe	1.0e-8	mol/L	Half-sat for Fe uptake (~0.5–1 µg/L for most algae)
K_Mo (NO₃ reductase)	2.0e-9	mol/L	Cole 1976; Howarth & Cole 1985 — 1–5 nM Mo for nitrate reductase
K_Zn (carbonic anhydrase)	1.0e-8	mol/L	Sunda & Huntsman 1992, 1995 — ~10 nM CA-activity half-sat
K_K	5.0e-6	mol/L	Healey 1973; Reynolds 2006 — middle of 1–20 µM range

Droop internal stores

Symbol	Value	Units	Source / Rationale
Q_P,min	0.005	mol P / mol C	Reynolds 2006; Sterner & Elser 2002 — 50% of Redfield structural P (cell-division floor)
Q_P,max	0.030	mol P / mol C	Reynolds 2006; Sterner & Elser 2002 — 3× structural (polyphosphate-saturated)
V_P,max	0.02	mol P / (mol C · h)	Healey 1973, Reynolds 2006 — mid-range for greens
K_PO4 (uptake)	5.0e-8	mol/L	Tight half-sat — transporters saturate against scarce P
Q_N,min	0.02	mol N / mol C	Reynolds 2006; Sterner & Elser 2002 — generic green phytoplankton
Q_N,max	0.15	mol N / mol C	Reynolds 2006; Sterner & Elser 2002 — generic greens (diatom / cyano subclasses raise)
V_N,max	0.05	mol N / (mol C · h)	Healey 1973, Goldman & McCarthy 1978, Falkowski & Raven 2007 — mid-range for greens
Q10 (uptake)	2.0	–	Eppley 1972 — transporter Q10 for V_N,max / V_P,max
k_catab (storage)	0.001	/h	Reynolds 2006 (polyphosphate t½ ~weeks); Allen 1984 / Mackerras 1990 (cyanophycin t½ ~days)
C_g (luxury viability gate)	1.0e-9	mol C	Numerical conditioning, not biology. Multiplies luxury uptake by `C²/(C_g²+C²)` so a functionally-dead cell pool loses its biomass-independent luxury Jacobian mode (LSODA die-off stiffness; see `docs/planning/performance.md` 2026-06-12). ~1000× below any viable biomass / seed inoculum, so live cells are bit-identical and only extinct pools are quenched. Mass-conserving (scales both sides of the flux).

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_HCO3	1.0e-3	mol/L	Mercado et al. 2003; Allen & Spence 1981; Madsen & Sand-Jensen 1991 — eukaryotic HCO₃⁻ transporter Km
CCM max conc factor	10.0	× ambient CO₂	CCM photorespiration relief. A bicarbonate user concentrates CO₂ at RuBisCO above bulk diffusive CO₂; photorespiration's O₂/CO₂ competition reads this elevated level (`Producer._ccm_effective_co2`), not bare CO₂. The effective level is the CO₂ that would, by diffusion alone, give the realized `CO2_fac` — `K_CO2·CO2_fac/(1−CO2_fac)` — which by construction equals ambient CO₂ exactly for a non-bicarbonate plant (so the relief is self-targeting to CCM use and inert otherwise), capped at this factor. Raven 1991; Maberly & Madsen 2002; Maberly 1996 — aquatic CCM internal:external CO₂ ratios ~3–40×; 10× conservative mid-range.

Thermal & physiological defaults

Symbol	Value	Units	Source / Rationale
T_opt	25.0	°C	Default; subclasses MUST override
T_lethal,photo	40.0	°C	Default temperature at which photosynthesis ceases
DOC excretion fraction	0.05	fraction	Fogg 1983 — 5–30% of fixed C excreted, routed to labile DOM

Mat / filament structure, allelopathy, viral lysis, death routing (defaults; subclasses override)

Symbol	Value	Units	Source / Rationale
Mat self-shading coefficient	0.0	m² / mol C	Disabled by default (unicellular); filamentous subclasses override
Allelo release fraction	0.0	fraction	Default off; subclasses (macrophytes for polyphenol, cyano for cyanotoxin) override
Allelochemical pool	polyphenol	–	Pool selector (no-op when release fraction = 0)
m_viral,max	0.0	/h	Default off; Suttle 2007, Brussaard 2004 — subclasses opt in
K_viral (host density)	1.0e-5	mol C / L	Default half-sat for density-dependent encounter
Surface death → suspended	0.10	fraction	Surface-attached mortality routing default

Planktonic green algae

The default freshwater unicellular green alga — fast-growing, mid-range nutrient affinity, sensitive to chloroviruses.

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.08	/h	Griffiths & Harrison 2009 — ~1.9/day, midrange of literature 1.0–2.0/day
I_K	40.0	µmol m⁻² s⁻¹	Low — adaptation to turbid / shaded freshwater

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	15e-6	mol/L	Raven et al. 2012 — typical 10–50 µmol/L
CCM efficiency	0.25	fraction	Giordano et al. 2005 — moderate CCM capability
K_HCO3	1.0e-3	mol/L	Mercado et al. 2003 — moderate-affinity transport (sits at base default)
Sc/o	80.0	–	Spreitzer & Salvucci 2002 — green algae moderate CCM range
PQ	1.0	mol O₂ / mol C	Photosynthetic quotient

N & P uptake

Symbol	Value	Units	Source / Rationale
K_N (total)	4e-5	mol/L	Total N half-sat for growth limitation
K_NH4	2e-5	mol/L	NH₄⁺ half-sat (preferred N source)
K_NO3	8e-5	mol/L	NO₃⁻ half-sat (requires reduction)
NO₃ preference (dark)	0.1	fraction	Light-dependent NO₃ source preference (low in dark)
NO₃ preference (light)	0.5	fraction	Light-dependent NO₃ source preference (high in light)

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	6.6	mol / mol	Redfield-like structural C:N
N:P	16.0	mol / mol	Redfield

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0012	/h	Hand-tuned maintenance respiration
K_O2 (respiration)	1.25e-5	mol/L	~0.4 mg/L O₂; high affinity (algae K_m 0.16–0.64 mg/L)

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_polyphenol	4.0e-6	mol C / L	Nakai 2000, Hilt 2006 — field-effective chronic exposure (~14 µg GAE/L)
K_cyanotoxin	2.0e-5	mol C / L	Sukenik et al. 2002 — PSII inhibition at ~0.4 mg MC-LR/L

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	24.0	°C	Goldman 1977; Reynolds 1984; Butterwick 2005; Lurling & Van Donk 2000; tuned 3 °C below cyano T_opt per Paerl & Huisman 2008
T_lethal,photo	38.0	°C	Hand-tuned upper photosynthesis limit
T_ref	25.0	°C	Engine reference temperature
Q10,photo	2.0	–	Standard
Q10,resp	2.2	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	10.0 / 35.0	°C	Mayo 1997; Converti et al. 2009
T_lethal (low / high)	0.0 / 42.0	°C	Freezing / hand-tuned upper
m_thermal,max	0.03	/h	~70%/day at lethal temperatures

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.0	–	Mayo 1997; Rachlin & Grosso 1991
pH lethal (low / high)	4.5 / 10.5	–	Mayo 1997; Rachlin & Grosso 1991
m_pH,max	0.03	/h	~70%/day at lethal pH

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	2.0	PSU	Kirst 1990 — freshwater
σ_S	8.0	PSU	Gaussian tolerance breadth
S_stress (low / high)	0.0 / 10.0	PSU	No low-salinity stress; upper threshold
S_lethal (low / high)	0.0 / 25.0	PSU	Freshwater fine; lethal high
m_salinity,max	0.15	/h	Salinity mortality cap
Osmoregulation cost	0.003	per PSU deviation	Respiratory cost multiplier

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.05 / 24	/h	~5%/day baseline
m_total,max	0.50	/h	Cap on summed mortality
Death → suspended fraction	0.3	fraction	30% lysis products suspended, 70% aggregates settled
DOC excretion fraction	0.05	fraction	Fogg 1983

Viral lysis

Symbol	Value	Units	Source / Rationale
m_viral,max	0.012	/h	Brussaard 2004, Van Etten et al. 2002 — chloroviruses 5–25%/day
K_viral (host density)	1.0e-5	mol C / L	Standard host density half-sat

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Dispersal fraction	0.25	fraction	Unicellular algae disperse readily
Settlement rate	0.001	/h	Minimal active attachment (passive sedimentation)
Detachment multiplier	3.0	–	Easily dislodged; no holdfast
Surface death → suspended	0.20	fraction	Biofilm mostly settles (80/20 settled/suspended)

Benthic green algae

Periphyton-forming greens — small cells embedded in an EPS biofilm matrix on hard substrates. (Only divergences from planktonic green algae are shown.)

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.065	/h	Biggs 1996, Stevenson 1996 — periphyton range 0.05–0.09/h; just above diatom 0.05
I_K	25.0	µmol m⁻² s⁻¹	Biggs 1996, Hill 1996 — shade-tolerant biofilm interior
Body size	0.001	cm	Fractal surface-area scaling for ~10 µm cells

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	12e-6	mol/L	Lower for small efficient cells
CCM efficiency	0.30	fraction	Giordano et al. 2005, Raven et al. 2012
K_HCO3	0.8e-3	mol/L	Higher affinity than planktonic greens — diffusion-boundary-layer benefit

N uptake

Symbol	Value	Units	Source / Rationale
K_N (total)	3e-5	mol/L	High affinity (small cells)
K_NH4	1.5e-5	mol/L	High affinity
K_NO3	6e-5	mol/L	High affinity

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0015	/h	Higher maintenance (small cells)
osmo_cost_per_PSU_deviation	0.003	× per PSU	Osmoregulation cost multiplier required by the shared Producer maintenance kernel (PROD-1 collapse). Matches planktonic green / diatom; the former benthic fork computed maintenance inline without an osmoregulation term.

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_polyphenol	6.0e-6	mol C / L	~1.5× higher than planktonic baseline (biofilm boundary protection)
K_cyanotoxin	3.0e-5	mol C / L	~1.5× higher than planktonic baseline

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	22.0	°C	Broad cool-temperate optimum for epilithic green community
T_lethal,photo	40.0	°C	Hand-tuned
T_stress (low / high)	8.0 / 32.0	°C	Typical freshwater periphyton
T_lethal (high)	40.0	°C	Typical freshwater periphyton

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	Typical freshwater green algae
pH lethal (low / high)	5.0 / 10.0	–	Typical freshwater green algae
m_pH,max	0.025	/h	Slightly lower than planktonic greens

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	1.0	PSU	Freshwater
σ_S	6.0	PSU	Narrower than planktonic
S_stress (high)	8.0	PSU	Freshwater
S_lethal (high)	20.0	PSU	Freshwater
m_salinity,max	0.12	/h	Slightly lower than planktonic

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Death → suspended fraction	0.50	fraction	Small planktonic cells fragment easily (applies to the planktonic pool; surface pools use the base `surface_death_suspended_frac` = 0.10)
DOC excretion fraction	0.12	fraction	Fogg 1983, Hoagland et al. 1993 — elevated due to EPS biofilm matrix

PROD-1 (2026-05-31): benthic green now runs the shared Producer.flux() pipeline. The former death_to_DOM_frac = 0.20 (biofilm-lysis-to-DOM split) was removed — the base routes all mortality to detritus (its only DOM mortality path is viral lysis, which this species does not have). DON/DOP are now excreted alongside DOC. See the PROD-1 session-log entry in docs/planning/tech_debt.md for the full list of adopted base conventions and the measured Walstad delta.

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Dispersal fraction	0.15	fraction	Biggs 1996, Hoagland et al. 1982 — biofilm formers disperse less
Settlement rate	0.008	/h	Hoagland et al. 1982, Biggs 1996 — ~19%/day; 2× diatom (EPS-mediated fast adhesion)
Detachment multiplier	2.0	–	Vs planktonic 3.0, diatom 1.5, Cladophora 0.7 — EPS improves adhesion

Biofilm shelter (see species/access.py::surface_protection)

Symbol	Value	Units	Source / Rationale
biofilm_predation_protection	0.40	fraction	M=1 EPS-shelter ceiling — filamentous green periphyton-formers (Cladophora, Oedogonium) build EPS-bound mats with cells partially embedded (Stevenson et al. 1996 Algal Ecology; Hoagland et al. 1993). Slightly lower than HB's 0.50 because outermost mat surface is always exposed. Same coefficient gates grazing access and the species' base + viral self-mortality.
geometric_predation_shield_scale	0.40	–	M=0 cold-start floor multiplier on substrate roughness — filament tangles settle into crevices

Diatom base

Shared diatom physiology — silica frustule, tight Fe affinity, large vacuolar luxury N and P stores, weaker CCM than greens, cold-adapted.

Growth defaults

Symbol	Value	Units	Source / Rationale
Q10,photo	1.8	–	Slightly lower than greens (cold-adapted)
Q10,resp	2.2	–	Standard
Q10,mort	1.5	–	Standard
T_ref	25.0	°C	Engine reference

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	15e-6	mol/L	Standard freshwater algae
CCM efficiency	0.15	fraction	Lower CCM than greens — relies more on CO₂
K_HCO3	1.2e-3	mol/L	Burkhardt et al. 2001, Tortell 2000 — high end of eukaryotic range
Sc/o	60.0	–	Lower than greens (weaker CCM)
PQ	1.0	mol O₂ / mol C	–

N & P uptake (diatom-typical high-affinity, fast V_max)

Symbol	Value	Units	Source / Rationale
K_N (total)	2e-5	mol/L	High affinity total N
K_NH4	2e-5	mol/L	–
K_NO3	8e-5	mol/L	–
NO₃ preference (dark / light)	0.1 / 0.5	fraction	Standard producer source preference
Q_P,max	0.050	mol P / mol C	Sicko-Goad 1986, Powell et al. 2009 — diatoms accumulate polyphosphate higher than greens
V_P,max	0.030	mol P / (mol C · h)	Diatoms drain water-column PO₄ aggressively in pulse events
Q_N,max	0.12	mol N / mol C	Lomas & Glibert 1999, Kamp et al. 2011; CAEDYM table — vacuolar NO₃ reservoir
V_N,max	0.07	mol N / (mol C · h)	High — diatoms drain NO₃ aggressively when pulsed

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	6.6	mol / mol	Redfield
N:P	16.0	mol / mol	Redfield
Si:N	1.0	mol Si / mol N	Brzezinski 1985 — ~2 g Si per g N

Trace-metal:C overrides (diatom-specific deviations from universal anchor)

Symbol	Value	Units	Source / Rationale
Fe:C	5.0e-6	mol Fe / mol C	Sunda & Huntsman 1995, Quigg et al. 2003 — diatoms Fe-frugal (frustule reduces demand)
Mo:C	2.0e-9	mol Mo / mol C	Quigg 2003 — Mo:C ≈ 1–3 nmol/mol (Mo-frugal)
Zn:C	8.0e-7	mol Zn / mol C	Morel et al. 1994, Sunda & Huntsman 1995 — Zn-hungry (CCM/CA dependent), ~2× anchor
Cu:C	3.0e-8	mol Cu / mol C	Annett et al. 2008, Peers & Price 2006 — Cu-frugal (cyt c₆ substitute)
K:C	2.0e-2	mol K / mol C	Quigg 2003 — slightly below anchor (frustule silica dilutes K demand)
B:C	1.5e-5	mol B / mol C	Loucaides 2008, Martin-Jézéquel 2017 — B-rich (frustule construction), ~3× anchor

Trace-metal Monod overrides

Symbol	Value	Units	Source / Rationale
K_Fe	8.0e-9	mol/L	Tighter than base — sub-nM Fe adaptation
K_Mo (NO₃ reductase)	1.0e-9	mol/L	High-affinity NO₃ reductase ~1 nM (Mo-poor offshore regimes)
K_Zn (carbonic anhydrase)	3.0e-8	mol/L	Morel et al. 2002, Lane & Morel 2000 — ~30 nM, heavier CCM commitment

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.001	/h	Hand-tuned
K_O2 (respiration)	1.25e-5	mol/L	~0.4 mg/L O₂

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_polyphenol	3.0e-6	mol C / L	Gross 2003 — tannins inhibit silica-deposition vesicles; tighter than greens
K_cyanotoxin	1.5e-5	mol C / L	Microcystin disrupts PP1/PP2A in eukaryotic algae (~0.3 mg MC-LR/L half-suppression)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_lethal,photo	35.0	°C	Less heat-tolerant than greens
T_stress (low)	5.0	°C	Cold-adapted shared trait
T_lethal (low)	0.0	°C	Cold-adapted
m_thermal,max	0.03	/h	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.0	–	Similar to greens
pH lethal (low / high)	4.5 / 10.5	–	Similar to greens
m_pH,max	0.03	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Strictly freshwater
σ_S	5.0	PSU	Narrow tolerance
S_stress (high)	5.0	PSU	Strictly freshwater
S_lethal (high)	15.0	PSU	Strictly freshwater
m_salinity,max	0.15	/h	Standard
Osmoregulation cost	0.003	per PSU deviation	Standard

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_total,max	0.50	/h	Mortality cap
Death → suspended fraction	0.3	fraction	Standard

Viral lysis

Symbol	Value	Units	Source / Rationale
m_viral,max	0.012	/h	Tomaru et al. 2015 — diatom-virus rates 5–25%/day (silica frustule no protection)
K_viral (host density)	1.0e-5	mol C / L	Standard density half-sat

Biofilm shelter (see species/access.py::surface_protection)

Symbol	Value	Units	Source / Rationale
biofilm_predation_protection	0.20	fraction	M=1 EPS-shelter ceiling — silica frustule offers some structural defence but diatoms are biofilm occupants, not mat-builders (Marker 1976; Hoagland et al. 1982). Lower than benthic green algae's 0.40. Same coefficient gates grazing access and base + viral self-mortality.
geometric_predation_shield_scale	0.30	–	M=0 cold-start floor multiplier on substrate roughness — frustules settle into micro-crevices

Centric diatoms — divergent only

Planktonic r-strategists — cold-water spring bloomers with boom-bust dynamics. (Only divergences from Diatom base are shown.)

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.085	/h	Fast bloom growth (~2.0/day)
I_K	30.0	µmol m⁻² s⁻¹	Less shade-tolerant than pennate

Si uptake

Symbol	Value	Units	Source / Rationale
K_DSi	3e-6	mol/L	Weaker Si affinity than pennate (~0.084 mg Si/L)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	16.0	°C	Cold-water spring bloomer
T_stress (high)	24.0	°C	Spring / cold-water community
T_lethal (high)	32.0	°C	Spring / cold-water community

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.06 / 24	/h	Boom-bust dynamics
DOC excretion fraction	0.05	fraction	Low mucilage
Surface death → suspended	0.40	fraction	Debris easily resuspends

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Settlement rate	0.002	/h	Weak mucilage adhesion, easy resuspension
Detachment multiplier	2.5	–	Easy resuspension
Dispersal fraction	0.30	fraction	Spreads readily between surfaces

Pennate diatoms — divergent only

Benthic K-strategists — shade-tolerant biofilm interior with aggressive mucilage adhesion and high Si affinity. (Only divergences from Diatom base are shown.)

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.045	/h	Slow K-strategist (~1.1/day)
I_K	12.0	µmol m⁻² s⁻¹	Shade-tolerant biofilm interior

Si uptake

Symbol	Value	Units	Source / Rationale
K_DSi	1.5e-6	mol/L	High Si affinity (~0.042 mg Si/L)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	22.0	°C	Temperate biofilm
T_stress (high)	30.0	°C	Temperate biofilm
T_lethal (high)	38.0	°C	Temperate biofilm

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.03 / 24	/h	Persistent communities
DOC excretion fraction	0.08	fraction	Heavy mucilage for biofilm scaffold
Surface death → suspended	0.10	fraction	Debris stays in place

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Settlement rate	0.008	/h	Aggressive mucilage attachment
Detachment multiplier	1.0	–	Strong adhesion
Dispersal fraction	0.10	fraction	Stay local

Cyanobacteria base

Shared cyanobacterial physiology — carboxysome CCM, cyanophycin luxury-N storage, N₂-fixation machinery, asymmetric high-pH tolerance, and dedicated cyanophage virus mortality.

Growth defaults

Symbol	Value	Units	Source / Rationale
Q10,photo	2.0	–	Standard
Q10,resp	2.0	–	Standard
Q10,mort	1.5	–	Standard
T_ref	25.0	°C	Engine reference

Carbon kinetics (high-affinity CCM)

Symbol	Value	Units	Source / Rationale
K_CO2	8e-6	mol/L	Strong carboxysome CCM — low half-sat survives high-pH CO₂ depletion
CCM efficiency	0.60	fraction	Giordano et al. 2005 — strong CCM via carboxysomes
K_HCO3	0.2e-3	mol/L	Price 2011, Mangan & Brenner 2014 — BCT1 / SbtA / BicA highest HCO₃⁻ affinity of any phototroph
Sc/o	120.0	–	Higher — carboxysome concentrates CO₂ for RuBisCO
PQ	1.0	mol O₂ / mol C	–

N & P uptake

Symbol	Value	Units	Source / Rationale
K_N (total)	4e-5	mol/L	Same as green algae
K_NH4	2e-5	mol/L	–
K_NO3	8e-5	mol/L	–
NO₃ preference (dark / light)	0.1 / 0.5	fraction	Standard producer source preference
Q_P,max	0.040	mol P / mol C	Stewart & Alexander 1971, Healey 1973, Sicko-Goad 1986 — cyano polyphosphate well-studied
V_P,max	0.025	mol P / (mol C · h)	CCM-coupled fast P uptake, slightly elevated vs greens
Q_N,max	0.18	mol N / mol C	Simon 1971, Allen 1984; AED2 / CAEDYM tables — cyanophycin granules (largest luxury-N reservoir)
V_N,max	0.04	mol N / (mol C · h)	Goldman & McCarthy 1978 — slightly lower than greens / diatoms
Q_N repression K (nifH)	0.07	mol N / mol C	Allen 1984, Muro-Pastor & Hess 2012 — nifH repression Hill² K

N₂ fixation kinetics

Symbol	Value	Units	Source / Rationale
I_K (nif)	15.0	µmol m⁻² s⁻¹	Staal et al. 2002 — nitrogenase light half-sat
nif energy cost fraction	0.25	fraction	Postgate 1982 — ~16 ATP + 8 e⁻ per N₂ at max ~25% of cellular energy
K_Fe (nif)	5.0e-8	mol/L	Kustka et al. 2003 — nitrogenase Fe half-sat ~0.5 µg/L (FeMo-cofactor, ~10× generic Fe demand)
K_Mo (nif)	2.0e-9	mol/L	Howarth & Cole 1985 — Mo-gate on nitrogenase ~2 nM

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	7.5	mol / mol	Sheaths and storage polymers raise C per N
N:P	16.0	mol / mol	Redfield

Trace-metal:C overrides (cyano-specific deviations from universal anchor)

Symbol	Value	Units	Source / Rationale
Fe:C	4.0e-5	mol Fe / mol C	Kustka et al. 2003, Berman-Frank et al. 2001 — 2–5× eukaryotic algae (PSI Fe-S + nitrogenase)
Mo:C	5.0e-9	mol Mo / mol C	Quigg 2003, Howarth & Cole 1985 — Mo-rich (FeMo-cofactor of nitrogenase), ~5× anchor
Zn:C	3.0e-7	mol Zn / mol C	Yee & Morel 1996, Xu et al. 2008 — Zn-frugal (Co / Cd-substituted CA), slightly below anchor
Cu:C	1.0e-7	mol Cu / mol C	Peers & Price 2006, Duckworth et al. 2009 — Cu-rich (obligate plastocyanin), ~2× anchor
K:C	3.0e-2	mol K / mol C	Sterner & Elser 2002 — slightly above anchor (Na/K antiport for high-pH habitat)
Ni:C	3.0e-7	mol Ni / mol C	Tuit et al. 2004, Ho et al. 2003 — Ni-rich (HupSL hydrogenase + urease), ~3× anchor
Co:C	3.0e-8	mol Co / mol C	Saito & Moffett 2002 — Co-rich (B12 synthesis + Co-substituted CA), ~6× anchor
B:C	2.0e-5	mol B / mol C	Mateo et al. 1986, Bonilla 1990 — B-rich (heterocyst-envelope glycolipids), ~4× anchor
S:C	7.0e-3	mol S / mol C	Cunningham & Capone 1992, Stal 2009 — S-rich (nitrogenase Fe-S clusters), ~1.4× anchor

Trace-metal Monod overrides

Symbol	Value	Units	Source / Rationale
K_Mo (NO₃ reductase)	2.0e-9	mol/L	Same scale as other phytoplankton
K_Zn (carbonic anhydrase)	5.0e-9	mol/L	Cyano CA is Co / Cd-swappable; below producer default — tolerates low-Zn water
K_K	3.0e-6	mol/L	Tighter than producer default — Na/K antiport gives kinetic edge at low ambient K

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.005	fraction	Rohrlack 1999, Sivonen & Jones 1999, Schatz 2007, Burford 2014 — places dissolved MC in µg/L envelope
Allelochemical pool	cyanotoxin	–	Routes to cyanotoxin pool
K_polyphenol	4.0e-5	mol C / L	Hilt & Gross 2008 — cyano relatively tolerant to plant polyphenols (~1.0 mg GAE/L half-suppression)

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0015	/h	Higher than diatoms — thick walls
K_O2 (respiration)	1.25e-5	mol/L	~0.4 mg/L O₂

Thermal envelope (warm-adapted)

Symbol	Value	Units	Source / Rationale
T_lethal,photo	40.0	°C	Warm-adapted
T_stress (high)	36.0	°C	Warm-adapted
T_lethal (low / high)	0.0 / 42.0	°C	Cold lethal / warm-adapted upper
m_thermal,max	0.03	/h	Standard

pH envelope (asymmetric high-pH tolerance)

Symbol	Value	Units	Source / Rationale
pH stress (low)	5.5	–	Asymmetric — high-pH side tolerates further
pH lethal (low)	4.5	–	–
pH lethal (high)	12.0	–	Very high tolerance (carboxysomes function at high pH)
m_pH,max	0.03	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	2.0	PSU	Freshwater
σ_S	8.0	PSU	Similar to greens
S_stress (high)	10.0	PSU	Freshwater
S_lethal (high)	20.0	PSU	Freshwater
m_salinity,max	0.15	/h	Standard
Osmoregulation cost	0.003	per PSU deviation	Standard

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_total,max	0.50	/h	Mortality cap
Death → suspended fraction	0.2	fraction	Dense sheaths → more settled debris

Viral lysis

Symbol	Value	Units	Source / Rationale
m_viral,max	0.025	/h	Suttle 2007, Brussaard 2004 — cyanophages strongest virus mortality (60%/day at saturation)
K_viral (host density)	5.0e-6	mol C / L	Tighter than greens — phage encounter at lower densities

Planktonic cyanobacteria — divergent only

Bloom-forming r-strategists — surface-scum / high-light adapted with heterocystous N₂ fixation. (Only divergences from Cyanobacteria base are shown.)

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.065	/h	Bloom r-strategist (~1.6/day)
I_K	35.0	µmol m⁻² s⁻¹	Surface-scum / high-light adapted

N₂ fixation

Symbol	Value	Units	Source / Rationale
N₂ fix rate max	3.5e-3	/h	Howarth et al. 1988, Carpenter 1983 — heterocystous forms sustain ~8% biomass N/day at peak
K_O2 (nif)	5.0e-4	mol/L	Fay 1992, Wolk et al. 1994; tuned for ~67% inhibition at 8 mg O₂/L (heterocysts decouple from bulk O₂)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	27.0	°C	Paerl & Huisman 2008 — cyano T_opt 28–32 °C; tuned to maintain warm-water advantage vs greens (24 °C)
T_stress (low)	14.0	°C	Less cold-tolerant than benthic mats

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (high)	10.5	–	Bloom species drive high-pH eutrophic lakes

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.03 / 24	/h	Tuned to preserve boom-bust character (~3%/day) — higher than benthic 2.5%/day
DOC excretion fraction	0.10	fraction	Moderate EPS (colonies, mucilage)
Surface death → suspended	0.40	fraction	Debris resuspends readily

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Settlement rate	0.002	/h	Weak attachment, easy resuspension
Detachment multiplier	2.5	–	Easy resuspension
Dispersal fraction	0.25	fraction	Spreads readily through water column

Benthic cyanobacteria — divergent only

Mat-forming K-strategists (Phormidium / Oscillatoria) with non-heterocystous N₂ fixation in the mat-interior microaerobic gradient. (Only divergences from Cyanobacteria base are shown.)

Growth & light

Symbol	Value	Units	Source / Rationale
P_max	0.030	/h	Slow K-strategist (~0.72/day)
I_K	12.0	µmol m⁻² s⁻¹	Shade-adapted mat interior

N₂ fixation

Symbol	Value	Units	Source / Rationale
N₂ fix rate max	2.0e-3	/h	Paerl & Bebout 1988 — non-heterocystous mats ~5% biomass N/day at peak (mat-interior microaerobic)
K_O2 (nif)	1.0e-3	mol/L	Paerl & Bebout 1988; tuned higher than planktonic (mat-interior O₂ gradient decouples from bulk)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	26.0	°C	Hudon et al. 2014, Quiblier et al. 2013 — Phormidium / Oscillatoria mats most vigorous 24–28 °C
T_stress (low)	10.0	°C	More cold-tolerant than planktonic

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (high)	9.5	–	Mats less alkaliphile than bloom species

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.025 / 24	/h	Persistent mats (~2.5%/day)
DOC excretion fraction	0.22	fraction	Heavy EPS scaffold + grazing deterrent
Surface death → suspended	0.05	fraction	Debris stays in place as settled detritus

Dispersal & surface attachment

Symbol	Value	Units	Source / Rationale
Settlement rate	0.012	/h	Aggressive EPS adhesion, cohesive mats
Detachment multiplier	0.8	–	Strong adhesion
Dispersal fraction	0.05	fraction	Mats stay local

Biofilm shelter (see species/access.py::surface_protection)

Symbol	Value	Units	Source / Rationale
biofilm_predation_protection	0.60	fraction	M=1 EPS-shelter ceiling — mature Phormidium / Oscillatoria / Lyngbya mats develop thick mucilaginous sheaths with well-documented grazing resistance (Dodds 2002 Freshwater Ecology ch. 12; Stevenson et al. 1996). Highest algal shelter in the model — sits between HB (0.50) and nitrifier (0.90). Same coefficient gates grazing access and base + viral self-mortality.
geometric_predation_shield_scale	0.50	–	M=0 cold-start floor multiplier on substrate roughness — sheath cohesion helps mats anchor in pits/crevices early

Macrophytes

Macrophytes — floating, submerged, and rooted vascular plants — share the producer kinetic skeleton but add multi-compartment structure (shoot / root / frond / stem), dual-source uptake (water-column leaves + pore-water roots), aerenchyma-mediated rhizosphere oxygen / CO₂ exchange, and (for rooted plants) phloem translocation between compartments. The conventions below extend the Producer glossary; species sections only spell out divergences.

Macrophyte symbol glossary

Symbol	Meaning
P_max, I_K, K_X, V_X,max, Q_X,min/max, Q10, T_opt, R_maint, m_X	Same as Producer glossary
Q_N,max / V_N,max (water) / V_N,max (root)	Cellular quota ceiling and parallel water- vs root-uptake rates (mol N per mol C per h)
K_NH4 (water) / K_NH4 (pore)	Leaf vs root NH₄ Monod half-sats (root system I is sub-µM affinity)
K_K (water) / K_K (pore)	Leaf vs root K Monod half-sats
f_water / f_root	Acquisition split for N and P uptake (sum to 1.0) — pore-dominated in Walstad-style rooted plants
f_root,CO2	Fraction of photosynthetic C drawn from pore CO₂ via aerenchyma (Cryptocoryne high; Vallisneria moderate)
f_root,O2 release	Fraction of GPP exuded as radial oxygen loss into rhizosphere
k_translocate	First-order phloem-borne mobilisation of N+P stored pools between root and shoot (rooted only)
α_root	Below-ground C allocation fraction
k_frond,atten / k_stem,atten / k_shoot,atten / k_canopy,atten	Beer-Lambert light attenuation coefficients (m² per mol C for fronds/canopy, L per mol C per m for stems/shoots)
SLA (canopy)	Specific leaf area (m² per mol C) for canopy light interception
SLA_cm2_per_mg_C	Specific leaf area for epiphytic biofilm carrying capacity on `macrophyte_leaf_surface` — multiplied by current leaf C (mg) and (for floating species) by `(1 − aerial_C_fraction)` to sum into the aggregated dynamic surface area. Per-grazer access on this surface is set in `interactions.yaml` (not codegen) and anchored to feeding-mode literature — see `docs/environment/surfaces.md` for the per-grazer table
max cover fraction	Areal cap on water-surface coverage by floating species
kLa block at full cover	Fractional suppression of air-water gas exchange under a mature floating mat
Competitive displacement	First-order suppression of a sub-dominant floating species by a dominant one
Aerial C fraction	Fraction of frond surface above the water line (stomata-bearing in floating C3 plants)
Dark respiration factor	LEDR — light-enhanced dark respiration ratio (Heskel 2013; Atkin & Tjoelker 2003)
Allelo release fraction	Fraction of net production released as polyphenol allelochemical (Hilt & Gross 2008)

Floating macrophyte base

Generic floating-plant kinetic skeleton — sets defaults for fronds resting on the water surface with aerial stomata, water-column nutrient uptake, and a mat-coverage cap.

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
K:C	5.0e-2	mol K / mol C	Macrophyte K:C anchor (vacuolar luxury K); ~2× universal anchor
B:C	5.0e-5	mol B / mol C	Marschner 1995 — vascular cell-wall pectin (RG-II) B crosslinking, ~10× detritus anchor
K_K (growth)	1.0e-5	mol/L	~0.4 mg K/L; matches K_K_water leaf scale

Canopy & light

Symbol	Value	Units	Source / Rationale
P_max	0.010	/h	~0.24/day generic floating-macrophyte rate; subclasses override
I_K	40.0	µmol m⁻² s⁻¹	No direct source — floating-plant range
k_frond,atten	10.0	m² / mol C	Calibration target: τ ~2–4 at full coverage (86–98% interception)
SLA	2.0	m² / mol C	Geometric monolayer footprint (reporting only)
Max cover fraction	1.0	fraction	Default disables spatial cap (Beer-Lambert only); subclasses override
Uses total cover for space	True	bool	Combined cover for large-frond species (Salvinia)
Competitive displacement	0.0	/h	Disabled by default; set on dominant species
Competition threshold	0.5	cover frac	Activation threshold for displacement
kLa block at full cover	0.85	fraction	At full cover, kLa drops to 15% of open-water value (literature mid-range)

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	8e-6	mol/L	Low half-sat (surface CO₂ access)
CCM efficiency	0.15	fraction	Modest C3-plant HCO₃⁻ use
K_HCO3	2.0e-3	mol/L	Maberly & Madsen 2002 — floating C3 plants are weak HCO₃⁻ users
Sc/o	80.0	–	Standard C3 RuBisCO
Internal air-CO₂	1.0e-5	mol/L	Ci/Ca ≈ 0.7 of atmospheric 400 ppm at 23 °C dissolved-phase equivalent
Aerial C fraction	0.85	fraction	Salvinia-style hairs lift fronds; stomata on aerial side dominate
PQ	1.0	mol O₂ / mol C	Standard photosynthesis stoichiometry
DOC excretion fraction	0.05	fraction	Generic algal/macrophyte DOC excretion fraction

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	10.0	mol / mol	N-rich non-lignified frond tissue
C:N (max under N starvation)	22.0	mol / mol	Maximum C:N under N starvation
N:P	14.0	mol / mol	Near-Redfield for fast growers

N & P uptake

Symbol	Value	Units	Source / Rationale
V_N,max (water)	1.5e-3	mol N / (mol C · h)	Epstein & Hagen 1952; Cedergreen & Madsen 2002 (Lemna)
V_P,max (water)	1.0e-4	mol P / (mol C · h)	Macrophyte literature high-affinity scale
K_N (water)	4e-6	mol/L	~0.056 mg N/L; high-affinity NH4 (root system I analogue)
K_NO3 (water)	1.5e-5	mol/L	Lower NO3 affinity vs. NH4
K_P (water)	3e-7	mol/L	~0.009 mg P/L; high P affinity
NO₃ preference (dark / light)	0.1 / 0.4	fraction	Standard producer source preference
K_N (total, helper)	8e-6	mol/L	Producer helper half-sat
K_NH4 (helper)	4e-6	mol/L	Producer helper half-sat
K_NO3 (helper)	1.5e-5	mol/L	Producer helper half-sat
K_PO4 (helper)	3e-7	mol/L	Producer helper half-sat
Min photo N factor	0.10	fraction	Floor on photo-N factor

Droop internal stores

Symbol	Value	Units	Source / Rationale
Q_P,min	0.005	mol P / mol C	Gerloff 1966 critical tissue P at ~40% C DW
Q_P,max	0.030	mol P / mol C	Lemna 2.8% DW upper P (Skillicorn 1993; Cedergreen & Madsen 2002)
Q_N,min	0.005	mol N / mol C	~0.25 × Q_N,max (Droop curve shape preserved)
Q_N,max	0.020	mol N / mol C	Skillicorn 1993; Cedergreen & Madsen 2002; Landolt 1986; Sale & Wetzel 1983
V_P,max (luxury)	5.0e-4	mol P / (mol C · h)	Paterson et al. 2020 ~10× baseline luxury rate (mid-range default)
V_N,max (luxury)	3.0e-3	mol N / (mol C · h)	Generic luxury-N rate, mid-range default
K_PO4 (luxury uptake)	1.0e-7	mol/L	Paterson et al. 2020 high-affinity Pi transporter
K_NH4 (luxury uptake)	4.0e-6	mol/L	Source-preference half-sat (mirrors K_N water)
K_NO3 (luxury uptake)	1.5e-5	mol/L	Source-preference half-sat
Q10 (uptake)	2.0	–	Eppley 1972 transporter scaling
k_catab (storage)	0.001	/h	Slow stored-pool hydrolysis under starvation
k_N homeostasis	0.01	/h	~3-day timescale; allows diurnal drift, corrects long-term

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	1.5e-3	/h	~0.15%/h base maintenance
K_O2 (respiration)	1.0e-5	mol/L	O2 half-sat for respiration
Osmoregulation cost	0.002	per PSU deviation	Osmoregulation respiratory load multiplier
Dark respiration factor	0.70	fraction	Heskel et al. 2013 LEDR; Atkin & Tjoelker 2003

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Frond mortality	1.25e-4	/h	~0.3%/day baseline senescence
O2 stress threshold	1.5	mg/L	O2 below this → mortality ×2
m_total,max	0.30	/h	Cap on combined mortality
Death → suspended fraction	0.10	fraction	10% suspended / 90% settled (fronds sink)
Surface death → suspended	0.10	fraction	Mirror of death-to-suspended

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	26.0	°C	Generic floating-plant optimum
T_lethal,photo	42.0	°C	Generic upper photosynthesis lethal
T_ref	T_REF_C (25)	°C	Standard biology reference temperature
Q10,photo	2.0	–	Standard
Q10,resp	2.2	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	12.0 / 35.0	°C	Stress onset
T_lethal (low / high)	3.0 / 42.0	°C	Lethal thresholds
m_thermal,max	0.02	/h	Max thermal mortality

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.5	–	Stress thresholds
pH lethal (low / high)	4.5 / 11.0	–	Lethal thresholds
m_pH,max	0.015	/h	Max pH-driven mortality

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater optimum
σ_S	4.0	PSU	Tolerance width
S_stress (low / high)	0.0 / 5.0	PSU	Stress thresholds
S_lethal (low / high)	0.0 / 10.0	PSU	Lethal thresholds
m_salinity,max	0.10	/h	Max salinity-driven mortality

Salvinia — divergent only

Free-floating water fern with hydrophobic-haired fronds that lift the leaf above the water line; sub-dominant in competition with Lemna. (Only divergences from the Floating macrophyte base are shown.)

Canopy & light

Symbol	Value	Units	Source / Rationale
k_frond,atten	1.5	m² / mol C	Geometrically derived from S. natans frond size + hair structures
SLA	1.3	m² / mol C	Geometric: ~1 cm frond, 1.33e-4 mol C per frond
Max cover fraction	0.95	fraction	Single-layer mat; τ=3 → 95% interception
kLa block at full cover	0.70	fraction	Janes 1998; Mitchell & Tur 1975 — Salvinia mats more porous than Lemna
P_max	3.0e-2	/h	~7–10 day doubling under 10h photoperiod (Lemon & Posluszny 2000; Walstad 1999)
I_K	30.0	µmol m⁻² s⁻¹	Floating plants near-saturate at low I

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	6e-6	mol/L	Low half-sat; surface atmospheric CO₂ access
CCM efficiency	0.15	fraction	C3 fern; primarily dissolved CO₂
K_HCO3	2.5e-3	mol/L	Madsen & Sand-Jensen 1991 — C3 ferns lack strong CCM
Aerial C fraction	0.90	fraction	Hydrophobic hairs lift fronds; stomata on aerial side
SLA_cm2_per_mg_C	2.0	cm² / mg C	Rhizoid-dominated; scaled by (1 − aerial_C_fraction) = 0.10 ⇒ ~0.2 cm² effective per mg frond C. Recalibrated from V1=5 (May 2026) in lockstep with rooted/submerged SLA reductions

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.0002	fraction	Smith et al. 1991 — floating plants invest little in allelochemistry; sub-hornwort

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	10.0	mol / mol	N-rich fast-growing tissue
C:N (max under N starvation)	20.0	mol / mol	Maximum C:N under N starvation
N:P	14.0	mol / mol	Near-Redfield

N & P uptake

Symbol	Value	Units	Source / Rationale
V_N,max (water)	1.5e-3	mol N / (mol C · h)	Dense root-hair-like absorptive tissue
K_N (water)	4e-6	mol/L	~0.056 mg N/L; high-affinity NH4
K_NO3 (water)	1.2e-5	mol/L	Lower NO3 affinity vs. NH4
K_P (water)	2.5e-7	mol/L	High P affinity
Q_P,max	0.025	mol P / mol C	Smaller P reservoir than Lemna (calibration knob for competition)
Q_N,min	0.004	mol N / mol C	Sale & Wetzel 1983; Cary & Weerts 1984 — Salvinia C:N 12–25
Q_N,max	0.015	mol N / mol C	Sale & Wetzel 1983; Cary & Weerts 1984 — replete tissue near C:N 12
V_P,max (luxury)	3.0e-4	mol P / (mol C · h)	Slower than Lemna (sub-dominant in competition)
V_N,max (luxury)	2.0e-3	mol N / (mol C · h)	Sub-Lemna luxury N rate
K_PO4 (luxury uptake)	1.5e-7	mol/L	Looser than Lemna (drives competitive outcome)

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	1.0e-3	/h	3.3% of P_max; preserves ratio used in floating base

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Frond mortality	1.25e-4	/h	~0.3%/day baseline (hardy in aquarium)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	24.0	°C	Calibrated for 22–26 °C aquarium range
T_lethal,photo	40.0	°C	Warm-water lethal
T_stress (low / high)	13.0 / 34.0	°C	Cold-intolerant lower; upper stress
T_lethal (low / high)	4.0 / 40.0	°C	Killed by frost; upper mirror
Q10,photo	2.2	–	Slightly elevated vs base
Q10,resp	2.2	–	Mirror

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.5	–	S. natans naturally pH 5–9
pH lethal (low / high)	4.5 / 11.0	–	–

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Strictly freshwater
σ_S	3.0	PSU	Narrower than base
S_stress (low / high)	0.0 / 4.0	PSU	No marine tolerance
S_lethal (low / high)	0.0 / 8.0	PSU	–

Duckweed / Lemna minor — divergent only

Tiny fast-growing angiosperm that displaces Salvinia by aggressive light pre-emption and tighter nutrient affinity. (Only divergences from the Floating macrophyte base are shown.)

Canopy & light

Symbol	Value	Units	Source / Rationale
k_frond,atten	10.0	m² / mol C	Tiny dense fronds intercept more light per unit C than Salvinia
SLA	3.8	m² / mol C	Geometric: ~2 mm diameter frond, 0.5 mg fresh each
Max cover fraction	0.90	fraction	Single-layer dense mat
Uses total cover for space	False	bool	Lemna grows in gaps of larger competitor mats
kLa block at full cover	0.92	fraction	Pokorný & Rejmánková 1983; Morris & Barker 1977 — Lemna nearly true lid
Competitive displacement	0.015	/h	Calibrated for 60–90 d Salvinia decline under Lemna dominance (aquarist observation)
Competition threshold	0.45	cover frac	Activation at 45% total cover
P_max	4.5e-2	/h	2–3 day doubling at 16h photoperiod (Hillman 1961; Landolt 1986; Skillicorn 1993)
I_K	25.0	µmol m⁻² s⁻¹	Thin fronds (~0.3 mm) saturate at low I

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	5e-6	mol/L	Low half-sat; surface atmospheric CO₂ access
CCM efficiency	0.25	fraction	Angiosperm; greater HCO₃ use than Salvinia (C3 fern)
K_HCO3	1.5e-3	mol/L	Angiosperm with modest CCM (intermediate)
Aerial C fraction	0.80	fraction	Thin fronds lie flat; some submerged surface
SLA_cm2_per_mg_C	1.0	cm² / mg C	Single short rhizoid; ~30 cm²/g dry. Scaled by (1 − aerial_C_fraction) = 0.20 ⇒ ~0.2 cm² effective per mg frond C. Recalibrated from V1=2 (May 2026) in lockstep with rooted/submerged SLA reductions

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.0002	fraction	Mussatto et al. 2017 — low but detectable Lemnaceae phenolic exudation

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	8.0	mol / mol	Skillicorn 1993; Landolt 1986 — C:N 7–10 N-replete
C:N (max under N starvation)	18.0	mol / mol	Maximum C:N under N starvation
N:P	14.0	mol / mol	Near-Redfield

N & P uptake

Symbol	Value	Units	Source / Rationale
V_N,max (water)	2.0e-3	mol N / (mol C · h)	Dense rootlet absorptive tissue
K_N (water)	3e-6	mol/L	Cedergreen & Madsen 2002 — Lemna direct measurement, higher affinity than Salvinia
K_NO3 (water)	1.0e-5	mol/L	Mirror low-K
K_P (water)	2.0e-7	mol/L	High P affinity
K_N (total, helper)	6e-6	mol/L	Matches water uptake parameters
K_NH4 (helper)	3e-6	mol/L	Matches water uptake parameters
K_NO3 (helper)	1.0e-5	mol/L	Matches water uptake parameters
K_PO4 (helper)	2e-7	mol/L	Matches water uptake parameters
Q_P,max	0.030	mol P / mol C	Paterson 2020 + Skillicorn 1993 polyphosphate uncoupling, P% DW 0.03–2.8%
Q_N,min	0.010	mol N / mol C	Set so total C:N floor ≈ 6 (documented Lemna minimum)
Q_N,max	0.040	mol N / mol C	Skillicorn 1993; Cedergreen & Madsen 2002 — total C:N ~6–7 max-N
V_P,max (luxury)	6.0e-4	mol P / (mol C · h)	Faster than Salvinia luxury kernel
V_N,max (luxury)	4.0e-3	mol N / (mol C · h)	Faster luxury N than Salvinia
K_PO4 (luxury uptake)	8.0e-8	mol/L	Tighter than Salvinia (high-affinity transporter)
K_NH4 (luxury uptake)	3.0e-6	mol/L	Matches K_N water
K_NO3 (luxury uptake)	1.0e-5	mol/L	Matches K_NO3 water

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	1.5e-3	/h	3.3% of P_max; preserves ratio

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Frond mortality	1.5e-4	/h	~0.36%/day; tiny fragile fronds turn over slightly faster

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	25.0	°C	Generic warm temperate optimum
T_lethal,photo	40.0	°C	Upper lethal photo
T_stress (low / high)	10.0 / 33.0	°C	Cold-hardier than Salvinia
T_lethal (low / high)	2.0 / 40.0	°C	Cold-hardy via turion formation
Q10,photo	2.1	–	Slightly below Salvinia
Q10,resp	2.2	–	Mirror base

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.0 / 9.5	–	Wider low-end than Salvinia
pH lethal (low / high)	4.0 / 10.5	–	–

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	2.5	PSU	Narrow (salt-sensitive)
S_stress (low / high)	0.0 / 3.0	PSU	More sensitive than Salvinia
S_lethal (low / high)	0.0 / 6.0	PSU	–

Submerged macrophyte base

Generic submerged-plant kinetic skeleton — stems suspended in the water column with leaf-borne uptake and Beer-Lambert self-shading.

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
K:C	5.0e-2	mol K / mol C	Macrophyte K:C anchor (mirrors floating/rooted)
B:C	5.0e-5	mol B / mol C	Marschner 1995 — vascular cell-wall pectin RG-II
K_K (growth)	1.0e-5	mol/L	Mirror of floating base K leaf scale

Stem geometry & light

Symbol	Value	Units	Source / Rationale
Stem depth	7.5	cm	Mid-tank in 15 cm tank (scenario-overridable)
k_stem,atten	120.0	L / (mol C · m)	Kirk 1994; Spence 1975 — macrophyte tissue ~40% of phytoplankton absorbance per mol C
P_max	0.006	/h	~0.14/day generic submerged-macrophyte rate
I_K	30.0	µmol m⁻² s⁻¹	Generic submerged-macrophyte half-sat

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	5e-6	mol/L	Generic submerged CO₂ half-sat
CCM efficiency	0.35	fraction	Moderate HCO₃ use; subclasses override
K_HCO3	1.5e-3	mol/L	Madsen & Sand-Jensen 1991 — mid-range for submerged macrophytes with CCM
Sc/o	80.0	–	Standard C3 RuBisCO
PQ	1.0	mol O₂ / mol C	Standard
DOC excretion fraction	0.05	fraction	Generic excretion fraction

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	17.0	mol / mol	Submerged macrophyte structural ratio
C:N (max under N starvation)	35.0	mol / mol	Maximum C:N under N starvation
N:P	22.0	mol / mol	Generic submerged ratio

N & P uptake

Symbol	Value	Units	Source / Rationale
V_N,max (water)	1.2e-3	mol N / (mol C · h)	Generic high-affinity submerged macrophyte uptake
V_P,max (water)	8e-5	mol P / (mol C · h)	Generic submerged macrophyte P uptake
K_N (water)	5e-6	mol/L	~0.07 mg N/L (high-affinity leaf system)
K_NO3 (water)	2e-5	mol/L	Lower NO3 affinity
K_P (water)	4e-7	mol/L	~0.012 mg P/L
NO₃ preference (dark / light)	0.1 / 0.4	fraction	Standard producer source preference
K_N (total, helper)	8e-6	mol/L	Producer helper
K_NH4 (helper)	5e-6	mol/L	Producer helper
K_NO3 (helper)	2e-5	mol/L	Producer helper
K_PO4 (helper)	4e-7	mol/L	Producer helper
Min photo N factor	0.10	fraction	Floor on photo-N factor

Droop internal stores

Symbol	Value	Units	Source / Rationale
Q_P,min	0.004	mol P / mol C	Gerloff 1966 critical tissue P, slightly lower than floating (more cellulose)
Q_P,max	0.025	mol P / mol C	Madsen & Cedergreen 2002; Pedersen et al. 2013 vacuolar Pi
Q_N,min	0.0015	mol N / mol C	~0.3 × Q_N,max
Q_N,max	0.005	mol N / mol C	Gerloff & Krombholz 1966; Best 1979; Madsen & Cedergreen 2002 — C:N 16–25
V_P,max (luxury)	2.0e-4	mol P / (mol C · h)	Proportional to lower P_max vs. Lemna
V_N,max (luxury)	1.5e-3	mol N / (mol C · h)	Generic submerged-macrophyte luxury rate
K_PO4 (luxury uptake)	1.5e-7	mol/L	Pedersen et al. 2013 — Lk ≈ 0.15 µM for M. spicatum
K_NH4 (luxury uptake)	5.0e-6	mol/L	Source preference half-sat
K_NO3 (luxury uptake)	2.0e-5	mol/L	Source preference half-sat
Q10 (uptake)	2.0	–	Eppley 1972 transporter scaling
k_catab (storage)	0.001	/h	Slow stored-pool hydrolysis
k_N homeostasis	0.01	/h	4-day timescale matched to recalibrated Q_N,max

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	6e-4	/h	~0.06%/h (10% of P_max)
K_O2 (respiration)	1.0e-5	mol/L	O₂ half-sat for respiration
Osmoregulation cost	0.002	per PSU deviation	Osmoregulation cost
Dark respiration factor	0.65	fraction	Heskel et al. 2013; Atkin & Tjoelker 2003 LEDR

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Stem mortality	1.5e-4	/h	~0.36%/day baseline senescence
O2 stress threshold	1.5	mg/L	Mortality ×2 threshold
m_total,max	0.30	/h	Mortality cap
Death → suspended fraction	0.30	fraction	Higher than floating (fragments, no fronds to sink)
Surface death → suspended	0.30	fraction	Mirror

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	22.0	°C	Temperate submerged optimum
T_lethal,photo	38.0	°C	Upper lethal photo
T_ref	T_REF_C (25)	°C	Standard biology reference
Q10,photo	2.0	–	Standard
Q10,resp	2.2	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	8.0 / 32.0	°C	Stress thresholds (temperate)
T_lethal (low / high)	2.0 / 38.0	°C	Cold-hardy lower; upper lethal
m_thermal,max	0.02	/h	Max thermal mortality

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.5	–	Broad tolerance (hallmark)
pH lethal (low / high)	4.5 / 11.0	–	–
m_pH,max	0.015	/h	Max pH mortality

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	4.0	PSU	Broad salinity tolerance width
S_stress (low / high)	0.0 / 5.0	PSU	–
S_lethal (low / high)	0.0 / 10.0	PSU	–
m_salinity,max	0.10	/h	Max salinity mortality

Hornwort / Ceratophyllum — divergent only

Rootless K-strategist submerged angiosperm that drives high-pH soft-water systems via aggressive HCO₃⁻ stripping and a strong polyphenol allelopathy. (Only divergences from the Submerged macrophyte base are shown.)

Stem geometry & light

Symbol	Value	Units	Source / Rationale
k_stem,atten	120.0	L / (mol C · m)	Spence 1975 — dense hornwort mats ~70–80% attenuation per 20 cm
P_max	6e-3	/h	Nichols & Shaw 1986; Barko & Smart 1981 — net doubling 15–25 d
I_K	20.0	µmol m⁻² s⁻¹	Shade-tolerant; persists under floating mats and turbid water
SLA_cm2_per_mg_C	100.0	cm² / mg C	Brönmark 1985; Mony et al. 2010 — highly dissected filiform leaves; the largest epiphytic substrate of any tracked macrophyte. Recalibrated from V1=300 (May 2026) against Walstad-target leaf area (~10× static substrate at peak macrophyte biomass)

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	5e-6	mol/L	Generic submerged CO₂ half-sat
CCM efficiency	0.45	fraction	Prins & Elzenga 1989 — strong HCO₃⁻ user; raises pH in hard water
K_HCO3	0.6e-3	mol/L	Maberly & Madsen 2002 — one of most aggressive HCO₃⁻ strippers
DOC excretion fraction	0.06	fraction	Slightly elevated; phenolic exudates

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.001	fraction	Hilt & Gross 2008; Nakai 2000; Hilt 2006 — calibrated to <50 µg GAE/L field window

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	17.0	mol / mol	Duarte 1992; Vestergaard & Sand-Jensen 2000 — C:N 15–20
C:N (max under N starvation)	35.0	mol / mol	Maximum under N starvation
N:P	22.0	mol / mol	N:P 20–25 (Duarte 1992)

N & P uptake

Symbol	Value	Units	Source / Rationale
V_N,max (water)	1.2e-3	mol N / (mol C · h)	Rattray et al. 1991 — high-affinity stem uptake
V_P,max (water)	8e-5	mol P / (mol C · h)	Generic submerged P uptake
K_N (water)	5e-6	mol/L	~0.07 mg N/L — high affinity
K_NO3 (water)	2e-5	mol/L	Lower NO3 affinity
K_P (water)	4e-7	mol/L	~0.012 mg P/L
Q_P,min	0.004	mol P / mol C	Generic submerged structural floor
Q_P,max	0.025	mol P / mol C	Best 1977 — vacuolar Pi in Ceratophyllum
Q_N,min	0.0015	mol N / mol C	Mirror of submerged base
Q_N,max	0.005	mol N / mol C	Gerloff & Krombholz 1966; Best 1979 — C:N 16–25 for C. demersum
V_P,max (luxury)	2.0e-4	mol P / (mol C · h)	Proportional to lower P_max
V_N,max (luxury)	1.5e-3	mol N / (mol C · h)	Generic submerged luxury rate
K_PO4 (luxury uptake)	1.5e-7	mol/L	Pedersen et al. 2013 (M. spicatum)
K_NH4 (luxury uptake)	5.0e-6	mol/L	Source preference half-sat
K_NO3 (luxury uptake)	2.0e-5	mol/L	Source preference half-sat

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	6e-4	/h	10% of P_max ratio
K_O2 (respiration)	1e-5	mol/L	O₂ half-sat for respiration

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Stem mortality	1.5e-4	/h	~0.36%/day baseline
O2 stress threshold	1.5	mg/L	Tolerates moderate hypoxia
Death → suspended fraction	0.35	fraction	Slightly higher than base (fragmenting stems)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	22.0	°C	Best 1977 — temperate hardy, optimum 20–24 °C
T_lethal,photo	38.0	°C	Upper lethal
T_ref	20.0	°C	Hornwort-specific reference
T_stress (low / high)	8.0 / 32.0	°C	–
T_lethal (low / high)	2.0 / 38.0	°C	Survives near-freezing

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.5	–	Thrives at pH 6–9
pH lethal (low / high)	4.5 / 11.0	–	–

Salinity envelope

Symbol	Value	Units	Source / Rationale
σ_S	2.0	PSU	Narrow (no marine tolerance)
S_stress (low / high)	0.0 / 3.0	PSU	–
S_lethal (low / high)	0.0 / 6.0	PSU	–

Rooted macrophyte base

Two-compartment plant with shoot (leaf-borne water-column uptake) and root (sediment pore-water uptake), aerenchyma-mediated rhizosphere O₂ release and pore CO₂ access, and phloem translocation between compartments.

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
K:C	5.0e-2	mol K / mol C	Quigg / Sterner & Elser / Marschner 2012 — plant K:C anchor, ~2× universal; ~50 mg K/g tissue C
B:C	5.0e-5	mol B / mol C	O'Neill 2004; Kobayashi 1996; Marschner 1995 — RG-II pectin crosslinker, ~50 µg B/g DW

Attachment

Symbol	Value	Units	Source / Rationale
Attached surface	""	string	Empty = first non-dynamic static surface

Canopy & light

Symbol	Value	Units	Source / Rationale
P_max	0.010	/h	~0.24/day generic rooted-macrophyte rate (10–100× slower than algae)
I_K	20.0	µmol m⁻² s⁻¹	Low-light adapted
k_canopy,atten	0.0	m² / mol C	Default: rosette plants don't form a water-column canopy
k_shoot,atten	0.0	L / (mol C · m)	Default: rosette plants don't attenuate at depth

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	8e-6	mol/L	Generic rooted CO₂ half-sat
CCM efficiency	0.25	fraction	Moderate CCM HCO₃⁻ use
K_HCO3	1.5e-3	mol/L	Madsen & Sand-Jensen 1991; Maberly & Madsen 2002 — Elodea/Potamogeton range
Sc/o	80.0	–	Standard C3 RuBisCO
PQ	1.0	mol O₂ / mol C	Standard
DOC excretion fraction	0.05	fraction	Standard producer excretion
f_root,CO2	0.0	fraction	Default: no pore-CO2 access; subclasses override
f_root,O2 release	0.0	fraction	Default: no aerenchyma ROL; subclasses set per literature (1–8% of GPP)

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N (shoot)	15.0	mol / mol	Structural C:N (rooted shoot tissue)
C:N (shoot, max under N starvation)	30.0	mol / mol	Maximum under N starvation
N:P (shoot)	20.0	mol / mol	Redfield-like; macrophytes P-poor
C:N (root)	20.0	mol / mol	Roots more C-rich / N-poor than shoots
N:P (root)	30.0	mol / mol	Generic root stoichiometry

Acquisition split (shoot vs root)

Symbol	Value	Units	Source / Rationale
f_water	0.30	fraction	Barko & Smart 1985; Carignan & Kalff 1980 — sediment-dominated default
f_root	0.70	fraction	Barko & Smart 1985 — 60–90% of P from sediment in most species
α_root	0.25	fraction	Lambers et al. 2008 — 20–40% below-ground C allocation
k_translocate	0.005	/h	Marschner 1995 — phloem mass-flow ~3-day timescale. Conductance scales by the phloem bottleneck `min(shoot_C, root_C)` (narrower conduit limits transport), so the flux vanishes as either compartment senesces — equals the legacy `× root_C` scaling whenever shoot ≥ root (the established case) and bounds the term's Jacobian to ±k, removing a die-off stiffness trap

N & P uptake (shoot, water-column)

Symbol	Value	Units	Source / Rationale
V_N,max (water)	5e-4	mol N / (mol C · h)	Lower than microalgae (leaf area-limited)
V_P,max (water)	3e-5	mol P / (mol C · h)	Lower than microalgae
K_N (water)	1e-5	mol/L	Nurnberg 1984 — K_NH4 10–50 µmol/L for submersed leaves
K_NO3 (water)	4e-5	mol/L	Lower NO3 affinity
K_P (water)	5e-7	mol/L	Bole & Allan 1978 — leaf K_P
K_K (water)	1e-5	mol/L	~0.39 mg K/L; leaf uptake (higher than phytoplankton)
V_P,max (luxury, water)	8.0e-5	mol P / (mol C · h)	Generic shoot luxury P
V_N,max (luxury, water)	6.0e-4	mol N / (mol C · h)	Generic shoot luxury N
K_PO4 (luxury water uptake)	5.0e-7	mol/L	Leaf transporter half-sat
K_NH4 (luxury water uptake)	1.0e-5	mol/L	Leaf transporter half-sat
K_NO3 (luxury water uptake)	4.0e-5	mol/L	Leaf NO3 half-sat
K_N (helper)	1e-5	mol/L	Inline-uptake half-sat (dual-uptake logic)
K_NH4 (helper)	5e-6	mol/L	Inline-uptake half-sat
K_NO3 (helper)	2e-5	mol/L	Inline-uptake half-sat
K_PO4 (helper)	5e-7	mol/L	Inline-uptake half-sat
NO₃ preference (dark / light)	0.1 / 0.4	fraction	Source preference
Min photo N factor	0.15	fraction	Floor on photo N factor (slightly higher than algae)

N & P uptake (root, pore-water)

Symbol	Value	Units	Source / Rationale
K_N (pore)	2e-6	mol/L	Epstein & Hagen 1952; Caffrey & Kemp 1992 — high-affinity root system I
K_NO3 (pore)	8e-6	mol/L	Root NO3 half-sat
K_P (pore)	1e-7	mol/L	Barko et al. 1991 — K_P_pore ~0.1 µmol/L
K_K (pore)	2e-6	mol/L	Schroeder & Fang 1991; Britto & Kronzucker 2008 — HAK/KUP at ~0.05 mg K/L
V_P,max (luxury, root)	2.0e-4	mol P / (mol C · h)	~3× shoot (Epstein & Hagen 1952; Caffrey & Kemp 1992)
V_N,max (luxury, root)	1.5e-3	mol N / (mol C · h)	~3× shoot luxury rate
K_PO4 (luxury pore uptake)	1.0e-7	mol/L	Pedersen et al. 2013 — root high-affinity Pi (M. spicatum)
K_NH4 (luxury pore uptake)	2.0e-6	mol/L	Root high-affinity
K_NO3 (luxury pore uptake)	8.0e-6	mol/L	Root NO3 half-sat
V_K,max	1.5e-3	mol K / (mol C · h)	~3× V_N,max to accommodate K:C anchor + luxury

Droop internal stores

Symbol	Value	Units	Source / Rationale
Q_P,min	0.003	mol P / mol C	Gerloff 1966 critical tissue P
Q_P,max	0.020	mol P / mol C	Madsen & Cedergreen 2002; Barko et al. 1991; Carignan & Kalff 1980
Q_N,min	0.002	mol N / mol C	~0.25 × Q_N,max
Q_N,max	0.008	mol N / mol C	Barko & Smart 1981; Madsen & Cedergreen 2002; Lambers 2008 — C:N 15–30
Q10 (uptake)	2.0	–	Eppley 1972
k_catab (storage)	0.001	/h	Slow stored-pool hydrolysis
k_N homeostasis	0.01	/h	4-day timescale (recalibrated with Q_N,max anchor)

Sediment coupling

Symbol	Value	Units	Source / Rationale
Pore-water volume	0.02	L	Default; should match PoreWaterDiffusion process
Fe-oxide sufficient	1.0e-5	mol	Rhizosphere Fe acquisition threshold (proxy for pore Fe²⁺)

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	8e-4	/h	~0.08%/h base; must scale with P_max in subclasses
K_O2 (respiration)	1.0e-5	mol/L	O₂ half-sat for respiration
Root respiration	0.001/24 (~4.17e-5)	/h	Lambers et al. 2008 — roots ~30–50% of 0.5–2%/day whole-plant respiration
Osmoregulation cost	0.002	per PSU deviation	Osmoregulation cost
Dark respiration factor	0.65	fraction	Heskel 2013; Atkin & Tjoelker 2003; Turnbull et al. 2005 LEDR

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Root mortality	0.005/24 (~2.08e-4)	/h	Sand-Jensen 1975; Chambers & Kalff 1985 — 0.3–1%/day temperate
Shoot mortality	0.003/24 (~1.25e-4)	/h	~0.3%/day baseline leaf senescence
O2 stress threshold	2.0	mg/L	O2 below → shoot mortality ×3
m_total,max	0.30	/h	Mortality cap
Death → suspended fraction	0.05	fraction	Mostly settled (heavy leaf litter)
Surface death → suspended	0.05	fraction	Mirror

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	24.0	°C	Generic rooted-macrophyte optimum
T_lethal,photo	38.0	°C	Upper lethal photo
T_ref	T_REF_C (25)	°C	Standard biology reference
Q10,photo	2.0	–	Standard
Q10,resp	2.2	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	15.0 / 30.0	°C	Tropical-aroid lower stress; upper
T_lethal (low / high)	5.0 / 38.0	°C	–
m_thermal,max	0.02	/h	Max thermal mortality

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	–
pH lethal (low / high)	5.0 / 10.5	–	–
m_pH,max	0.015	/h	Max pH mortality

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	3.0	PSU	Tolerance width
S_stress (low / high)	0.0 / 5.0	PSU	–
S_lethal (low / high)	0.0 / 15.0	PSU	Slightly more tolerant than other macrophytes
m_salinity,max	0.10	/h	Max salinity mortality

Vallisneria — divergent only

Tall strap-leaved rooted angiosperm with a canopy that attenuates water-column light and balanced shoot/root uptake. (Only divergences from the Rooted macrophyte base are shown.)

Canopy & light

Symbol	Value	Units	Source / Rationale
P_max	1.5e-3	/h	Titus & Adams 1979 — optimal 0.04–0.10/day for V. americana
I_K	45.0	µmol m⁻² s⁻¹	Light-demanding (higher than shade-tolerant rosettes)
Light saturation	200.0	µmol m⁻² s⁻¹	Informational saturation point
Photoinhibition threshold	1200.0	µmol m⁻² s⁻¹	Informational photoinhibition threshold
k_canopy,atten	0.45	m² / mol C	Sand-Jensen 1998; Madsen et al. 2001; Titus & Adams 1979 — SLA × k_extinction
k_shoot,atten	40.0	L / (mol C · m)	Tall strap-leaves attenuate at depth (Beer-Lambert)
SLA_cm2_per_mg_C	17.0	cm² / mg C	Madsen & Brix 1997 — strap leaves, ~100–200 cm²/g dry weight. Recalibrated from V1=50 (May 2026) against Walstad-target leaf area (~10× static substrate at peak macrophyte biomass)

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	2.5e-5	mol/L	Generic Vallisneria-scale half-sat (with HCO3 supplementation)
CCM efficiency	0.40	fraction	Prins & Elzenga 1989 — strong bicarbonate user
K_HCO3	0.8e-3	mol/L	Maberly 1985 — Elodea/Potamogeton high-affinity CCM
f_root,CO2	0.30	fraction	Prins & Elzenga 1989; Smits et al. 1990 — supplemental pore CO2 (less than Crypt)
f_root,O2 release	0.06	fraction	Sand-Jensen et al. 1982 — Vallisneria ROL ~5–8% of GPP

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.0003	fraction	Hilt 2006 — ~1/3 of hornwort baseline; field-realistic

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N (shoot)	20.0	mol / mol	Structural shoot ratio
C:N (shoot, max under N starvation)	40.0	mol / mol	Maximum under N starvation
N:P (shoot)	28.0	mol / mol	Leaf N:P
C:N (root)	16.0	mol / mol	Roots slightly less C-rich than leaves
N:P (root)	22.0	mol / mol	Root N:P

Acquisition split

Symbol	Value	Units	Source / Rationale
f_water	0.45	fraction	More balanced than Crypt; exploits open-water NH4 via leaves
f_root	0.55	fraction	Less sediment-dominated than Crypt
α_root	0.22	fraction	Slightly less rhizome-heavy than Crypt; runners carry own C

N & P uptake

Symbol	Value	Units	Source / Rationale
K_N (water)	1.2e-5	mol/L	Vallisneria-scale leaf half-sat
K_N (pore)	1.8e-6	mol/L	High-affinity root
K_P (water)	2.5e-7	mol/L	Vallisneria-scale leaf P
K_P (pore)	4.0e-8	mol/L	High-affinity root P
Q_P,min	0.003	mol P / mol C	Mirror of rooted base
Q_P,max	0.020	mol P / mol C	Mirror of rooted base
Q_N,min	0.0015	mol N / mol C	~0.25 × Q_N,max
Q_N,max	0.006	mol N / mol C	Barko & Smart 1981; Tessier et al. 2008 — V. americana C:N 18–25
V_P,max (luxury, water)	8.0e-5	mol P / (mol C · h)	Faster luxury kinetic vs base
V_P,max (luxury, root)	2.0e-4	mol P / (mol C · h)	Root luxury P
V_N,max (luxury, water)	6.0e-4	mol N / (mol C · h)	Fast-grower luxury N
V_N,max (luxury, root)	1.5e-3	mol N / (mol C · h)	Root luxury N
K_PO4 (luxury water uptake)	2.5e-7	mol/L	Leaf transporter half-sat
K_PO4 (luxury pore uptake)	4.0e-8	mol/L	Root high-affinity
K_NH4 (luxury water uptake)	1.2e-5	mol/L	Leaf NH4 half-sat
K_NH4 (luxury pore uptake)	1.8e-6	mol/L	Root NH4 high-affinity
K_NO3 (luxury water uptake)	4.0e-5	mol/L	Leaf NO3 half-sat
K_NO3 (luxury pore uptake)	8.0e-6	mol/L	Root NO3 half-sat

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	1.875e-4	/h	Preserves 0.125 ratio with P_max (matches Crypt scaling)
Root respiration	2.0e-4	/h	Somewhat faster turnover than Crypt

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Root mortality	5.0e-5	/h	~0.12%/day
Shoot mortality	3.5e-5	/h	~0.084%/day
O2 stress threshold	1.5	mg/L	O2 below → shoot mortality ×3
O2 anoxia threshold	0.2	mg/L	Informational anoxia threshold

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	24.0	°C	Warm optimum
T_stress (low / high)	15.0 / 28.0	°C	–
T_lethal (low / high)	12.0 / 32.0	°C	Cooler-tolerant than Crypt
Q10,photo	2.1	–	Slightly elevated
Q10,resp	2.1	–	Mirror

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	Tolerates hard water well
pH lethal (low / high)	5.5 / 10.5	–	More alkaline-tolerant

Cryptocoryne — divergent only

Tropical rosette aroid that anchors the Walstad-tank archetype — sediment-dominated uptake, no CCM, primary CO₂ acquired via aerenchyma from pore water. (Only divergences from the Rooted macrophyte base are shown.)

Canopy & light

Symbol	Value	Units	Source / Rationale
P_max	5.0e-4	/h	Barko & Smart 1985; Sand-Jensen 1983 — submersed macrophyte low end (~0.14%/day net)
I_K	22.0	µmol m⁻² s⁻¹	Very shade-tolerant
Light saturation	80.0	µmol m⁻² s⁻¹	Informational saturation point
Photoinhibition threshold	800.0	µmol m⁻² s⁻¹	Informational high-light inhibition
SLA_cm2_per_mg_C	13.0	cm² / mg C	Madsen & Cedergreen 2002 — broad rosette leaves, ~80–150 cm²/g dry weight. Recalibrated from V1=40 (May 2026) against Walstad-target leaf area (~10× static substrate at peak macrophyte biomass)

Carbon kinetics

Symbol	Value	Units	Source / Rationale
K_CO2	3.5e-5	mol/L	~1.5 mg CO2/L half-sat
CCM efficiency	0.0	fraction	Uses CO2 only (no CCM)
K_HCO3	1.5e-3	mol/L	Irrelevant (CCM efficiency=0); kept at base default
f_root,CO2	0.70	fraction	Walstad 1999; Smits et al. 1990 — primary CO2 source from pore water (no CCM)
f_root,O2 release	0.03	fraction	Sand-Jensen et al. 1982; Caffrey & Kemp 1991 — slow rosette ROL ~2–4% of GPP

Allelochemistry

Symbol	Value	Units	Source / Rationale
Allelo release fraction	0.0003	fraction	Walstad 1999 — phenolic suppression in low-tech tanks; ~1/3 hornwort baseline

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N (shoot)	18.0	mol / mol	Leaf C:N
C:N (shoot, max under N starvation)	35.0	mol / mol	Maximum under N stress
N:P (shoot)	30.0	mol / mol	P-conservative species
C:N (root)	15.0	mol / mol	Roots more N-rich than leaves
N:P (root)	25.0	mol / mol	Root N:P

Acquisition split

Symbol	Value	Units	Source / Rationale
f_water	0.20	fraction	Strongly substrate-dominated
f_root	0.80	fraction	80% N from pore water (Walstad-tank archetype)
α_root	0.28	fraction	Rhizome-heavy plant (high end of 25–35%)

N & P uptake

Symbol	Value	Units	Source / Rationale
K_N (water)	1.5e-5	mol/L	Lower leaf affinity
K_N (pore)	2.0e-6	mol/L	High-affinity root
K_P (water)	3.0e-7	mol/L	Leaf P half-sat
K_P (pore)	5.0e-8	mol/L	High-affinity root P
Q_P,min	0.003	mol P / mol C	Mirror of rooted base
Q_P,max	0.025	mol P / mol C	Walstad 1999 — long persistence under pulse-feeding (bigger Pi store than Vallisneria)
Q_N,min	0.0015	mol N / mol C	~0.3 × Q_N,max
Q_N,max	0.005	mol N / mol C	Madsen & Cedergreen 2002; Lambers et al. 2008 — tropical-aroid C:N 18–30
V_P,max (luxury, water)	6.0e-5	mol P / (mol C · h)	Slow K-strategist luxury P
V_P,max (luxury, root)	1.5e-4	mol P / (mol C · h)	Root luxury P (slower than Vallisneria)
V_N,max (luxury, water)	4.0e-4	mol N / (mol C · h)	Slow luxury N
V_N,max (luxury, root)	1.0e-3	mol N / (mol C · h)	Root luxury N
K_PO4 (luxury water uptake)	3.0e-7	mol/L	Leaf transporter half-sat
K_PO4 (luxury pore uptake)	5.0e-8	mol/L	High-affinity Pi (upregulated under low-PO4)
K_NH4 (luxury water uptake)	1.5e-5	mol/L	Leaf NH4 half-sat
K_NH4 (luxury pore uptake)	2.0e-6	mol/L	Root high-affinity
K_NO3 (luxury water uptake)	4.0e-5	mol/L	Leaf NO3 half-sat
K_NO3 (luxury pore uptake)	8.0e-6	mol/L	Root NO3 half-sat

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	6.25e-5	/h	Preserves 0.125 ratio with P_max
Root respiration	5.0e-5	/h	~0.12%/day; rhizome has low respiration

Mortality & death routing

Symbol	Value	Units	Source / Rationale
Root mortality	3.0e-5	/h	~0.07%/day; very slow turnover
Shoot mortality	2.0e-5	/h	~0.048%/day; very hardy
O2 stress threshold	1.0	mg/L	Less O2-sensitive than algae
O2 anoxia threshold	0.1	mg/L	Informational anoxia threshold

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_opt	24.0	°C	Tropical optimum
T_stress (low / high)	15.0 / 30.0	°C	–
T_lethal (low)	10.0	°C	Lower lethal (warmer than Vallisneria)
Q10,photo	2.0	–	Standard
Q10,resp	2.0	–	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 8.5	–	Kasselmann 2003 — accelerated senescence above pH 8.5
pH lethal (low / high)	4.5 / 9.5	–	Upper lethal narrower than Vallisneria

Consumers

Consumers — grazers, detritivores, and the first predator (hydra) — share a Holling-II ingestion / SDA-respiration / stoichiometric-homeostasis skeleton, layered with hypoxia, NH₃, NO₂, Cu²⁺, H₂S, and allelochemical tolerance kernels. Stage-structured zooplankton (daphnia, copepod, ostracod) add a dormant resting-pool channel; shrimp and snails add molting + shell Ca stoichiometry; gape-limited predators (hydra) target a specific prey life-stage.

Consumer symbol glossary

Symbol	Meaning
Imax	Maximum specific ingestion rate (per h per mol body C)
K_C	Holling-II food-density half-saturation (mol C/L)
SDA fraction	Specific dynamic action — heat increment of feeding (fraction of assimilated C)
Nocturnal feeding fraction	Day-to-night ingestion ratio (>1 means more active at night)
Assim N / P multiplier	Per-element assimilation efficiency relative to C (typically 1.10–1.15)
RQ	Respiratory quotient — mol CO₂ released per mol O₂ consumed
R_maint, K_O2 (resp)	Maintenance respiration rate and O₂ Monod for respiration
Q10,ingestion / resp / mort	Temperature sensitivities per process
K_O2 (activity)	O₂ Monod for ingestion (separate from respiration)
K_NH3,tox / K_NO2,tox / K_Cu,tox / K_H2S,tox	Mortality half-saturations for each toxicant (Hill-2 with same K)
m_X,max	Maximum mortality rate from stressor X (NH3, NO2, Cu, H2S, hypoxia, thermal, pH, salinity, viral, starvation, crowding)
K_allelo,polyphenol / K_allelo,cyanotoxin / K_allelo,cyanotoxin,feeding	Half-sats for allelochemical kernels (mortality and feeding suppression)
K_crowding	Density half-saturation for crowding mortality (per-volume or per-area)
Fe:C, Cu:C, ...	Per-element body composition ratios (subset of producer trace-metal anchor for consumers)
Shell Ca per body C	Calcareous structure routed to CaCO₃ substrate on death
Molt rate, molt Ca per C	Crustacean molting interval (Q10-scaled) and Ca cost per molt
dev_a, dev_α, dev_b	Belehrádek juvenile-to-adult development parameters (h·°C^
τ_brood	Mean berried period for Erlang-3 reproduction pipeline (days)
t_mature	Sexual maturity age (days)
Dormant base / max fraction	Resting-egg (ephippia / cyst) allocation floor and ceiling
Hatch rate (max)	Maximum specific hatching rate of dormant pool (per h)
Dormant mortality	Resting-pool turnover (per h; viability often years to centuries)
Feces C:N, Feces → suspended fraction	Egesta stoichiometry and routing between suspended/settled detritus
Sloppy feeding DOM fraction	Fraction of egesta released as cytoplasmic DOM (Møller 2005)
K_viral, m_viral,max	Density half-sat and max rate for viral-lysis kernel (only ciliate / nanoflagellate)
SURFACE_PROTECTION_PROFILE	Dispatcher for prey-access modifier — `NONE` (planktonic / macrophyte / consumer prey, no surface kernel) or `BIOFILM_RESIDENT` (everything that lives on a surface — bacteria, nitrifiers, periphyton-forming algae — gets `1 − protection` shelter that interpolates from a roughness-based M=0 floor up to a species-specific M=1 cap)

The shared consumer machinery lives in species/consumer.py (Holling-II / SDA / homeostasis / mortality), species/consumer_food.py (the catalogue of food-type structural recipes), species/consumer_removal.py (the mixin that routes intake back into prey pools, including stage-targeted juvenile prey), species/_element_release.py (per-element respiration release + mortality close-out), and species/access.py (single source of truth for prey accessibility: effective_access = static_access × density_refugia × M-modifier).

Consumer base

Shared anchors for every grazer / detritivore / predator. Concrete species override individual rows where they deviate.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
SDA fraction	0.20	fraction of assim C	Specific dynamic action — heat increment of feeding, 10–25% of assimilated energy in crustaceans (Gnaiger 1983)
Nocturnal feeding fraction	0.7	fraction of day rate	Diel ingestion scaling
O2-limited waste excretion	False	bool	Excrete excess C as DIC under O2 limit
RQ	0.85	mol CO₂ / mol O₂	Mixed protein/lipid catabolism (Gnaiger 1983)
Assim N multiplier	1.10	× C assim	N assimilated ~10% more efficiently than C (Sterner & Elser 2002; Urabe et al. 1995)
Assim P multiplier	1.15	× C assim	P assimilated ~15% more efficiently than C (Sterner & Elser 2002; Urabe et al. 1995)
Sloppy feeding DOM fraction	0.10	fraction of egest	Sloppy-feeding cytoplasmic leakage to DOM (Møller 2005)
Bare-surface algae access max	3.0	× access	Max bare-surface algae access boost on smooth substrate (roughness→0)

Trace-metal:C overrides (consumer-specific deviations from universal detritus anchor)

Symbol	Value	Units	Source / Rationale
Fe:C	3.0e-5	mol Fe / mol C	Above universal detritus anchor (haemoproteins, cytochromes)
Mo:C	2.0e-8	mol Mo / mol C	Xanthine / sulfite / aldehyde oxidase Mo holdings
Zn:C	1.0e-6	mol Zn / mol C	Zinc-fingers, metalloproteases, Cu/Zn-SOD (Sterner & Elser 2002; Martin & Knauer 1973)
Cu:C	2.0e-7	mol Cu / mol C	Crustacean haemocyanin, cyt-c oxidase (Sterner & Elser 2002; White & Rainbow 1987)
K:C	1.0e-2	mol K / mol C	Below universal anchor — shells/chitin dilute K demand (Sterner & Elser 2002)
Ni:C	2.0e-7	mol Ni / mol C	Digestive urease + Ni metalloproteins (Sterner & Elser 2002)
Co:C	1.0e-8	mol Co / mol C	Cobalamin (B12) cofactor (Sterner & Elser 2002)
B:C	5.0e-6	mol B / mol C	At universal anchor — incidental dietary B
S:C	5.0e-3	mol S / mol C	At universal anchor — protein S close to bulk biomass

Mortality routing & NO₂ toxicity defaults

Symbol	Value	Units	Source / Rationale
Exposure mortality max	0.0	/h	Biofilm-immaturity mortality on bare surfaces; ostracod overrides (Roca et al. 1993)
Death → DOM fraction	0.0	fraction	Direct lysis-to-DOM at death; protist overrides (Nagata 2000; Fuhrman 1992)
Shell Ca per body C	0.0	mol Ca / mol C	Calcareous-structure Ca routed to CACO3_SUBSTRATE on death
K_NO2,tox (stress)	3.6e-5	mol/L	~0.5 mg NO2-N/L invertebrate stress
K_NO2,tox (lethal)	3.6e-4	mol/L	~5 mg NO2-N/L invertebrate lethal
m_NO2,max	0.04	/h	Slightly gentler than NH3 (Cl⁻ competes, reversible)

Rotifer

Smallest planktonic grazer — high mass-specific metabolism, exquisitely cyano-sensitive, mechanically suppressed by Daphnia.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.015	cm	~100–200 µm
Imax	0.07	/h	~1.7/day; higher than Daphnia (Starkweather & Gilbert 1977)
K_C	4.0e-5	mol C/L	~0.48 mg C/L half-sat
SDA fraction	0.20	fraction	No direct source
Nocturnal feeding fraction	0.9	fraction	No direct source

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Yufera & Pascual 1989
N:P	16.0	mol / mol	Redfield

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.004	/h	Higher mass-specific metabolism than Daphnia
K_O2 (respiration)	3.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	4.0e-5	mol/L	No direct source
O2 stress	4.0e-5	mol/L	No direct source
O2 lethal	1.5e-5	mol/L	No direct source
m_hypoxia,max	0.08	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion	2.3	–	No direct source
Q10,resp	2.0	–	No direct source
Q10,mort	1.8	–	No direct source
T_stress (low / high)	8.0 / 30.0	°C	No direct source
T_lethal (low / high)	2.0 / 38.0	°C	No direct source
m_thermal,max	0.04	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater optimum
σ_S	2.5	PSU	No direct source
S_stress (low / high)	0.0 / 3.0	PSU	Stenohaline
S_lethal (low / high)	0.0 / 8.0	PSU	No direct source
m_salinity,max	0.30	/h	No direct source
Osmoregulation cost	0.005	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	No direct source
pH lethal (low / high)	5.0 / 10.0	–	No direct source
m_pH,max	0.05	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	3.5e-6	mol/L	No direct source
NH3 lethal	7.0e-5	mol/L	No direct source
m_NH3,max	0.10	/h	No direct source

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_allelo,cyanotoxin	5.0e-6	mol C/L	Most cyano-sensitive grazer (Gilbert 1990; Pereira et al. 2004)
K_allelo,cyanotoxin,feeding	2.0e-6	mol C/L	Cilia paralysis sub-µg/L (Gilbert 1990)

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.06 / 24	/h	~6%/day (Galkovskaya 1995)
Feces C:N	10.0	mol / mol	No direct source
Feces → suspended fraction	0.70	fraction	Small body — most feces stays suspended
Death → suspended fraction	0.50	fraction	No direct source
Starvation m_max	0.10/24	/h	No direct source
Crowding m_max	0.06/24	/h	No direct source
K_crowding	1.0e-4	mol/L	No direct source
Daphnia interference m_max	0.04/24	/h	Mechanical-interference suppression (Gilbert 1988)
K_Daphnia interference	1.5e-4	mol C/L	~1.8 mg C Daphnia density half-sat
m_total,max	0.50	/h	Cap

Daphnia

Filter-feeding cladoceran with high-P body and ephippial dormancy; tightly linked to chlorophyll and prone to crash under cyanobacterial blooms.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.15	cm	~1–2 mm adult
Imax	0.06	/h	~1.4/day max ingestion
K_C	5.0e-5	mol C/L	~0.6 mg C/L half-sat (Lampert 2006)
SDA fraction	0.20	fraction	No direct source
Nocturnal feeding fraction	0.7	fraction	No direct source

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	No direct source
N:P	12.0	mol / mol	P-rich (Elser et al. 2000)

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.003	/h	No direct source
K_O2 (respiration)	5.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	6.0e-5	mol/L	~2 mg/L
O2 stress	7.0e-5	mol/L	~2.2 mg/L
O2 lethal	2.0e-5	mol/L	~0.6 mg/L
m_hypoxia,max	0.08	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion	2.0	–	Bottrell 1975; Lampert 1977 (ingestion Q10 ≈ 1.9–2.1, 10–25 °C)
Q10,resp	2.0	–	No direct source
Q10,mort	1.8	–	No direct source
T_stress (low / high)	4.0 / 25.0	°C	No direct source
T_lethal (low / high)	0.0 / 30.0	°C	No direct source
m_thermal,max	0.04	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	3.0	PSU	No direct source
S_stress (low / high)	0.0 / 4.0	PSU	No direct source
S_lethal (low / high)	0.0 / 10.0	PSU	No direct source
m_salinity,max	0.30	/h	No direct source
Osmoregulation cost	0.005	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	No direct source
pH lethal (low / high)	5.0 / 10.0	–	No direct source
m_pH,max	0.05	/h	No direct source

NH₃ / NO₂ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	3.5e-6	mol/L	No direct source
NH3 lethal	7.0e-5	mol/L	No direct source
m_NH3,max	0.10	/h	No direct source
NO2 stress	2.1e-5	mol/L	~0.3 mg N/L (Dowden & Bennett 1965; Russo 1985)
NO2 lethal	2.1e-4	mol/L	~3 mg N/L
m_NO2,max	0.06	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	1.6e-7	mol/L	Borgmann et al. 1993
K_H2S,tox	5.0e-7	mol/L	No direct source

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_allelo,cyanotoxin	8.0e-6	mol C/L	~0.16 mg MC-LR/L; 50% mortality 24h (Rohrlack et al. 2003)
K_allelo,cyanotoxin,feeding	3.0e-6	mol C/L	Feeding suppression below mortality K (Rohrlack 1999; DeMott 1991)

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.02/24	/h	~2%/day
Feces C:N	10.0	mol / mol	No direct source
Feces → suspended fraction	0.25	fraction	No direct source
Death → suspended fraction	0.10	fraction	No direct source
Starvation m_max	0.07/24	/h	No direct source
Crowding m_max	0.05/24	/h	~5%/day at high density
K_crowding	2.0e-4	mol N/L	~4 mg N/L half-sat
m_total,max	0.50	/h	Cap

Reproduction & life-stage (Belehrádek + ephippia)

Symbol	Value	Units	Source / Rationale
dev_a	10650.0	h·°C^\|b\|	Belehrádek a; egg→primipara ~10 d at 20 °C (Bottrell 1975; Goss & Bunting 1983)
dev_α	-10.0	°C	Belehrádek biological-zero
dev_b	-2.05	–	Belehrádek exponent
Dormant food-limit threshold	0.30	fraction	Ephippial-cue food limit (Stross & Hill 1965)
Dormant density threshold	1.0e-3	mol N/L	Crowding cue
Dormant T-drop threshold	12.0	°C	Cool-T cue
Dormant short-day threshold	12.0	h	Short-day cue (Hobæk & Larsson 1990)
Dormant max fraction	0.40	fraction	Max ephippial allocation
Dormant base fraction	0.03	fraction	Constitutive ephippia (3%)
T_hatch (min)	10.0	°C	No direct source
K_food (hatch)	2.0e-5	mol C/L	Food-Monod for hatching
k_hatch,max	1.4e-4	/h	~10%/month under ideal (Cáceres 1998)
Dormant mortality	1.4e-7	/h	~0.1%/yr; ephippia viable for centuries (Hairston et al. 1995)
Initial adult fraction	1.0	fraction	Hobbyist adds adults
Initial dormant fraction	0.0	fraction	No pre-existing egg bank by default
Introduction adult fraction	1.0	fraction	–
Introduction dormant fraction	0.0	fraction	–

Copepod

Cyclopoid-leaning omnivore with adult cannibalism on nauplii, broader thermal tolerance than Daphnia, and longer-lived resting eggs.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.10	cm	~1 mm
Imax	0.058	/h	Cyclopoid-leaning defaults
K_C	2.0e-5	mol C/L	No direct source
SDA fraction	0.18	fraction	No direct source
Nocturnal feeding fraction	0.8	fraction	No direct source

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	4.5	mol / mol	No direct source
N:P	22.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0025	/h	No direct source
K_O2 (respiration)	4.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	5.0e-5	mol/L	No direct source
O2 stress	5.5e-5	mol/L	No direct source
O2 lethal	1.5e-5	mol/L	No direct source
m_hypoxia,max	0.06	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion	2.0	–	No direct source
Q10,resp	1.8	–	No direct source
Q10,mort	1.6	–	No direct source
T_stress (low / high)	1.0 / 30.0	°C	No direct source
T_lethal (low / high)	0.0 / 34.0	°C	No direct source
m_thermal,max	0.03	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	4.0	PSU	No direct source
S_stress (low / high)	0.0 / 6.0	PSU	No direct source
S_lethal (low / high)	0.0 / 15.0	PSU	No direct source
m_salinity,max	0.25	/h	No direct source
Osmoregulation cost	0.004	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.5	–	No direct source
pH lethal (low / high)	4.5 / 10.5	–	No direct source
m_pH,max	0.04	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	5.0e-6	mol/L	No direct source
NH3 lethal	1.0e-4	mol/L	No direct source
m_NH3,max	0.08	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	2.4e-7	mol/L	~15 µg Cu/L; less Cu-sensitive than Daphnia (Hutchinson 1947; Williamson 1986)
K_H2S,tox	8.0e-7	mol/L	No direct source

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_allelo,cyanotoxin	1.2e-5	mol C/L	Less acute than Daphnia (Reinikainen et al. 2002; DeMott 1991)
K_allelo,cyanotoxin,feeding	5.0e-6	mol C/L	Feeding suppression earlier than mortality

Mortality, feces, cannibalism

Symbol	Value	Units	Source / Rationale
m_base	0.015/24	/h	No direct source
Feces C:N	9.0	mol / mol	No direct source
Feces → suspended fraction	0.35	fraction	No direct source
Death → suspended fraction	0.20	fraction	No direct source
Starvation m_max	0.04/24	/h	No direct source
Cannibalism m_max	0.05/24	/h	Cyclopoid adults predate nauplii
K_cannibalism	2.0e-5	mol N/L	Calibrated to planted-aquarium cyclopoid densities (~10-100 ind/L × ~0.5 µg N each → ~5e-6 to 5e-5 mol N/L). The legacy 3e-4 was anchored to eutrophic-pond bloom densities and never engaged in 20 L tanks. May 2026: validated via Walstad 365d diagnostic where the new K reduced copepod peak by 74%.
m_total,max	0.50	/h	Cap

Reproduction & life-stage (Belehrádek + resting eggs)

Symbol	Value	Units	Source / Rationale
dev_a	26600.0	h·°C^\|b\|	Belehrádek a; calanoid egg→adult ~25 d at 20 °C (Munro 1974; Hart 1990)
dev_α	-10.0	°C	Belehrádek biological-zero
dev_b	-2.05	–	Belehrádek exponent
Dormant food-limit threshold	0.30	fraction	No direct source
Dormant density threshold	1.5e-3	mol N/L	Widened vs Daphnia (Frisch 2002; Hansen 1998)
Dormant T-drop threshold	8.0	°C	Widened — cyclopoids encyst at both ends
Dormant short-day threshold	12.0	h	No direct source
Dormant max fraction	0.50	fraction	Higher ceiling than Daphnia (Frisch 2002)
Dormant base fraction	0.04	fraction	Constitutive 4%
T_hatch (min)	10.0	°C	No direct source
K_food (hatch)	2.0e-5	mol C/L	No direct source
k_hatch,max	1.4e-4	/h	Same envelope as Daphnia
Dormant mortality	1.4e-7	/h	Hairston 1987/1996 (centuries-viable)
Initial adult / dormant fraction	1.0 / 0.0	fraction	–
Introduction adult / dormant fraction	1.0 / 0.0	fraction	–

Ostracod

Benthic seed-shrimp browser/picker — durable resting eggs and a constitutive bare-substrate exposure mortality (vulnerable to predation when biofilm immature).

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.075	cm	~0.75 mm
Imax	0.030	/h	No direct source
K_C	1.0e-5	mol C/L	No direct source
SDA fraction	0.18	fraction	No direct source
Nocturnal feeding fraction	0.7	fraction	No direct source
Water-change removal fraction	0.15	fraction	Benthic crawler, mostly avoids siphon
Exposure mortality max	0.001	/h	Bare-substrate vulnerability (Roca et al. 1993)

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.5	mol / mol	No direct source
N:P	20.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0022	/h	No direct source
K_O2 (respiration)	3.5e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	4.0e-5	mol/L	No direct source
O2 stress	4.0e-5	mol/L	No direct source
O2 lethal	1.0e-5	mol/L	No direct source
m_hypoxia,max	0.05	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.1 / 2.15 / 1.7	–	No direct source
T_stress (low / high)	5.0 / 28.0	°C	No direct source
T_lethal (low / high)	0.0 / 33.0	°C	No direct source
m_thermal,max	0.03	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	No direct source
σ_S	4.0	PSU	No direct source
S_stress (low / high)	0.0 / 6.0	PSU	No direct source
S_lethal (low / high)	0.0 / 15.0	PSU	No direct source
m_salinity,max	0.25	/h	No direct source
Osmoregulation cost	0.004	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.5	–	No direct source
pH lethal (low / high)	4.5 / 10.5	–	No direct source
m_pH,max	0.04	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	4.0e-6	mol/L	No direct source
NH3 lethal	8.0e-5	mol/L	No direct source
m_NH3,max	0.08	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	3.1e-7	mol/L	No direct source
K_H2S,tox	1.0e-6	mol/L	No direct source

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.015/24	/h	No direct source
Feces C:N	10.0	mol / mol	No direct source
Feces → suspended fraction	0.15	fraction	Benthic
Death → suspended fraction	0.10	fraction	No direct source
Starvation m_max	0.05/24	/h	No direct source
Crowding m_max	0.10/24	/h	No direct source
K_crowding (benthic areal)	4.0e-7	mol N / cm²	Benthic areal density half-sat
m_total,max	0.50	/h	Cap

Reproduction & resting eggs

Symbol	Value	Units	Source / Rationale
Dormant food-limit threshold	0.30	fraction	No direct source
Dormant density threshold	1.5e-3	mol N/L	No direct source
Dormant T-drop threshold	8.0	°C	No direct source
Dormant short-day threshold	12.0	h	No direct source
Dormant max fraction	0.50	fraction	No direct source
Dormant base fraction	0.05	fraction	Higher base — textbook resting-egg producer (Brendonck & De Meester 2003)
T_hatch (min)	10.0	°C	No direct source
K_food (hatch)	2.0e-5	mol C/L	No direct source
k_hatch,max	1.4e-4	/h	No direct source
Dormant mortality	7.0e-8	/h	Half Daphnia — exceptionally durable (Brendonck & De Meester 2003)
Initial / introduction dormant fraction	0.0 / 0.0	fraction	–

Ciliate

Bacterivorous protist with strong temperature dependence and density-dependent giant-virus lysis; routes a larger lysate share to DOM than larger consumers.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.005	cm	~50 µm
Imax	0.08	/h	~1.9/day; Fenchel 1987 mixed-community ingestion 2–20× body C/day
K_C	1.2e-5	mol C/L	~0.15 mg C/L; higher K than HNF for trophic-cascade realism (Fenchel 1987)
SDA fraction	0.15	fraction	No direct source
Nocturnal feeding fraction	0.95	fraction	Active day and night
RQ	0.90	mol CO₂ / mol O₂	Protist mixed substrates

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	4.5	mol / mol	High protein
N:P	16.0	mol / mol	Redfield

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.004	/h	Higher than copepods
K_O2 (respiration)	2.0e-5	mol/L	~0.64 mg/L (Fenchel & Finlay 1995)

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	4.0e-5	mol/L	~1.3 mg/L
O2 stress	4.0e-5	mol/L	~1.3 mg/L
O2 lethal	1.0e-5	mol/L	~0.3 mg/L
m_hypoxia,max	0.10	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.5 / 2.2 / 1.8	–	Strong T dependence for protists (Weisse 2002)
T_stress (low / high)	8.0 / 30.0	°C	No direct source
T_lethal (low / high)	2.0 / 38.0	°C	No direct source
m_thermal,max	0.05	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater stenohaline
σ_S	3.0	PSU	No direct source
S_stress (low / high)	0.0 / 4.0	PSU	No direct source
S_lethal (low / high)	0.0 / 10.0	PSU	No direct source
m_salinity,max	0.30	/h	No direct source
Osmoregulation cost	0.005	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.8 / 9.0	–	No direct source
pH lethal (low / high)	5.0 / 10.0	–	No direct source
m_pH,max	0.06	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	8.0e-6	mol/L	~0.11 mg/L NH3-N
NH3 lethal	1.5e-4	mol/L	~2.1 mg/L NH3-N
m_NH3,max	0.10	/h	No direct source

Viral lysis

Symbol	Value	Units	Source / Rationale
m_viral,max	0.02	/h	Density-dependent giant-virus lysis (Montagnes et al. 2008)
K_viral	5.0e-6	mol C/L	No direct source

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.04/24	/h	~4%/day
Feces C:N	8.0	mol / mol	C-rich
Feces → suspended fraction	0.80	fraction	Small fecal pellets
Death → suspended fraction	0.70	fraction	Small cells lyse
Death → DOM fraction	0.25	fraction	Lower than HNF — denser pellicle (Nagata 2000)
Starvation m_max	0.20/24	/h	~20%/day; active ciliates die 3–7 d w/o prey (Fenchel 1987; Weisse 2002)
m_total,max	0.60	/h	Cap

Nanoflagellate

Smallest heterotrophic flagellate — primary bacterivore in the microbial loop, fragile, strong T dependence, lyses to DOM at death.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.0005	cm	~5 µm
Imax	0.10	/h	~2.4/day; 10–100 bacteria/cell/h (Fenchel 1982)
K_C	8.0e-6	mol C/L	~0.10 mg C/L; mixed-community (Fenchel 1982)
SDA fraction	0.15	fraction	No direct source
Nocturnal feeding fraction	0.95	fraction	Active day and night
RQ	0.90	mol CO₂ / mol O₂	Protist mixed substrates

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Caron et al. 1990
N:P	16.0	mol / mol	Redfield

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.005	/h	Allometric (Fenchel & Finlay 1983)
K_O2 (respiration)	2.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	4.0e-5	mol/L	~1.3 mg/L
O2 stress	4.0e-5	mol/L	~1.3 mg/L
O2 lethal	1.0e-5	mol/L	~0.3 mg/L
m_hypoxia,max	0.10	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.5 / 2.2 / 1.8	–	Strong T dependence (Weisse 2002)
T_stress (low / high)	8.0 / 30.0	°C	No direct source
T_lethal (low / high)	2.0 / 38.0	°C	No direct source
m_thermal,max	0.05	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	3.0	PSU	No direct source
S_stress (low / high)	0.0 / 4.0	PSU	No direct source
S_lethal (low / high)	0.0 / 10.0	PSU	No direct source
m_salinity,max	0.30	/h	No direct source
Osmoregulation cost	0.005	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.8 / 9.0	–	No direct source
pH lethal (low / high)	5.0 / 10.0	–	No direct source
m_pH,max	0.06	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	8.0e-6	mol/L	~0.11 mg/L NH3-N
NH3 lethal	1.5e-4	mol/L	~2.1 mg/L NH3-N
m_NH3,max	0.10	/h	No direct source

Viral lysis

Symbol	Value	Units	Source / Rationale
m_viral,max	0.03	/h	NCLDV / giant-virus lysis, 10–60% HNF mortality (Massana et al. 2007; Montagnes et al. 2008)
K_viral	5.0e-6	mol C/L	No direct source

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.05/24	/h	~5%/day, higher turnover than ciliate
Feces C:N	8.0	mol / mol	No direct source
Feces → suspended fraction	0.90	fraction	Tiny pellets
Death → suspended fraction	0.85	fraction	Naked flagellates lyse
Death → DOM fraction	0.30	fraction	No cell wall (Nagata 2000)
Starvation m_max	0.30/24	/h	20–50%/day starvation (Zubkov & Sleigh 1995; Weisse 2002)
m_total,max	0.60	/h	Cap

Amphipod / Scuds

First detrital shredder — fragments settled detritus mechanically (parallel flux on top of biological feeding) at a calibrated 1/3 share of the amphipod–detritus interaction (Wallace & Webster 1996).

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.5	cm	~5 mm adult
Imax	0.005	/h	~0.12/day at 22°C on detritus (Othman & Pascoe 2001)
K_C	1.5e-5	mol C/L	~0.18 mg C/L; benthic forager
SDA fraction	0.10	fraction	Low SDA on detrital diet
Nocturnal feeding fraction	1.10	fraction	Nocturnal — more active at night
Water-change removal fraction	0.0	fraction	Fully benthic — hides in litter

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Protein-rich crustacean
N:P	22.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0006	/h	Moderate basal metabolism
K_O2 (respiration)	3.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	6.0e-5	mol/L	~1.9 mg/L
O2 stress	9.4e-5	mol/L	3.0 mg/L
O2 lethal	3.13e-5	mol/L	1.0 mg/L
m_hypoxia,max	0.03	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.2 / 2.2 / 1.7	–	No direct source
T_stress (low / high)	8.0 / 26.0	°C	Cool-water taxon
T_lethal (low / high)	1.0 / 32.0	°C	Overwinters under ice
m_thermal,max	0.025	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.2	PSU	Freshwater; some brackish tolerance
σ_S	2.5	PSU	No direct source
S_stress (low / high)	0.0 / 4.0	PSU	No direct source
S_lethal (low / high)	0.0 / 8.0	PSU	No direct source
m_salinity,max	0.12	/h	No direct source
Osmoregulation cost	0.003	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.2 / 9.0	–	Ca uptake fails in acidic (chronic ~pH 5.8)
pH lethal (low / high)	5.5 / 10.0	–	No direct source
m_pH,max	0.04	/h	No direct source

NH₃ / NO₂ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	5.0e-6	mol/L	~0.07 mg N/L; 96-h LC50 (Borgmann 1994)
NH3 lethal	1.5e-4	mol/L	No direct source
m_NH3,max	0.06	/h	No direct source
NO2 stress	3.6e-5	mol/L	~0.5 mg N/L; matches Daphnia / Neocaridina
NO2 lethal	3.6e-4	mol/L	~5 mg N/L
m_NO2,max	0.05	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	1.5e-7	mol/L	96-h LC50 ~25–35 µg Cu/L; EPA reference organism (Borgmann et al. 1991)
K_H2S,tox	2.5e-7	mol/L	No direct source

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	2.0e-4	/h	~0.5%/day; ~1-yr lifespan
Feces C:N	14.0	mol / mol	High-C detrital diet
Feces → suspended fraction	0.10	fraction	90% settles (benthic)
Death → suspended fraction	0.05	fraction	Carcasses settle
Starvation m_max	0.025/24	/h	~10 d tolerance (lipid reserves)
Crowding m_max	0.04/24	/h	No direct source
K_crowding (benthic areal)	2.0e-6	mol N / cm²	~150 ind / 1000 cm² (typical density)
m_total,max	0.50	/h	Cap

Molting & shredding

Symbol	Value	Units	Source / Rationale
Molt rate (ref)	1/(14·24)	/h	~14-day molt at 22°C (Othman & Pascoe 2001)
T_ref (molt)	22.0	°C	Othman & Pascoe 2001
Q10,molt	2.0	–	No direct source
Molt Ca per C	0.003	mol Ca / mol C / molt	Thin cuticle vs shrimp/crayfish
Molt mortality	0.004	/h	Post-molt soft-shell vulnerability
Molt Ca stress threshold	2.5e-4	mol/L	~1.4 °dGH; Hyalella need >0.5 mg Ca/L
Molt Ca-stress rate factor	0.5	×	Molt-rate halving under Ca stress
Molt Ca-stress mortality factor	2.0	×	Post-molt mortality doubling under Ca stress
Shell Ca per body C	0.003	mol Ca / mol C	Lightly calcified cuticle
Shredding rate	0.0028	/h per mol C	Calibrated so ~1/3 of amphipod-detritus interaction is shredding (Wallace & Webster 1996; Graça 2001)
K_shred (settled C)	1.5e-5	mol C/L	Half-sat on settled-detritus availability

Bladder snail

Hardy radula-grazing gastropod with shell Ca demand and Physella-style tolerance to poor water quality (notably high NO₂).

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.5	cm	~5 mm adult
Imax	0.012	/h	~0.29/day max; gen time 2–3 wks (Dillon 2000)
K_C	1.2e-5	mol C/L	~0.14 mg C/L; raised vs 5e-6 to avoid over-grazing periphyton (Feminella & Hawkins 1995)
SDA fraction	0.15	fraction	Lower than copepods — simpler digestion
Nocturnal feeding fraction	0.9	fraction	Snails more active at night
Water-change removal fraction	0.0	fraction	Benthic crawler

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.5	mol / mol	Protein-rich mollusc body
N:P	20.0	mol / mol	P-rich due to shell

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0003	/h	Low ectotherm basal
K_O2 (respiration)	2.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	2.5e-5	mol/L	Lower than copepods — more tolerant
O2 stress	4.69e-5	mol/L	1.5 mg/L
O2 lethal	9.38e-6	mol/L	0.3 mg/L
m_hypoxia,max	0.03	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.2 / 2.2 / 1.6	–	No direct source
T_stress (low / high)	5.0 / 30.0	°C	Warm-water species
T_lethal (low / high)	0.0 / 35.0	°C	No direct source
m_thermal,max	0.02	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.3	PSU	Freshwater
σ_S	3.0	PSU	No direct source
S_stress (low / high)	0.0 / 4.0	PSU	No direct source
S_lethal (low / high)	0.0 / 8.0	PSU	No direct source
m_salinity,max	0.20	/h	No direct source
Osmoregulation cost	0.003	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.5 / 9.0	–	Shells dissolve below 6.5 (Dillon 2000); thrives in alkaline (Byers & Herbst 2002)
pH lethal (low / high)	5.5 / 10.0	–	No direct source
m_pH,max	0.05	/h	No direct source

NH₃ / NO₂ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	5.0e-6	mol/L	No direct source
NH3 lethal	1.0e-4	mol/L	No direct source
m_NH3,max	0.06	/h	No direct source
NO2 stress	1.4e-4	mol/L	2 mg N/L — Physella notoriously tolerant of poor water
NO2 lethal	1.4e-3	mol/L	20 mg N/L
m_NO2,max	0.04	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	4.7e-7	mol/L	~30 µg Cu/L; EPA mollusc acute AWQC 20–50 µg/L
K_H2S,tox	2.0e-6	mol/L	No direct source

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.0002	/h	~0.48%/day; hardy
Feces C:N	12.0	mol / mol	No direct source
Feces → suspended fraction	0.10	fraction	90% settles
Death → suspended fraction	0.05	fraction	Shells + tissue settle
Starvation m_max	0.03/24	/h	Can weather starvation
K_crowding,feeding (areal)	2.3e-7	mol N / cm²	Brown, Carman & Inchausty (1994, Oecologia 99:158) — per-capita grazing halves above ~4 Physella/25 cm²; 4×0.02 mg N / 25 cm². Self-limitation acts on FEEDING (interference), not survival → boom-then-plateau
Crowding feeding Hill n	1.5	–	Interference steepness (calibrated)
Crowds over full surface	true	–	Pulmonate crawls glass/hardscape/plants, not just floor
Density-dependent mortality	disabled	–	Replaced by feeding interference above (was 0.08/24 /h crowding-death, K 1.0e-6 — killed snails at hobby density instead of plateauing)
m_total,max	0.50	/h	Cap

Detrital shredding / facilitation

Symbol	Value	Units	Source / Rationale
Shred rate	0.0010	/h per mol snail C	Settled→suspended detritus fragmentation; subsidises collector-grazers (shrimp). Shredder→collector facilitation (Ecol. Res. 2001); cross-species coprophagy of snail-conditioned egesta (Aquat. Sci. 2022). Gentler than amphipod (0.0028) — snails rasp, not tear
K_shred (settled det.)	1.5e-5	mol C/L	Half-sat on settled-detritus availability (matches amphipod)

Shell / Ca stoichiometry

Symbol	Value	Units	Source / Rationale
Shell TA per C	0.05	mol TA / mol C	CaCO₃ stoichiometry: −2 TA per mol CaCO₃
Shell Ca per C	0.025	mol Ca / mol C	−1 Ca²⁺ per mol CaCO₃ = shell_TA/2
Shell Ca stress threshold	5.0e-4	mol/L	~2.8 °dGH soft-water threshold
Shell low-Ca growth factor	0.5	×	Growth halved under soft-water stress
Shell Ca per body C (on death)	0.025	mol Ca / mol C	Ca routed to CACO3_SUBSTRATE on death

Malaysian trumpet snail

Burrowing tropical operculate snail — drives the first bioturbation kernel; tighter O2 affinity and broader NO₂ tolerance than Physella.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	1.5	cm	Population mean (juveniles + adult ~2–3 cm)
Imax	0.010	/h	Slightly slower than Physa per unit C
K_C	1.5e-5	mol C/L	Raised vs Physa — buried particle encounter
SDA fraction	0.15	fraction	No direct source
Nocturnal feeding fraction	0.95	fraction	Markedly nocturnal — surfaces at night
Water-change removal fraction	0.0	fraction	Burrower

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.5	mol / mol	No direct source
N:P	20.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0003	/h	No direct source
K_O2 (respiration)	1.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	1.5e-5	mol/L	Tighter than Physa — efficient at low O2
O2 stress	3.13e-5	mol/L	1.0 mg/L
O2 lethal	4.69e-6	mol/L	0.15 mg/L
m_hypoxia,max	0.02	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.2 / 2.2 / 1.6	–	No direct source
T_stress (low / high)	12.0 / 32.0	°C	Tropical / subtropical native
T_lethal (low / high)	5.0 / 38.0	°C	No direct source
m_thermal,max	0.02	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Tolerates up to ~15 PSU — invasive in brackish
σ_S	6.0	PSU	No direct source
S_stress (low / high)	0.0 / 12.0	PSU	No direct source
S_lethal (low / high)	0.0 / 18.0	PSU	No direct source
m_salinity,max	0.10	/h	No direct source
Osmoregulation cost	0.002	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.5 / 9.5	–	Calcareous tropical streams native
pH lethal (low / high)	5.5 / 10.0	–	No direct source
m_pH,max	0.04	/h	No direct source

NH₃ / NO₂ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	5.0e-6	mol/L	No direct source
NH3 lethal	1.5e-4	mol/L	No direct source
m_NH3,max	0.05	/h	No direct source
NO2 stress	2.0e-4	mol/L	MTS notoriously survive uncycled tanks
NO2 lethal	2.0e-3	mol/L	No direct source
m_NO2,max	0.03	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	4.7e-7	mol/L	Same gastropod-class as Physa
K_H2S,tox	2.0e-6	mol/L	No direct source

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.00012	/h	~0.29%/day; hardier than Physa
Feces C:N	12.0	mol / mol	No direct source
Feces → suspended fraction	0.05	fraction	Deep deposition
Death → suspended fraction	0.02	fraction	Sinks immediately
Starvation m_max	0.02/24	/h	Weathers long fasts
Crowding m_max	0.10/24	/h	No direct source
K_crowding (benthic areal)	3.0e-6	mol N / cm²	Higher than Physa — 3D substrate use
Bare-bottom crowding multiplier	5.0	×	Amplified crowding on bare glass / ceramic — obligate burrower
m_total,max	0.50	/h	Cap

Shell / Ca stoichiometry & bioturbation

Symbol	Value	Units	Source / Rationale
Shell TA per C	0.06	mol TA / mol C	Thicker shell than Physa
Shell Ca per C	0.030	mol Ca / mol C	TA/2
Shell Ca stress threshold	5.0e-4	mol/L	~2.8 °dGH
Shell low-Ca growth factor	0.5	×	No direct source
Shell Ca per body C (on death)	0.030	mol Ca / mol C	Ca → CACO3_SUBSTRATE on death
K_bioturbation	5.0e-7	mol C / cm²	Half-sat for bioturbation intensity tanh; tuned to 5→50 MTS arc

Neocaridina / Cherry shrimp

Detritus-grazing tropical shrimp with rich reproduction kinetics — Erlang-3 brood pipeline, NO₃-suppressed breeding, and a Ca-dependent molting cycle.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	2.5	cm	~2.5 cm adult
Imax	0.008	/h	~0.19/day; gen time ~3–4 wk (Wester 2013; Pantaleão et al. 2015)
K_C	1.0e-5	mol C/L	~0.12 mg C/L. No published functional-response half-sat for N. davidi. Lowered from 2.0e-5: a specialised biofilm scraper should not be a worse low-food feeder than the smaller co-occurring snail (K_C 1.2e-5). Viau et al. (2020, Aquac. Res.) — biofilm as SOLE diet sustains full somatic growth + reproduction → efficient feeding at modest periphyton. Calibrated to a biofilm specialist
SDA fraction	0.12	fraction	Crustacean digestion
Nocturnal feeding fraction	0.85	fraction	Slightly more active at night
Water-change removal fraction	0.0	fraction	Hides in substrate / plants

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	4.5	mol / mol	Protein-rich crustacean
N:P	20.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0008	/h	Moderate ectotherm basal
K_O2 (respiration)	2.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	2.0e-5	mol/L	~0.64 mg/L
O2 stress	3.13e-5	mol/L	1.0 mg/L
O2 lethal	6.25e-6	mol/L	0.2 mg/L
m_hypoxia,max	0.025	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.1 / 2.1 / 1.6	–	No direct source
T_stress (low / high)	15.0 / 28.0	°C	Activity decline outside
T_lethal (low / high)	5.0 / 32.0	°C	No direct source
m_thermal,max	0.02	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.2	PSU	Pure freshwater
σ_S	2.0	PSU	No direct source
S_stress (low / high)	0.0 / 3.0	PSU	No direct source
S_lethal (low / high)	0.0 / 6.0	PSU	No direct source
m_salinity,max	0.15	/h	No direct source
Osmoregulation cost	0.003	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	No direct source
pH lethal (low / high)	5.5 / 10.0	–	No direct source
m_pH,max	0.04	/h	No direct source

NH₃ / NO₂ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	4.0e-6	mol/L	No direct source
NH3 lethal	1.0e-4	mol/L	No direct source
m_NH3,max	0.06	/h	No direct source
NO2 stress	3.6e-5	mol/L	~0.5 mg N/L; sensitive onset / lower "safe" bound (Lewis & Morris 1986); haemocyanin disruption
NO2 lethal	5.7e-4	mol/L	~8 mg N/L; near M. rosenbergii larvae 96 h LC50 8.6 (Armstrong et al. 1976)
m_NO2,max	0.021	/h	Anchored so the linear ramp passes through ln(2)/96h = 0.0072/h at the M. malcolmsonii 96 h LC50 of 3.14 mg NO2-N/L. Was 0.05 (unsourced): gave ~0.029/h (70 %/day) at that LC50 (~4× too steep), wiping shrimp out at the literature-"safe" 1–1.5 mg-N/L band

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	1.9e-7	mol/L	~12 µg Cu/L; 96-h LC50 ~15 µg/L (Lauer et al. 2012)
K_H2S,tox	3.0e-7	mol/L	No direct source

Allelochemical sensitivity

Symbol	Value	Units	Source / Rationale
K_allelo,cyanotoxin	2.0e-5	mol C/L	Larger body dilutes toxin (Lürling 2003)
K_allelo,cyanotoxin,feeding	8.0e-6	mol C/L	No direct source

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	1.4e-4	/h	~0.33%/day; ~1.5-yr lifespan
Feces C:N	12.0	mol / mol	No direct source
Feces → suspended fraction	0.05	fraction	95% settles
Death → suspended fraction	0.05	fraction	Exuvia + carcass settle
Starvation m_max	0.03/24	/h	~1 wk tolerance
K_crowding,feeding (areal)	4.0e-6	mol N / cm²	Half-feeding density over the full crawlable surface. No published carrying-capacity constant for N. davidi; calibrated to a hobby-realistic plateau (~2–5/L). Self-limitation acts on FEEDING (Brown et al. 1994 mechanism), not survival
Crowding feeding Hill n	1.5	–	Interference steepness (calibrated)
Crowds over full surface	true	–	Shrimp crawl glass/hardscape/plants, not just floor
Density-dependent mortality	disabled	–	Replaced by feeding interference above. The old areal crowding-DEATH kernel (0.05/24 /h, K 1.0e-6, benthic-FLOOR only) killed adults at normal hobby stocking — e.g. 8 shrimp in a 600 cm² footprint sat at the half-saturation density — driving spurious extinction
m_total,max	0.50	/h	Cap

Reproduction (Erlang-3 brood pipeline)

Symbol	Value	Units	Source / Rationale
t_mature	92.0	days	Sexual maturity 4–5 mo (Pantaleão et al. 2015; Wester 2013); erlang3 mode separates 28-d brood
Initial / introduction adult fraction	1.0 / 1.0	fraction	Hobbyist purchases adults
Reproduction mode	"erlang3"	str	Gamma(3) smoothed delay through 3-cohort brood pipeline
τ_brood	28.0	days	Mean berried period (Wester 2013)
Brood cap fraction	0.50	fraction	Cap on berried biomass per adult
NO3 repro onset	3.23e-4	mol N/L	20 ppm — reproduction suppression begins
NO3 repro zero	6.45e-4	mol N/L	40 ppm — full suppression
pH repro (low / high)	6.5 / 8.8	–	Below / above → reduced breeding (Wester 2013, hobby consensus 6.5–8.5)
T repro (low / high)	18.0 / 27.0	°C	Outside → reduced breeding
NH3 repro threshold	3.0e-6	mol/L	~0.05 ppm NH3 → breeding stops
Repro maturity threshold (M)	0.30	fraction	Biofilm-maturity threshold for full reproduction
Repro maturity Hill exponent	2.0	–	Hill exponent on M ramp

Molting & shell

Symbol	Value	Units	Source / Rationale
Molt rate (ref)	1/(21·24)	/h	One molt per 21 d at T_ref,molt
T_ref (molt)	22.0	°C	No direct source
Q10,molt	2.0	–	No direct source
Molt Ca per C	0.010	mol Ca / mol C / molt	No direct source
Molt mortality	0.005	/h	Soft-shell vulnerability
Molt Ca stress threshold	3.6e-4	mol/L	~2 °dGH
Molt Ca-stress rate factor	0.5	×	No direct source
Molt Ca-stress mortality factor	2.0	×	No direct source
Shell Ca per body C (on death)	0.010	mol Ca / mol C	Ca → CACO3_SUBSTRATE on death

Hydra

Sit-and-wait gape-limited cnidarian — first invertebrate predator; lowest Cu tolerance in the codebase; targets juvenile daphnia/copepod.

Ingestion & assimilation

Symbol	Value	Units	Source / Rationale
Body size	0.6	cm	Polyp ~5–15 mm extended
Imax	0.025	/h	~0.6/day; population doubling 2–4 d (Bossert & Galliot 2012)
K_C	1.5e-5	mol C/L	Encounter-limited, not filter-limited
SDA fraction	0.18	fraction	No direct source
Nocturnal feeding fraction	1.0	fraction	Tentacles deployed continuously

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.5	mol / mol	No direct source
N:P	17.0	mol / mol	No direct source

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0025	/h	No direct source
K_O2 (respiration)	3.0e-5	mol/L	No direct source

Hypoxia

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	4.5e-5	mol/L	No direct source
O2 stress	5.0e-5	mol/L	No direct source
O2 lethal	2.0e-5	mol/L	No direct source
m_hypoxia,max	0.07	/h	No direct source

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	T_REF_C
Q10,ingestion / resp / mort	2.2 / 2.0 / 1.8	–	No direct source
T_stress (low / high)	6.0 / 28.0	°C	Brown / common hydra collapse > 28 °C (Slobodkin & Bossert 1991)
T_lethal (low / high)	1.0 / 33.0	°C	No direct source
m_thermal,max	0.05	/h	No direct source

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.1	PSU	Strictly freshwater
σ_S	1.5	PSU	No direct source
S_stress (low / high)	0.0 / 2.0	PSU	No direct source
S_lethal (low / high)	0.0 / 5.0	PSU	No direct source
m_salinity,max	0.30	/h	No direct source
Osmoregulation cost	0.006	× maint	No direct source

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	No direct source
pH lethal (low / high)	5.0 / 10.0	–	No direct source
m_pH,max	0.05	/h	No direct source

NH₃ toxicity

Symbol	Value	Units	Source / Rationale
NH3 stress	2.0e-6	mol/L	Comparable to / tighter than Daphnia (Karntanut & Pascoe 2002)
NH3 lethal	4.0e-5	mol/L	No direct source
m_NH3,max	0.10	/h	No direct source

Cu / H₂S toxicity

Symbol	Value	Units	Source / Rationale
K_Cu,tox	1.0e-7	mol/L	Lowest in codebase; 96-h LC50 ~13 µg/L (Karntanut & Pascoe 2002; Holdway 2001)
K_H2S,tox	8.0e-7	mol/L	Mirrors copepod

Mortality, feces, density-dependence

Symbol	Value	Units	Source / Rationale
m_base	0.015/24	/h	Long-lived under good conditions (Martinez 1998)
Feces C:N	9.0	mol / mol	No direct source
Feces → suspended fraction	0.40	fraction	Compact regurgitation pellets
Death → suspended fraction	0.30	fraction	Detached sinking polyps
Starvation m_max	0.08/24	/h	No direct source
Crowding m_max	0.05/24	/h	Sessile, contact-mediated; budding rate drops
K_crowding	1.0e-4	mol/L	No direct source
m_total,max	0.50	/h	Cap

Fish

Fish are modelled as a boundary condition on the ecosystem, not a closed-mass-balance member (see docs/consumers/fish_and_feeding.md and docs/planning/archive/fish_and_feeding_spec.md). Biomass is a user-set stocking level held fixed except by death (no growth/reproduction in V1); the ecosystem-facing output is bioload (an O₂ sink + NH₄/CO₂/PO₄ source), the fish-facing output is a continuous health gauge ∈ [0, 1]. FishSpecies subclasses Consumer to reuse the feeding/respiration/tolerance pipeline and overrides the biomass-change, feeding-suppression, and mortality stages.

Status (June 2026): Phases 1–3 shipped. The base health-ODE / metabolism / mortality constants below remain hand-tuned estimates (no fish-by-fish literature exists for the health-gauge coefficients — they are calibrated so the gauge behaves like a real fish: sick-fast, recover-slow, die near lethal through the health pathway). The per-species tolerance thresholds (NH₃ / NO₂ / O₂ / T / pH bands) were calibrated in P3 against species or congener LC50 / tolerance literature where it exists, and flagged "hand-tuned" otherwise — see each species' divergent table. The acute-kernel rates (*_mort_max) are deliberately kept uniform and gentle across the roster: in the fish model the health gauge is the primary chronic-stress integrator and mortality driver, so the per-species spread (fragile neon ↔ hardy danio) comes from the thresholds feeding the health stress blend, not from per-species kernel rates. starvation m_max is 0 (a fixed-biomass boundary condition does not lose mass to starvation; under-feeding manifests through reduced appetite and the health gauge).

Fish symbol glossary

Symbol	Meaning
H	Health gauge, a per-population ODE state ∈ [0, 1] (1 = perfectly healthy, 0 = dead). Non-mass scalar slot (the biofilm-maturity precedent), excluded from mass balance.
stress(t)	Max over normalized water-quality stressor intensities (NH₃/NO₂/O₂/T/pH/Cu/H₂S), each 0 at comfort → 1 at that species' lethal threshold (reuses the `biology.py` kernel thresholds).
comfort(t)	1 − stress(t).

Fish base — health ODE

dH/dt = k_recover·(1−H)·comfort − (k_damage·stress + k_acute·relu(stress − s_lethal))·H. The asymmetry (k_damage > k_recover) is the point: a fish gets sick fast and recovers slowly, staying sick for days after a spike clears (chronic memory). Health drives an added mortality term ramping as H falls below the onset. Every loss term is scaled by H (recovery by 1−H), so the derivative vanishes at both ends and the gauge stays in [0, 1] by construction — under lethal water H asymptotes toward 0 (a ~5 h half-life collapse) instead of being driven through it. That smooth landing is also a numerical necessity: a derivative that stayed strongly negative at H = 0 collided with the rhs non-negativity floor guard, creating a step discontinuity at the H = 0 surface that LSODA chatters across (step size collapses → the sim appears to freeze). This bit sealed high-bioload tanks the moment bulk O₂ went lethal; open-top tanks never reach lethal O₂, so health never touches the boundary.

Symbol	Value	Units	Source / Rationale
k_recover	0.006	/h	Recovery t½ ≈ 5 d in full comfort; estimate
k_damage	0.070	/h	~12× faster than recovery (sick-fast). Calibrated (Jun 2026) so the gauge faithfully displays condition: the equilibrium under a sustained stress s, `H* = k_recover·(1−s)/(k_recover·(1−s)+k_damage·s)`, maps a slow ammonia die-off (~0.18 normalized stress, e.g. betta_bowl) into the "stressed" band (~0.4) rather than reading mid-"healthy" through a 30 %-biomass decline. Display recalibration — paired with the lowered onset below it leaves the mortality model neutral
k_acute	0.50	/h	Near-instant collapse past s_lethal (hours); estimate
s_lethal	0.75	–	Normalized-stress threshold engaging the acute term (approaching lethal water); estimate
m_health,max	0.05	/h	Health-driven mortality as H→0 (~120%/day, enables die-off); estimate
Health-mortality onset	0.13	–	H above this → ~no health mortality; quadratic ramp below. Lowered 0.35→0.13 (Jun 2026) in lock-step with the steeper k_damage so the coupling engages at the same stress severity (s≈0.36) as before — mortality-neutral by construction, while freeing the gauge to display "stressed" under chronic sublethal load without spuriously adding mortality
Appetite floor	0.15	fraction	Ration multiplier as H→0 (a sick fish eats less → slower recovery feedback); estimate
Aerial O₂ access	0.0	fraction	Scales the O₂ contribution to stress (air-breathers > 0; Betta ≈ 0.9 in P3)

Fish base — body, ingestion, metabolism

Symbol	Value	Units	Source / Rationale
C:N	5.5	mol / mol	Fish body C:N 5–6 (Sterner & Elser 2002); estimate
N:P	20.0	mol / mol	Fish body N:P 15–25 (Sterner & Elser 2002); estimate
Imax	0.020	/h	Lower per-mass turnover than zooplankton; estimate
K_C	8.0e-5	mol C/L	Holling-II half-saturation; estimate
R_maint	0.0020	/h	Maintenance respiration; estimate
SDA fraction	0.15	fraction	Heat increment of feeding, fish ~15% (Jobling 1981); estimate
Nocturnal feeding fraction	0.5	fraction	Most community fish are diurnal; estimate

Fish base — O₂, thermal, salinity, pH, toxicity

In the fish model the health gauge is the primary integrator of sublethal stress and the primary chronic-mortality driver; the direct biology.py acute kernels are retained (an acute lethal slug still kills directly) but tuned gentle so a hardy fish is not killed by a routine cycling spike — fast death near/above lethal comes through the health pathway (stress → acute collapse → health mortality). The *_mort_max values are therefore deliberately low.

Symbol	Value	Units	Source / Rationale
K_O2 (activity)	9.0e-5	mol/L	Fish need more O₂ than inverts; estimate
K_O2 (respiration)	6.0e-5	mol/L	estimate
O2 stress / lethal	1.25e-4 / 6.25e-5	mol/L	~4 / ~2 mg/L; estimate
m_hypoxia,max	0.02	/h	Gentle (health-led); estimate
T_ref	25	°C	T_REF_C
Q10 ingestion / resp / mort	2.0 / 2.0 / 2.0	–	estimate
T_stress (low / high)	18 / 28	°C	estimate (overridden per species)
T_lethal (low / high)	10 / 36	°C	estimate (overridden per species)
m_thermal,max	0.02	/h	Gentle (health-led); estimate
S_opt / σ_S	0.3 / 2.5	PSU	Freshwater; estimate
S_stress (low / high)	0.0 / 3.0	PSU	estimate
S_lethal (low / high)	0.0 / 12.0	PSU	estimate
m_salinity,max	0.10	/h	estimate
Osmoregulation cost	0.004	× maint	estimate
pH stress (low / high)	6.0 / 8.5	–	estimate
pH lethal (low / high)	4.5 / 9.5	–	estimate
m_pH,max	0.02	/h	Gentle (health-led); estimate
NH3 stress / lethal	4.3e-6 / 2.9e-5	mol/L	~0.06 / ~0.4 mg NH₃-N/L; estimate (overridden per species)
m_NH3,max	0.008	/h	Gentle (health-led); estimate
NO2 stress / lethal	7.1e-5 / 7.1e-4	mol/L	~1 / ~10 mg NO₂-N/L; looser than inverts (Cl⁻ protective); estimate
m_NO2,max	0.005	/h	Gentle (health-led); estimate

Fish base — mortality & routing

Symbol	Value	Units	Source / Rationale
m_base	0.0005/24	/h	Fish are long-lived (years), ~0.05%/day; estimate
Starvation m_max	0.0	/h	Off in P1 (nutrition coupling lands with feeding, P2)
m_total,max	0.50	/h	Cap
Feces → suspended fraction	0.10	fraction	Fish feces sink; estimate
Death → suspended fraction	0.10	fraction	Carcasses sink to settled detritus; estimate
Water-change removal fraction	0.0	fraction	Fish are not netted out during a water change

Zebra danio (Danio rerio) — divergent only

The hardiest of the V1 roster — wide thermal window, high NH₃/NO₂ tolerance; the recommended fish-in-cycling species and the P1 end-to-end species.

Symbol	Value	Units	Source / Rationale
Individual N mass	14	mg N	Wet ~0.7 g × ~20% dry × ~10% N; count→mg-N anchor (frontend)
Body size	3.5	cm	Adult ~3–4 cm
T_stress (low / high)	15 / 30	°C	Wide window; §5 roster (opt ~22 °C)
T_lethal (low / high)	10 / 38	°C	§5 roster
NH3 stress / lethal	0.06 / 0.40	mg NH₃-N/L	§5 roster; estimate
NO2 stress / lethal	1 / 10	mg NO₂-N/L	§5 roster; tolerant; estimate
O2 stress / lethal	3.5 / 2.0	mg/L	§5 roster (lethal ~2 mg/L); estimate
K_Cu,tox	1.0e-6	mol/L	Fish ~5–10× more Cu-tolerant than inverts; estimate (P3 citation)
K_H2S,tox	2.0e-6	mol/L	estimate (P3 citation)

Betta (Betta splendens) — divergent only

The roster's air-breather (§3.5): a labyrinth organ lets it survive a low-oxygen bowl. Solo, low-bioload, ammonia/nitrite-tolerant. Calibration anchor: Anh et al. (2023) BMC Zoology 10:60 — 96 h LC50 = 123.4 mM total ammonia-N (~1.7 g/L) and 24.6 mM NO₂-N (~344 mg/L); betta is among the most ammonia/nitrite-tolerant freshwater fish.

Symbol	Value	Units	Source / Rationale
Individual N mass	25	mg N	Wet ~1.2 g × ~20 % dry × ~10 % N; count→mg-N anchor (frontend)
Body size	6.0	cm	Adult ~6 cm incl. finnage
T_stress (low / high)	20 / 31	°C	Warm-preferring tropical (opt ~26 °C); §5 roster
T_lethal (low / high)	16 / 35	°C	§5 roster
NH3 stress / lethal	0.10 / 0.80	mg NH₃-N/L	Tolerant (Anh et al. 2023), but kept only moderately relaxed so an uncycled bowl still drives a slow health decline (betta_bowl demonstrator)
NO2 stress / lethal	5 / 40	mg NO₂-N/L	Very tolerant (Anh et al. 2023 LC50 ~344 mg/L); capped at an aquarium-relevant band, not the literal LC50
O2 stress / lethal	1.5 / 0.5	mg/L	Air-breather survives near-anoxic water; §3.5
Aerial O₂ access	0.9	fraction	§3.5 labyrinth air-breather — scales the O₂ contribution to health stress down 10×
pH stress (low / high)	5.5 / 8.2	–	Soft-to-neutral blackwater origin; hand-tuned
pH lethal (low / high)	4.5 / 9.0	–	hand-tuned
K_Cu,tox	1.0e-6	mol/L	Fish ~5–10× more Cu-tolerant than inverts; hand-tuned
K_H2S,tox	2.0e-6	mol/L	hand-tuned

Neon tetra (Paracheirodon innesi) — divergent only

The fragile end of the roster — a soft-water characin that needs a mature tank; the "wrong fish, too soon" cautionary case. Calibration anchor: Oliveira et al. (2008) Acta Amazonica 38(4):773–780 on the congeneric cardinal tetra (P. axelrodi) — the most ammonia-sensitive species tested, nitrite > ~1.1 mg/L NO₂ compromises survival, survival drops below ~19.6 °C.

Symbol	Value	Units	Source / Rationale
Individual N mass	4	mg N	Wet ~0.2 g × ~20 % dry × ~10 % N; count→mg-N anchor
Body size	3.0	cm	Adult ~3 cm
T_stress (low / high)	20 / 29	°C	Narrow tropical window (opt ~23 °C); §5; congener survival falls < ~19.6 °C (Oliveira 2008), neon slightly more cold-hardy
T_lethal (low / high)	14 / 32	°C	§5 roster
NH3 stress / lethal	0.02 / 0.15	mg NH₃-N/L	Most sensitive of the roster (Oliveira 2008: congener the most ammonia-sensitive tested); §5
NO2 stress / lethal	0.3 / 3	mg NO₂-N/L	Sensitive — congener survival compromised above ~1.1 mg/L NO₂ (~0.33 mg/L NO₂-N); §5
O2 stress / lethal	4 / 3	mg/L	More O₂-demanding than the hardy danio; §5
pH stress (low / high)	5.5 / 7.8	–	Soft acidic blackwater species; intolerant of hard alkaline water; congener tolerates pH 2.9–8.8 (Oliveira 2008)
pH lethal (low / high)	4.0 / 8.8	–	Oliveira 2008 (congener)
K_Cu,tox	6.0e-7	mol/L	Soft-water characin, more Cu-sensitive (less DOC/Ca to bind free Cu²⁺); hand-tuned, still ~3–5× more tolerant than inverts
K_H2S,tox	1.2e-6	mol/L	hand-tuned

Guppy / Endler (Poecilia reticulata) — divergent only

A hardy hard-water livebearer — one of the more pollution-tolerant community fish. Calibration anchors: Frances et al. (2023) Acta Biológica Colombiana 28(1):57–64 — ammonia 96 h LC50 ≈ 1.17 mg/L unionized NH₃-N; nitrite 96 h LC50 ≈ 30 mg/L NO₂ (~9 mg/L NO₂-N), rising strongly with chloride.

Symbol	Value	Units	Source / Rationale
Individual N mass	6	mg N	Wet ~0.3 g × ~20 % dry × ~10 % N; count→mg-N anchor
Body size	3.5	cm	Adult (females larger than males)
T_stress (low / high)	18 / 31	°C	Wide warm-preferring window (opt ~25 °C); §5
T_lethal (low / high)	16 / 34	°C	§5 roster
NH3 stress / lethal	0.10 / 1.0	mg NH₃-N/L	Hardy — Frances et al. (2023) 96 h LC50 ~1.17 mg NH₃-N/L; lethal set at ~the LC50
NO2 stress / lethal	2 / 9	mg NO₂-N/L	Tolerant in hard water — LC50 ~9 mg/L NO₂-N at moderate Cl⁻ (Cl⁻ protective)
O2 stress / lethal	3.5 / 2.5	mg/L	Tolerant surface-dwelling livebearer; §5
pH stress (low / high)	6.5 / 8.6	–	Hard-water / high-GH lover; tolerates alkaline water, less happy in soft acidic; hand-tuned
pH lethal (low / high)	5.5 / 9.2	–	hand-tuned
K_Cu,tox	1.0e-6	mol/L	Hard-water fish, well Cu-buffered; hand-tuned
K_H2S,tox	2.0e-6	mol/L	hand-tuned

Corydoras (Corydoras spp.) — divergent only

The benthic detritivore (§4.4) — the only roster fish that grazes in-tank (settled detritus + incidental periphyton, wired in interactions.yaml) on top of the prepared feed. Calibration: temperature from keeper consensus (Aqueon / Aquarium Co-op care guides; cooler-preferring); ammonia/nitrite hand-tuned to a moderate tolerance (between fragile neon and hardy danio) as no species-specific LC50 exists; tighter Cu_tox because scaleless armoured catfish are Cu/medication-sensitive.

Symbol	Value	Units	Source / Rationale
Individual N mass	50	mg N	Wet ~2.5 g × ~20 % dry × ~10 % N; largest of the roster; count→mg-N anchor
Body size	6.0	cm	Adult ~5–7 cm
T_stress (low / high)	19 / 28	°C	Cooler-preferring tropical (opt ~24 °C); keeper consensus
T_lethal (low / high)	12 / 30	°C	§5 roster
NH3 stress / lethal	0.04 / 0.30	mg NH₃-N/L	Moderate; §5; hand-tuned (no species LC50)
NO2 stress / lethal	0.5 / 5	mg NO₂-N/L	Moderate; §5; hand-tuned
O2 stress / lethal	3.5 / 2.5	mg/L	Benthic fish near the lower-O₂ substrate boundary; §5. (Real cory gulp air via intestinal respiration — not modelled in V1; only Betta is an air-breather here, §3.5)
pH stress (low / high)	5.5 / 8.0	–	Soft-to-neutral; tolerant but not a hard-alkaline-water fish; hand-tuned
pH lethal (low / high)	4.5 / 8.8	–	hand-tuned
K_Cu,tox	6.0e-7	mol/L	Scaleless armoured catfish, Cu/medication-sensitive (no scales over trunk); hand-tuned
K_H2S,tox	1.5e-6	mol/L	Benthic — more sediment-H₂S contact; hand-tuned

Corydoras interactions.yaml benthic foods (in-tank grazing, §4.4; on top of fish_feed at preference 1.0 / assim 0.80 / access 1.0):

Food	preference	assimilation	access	Rationale
detritus_settled	0.70	0.25	0.80	Primary in-tank food — sifts the substrate; low assimilation (detrital C largely refractory/microbially bound), as for the amphipod shredder
surface_algae	0.20	0.30	0.25	Incidental periphyton taken while sifting; cory is not a specialised scraper, so most biofilm cells stay refuge-protected (`refugia` K 5e-4, min_frac 0.10)

Fish feeding (Phase 2) — external feed & bioload

External feed is the model's only organic input. A feed event (feeding: scenario block) adds dry food of fixed C:N:P stoichiometry to the transient fish_feed pool; fish graze it (high preference, fast), and uneaten feed decays to suspended detritus. Because fish are a fixed-biomass boundary condition with no growth sink, every feed-N atom becomes ammonia (assimilated N excreted ammonotelically + egested N → detritus → mineralised), reproducing the empirical RAS bioload factor (~25–35 g TAN/kg feed/day; Merino 2007) mechanistically rather than by fiat. Constants live in engine/dosing.py; the decay process in processes/fish_feed.py. See docs/consumers/fish_and_feeding.md.

Symbol	Value	Units	Source / Rationale
Feed C:N:P (molar)	9 : 1.6 : 0.1	mol/mol	Default dry prepared food ≈ 45 % protein; N:C 0.18 molar, C:P ~90 (≈ 9 % N, ~1 % P by dry mass). Roberts 2018 feed tables; overridable per scenario (`cnp_molar`)
Feed C fraction (dry)	0.45	g C / g dry	Carbon mass fraction of dry prepared food (high-protein organic matter); with the C:N:P ratio fixes the N/P mass fractions and hence the RAS factor. Hand-tuned anchor
k_feed_decay	0.173	/h	Uneaten feed → suspended detritus; ~4 h half-life (flake/pellet saturates and fragments within hours). Second-order knob — all routes lead to the same detritus → NH4 fate, only the lag differs
Auto feed rate	1.5	% fish wet mass / day	Maintenance ration for adult community fish at ~24 °C (`auto.pct_fish_biomass_per_day`); the hobbyist default when grams are not given
Fish wet mass per body N	0.05	g wet / mg N	From the §5 anchor (`individual_N_mg` = wet_g × 20); converts a fish stocking (tracked in mg N) into the wet mass the auto rate scales against
Danio `fish_feed` preference	1.0	—	Prepared food taken avidly; not a refuge-protected prey (`interactions.yaml`)
Danio `fish_feed` assimilation	0.80	fraction	Prepared food is highly digestible (NRC 2011 fish nutrition); assimilated → NH4, egested 20 % → feces/detritus
Danio `fish_feed` access	1.0	fraction	Fully accessible (formulated food, no refuge)

(Starvation mortality stays 0 in P2 — a fixed-biomass boundary condition does not starve to lose mass; under-feeding instead manifests through reduced appetite and the health gauge. True nutrition→condition coupling is future work.)

Microbes

Microbes — nitrifiers, the heterotrophic-bacteria pool, the diagenetic-ladder anaerobes (denitrifier, DNRA, Fe-reducer, sulfate-reducer, methanogen), and aquatic fungi — share a μ_max / Monod-substrate / O₂-gated growth skeleton, layered with terminal-electron-acceptor ladder inhibition, biofilm protection from grazing, and (for nitrifiers, sediment anaerobes) a bulk-vs-pore biomass split.

Microbe symbol glossary

Symbol	Meaning
μ_max	Maximum specific growth rate (per h)
K_X	Monod half-saturation for substrate X (NH₄, NO₂, DOM, settled detritus, soil OM…)
K_O2	O₂ Monod half-sat for growth (separate K_O2 for respiration)
BGE (Y_C/X)	Bacterial growth efficiency — mol cell C per mol substrate processed
O₂:X	Mol O₂ consumed per mol substrate oxidised
TA:X	TA change per mol substrate (negative releases H⁺, positive consumes H⁺)
Acceptor:C	Mol terminal electron acceptor reduced per mol C oxidised (NO₃, Fe(III), SO₄, CO₂)
TA:C	TA change per mol C oxidised through the ladder reaction
Pore fraction	Biomass share resident in soil pore-water zone (vs bulk) — drives substrate access
K_NH3,inhib / K_HNO2,inhib	Free-ammonia / nitrous-acid inhibition Hill K for NOB/Comammox (Anthonisen 1976; Vadivelu 2006/2007)
K_NO3,inhib	Cascade gate disabling lower-rung anaerobes while NO₃ is available
K_oxide,inhib (pore)	Cascade gate disabling SR while reducible Fe(III) is available (pore-concentration basis)
K_pore SO4,inhib	Cascade gate disabling methanogens while pore SO₄ is available
Biofilm predation protection	Maximum M-modifier — fraction of biomass unreachable to grazers at full biofilm maturity (Schramm 1996; Matz & Kjelleberg 2005)
Geometric predation shield	M=0 floor for the same kernel — roughness-scaled shelter even on immature surfaces
Biofilm light attenuation	M=1 light shading factor for nitrifier biofilm
Induction lag	Enzyme-induction delay for fresh inoculum (h)
K_viral, m_viral,max	Density half-sat and max rate for phage / NCLDV lysis kernel
Settlement / detachment rate	First-order kinetics for biofilm colonisation and detachment

Nitrifier base

Shared base for AOB / NOB / Comammox — pore-attached chemoautotrophs with explicit biofilm light attenuation, predation protection, and an induction-lag floor. Refs: Prosser 1989, Daims 2015, Schramm 1996.

Growth & stoichiometry (base defaults — overridden per subclass)

Symbol	Value	Units	Source / Rationale
Pore fraction	0.0	fraction	Phase 3 sediment realism: biomass share in soil pore zone. Auto-injected to ~0.5–0.7 in soil scenarios (textbook: ~80% of aquarium nitrification in substrate biofilm)
O₂:X (base)	2.0	mol O₂ / mol N	Sum of AOB+NOB half-reactions (1.5 + 0.5)
TA:X (base)	−2.0	eq TA / mol N	Full NH₄→NO₃ releases 2 H⁺
Body size	0.0001	cm	~1 µm nitrifier cell
μ_max (base)	0.55/24	/h	Overridden per subclass
K_substrate (base)	2.5e-5	mol/L	Overridden per subclass
K_O2	3.0e-5	mol/L	~1 mg O2/L; AMO/NXR aerobic affinity
K_Fe (AMO)	5.0e-9	mol/L	Wagner et al. 2002; Ensign 1993 — purified AMO/NXR Fe affinity 1–5 nM midpoint; nitrifiers tighter than producer baseline due to higher Fe-S cluster load
BGE (base)	0.08	mol C / mol N	Prosser 1989 AOB default; overridden per subclass
C:N	5.0	mol / mol	Bacterial C:N
N:P	16.0	mol / mol	Redfield-style N:P

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	5.0e-5	mol Fe / mol C	AMO di-iron + electron transport Fe-S clusters
Mo:C	1.0e-8	mol Mo / mol C	Universal anchor (base; NOB/Comammox elevate)
Zn:C	4.0e-7	mol Zn / mol C	Universal anchor
Cu:C	2.0e-7	mol Cu / mol C	AOB AMO Cu; overridden per subclass
Ni:C	1.0e-7	mol Ni / mol C	Universal anchor
Co:C	5.0e-9	mol Co / mol C	Universal anchor
B:C	5.0e-6	mol B / mol C	Universal anchor
S:C	5.0e-3	mol S / mol C	Universal anchor

Inhibition (sentinels; subclasses opt in)

Symbol	Value	Units	Source / Rationale
K_NH3,inhib (base)	0.0	mol/L	Sentinel disables; only NOB/Comammox opt in (Anthonisen 1976)
K_HNO2,inhib (base)	0.0	mol/L	Sentinel; NOB activates

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0005	mol O₂ / mol C / h	Low maintenance for chemoautotroph
K_O2 (respiration)	1e-5	mol/L	High maintenance O2 affinity (~0.3 mg/L)

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	T_REF_C (25)	°C	Standard reference
Q10,growth	2.5	–	Nitrifier literature midrange (sub-optimal limb)
T_opt,growth	30.0	°C	Growth thermal optimum; below it the factor is identical to the bare Q10, above it the rate declines linearly to 0 at T_max (asymmetric curve, R6). Community/aquarium optimum ~28–30 °C; pure-culture Nitrosomonas ~35 (Grunditz & Dalhammar 2001; EPA Nitrification)
T_max,growth	49.0	°C	Temperature where growth rate reaches 0 (audit §9.4 anchor ~49 °C). Respiration/maintenance keep the plain monotonic Q10, so the growth–maintenance gap above the optimum drives the hot-tank stall
Q10,resp	2.0	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	10.0 / 38.0	°C	Wide tolerance
T_lethal (low / high)	0.0 / 45.0	°C	Wide tolerance
m_thermal,max	0.02	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	20.0	PSU	Brackish-tolerant
σ_S	30.0	PSU	Wide Gaussian
S_stress (low / high)	0.0 / 50.0	PSU	Wide tolerance
S_lethal (low / high)	0.0 / 150.0	PSU	Wide tolerance
m_salinity,max	0.05	/h	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.0 / 9.0	–	Standard nitrifier band
pH lethal (low / high)	5.0 / 10.0	–	Standard
m_pH,max	0.03	/h	Standard

pH–rate activity curve (pH_activity_points)

Direct pH dependence of the nitrification rate — distinct from the pH stress/mortality band above, which only kills at the extremes. Free NH3 (not NH4⁺) is the AMO substrate, and the NH3 fraction falls ~10× per pH unit, so the AOB/comammox step starves at low pH even when total ammonia is high; NOB physiology slows in acid too. Applied as a piecewise-linear multiplier on µ for all three guilds. Curve calibrated to the consistent literature/extension consensus (EPA Nitrification; OSU aquaponics; Fritz Aquatics): optimal pH 7.5–8.5, significant decline <6.8, severe inhibition <6.5, ceases ~6.0. High-pH limb deliberately gentle (free-NH3 toxicity to NOB is handled by the separate K_NH3_inhib kernel; penalising it twice would wrongly slow hard alkaline tanks that cycle fast in practice). Set pH_activity_enabled = False to disable.

pH	6.0	6.5	7.0	7.5	8.5	9.0	9.5	10.0
µ multiplier	0.0	0.20	0.50	1.0	1.0	0.85	0.55	0.30

Hypoxia

Symbol	Value	Units	Source / Rationale
O2 stress	6.0e-5	mol/L	~2 mg O2/L; aerobe stress threshold
O2 lethal	1.5e-5	mol/L	~0.5 mg O2/L
m_hypoxia,max	0.06	/h	Aerobe sensitivity

Light suppression

Symbol	Value	Units	Source / Rationale
K_light (inhibition)	500.0	µmol m⁻² s⁻¹	AOB/Nitrosomonas photoinhibition half-response (hyperbolic 1/(1+I/K)). 50 % inhibition at ~500 µmol; unaffected ≤15, ~11 % down at 60, tolerate ~200 (Merbt et al. 2012, FEMS Microbiol Lett 327:41; Vergara et al. 2016; algal-bacterial photobioreactor studies). NOB/comammox override tighter (their sections). Was 2.0 — implied 50 % inhibition at a near-dark 2 µmol (dimmer than a shaded substrate), leaving nitrifiers no oxic-lit niche and stalling planted-tank nitrite clearance for months.
Biofilm light attenuation	0.10	–	M=1 mature EPS light attenuation
Geometric light shield scale	0.90	–	Roughness-scaled light shelter
Pore-zone O2 source	bulk O2	–	Pore-resident (pore_fraction) nitrifiers breathe bulk-water O2, not lumped anoxic PORE_O2 — they occupy the thin oxic sediment-surface microzone fed by the overlying water (Jensen et al. 1994 L&O 39:573; Risgaard-Petersen & Jensen 1997 L&O 42:529). Keeps the in-situ pore NO3/NO2 they produce (denitrifier feed) while preventing the pore fraction from suffocating.
PORE_FRACTION_SOIL_DEFAULT	0.6	–	Share of biomass placed in the soil pore zone (soil tanks; config.py auto-injection per class). AOB / comammox 0.6 — their NH4 substrate concentrates in the pore (Schramm 1996). NOB overrides to 0.2 (its section) — NO2 is a transient intermediate that is not pore-stable.

Mortality & viral lysis

Symbol	Value	Units	Source / Rationale
m_base	0.01/24	/h	~1%/day persistent guild
m_viral,max	0.005	/h	Density-dependent lysis cap
K_viral	2e-5	mol/L	Half-sat on biomass density
m_total,max	0.50	/h	Hard cap
Death → suspended fraction	0.8	fraction	Most planktonic mortality stays suspended
Surface death → settled fraction	0.9	fraction	Surface-attached mortality mostly settles

Biofilm dynamics & predation protection

Symbol	Value	Units	Source / Rationale
Settlement rate	0.002	/h	Biofilm colonisation rate
Detachment rate	0.0002	/h	10× slower than settlement
Induction lag	48.0	h	Enzyme-induction lag for fresh inoculum
Induction lag min factor	0.10	fraction	Floor activity at t=0
Biofilm predation protection	0.90	fraction	Schramm 1996 / Matz & Kjelleberg 2005 — 90% biomass unreachable to grazers at full biofilm maturity
Geometric predation shield scale	0.70	–	M=0 floor — calibrated against skeptic_overstocked_nano scenario
GRAZING_SUBSTRATE_REFUGE_SOIL	0.85	fraction	Burial-refuge ceiling: max share of nitrifier biomass that can sit below the grazed surface skin (substrate interstitial biofilm + EPS basal layers), inaccessible to metazoan grazers (snails, shrimp, copepods, ostracods). Applied SYMMETRICALLY to AOB / NOB / comammox — they co-aggregate microns apart in the same nitrifying biofilm (Schramm et al. 1996 AEM 62:4641), so grazing exposure is guild-symmetric, unlike the kinetic `pore_fraction`. Scaled per-surface by `benthic_fraction`: the effective refuge on a surface is `0.85 × benthic_fraction`, so sand/gravel floor (benthic_fraction 1.0) gets the full 0.85, bare glass walls (0.0) get none (only their EPS shelter), and leaves (~0.3) get partial credit — burial is only possible where there is floor substrate to bury into. Auto-injected by config.py: 0.85 in soil tanks, 0.0 bare-bottom. Scales the grazing access modifier only (`species/access.py` `modifier_coeffs`/`effective_access`); the self-mortality path (`surface_protection`) is unscaled because base/viral mortality reaches buried cells. Stacks multiplicatively with the M-dependent EPS shelter: total protection = r_eff + (1−r_eff)·P_biofilm. Without it, a maturing invertebrate community grazes all three nitrifier guilds — including NOB, the sole NO2 sink — to local extinction, freezing a spurious ~0.17 mg-N/L residual nitrite in established planted tanks; with it the mature tank reaches kit-undetectable NO2 (~0.05 mg-N/L), the surviving nitrification concentrated on the protected substrate surface.

Recruitment / immigration floor

Symbol	Value	Units	Source / Rationale
recruitment_N_mgL_per_h	1.0e-9	mg N / L / h	Continuous tiny aerial deposition + water-change inoculation + biological vectoring into the planktonic pool, C and P added at species stoichiometry. ≈ 10 cells / L / h = 240 cells / L / day, sitting at the low (indoor) end of Bowers et al. 2013's measured 10²–10⁴ aerial cells / L of settled air / day. Hovanec et al. 1998 documented that sterile new freshwater aquaria establish functional nitrification within ~21 days from this background contamination alone. Defensive insurance against numerical extinction under transient hypoxia — negligible (~8.6e-6 mg N / L / year mass injection) when biomass is healthy; seeds recovery within days when a guild bottoms out.

AOB / ammonia oxidisers — divergent only

Nitrosomonas-class first-leg nitrifier (NH₄ + 1.5 O₂ → NO₂ + 2 H⁺). Refs: Prosser 1989, Ensign 1993, Wagner 2002, Martens-Habbena 2009, Könneke 2005, Arp & Stein 2003.

Substrate & stoichiometry

Symbol	Value	Units	Source / Rationale
Substrate / Product	NH₄ / NO₂	–	NH₄ + 1.5 O₂ → NO₂ + 2 H⁺
O₂:X	1.5	mol O₂ / mol N	Half-reaction stoichiometry
TA:X	−2.0	eq TA / mol N	2 H⁺ released
μ_max	0.50/24	/h	Prosser 1989: Nitrosomonas doubling 33–56 h → ~0.5/day
K_substrate	2.5e-5	mol/L NH₄	Martens-Habbena 2009; Könneke 2005
K_O2	1.0e-6	mol/L	≈0.03 mg O₂/L; AMO O₂-independent above ~1 mg/L (Hunik; Laanbroek & Gerards). ~13× more O₂-affine than NOB — the basis of low-DO nitrite accumulation. Override of base 3e-5 (which made AOB ~14% O₂-limited at 6 mg/L, collapsing the AOB/NOB asymmetry to ~2×)
BGE	0.08	mol C / mol NH₄	Prosser 1989

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Cu:C	2.0e-7	mol Cu / mol C	AMO Cu-monooxygenase (Ensign 1993, Arp & Stein 2003)

NOB / nitrite oxidisers — divergent only

Nitrospira-leaning second-leg nitrifier (NO₂ → NO₃) — more pH- and O₂-sensitive than AOB, with both NH₃ and HNO₂ inhibition gates. Refs: Knowles & Wakeham 1978, Daims 2015, Schramm 1996, Anthonisen 1976, Vadivelu 2006/2007, Park & Bae 2009, Pollice 2002, Sin 2008.

Substrate & stoichiometry

Symbol	Value	Units	Source / Rationale
Substrate / Product	NO₂ / NO₃	–	Charge-conserving redox
O₂:X	0.5	mol O₂ / mol N	Half-reaction
TA:X	0.0	eq TA / mol N	No proton release; biomass-N assimilation handles −1 separately
Uses biofilm NH₄ enrichment	False	–	No NO2 enrichment kernel in V1
PORE_FRACTION_SOIL_DEFAULT	0.2	–	Far lower than AOB/comammox (0.6). Pore-residency tracks where a guild's substrate concentrates. AOB's NH4 is concentrated in the substrate pore by mineralisation; NOB's NO2 is a transient intermediate that diffuses out of the well-mixed pore (PoreWaterDiffusion) into the bulk faster than pore-NOB can consume it — so a high pore_fraction left 60 % of NOB NO2-starved (perceived-NO2 Monod factor ~0.02 vs ~0.8 in the bulk) while bulk NO2 piled up to a spurious ~0.5–0.7 mg-N/L plateau in established planted tanks. The single-pore, well-mixed model can't reproduce microscale AOB↔NOB spatial coupling (Schramm 1996/1999), so NOB are placed where their substrate effectively ends up: the bulk / oxic-surface zone. With 0.2, established planted tanks reach the realistic ~0 NO2 (plant-dominated silent cycle) and shrimp persist robustly.
μ_max	0.45/24	/h	Doubling ~37 h — set just below AOB (0.50/24) so NOB trails AOB as a K-strategist, which is what now sources the new-tank NO₂ spike. Slightly slower than pure-culture Nitrospira (Nowka/Daims/Spieck 2015: 12–32 h); the gap stands in for the establishment lag (lower seed + NO₂-substrate dependency) not otherwise modelled. Was 0.85/24 (faster than AOB) — backwards for an aquarium K-strategist, which forced the model to manufacture the spike via chronic free-NH₃ poisoning (see K_NH3,inhib). Aquarium NOB is Nitrospira, not Nitrobacter (Hovanec 1998). Calibrated to the audit §9.4 target: baseline NO₂ peak 2–5 mg N/L, high-pH ≈ baseline (no inversion)
K_substrate	1.5e-5	mol/L NO₂	≈15 µM — measured Nitrospira affinity (Nowka 2015: Km 9–27 µM). Was 5e-6, tighter than the organism modelled; drained NO₂ too aggressively
BGE	0.02	mol C / mol NO₂	Knowles & Wakeham 1978; Wagner 2002 — ~4× lower than AOB (less free energy per electron)
K_O2	1.3e-5	mol/L	≈0.43 mg O₂/L (Hunik; Laanbroek & Gerards). ~13× less O₂-affine than AOB (1e-6) → low DO throttles NOB selectively → nitrite accumulation. Was 6e-5 (~2 mg/L), only ~2× the old AOB value
T_opt,growth	32.0	°C	Slightly above AOB's 30 °C — pure-culture Nitrobacter optimum (~38) sits above Nitrosomonas (~35) (Grunditz & Dalhammar 2001), scaled to community optima. Keeps NOB pace with AOB through the optimum (no warm-water nitrite pile-up) and makes very hot tanks AOB- not NOB-limited. Only the above-optimum limb differs from base, so every ≤26 °C scenario is unchanged. (Making the cold NO2 tail mechanistic via a steeper NOB cold falloff is deferred — it would shift the calibrated 18 °C run; today the cold tail comes from the establishment lag)
T_max,growth	49.0	°C	Growth → 0; same ceiling as AOB

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	4.0e-5	mol Fe / mol C	NXR Fe-S + ETC
Mo:C	5.0e-8	mol Mo / mol C	NXR molybdopterin (~5× anchor)
Cu:C	5.0e-8	mol Cu / mol C	Universal anchor (no AMO)

Inhibition

Symbol	Value	Units	Source / Rationale
K_NH3,inhib	5.0e-5	mol/L	≈0.7 mg NH3-N/L; Anthonisen onset band. Was 5e-6 (Vadivelu enriched-culture Ki) — over-fired at hobby doses (suppressed NOB ~52% at baseline, ~82% at pH 8.5), manufacturing the NO2 spike via chronic FA poisoning and inverting high-pH tanks. Spike now comes from establishment lag + Nitrospira affinity; FA only bites at genuinely high free ammonia
K_HNO2,inhib	7.0e-7	mol/L	≈0.01 mg HNO2-N/L (Vadivelu 2007; Park & Bae 2009) — left as-is; free nitrous acid genuinely is a sharp NOB inhibitor (the "keep NO2-N < 5 mg/L" self-stall rule)
K_light (inhibition)	50.0	µmol m⁻² s⁻¹	NOB are the most light-sensitive nitrifying guild — ~80 % suppressed at ~200 µmol where AOB tolerate (Vergara et al. 2016, basis of light-driven partial nitritation; Guerrero & Jones 1996, Nitrobacter ≫ Nitrosomonas sensitivity). ~10× tighter than the AOB base (500). At a shaded substrate surface (≈3–13 µmol) NOB still run ~79–94 % so the NO₂→NO₃ step establishes in the oxic biofilm, while bright water-column light strongly throttles the lit/planktonic fraction (preserving "NO2 lingers under high light").

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	6.5 / 9.0	–	Tightened vs base — NOB more pH-sensitive
pH lethal (low / high)	5.5 / 10.0	–	Tightened
m_pH,max	0.04	/h	Elevated vs base

Hypoxia

Symbol	Value	Units	Source / Rationale
O2 stress	9.0e-5	mol/L	Tightened vs base
O2 lethal	3.0e-5	mol/L	Tightened
m_hypoxia,max	0.02	/h	Elevated NOB O2 sensitivity but recoverable on a one-day timescale. Schramm 1996 micro-electrode work shows NOB in mature biofilm interiors tolerate brief hypoxia via micro-aggregate O2 gradients. Lowered from 0.08 (May 2026) after the prior value caused total NOB extinction during transient bulk-O2 dips in the Walstad 365d diagnostic; with no recovery pathway from sub-detection biomass, NO2 plateaued indefinitely. 0.02 = 48%/d max wipeout at full anoxia, still aggressive but allows recovery.

Comammox Nitrospira — divergent only

K-strategist single-cell complete oxidation (NH₄ → NO₃ in one cell); dominates mature aquarium biofilms. Refs: Daims 2015, van Kessel 2015, Kits 2017, Bartelme 2017, Sauder 2017, Sakoula 2021.

Substrate & stoichiometry

Symbol	Value	Units	Source / Rationale
Substrate / Product	NH₄ / NO₃	–	Single-cell complete oxidation
O₂:X	2.0	mol O₂ / mol N	Sum of AMO+NXR
TA:X	−2.0	eq TA / mol N	Only NH₄→NO₂ leg releases H⁺
μ_max	0.30/24	/h	Conservative ~55 h doubling; Kits 2017 reports ~24 h for N. inopinata, community estimates slower (Bartelme 2017)
K_substrate	5.0e-7	mol/L NH₄	Conservative community value (~50× tighter than AOB); Kits 2017 reports 6.3e-8 in pure culture — tuned upward to avoid day-1 dominance
K_O2	4.0e-5	mol/L	Kits 2017 measured ~1 µM for N. inopinata; intermediate AOB/NOB
BGE	0.10	mol C / mol NH₄	Thermodynamic ceiling: captures both half-reactions; ≈ AOB+NOB sum (0.08+0.02)

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Mo:C	4.0e-8	mol Mo / mol C	NXR molybdopterin (near NOB level)
Cu:C	1.5e-7	mol Cu / mol C	AMO Cu-monooxygenase, between AOB (2e-7) and NOB anchor

Inhibition

Symbol	Value	Units	Source / Rationale
K_NH3,inhib	2.0e-6	mol/L	Sakoula 2021 — comammox more NH3-sensitive than AOB/NOB; ~3× tighter than NOB. Mechanism: dual AMO+NXR sites compound inhibition
K_HNO2,inhib	0.0	mol/L	Sentinel — substrate is NH4, HNO2 branch self-skips
K_light (inhibition)	300.0	µmol m⁻² s⁻¹	Between AOB (500) and NOB (50). Yamamoto et al. 2022 (PMC9797979): >50 % photoinhibition of N. inopinata only under acute bright/direct sun (500–800 µmol), inhibition confined to <550 nm; but the Nitrospira lineage is chronically more light-sensitive than Nitrosomonas-type AOB. Shaded substrate (≈3–13 µmol) leaves comammox near-uninhibited so it holds the mature-tank niche; bright light throttles the lit fraction

Heterotrophic bacteria

Single-pool decomposer guild — labile / refractory DOM split BGE, settled-detritus access scaling, sediment-anoxia gate, viral-shunt routing of lysed C to DOM. Refs: Azam 1983, Cole 1988, Carlson & Ducklow 1996, del Giorgio & Cole 1998, Kirchman 2012, Flemming 2016, Fuhrman 1999, Weinbauer 2004, Wainright 1990, Fenchel & Finlay 1995.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Water-change removal fraction	0.40	fraction	Flemming 2016: 40–80% biofilm-associated; only free-living ~40% removed by water change
Body size	0.0001	cm	~1 µm
μ_max (substrate uptake)	0.25	/h	Kirchman 2012: doubling 0.5–3 h → 0.2–1.4/h; 0.25/h mixed community
K_DOM (labile)	8e-6	mol C / L	Labile DOM ~0.096 mg C/L; Carlson & Ducklow 1996, Kirchman 2012
K_DOM (refractory)	5e-7	mol C / L	Refractory ~0.006 mg C/L; tighter due to enzyme specialisation
K_detritus (suspended)	2e-5	mol C / L	Suspended detritus ~0.24 mg C/L
K_detritus (settled)	4e-5	mol C / L	Settled higher K due to lower surface:volume ratio (Wainright 1990)
DOM (labile) preference	2.0	weight	Labile prioritised 2× over suspended detritus
DOM (refractory) preference	0.1	weight	Refractory ~10× less preferred (humic enzymes)
Settled-detritus preference	0.3	weight	Settled ~3× less preferred (access limitation)
Settled-detritus access fraction	0.3	fraction	Only benthic-associated fraction accesses sediment
BGE (labile)	0.28	fraction	Carlson & Ducklow 1996; del Giorgio & Cole 1998 — 15–40% labile BGE
BGE (refractory)	0.08	fraction	Refractory BGE much lower (enzyme overhead)
K_O2 (growth)	3e-5	mol/L	~1 mg/L; del Giorgio & Cole 1998, Fenchel & Finlay 1995 — high O2 affinity

C:N-driven N immobilisation — when substrate C:N exceeds bacterial C:N (~5), the shortfall is drawn from bulk DIN; if even bulk DIN is insufficient, growth becomes C-limited and unbuildable C is respired. Floater detritus (C:N ≈ 20–30) becomes a transient N sink — the canonical Walstad "tank stripping" mechanism in mature planted systems.

Symbol	Value	Units	Source / Rationale
K_NH4,immob	3.0e-6	mol/L	~42 µg N/L; Kirchman 2012 Ch. 7, Vrede et al. 2002 AEM 68:2965 — aquatic heterotroph NH4 affinity 1–5 µM
K_NO3,immob	2.0e-5	mol/L	~280 µg N/L; ~7× K_NH4 — assimilatory NO3 reductase is energetically costly (Antia et al. 1991 Phycologia 30:1)
NO3 immobilisation preference	0.4	weight	NH4 preferred over NO3 even when bulk concentrations equal
max_frac_immob_per_h	0.20	fraction	Per-step pool-fraction safety cap; same pattern as nitrifier `cap_n` clamp

Sediment anoxia gate

Symbol	Value	Units	Source / Rationale
Sediment type	"sand"	–	Default; anoxia gate driver
Sediment area	0.0	cm²	Auto-injected from scenario
D_O2 (water)	7.2	cm²/h	O₂ diffusivity in water
k_sediment,resp	0.02	/h	Sediment respiration rate constant
Max O₂ penetration	10.0	cm	Cap on O2 penetration depth
Q10,sediment resp	2.0	–	Standard

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Bacterial C:N
N:P	10.0	mol / mol	Bacteria P-rich (lower N:P than Redfield)

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0008	mol O₂ / mol C / h	Low maintenance
K_O2 (respiration)	1e-5	mol/L	~0.3 mg/L

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	T_REF_C (25)	°C	Standard
Q10,uptake	2.2	–	Strong temperature dependence
Q10,resp	2.0	–	Standard
Q10,mort	1.6	–	Standard
T_stress (low / high)	5.0 / 35.0	°C	Wide tolerance — mixed community
T_lethal (low / high)	0.0 / 45.0	°C	Wide
m_thermal,max	0.02	/h	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.0	–	Wide
pH lethal (low / high)	4.5 / 10.0	–	Wide
m_pH,max	0.02	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	1.0	PSU	Freshwater
σ_S	8.0	PSU	–
S_stress (low / high)	0.0 / 10.0	PSU	Freshwater band
S_lethal (low / high)	0.0 / 25.0	PSU	–
m_salinity,max	0.10	/h	Standard

Hypoxia

Symbol	Value	Units	Source / Rationale
O2 stress	3e-5	mol/L	~1 mg/L — facultative anaerobe tolerance
O2 lethal	5e-6	mol/L	~0.15 mg/L
m_hypoxia,max	0.04	/h	Lower than aerobes

Mortality & viral lysis

Symbol	Value	Units	Source / Rationale
m_base	0.03/24	/h	~3%/day
m_viral,max	0.02	/h	Fuhrman 1999, Weinbauer 2004 — phages 10–50% mortality; max ~48%/day at saturating density
K_viral	2e-5	mol/L	~0.24 mg C/L half-sat
m_total,max	0.40	/h	Hard cap
Death → DOM fraction	0.80	fraction	Fuhrman 1999 — 60–95% lysed bacterial C → DOM; 80% central estimate
Death → suspended fraction	0.50	fraction	Of detritus remainder, half suspended

Predation protection

Symbol	Value	Units	Source / Rationale
Biofilm predation protection	0.50	fraction	Flemming 2016 — 60–80% embedded; conservative 0.50 for lumped pool
Geometric predation shield scale	0.30	–	Lower than nitrifier (0.70) because HB is partly planktonic

Sediment anaerobe base

Shared base for IronReducer / SulfateReducer / Methanogen (and DNRA) — pore-resident obligate anaerobes. Hypoxia kernel disabled; sentinel ACCEPTOR:C / TA:C zeros are overridden per subclass to encode the ladder-position stoichiometry. Refs: Lovley & Phillips 1988, Conrad 1999, Heijnen & Roels 1981, Whiticar 1999.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Water-change removal fraction	0.40	fraction	Matches denitrifier — pore-bound stays through exchange
Body size	0.0001	cm	~1 µm
μ_max (substrate uptake)	0.10	/h	Base default; subclasses override
K_DOM	1.0e-5	mol C / L	Half-sat on pore DOM
K_acceptor	1.0e-5	mol	Default acceptor half-sat; subclasses override
BGE	0.10	fraction	Anaerobic BGE — ~30% of NO3 BGE (Heijnen & Roels 1981)
Acceptor:C (sentinel)	0.0	mol / mol	Subclasses override
TA:C (sentinel)	0.0	eq / mol	Subclasses override
K_O2 (anoxia switch)	1.0e-5	mol/L	Hill² anoxia switch; matches abiotic kernels

Sediment binding

Symbol	Value	Units	Source / Rationale
Has soil substrate	False	–	Auto-injected per scenario
Soil anoxia factor	0.95	fraction	Floor for soil pore zone — genuinely anoxic buried bulk
Sediment type	"sand"	–	Auto-injected
Sediment area	0.0	cm²	Auto-injected

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Bacterial C:N
N:P	10.0	mol / mol	Bacterial N:P

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0004	/h	Anaerobic maintenance — runs on the catabolic acceptor

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	T_REF_C (25)	°C	Standard
Q10,uptake	2.5	–	Anaerobe sensitivity
Q10,resp	2.0	–	Standard
Q10,mort	1.6	–	Standard
T_stress (low / high)	5.0 / 35.0	°C	Wide tolerance
T_lethal (low / high)	0.0 / 45.0	°C	Wide
m_thermal,max	0.02	/h	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	5.5 / 9.0	–	Wide
pH lethal (low / high)	4.5 / 10.0	–	Wide
m_pH,max	0.02	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	1.0	PSU	Freshwater V1
σ_S	8.0	PSU	–
S_stress (low / high)	0.0 / 10.0	PSU	Freshwater band
S_lethal (low / high)	0.0 / 25.0	PSU	–
m_salinity,max	0.10	/h	Standard

Hypoxia (disabled)

Symbol	Units	Source / Rationale
O2 stress	mol/L	Sentinel — obligate anaerobes; hypoxia kernel disabled
O2 lethal	mol/L	Sentinel
m_hypoxia,max	/h	Disabled

Mortality & viral lysis

Symbol	Value	Units	Source / Rationale
m_base	0.025/24	/h	~2.5%/day persistent guild
m_viral,max	0.012	/h	Phage mortality cap
K_viral	2e-5	mol/L	Standard half-sat
m_total,max	0.40	/h	Hard cap
Death → DOM fraction	0.40	fraction	Lower than HB (0.80) — pore EPS retains lysate
Death → suspended fraction	0.20	fraction	Mostly settled; cells lyse in place

Predation protection

Symbol	Value	Units	Source / Rationale
Biofilm predation protection	0.50	fraction	EPS-embedded sediment community
Geometric predation shield scale	0.50	–	Higher than HB (0.30) — pore-obligate, no planktonic fraction

Denitrifier

Facultative anaerobe owning the NO₃ → N₂ flux — standalone Species (not a SedimentAnaerobeBase subclass), reads bulk + 50% pore NO₃, hypoxia kernel disabled. Refs: Seitzinger 1988, Tiedje 1988, Heijnen & Roels 1981, Korner & Zumft 1989, Zumft 1997, Carlson & Ducklow 1996, Nielsen 1992.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Water-change removal fraction	0.40	fraction	Pore-bound; matches HB
Body size	0.0001	cm	~1 µm
μ_max (substrate uptake)	0.18	/h	Korner & Zumft 1989 — Pseudomonas anaerobic doubling 3–6 h ≈ 0.12–0.23/h midpoint; slightly slower than HB aerobic 0.25/h
K_DOM	8e-6	mol C / L	Matches HB labile DOM
K_detritus (settled)	2e-5	mol C / L	Tighter than HB (no spatial access penalty — denitrifiers ARE the sediment community)
DOM (labile) preference	1.0	weight	Equal weight on DOM and settled detritus
Settled-detritus preference	1.0	weight	–
K_NO3	5.0e-5	mol/L	Seitzinger 1988 — sediment denitrifiers 10–100 µM; midpoint matches abiotic kernel
Pore-NO3 access fraction	0.5	fraction	Nielsen 1992 coupled nit-denit; matches retired abiotic kernel
BGE	0.30	fraction	Heijnen & Roels 1981 — NO3 anaerobic BGE ~70% of aerobic ATP per electron; close to HB labile 0.28
NO₃:C	0.8	mol / mol	Seitzinger 1988 — 5 CH2O + 4 NO3 → 2 N2 + 5 CO2
N₂:NO₃	0.5	mol / mol	Stoichiometric
TA:NO₃	1.0	eq / mol	+1 TA per NO3 (4 H⁺ consumed per 4 NO3)

Sediment binding

Symbol	Value	Units	Source / Rationale
Has soil substrate	False	–	Auto-injected
Soil anoxia factor	0.95	fraction	Floor — buried soil pore zone genuinely anoxic
Sediment type	"sand"	–	Auto-injected
Sediment area	0.0	cm²	Auto-injected
D_O2 (water)	7.2	cm²/h	Standard
k_sediment,resp	0.02	/h	Standard
Max O₂ penetration	10.0	cm	Standard
Q10,sediment resp	2.0	–	Standard

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	5.0	mol / mol	Bacterial
N:P	10.0	mol / mol	Bacterial

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	1.0e-4	mol Fe / mol C	NarG/NirS/NorB heme + Fe-S — 2× AOB anchor
Mo:C	5.0e-8	mol Mo / mol C	NarG molybdopterin (matches NOB)
Cu:C	4.0e-7	mol Cu / mol C	NosZ Cu-Z cluster (Zumft 1997) — distinctive complete denitrifier

Respiration & thermal envelope

Symbol	Value	Units	Source / Rationale
R_maint	0.0006	mol O₂ / mol C / h	Slightly below HB
K_O2 (respiration)	1e-5	mol/L	High maintenance O2 affinity
Q10,uptake	2.5	–	Anaerobe sensitivity
T / pH / salinity bands	(5/35, 0/45) °C; (5.5/9.0, 4.5/10) pH; freshwater	–	Match SedimentAnaerobeBase

Hypoxia (disabled)

Symbol	Value	Units	Source / Rationale
O2 stress / lethal / m_hypoxia,max	0.0 / 0.0 / 0.0	–	Hypoxia DISABLED — denitrifiers thrive in anoxia

Mortality & viral lysis

Symbol	Value	Units	Source / Rationale
m_base	0.025/24	/h	~2.5%/day
m_viral,max	0.015	/h	Phage parameterisation
K_viral	2e-5	mol/L	Standard
m_total,max	0.40	/h	Hard cap
Death → DOM fraction	0.40	fraction	Lower than HB — pore EPS retention
Death → suspended fraction	0.20	fraction	Mostly settled

Predation protection

Symbol	Value	Units	Source / Rationale
Biofilm predation protection	0.50	fraction	EPS-embedded
Geometric predation shield scale	0.50	–	Pore-resident, no planktonic dilution

DNRA — divergent only

Peer of denitrifier on the NO₃ rung — reduces NO₃ → NH₄ instead of N₂; niche partition emergent from per-NO₃ stoichiometry (DNRA more electron-efficient at high C, lower acceptor demand). Refs: Tiedje 1988, Burgin & Hamilton 2007, Kraft 2011, van den Berg 2015.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Acceptor:C	0.5	mol NO₃ / mol C	2 CH₂O + NO3 + 2 H⁺ → NH4 + 2 CO2; more electron-efficient than denitrifier (0.8)
TA:C	1.0	eq TA / mol C	+1 TA per mol C (2 H⁺ per 2 mol C). Chemically correct +2 TA per NO3 (retired abiotic kernel emitted +3)
μ_max (substrate uptake)	0.10	/h	van den Berg 2015 — fermentative DNRA genera slower than denitrifier (0.18); kinetic edge denitrifier exploits at high NO3
K_DOM	8e-6	mol C / L	Matches denitrifier — shared substrate channel
K_NO3	3.0e-5	mol/L	Tiedje 1988, Kraft 2011 — DNRA tighter NO3 affinity than denitrifiers; matches retired abiotic kernel
Pore-NO3 access fraction	0.5	fraction	Nielsen 1992 coupled nit-denit
BGE	0.25	fraction	van den Berg 2015 — comparable to denitrifier under acetate excess; slightly below 0.30 to reflect fermentative overhead

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	1.0e-4	mol Fe / mol C	Nrf 5×heme + NapB c-type heme + Fe-S
Mo:C	5.0e-8	mol Mo / mol C	NapA molybdopterin
Cu:C	2.0e-7	mol Cu / mol C	Universal anchor — no NosZ Cu-Z

Iron reducer — divergent only

Geobacter-style dissimilatory Fe(III) reducer — third rung of the ladder; releases Fe-bound P as a side effect. Refs: Lovley & Phillips 1988, Methé 2003, Reguera 2005.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Acceptor:C	4.0	mol Fe(III) / mol C	4 Fe(OH)3 + CH2O → 4 Fe²⁺ + CO2
TA:C	8.0	eq TA / mol C	+2 TA per Fe × 4 Fe = +8
μ_max (substrate uptake)	0.12	/h	Lovley/Methé 2003 — Geobacter sulfurreducens doubling 6–10 h ~0.1/h; slightly slower than denitrifier (Fe(III) yields ~50% of NO3 energy)
K_DOM	1.0e-5	mol C / L	Standard pore DOM half-sat
K_acceptor	1.0e-5	mol Fe-oxide	Saturated in young tanks; matters once 99% reservoir consumed
BGE	0.10	fraction	~30% of NO3 BGE

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	1.5e-4	mol Fe / mol C	OmcS/OmcB/OmcZ c-type cytochrome nanowires (Reguera 2005) — 3× anchor

Ladder inhibition & Fe-P release

Symbol	Value	Units	Source / Rationale
K_NO3,inhib	5.0e-6	mol/L	Matches methanogenesis/SR ladder gates — uniform NO3-rung threshold
Adsorbed P (Fe-bound) fraction	1.0	fraction	Auto-injected from soil preset (peat 0.10, walstad 0.60, volcanic 0.70); default = bare-bottom / fully Fe-mediated

Sulfate reducer — divergent only

Desulfovibrio analog — fourth rung; suppressed by NO₃ above and reducible Fe(III) loading (pore-concentration basis). Refs: Canfield 1991, Heidelberg 2004, Rabus 2015, Berner 1980, Roden 2003.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Acceptor:C	0.5	mol SO₄ / mol C	SO4 + 2 CH2O → HS + 2 HCO3 + H⁺
TA:C	−0.5	eq TA / mol C	One H⁺ released per 2 mol C
μ_max (substrate uptake)	0.06	/h	Canfield 1991 freshwater rates ~0.05/h pure culture; calibrated against abiotic kernel baseline
K_DOM	1.0e-5	mol C / L	Standard pore DOM
K_acceptor (pore SO₄)	5.0e-6	mol/L pore	Pore SO4 half-sat (saturates above ~1e-4 mol in tap-water tanks)
BGE	0.07	fraction	Heijnen & Roels 1981 — ~25% of NO3 BGE

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	1.0e-4	mol Fe / mol C	DsrAB siroheme + [4Fe-4S]; APS reductase Fe-S
Mo:C	5.0e-8	mol Mo / mol C	Matches denitrifier/NOB
Ni:C	5.0e-7	mol Ni / mol C	[NiFe]-hydrogenase distinctive — 5× anchor
S:C	6.0e-3	mol S / mol C	Cysteine-rich + Fe-S clusters; slightly above anchor

Ladder inhibition

Symbol	Value	Units	Source / Rationale
K_NO3,inhib	5.0e-6	mol/L	Matches ladder gates
K_oxide,inhib (pore)	0.05	mol/L pore	Berner 1980, Roden 2003 — SR onset in lake/marsh sediments at pore Fe(III) ~50–100 µmol/cm³; half-strength at ~7% fresh loading, full at ~50% depletion. Pore-concentration basis (not mol stock) — scale-invariant

Methanogen — divergent only

Acetoclastic Methanosaeta/Methanosarcina — bottom rung of the ladder; stronger T-sensitivity than other anaerobes (Q10 ≈ 4). Refs: Conrad 1999, Whiticar 1999, Thauer 2008, Bastviken 2004.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Acceptor:C	0.5	mol CH₄ / mol C	2 CH2O → CH4 + CO2 disproportionation
TA:C	0.0	eq TA / mol C	Acid-base balanced at C step
μ_max (substrate uptake)	0.03	/h	Bastviken 2004 freshwater rates ~0.02–0.04/h; Methanosaeta doubling 24–48 h
K_DOM	1.0e-5	mol C / L	Standard pore DOM
BGE	0.04	fraction	~13% of NO3 BGE — bottom of ladder
Q10,uptake	4.0	–	Bastviken 2004 lake sediment Q10 ≈ 4 — methanogens more T-sensitive than other anaerobes

Trace-metal:C overrides

Symbol	Value	Units	Source / Rationale
Fe:C	1.0e-4	mol Fe / mol C	F430 + [4Fe-4S] in MCR; less Fe-rich than Geobacter
Ni:C	5.0e-7	mol Ni / mol C	F430 cofactor in MCR — distinctive (5× anchor)
Co:C	5.0e-8	mol Co / mol C	Cobamides drive methyl-transfer — 10× anchor; distinctive methanogen signature

Ladder inhibition

Symbol	Value	Units	Source / Rationale
K_NO3,inhib	5.0e-6	mol/L	Matches ladder gates
K_pore SO4,inhib	1.0e-5	mol/L	Matches retired abiotic methanogenesis kernel default

Aquatic fungi

Hyphomycetes / chytrids — refractory-specialist decomposers that condition leaf litter and drive the fungal→bacterial succession. Cool-T competitive advantage (T_ref=20°C, below bacteria's 25°C). Refs: Bärlocher 1992, Suberkropp 1991/1998, Gulis & Suberkropp 2003, Gessner 1994/1999/2007, Krauss 2011, Kirk & Farrell 1987, Sinsabaugh 2002, Mille-Lindblom 2006, Gooday 1990, Six 2006, Von Lützow 2006, Reddy & DeLaune 2008, Bosatta & Agren 1999, Duarte 2016, Chauvet & Suberkropp 1998.

Growth & substrate kinetics

Symbol	Value	Units	Source / Rationale
Water-change removal fraction	0.05	fraction	Bärlocher 1992 — >95% hyphal biomass embedded in substrate; only zoospores/fragments removed
Body size	0.001	cm	~10 µm hyphal diameter
μ_max (substrate uptake)	0.035	/h	Suberkropp 1998: hyphomycete growth 0.05–0.20/day; Gulis & Suberkropp 2003: 0.03–0.12/day → ~0.84/day uptake supports ~0.1/day growth at 12% BGE
K_DOM (refractory)	3e-7	mol C / L	Sinsabaugh 2002; Krauss 2011 — high affinity for refractory (~0.004 mg C/L) via cellulases/laccases
K_detritus (settled)	1e-5	mol C / L	Settled detritus — physical access limitation
K_soil OM (refractory)	5e-4	mol C / L	Bosatta & Agren 1999; Sinsabaugh 2002 — particulate K 1–2 orders above dissolved (physical inaccessibility bottleneck). Gradual deceleration near pool exhaustion
K_DOM (labile)	5e-5	mol C / L	Low affinity for labile (bacteria outcompete)
DOM (refractory) preference	3.0	weight	Gessner 2007 — fungi dominate lignocellulose
Settled-detritus preference	2.0	weight	Bärlocher 1992 — hyphal colonisation of fresh detritus
Soil OM (refractory) preference	0.8	weight	Suberkropp 1998 — humified soil OM 5–10× lower fungal growth than fresh material
DOM (labile) preference	0.05	weight	Bacteria dominate labile substrates
α (recalcitrance)	0.0	–	Disabled by default — evolving K_soil modifier
β (recalcitrance)	2.5	–	Power exponent on depletion fraction when α>0
Initial soil-OM (refractory)	0.0	mol	Set by scenario init
Settled-detritus access fraction	0.7	fraction	Bärlocher 1992 — fungi primarily benthic
Soil-OM access fraction	0.15	fraction	Von Lützow 2006; Kirk & Farrell 1987; Reddy & DeLaune 2008 — peroxidases need O2, restricting decomposition to aerobic top 2–5 mm of 4 cm substrate ≈ 5–12%, plus root-channel access → ~15%
BGE (refractory)	0.15	fraction	Suberkropp 1998: 5–15% on leaf litter; Gulis & Suberkropp 2003: 10–18%
BGE (labile)	0.20	fraction	Secondary niche
Conditioning fraction	0.20	fraction	Gessner 1999; Gulis & Suberkropp 2003 — enzymatic conditioning fraction ~10–20% of fungal-processed C (excluding abiotic leaching)
K_O2 (growth)	3e-5	mol/L	Kirk & Farrell 1987 — peroxidases function at 0.5–1.0 mg/L; ~1 mg/L gives O2_fac≈0.89 at 8 mg/L

Space competition & bacterial interference

Symbol	Value	Units	Source / Rationale
Space carrying capacity	0.005	mol / mol	Gessner & Chauvet 1994; Suberkropp 1998; Six 2006 — upper bound 5 mg fungal C per g substrate C. Logistic suppression
Space includes detritus	True	bool	Settled detritus counts as colonisable
Bacterial suppression max	0.40	fraction	Mille-Lindblom 2006 — max 40% uptake reduction (substrate competition, not killing)
K_bacterial suppression	1e-5	mol C / L	Half-sat at ~0.12 mg C/L — gives 5–25% suppression at typical jar densities

Stoichiometry

Symbol	Value	Units	Source / Rationale
C:N	10.0	mol / mol	Suberkropp 1991 — hyphomycete C:N 8–12
N:P	15.0	mol / mol	Fungal N:P

Respiration

Symbol	Value	Units	Source / Rationale
R_maint	0.0005	mol O₂ / mol C / h	Metabolically conservative
K_O2 (respiration)	2e-5	mol/L	~0.64 mg/L; less tolerant than bacteria

Thermal envelope

Symbol	Value	Units	Source / Rationale
T_ref	20.0	°C	Suberkropp 1984; Chauvet & Suberkropp 1998 — community optimum 15–25°C; Duarte 2016. Lower than bacteria (25°C) → cool-water competitive advantage
Q10,uptake	2.0	–	Bärlocher 1992 — Q10 1.8–2.5
Q10,resp	2.0	–	Standard
Q10,mort	1.5	–	Standard
T_stress (low / high)	8.0 / 30.0	°C	Krauss 2011 — stress above 28–30°C
T_lethal (low / high)	2.0 / 38.0	°C	Bärlocher 1992 upper viability
m_thermal,max	0.02	/h	Standard

pH envelope

Symbol	Value	Units	Source / Rationale
pH stress (low / high)	4.5 / 8.5	–	Bärlocher 1992 — fungi tolerate mild acidity better than bacteria
pH lethal (low / high)	3.5 / 9.5	–	–
m_pH,max	0.02	/h	Standard

Salinity envelope

Symbol	Value	Units	Source / Rationale
S_opt	0.5	PSU	Freshwater
σ_S	5.0	PSU	–
S_stress (low / high)	0.0 / 8.0	PSU	Freshwater
S_lethal (low / high)	0.0 / 20.0	PSU	–
m_salinity,max	0.10	/h	Standard

Hypoxia

Symbol	Value	Units	Source / Rationale
O2 stress	5e-5	mol/L	~1.6 mg/L — obligate aerobe
O2 lethal	1.5e-5	mol/L	~0.5 mg/L
m_hypoxia,max	0.06	/h	Aerobe sensitivity

Mortality & death routing

Symbol	Value	Units	Source / Rationale
m_base	0.02/24	/h	Bärlocher 1992 — hyphal turnover 2–5%/day; low end for established mycelium
m_total,max	0.30	/h	Hard cap
Death → DOM (labile) fraction	0.20	fraction	Cytoplasmic lysis
Death → DOM (refractory) fraction	0.15	fraction	Gooday 1990 — chitin/melanin recalcitrant cell wall fragments
Death → DOM fraction (total)	0.35	fraction	Sum of lab + ref (consumed by base class)
Death → suspended fraction	0.15	fraction	Hyphae substrate-bound; mostly settled

Biogeochemical & Physical Processes

Process kernels — sediment / water-column chemistry, gas exchange across the air-water interface, light-driven photodegradation, mineral equilibria, allelochemical decay, biofilm maturation, and bioturbation. The conventions below are shared; per-process tables only spell out divergences.

Process symbol glossary

Symbol	Meaning
k_X	First-order rate constant for process X (per h)
K_X	Monod / Hill half-saturation for substrate or driver X
D_X	Molecular diffusivity of species X (m²/h or cm²/h)
Q10,X	Temperature sensitivity of process X (multiplicative rate increase per 10 °C)
T_ref	Reference temperature for Q10 scaling (default 25 °C)
pH_break	Sigmoid midpoint for pH-modulated ligand stability
pH_width	Sigmoid width for the same transition (pH units)
pKa1	First acid-dissociation constant
Hill n	Hill exponent for sigmoid response curve
Ω	Mineral saturation state (precipitation when Ω > 1, dissolution when Ω < 1)
f_X,max	Fractional ceiling on process X (e.g. maximum local re-oxidation share)
Henry's law constant	Air-water partitioning ratio for gas exchange

Decomposition

Abiotic first-order breakdown of suspended and settled detritus with separate O₂-aerobic and anaerobic-floor rates; products split between DOM and direct mineralization (DIC/NH₄/PO₄) and exchanged between suspended/settled pools via aggregation and resuspension.

Decomposition rates

Symbol	Value	Units	Source / Rationale
k_decomp (suspended)	0.12/24 (~12%/day)	/h	Cole et al. 1984 (5–20 %/day labile OM); Urban-Rich 1999
k_decomp (settled)	0.04/24 (~4%/day)	/h	Calibrated for ~50/50 biotic/abiotic split with HeterotrophicBacteria; pre-split literature value ~8 %/day

O₂ gating

Symbol	Value	Units	Source / Rationale
K_O2	1.0e-5	mol/L	Aerobic decomposition half-sat; standard sediment value
Min decomp fraction	0.15	–	Anaerobic decomposition floor as fraction of aerobic
Settled O₂ scaling	0.5	–	Hand-tuned to reflect partially anoxic sediment
Settled O₂ access fraction	0.3	–	Hand-tuned O₂ demand reduction for settled decomp

Product routing

Symbol	Value	Units	Source / Rationale
Fraction → DOM	0.70	–	70% DOM, 30% direct mineralization split
DOM labile fraction (suspended)	0.70	–	Kalbitz et al. 2003 / Hedges et al. 2001 — younger detritus more labile
DOM labile fraction (settled)	0.55	–	Kalbitz et al. 2003 / Hedges et al. 2001 — aged detritus more humified

Particle exchange

Symbol	Value	Units	Source / Rationale
k_resuspension	0.015/24 (~1.5%/day)	/h	Wainright 1990 (1–5 %/day shallow systems)
k_aggregation	0.015/24 (~1.5%/day)	/h	Hand-tuned to balance resuspension

Thermal

Symbol	Value	Units	Source / Rationale
T_ref	25	°C	Engine reference temperature
Q10,decomp	2.0	–	Typical microbial Q10

Soil mineralization

Slow first-order mineralization of labile and refractory soil OM into pore-water nutrients with bacterial stimulation, evolving recalcitrance, methanogenic CH₄ routing, and a Phase-2 pore-DOM intermediate.

Mineralization rates

Symbol	Value	Units	Source / Rationale
k_lab	1.0e-4 (~0.24%/day)	/h	Reddy & DeLaune 2008; Walstad 1999 — labile manure/compost rate
k_ref	5.0e-6 (~0.012%/day)	/h	Reddy & DeLaune 2008 — peat/bark ~20× slower than labile
Q10	2.0	–	Standard microbial Q10
T_ref	25	°C	Engine reference
Soil volume	0.05	L	Scenario default; bacterial-stim threshold scaling

Bacterial stimulation

Symbol	Value	Units	Source / Rationale
K_bacterial	1.0e-4	mol C / L soil	Hand-tuned bacterial-stim half-sat
Bacterial stim coeff (labile)	0.5	–	Max fractional stimulation of labile fraction
Bacterial stim coeff (refractory)	0.2	–	Max stimulation of refractory fraction

Recalcitrance evolution

Symbol	Value	Units	Source / Rationale
α (recalcitrance)	0.0 (disabled)	–	Schmidt et al. 2011; Boudreau & Ruddick 1991 — set by soil preset
β (recalcitrance)	2.5	–	Recalcitrance exponent
Initial soil-OM (refractory)	0.0 (disabled)	mol C	Soil preset overrides

O₂ switching

Symbol	Value	Units	Source / Rationale
O₂ aerobic threshold	1.0	mg/L	Hand-tuned aerobic-switch upper threshold
O₂ anaerobic threshold	0.2	mg/L	Hand-tuned anaerobic-floor lower threshold
O₂ factor (aerobic)	1.0	–	Full aerobic rate
O₂ factor (anaerobic)	0.15	–	Facultative-microbe floor

Methanogenic ladder routing

Symbol	Value	Units	Source / Rationale
Anaerobic DIC fraction	0.50	–	Conrad 1999 / Whiticar 1999 — acetoclastic methanogenesis (2 CH₂O → CH₄ + CO₂)
K_O2 (methanogenesis)	1.0e-5	mol/L	Mirrors Methanogenesis Hill² gate
K_NO3 (methanogenesis)	5.0e-6	mol/L	Terminal-electron-acceptor ladder ordering
K_pore SO4 (methanogenesis)	1.0e-5	mol/L	Ladder ordering, mirrors Methanogenesis
Pore-DOM (labile) fraction	0.5	–	Phase 2 sediment realism — fraction of labile mineralization routed through PORE_DOM_LAB (denitrifier substrate)

Soil P sorption

First-order desorption/adsorption between mineral-bound P and pore-water PO₄, linearised Langmuir isotherm with equilibrium concentration target; buffers pore PO₄ against root drawdown.

Symbol	Value	Units	Source / Rationale
k_desorb	5.0e-4 (~1.2%/day)	/h	Reddy & DeLaune 2008; McGechan & Lewis 2002
k_adsorb	2.0e-3 (~4.8%/day)	/h	Reddy & DeLaune 2008 — P binds Fe/Al oxides rapidly
PO4 equilibrium	3.23e-5 (≈ 1.0 mg P/L)	mol P / L	Froelich 1988 — typical pore-water equilibrium
Soil pore volume	0.02	L	Scenario default
Q10	1.5	–	Weak T-dependence (partly physical sorption)
T_ref	25	°C	Engine reference

Soil humic leaching

Physical extraction of water-soluble humic/fulvic acids from soil refractory OM into water-column refractory DOM; no O₂ consumption, no bacterial dependence — produces the "tea-coloured water" signature.

Symbol	Value	Units	Source / Rationale
k_humic leach	1.5e-5	/h	Kalbitz et al. 2000; Thurman 1985; Walstad 1999 — soil-preset overrides (peat 4e-5, walstad fresh 2e-5, aquarium substrate 1e-6)
Q10	1.5	–	Physical dissolution — milder T-dependence than biology
T_ref	25	°C	Engine reference

Pore-water diffusion

Series-resistance Fickian diffusion (soil + sand cap + DBL) of dissolved species between pore and bulk water, with rhizosphere physical-barrier interception and bioirrigation amplification.

Free-solution diffusivities

Symbol	Value	Units	Source / Rationale
D_NH4	2.45e-6	m²/h	Li & Gregory 1974
D_NO3	3.28e-6	m²/h	Li & Gregory 1974
D_NO2	3.28e-6	m²/h	Cussler / Li & Gregory 1974 — matched to NO3
D_PO4	2.20e-6	m²/h	Li & Gregory 1974 (H2PO4⁻ at pH 7)
D_CO2	6.84e-6	m²/h	Jähne et al. 1987
D_Fe	2.59e-6	m²/h	Li & Gregory 1974 (aquo Fe²⁺)
D_K	7.06e-6	m²/h	Li & Gregory 1974
D_SO4	3.6e-6	m²/h	Schulz & Zabel 2006
D_HS	6.5e-6	m²/h	Schulz & Zabel 2006
D_CH4	6.6e-6	m²/h	Witherspoon & Saraf 1965; Boudreau 1997
D_O2	7.56e-6	m²/h	Han & Bartels 1996; Boudreau 1997
D_DOM (labile)	1.8e-6	m²/h	Lerman 1979; Boudreau 1997 (amino-acid / small-organic-acid mixture)

Sediment geometry

Symbol	Value	Units	Source / Rationale
Max depletion fraction	0.5	–	Numerical safety cap
DBL thickness	0.5e-3	m	Jørgensen & Revsbech 1985 (0.2–1 mm range)
Default soil tortuosity	0.3	–	Boudreau 1996 (τ² ≈ 1 − ln(φ²) for φ=0.38)
Sand-cap thickness	1.5	cm	Default for typical Walstad
Sand porosity	0.38	–	Coarse sand typical
Sand tortuosity factor	0.5	–	Sand-pore tortuosity default
Soil depth	3.0	cm	Default soil layer
Soil porosity	0.38	–	Soil preset overrides
Soil tortuosity factor	0.3	–	Boudreau 1996
Sediment area	100.0	cm²	Scenario default
Soil pore volume	0.02	L	Scenario default
Q10,diffusion	1.3	–	Berner 1980 — weak T-dependence for diffusion
T_ref	25	°C	Engine reference

Rhizosphere & bioirrigation

Symbol	Value	Units	Source / Rationale
Max root trapping	0.2	–	Caffrey & Kemp 1992 — physical-barrier-only contribution (chemical share in RhizosphereOxidation)
K_root trap	5e-5	mol C / cm²	~15 g dry root/m² — half-sat calibrated for mature Vallisneria/Potamogeton
Bioirrigation α (gallery)	2.5	–	Mermillod-Blondin 2011 Table 2 (tubificid/chironomid bioirrigation)
Bioirrigation α (biodiffusor)	0.3	–	Hand-tuned — surface mixing weakly enhances pore↔column exchange

Rhizosphere oxidation

Four coupled chemical sinks (HS, NH₄, CH₄, Fe²⁺) driven by radial oxygen loss from rooted-macrophyte aerenchyma; demands scaled uniformly to fit the per-rhs ROL O₂ budget; Fe-P co-precipitation onto root iron plaque.

Symbol	Value	Units	Source / Rationale
k_nit	0.5	/h	Hand-set at per-pool depletion cap; supply-capped by ROL O2 budget
K_NH4 (nitrification)	5.0e-7 (~7 µg N/L)	mol/L	Sub-µM half-sat — O2-limited regime is the steady state
k_so	0.5	/h	Set at per-pool 0.5/h cap; Wium-Andersen et al. 1982 (textbook minute-scale)
k_mox	0.05	/h	Same magnitude as cryptic-interface kernel in Methanogenesis
k_Fe oxidation	0.5	/h	Set at per-pool cap; mirrors IronRedox.k_ox_free_per_h (Stumm & Morgan 1996)
P:Fe scavenge ratio	0.05	mol P / mol Fe	Mirrors IronRedox default (Gunnars & Blomqvist 1997)
Q10,chem	2.0	–	Standard chemical-kinetics Q10
Q10,bio	2.5	–	Microbial activity steeper than chemical
T_ref	25	°C	Engine reference
Pore O₂ routing fraction	0.5	–	Phase 2 sediment realism — fraction of unused ROL routed to PORE_O2 vs bulk

Gas exchange

Two-film model (Whitman 1923; Liss & Slater 1974) for O₂, CO₂, NH₃, H₂S, CH₄ across the air-water interface; uses Henry's law with overall KLa combining liquid- and gas-side resistance; open-top vs sealed headspace logic.

Symbol	Value	Units	Source / Rationale
D_NH3 / D_O2 ratio	0.78	–	Cussler 2009 (D_NH3=1.64e-9, D_O2=2.10e-9 m²/s)
D_H2S / D_O2 ratio	0.95	–	Cussler 2009; Schulz & Zabel 2006
D_CH4 / D_O2 ratio	0.88	–	Witherspoon & Saraf 1965
pKa1 (H₂S)	7.05	pH units	Millero 1986 — H2S ⇌ HS⁻ + H⁺
K_G / K_L ratio	100.0	–	Liss & Slater 1974 — still indoor air
Open-top threshold	0.5	/h	head_leak threshold above which tank is treated as open to atmosphere

Iron redox

End-to-end Fe speciation + redox: free/chelated oxidation, DOM-gated chelation equilibrium, sediment Fe-oxide reduction (biology owns; cryptic trap retained), photoreduction, settling, and Fe-PO₄ co-precipitation/release.

Oxidation kinetics

Symbol	Value	Units	Source / Rationale
k_ox (free)	0.5 (t½ ≈ 1.4 h)	/h	Stumm & Morgan 1996 (capped vs textbook minute-scale for LSODA stiffness)
k_ox (chelated)	0.008 (t½ ≈ 3.6 d)	/h	Rose & Waite 2003; Emmenegger et al. 2001
pH_ref (ox)	7.5	pH	Stumm & Morgan 1996 — calibration pH for [OH⁻]² rate law
pH ox factor (max)	20.0	–	Stiffness cap (~pH 8.15 equivalent)
pH ox factor (min)	0.01	–	Floor (~pH 6.5 equivalent)
K_O2 (Fe ox)	3.0e-5	mol/L	Stumm & Morgan 1996
Q10,Fe ox	2.0	–	Stumm & Morgan 1996; Millero et al. 1987
Q10,Fe red	2.0	–	Standard microbial Q10
Q10,photoreduction	1.5	–	Emmenegger et al. 2001 — photon-dominated kinetics
Q10,chelation	1.5	–	Ligand-exchange coordination kinetics

Chelation equilibrium

Symbol	Value	Units	Source / Rationale
k_chel (forward)	50.0	/h	Hand-tuned to match Rose & Waite 2003 / Emmenegger 2001 (>90% chelated in DOM-rich tanks)
k_chel (back)	0.02	/h	Hand-tuned dissociation rate
K_DOM (chelation)	5.0e-7	mol C/L	Hand-tuned — trace DOM saturates chelation

Sediment reduction & cryptic trap

Symbol	Value	Units	Source / Rationale
k_settle	1.0e-4 (~289 d t½)	/h	Hand-tuned (colloidal 1–10 nm ferrihydrite suspended indefinitely on simulation timescales)
k_red	5.0e-4 (~1%/day)	/h	Legacy (biology now owns reduction); Lovley & Phillips 1988 family
K_O2 (anoxia switch)	1.5e-5	mol/L	Hill-2 anoxia half-sat
K_detritus (settled)	5.0e-5	mol	Hand-tuned settled-det half-sat
Buried anoxia floor	0.5	–	Hand-tuned proxy for buried sediment oxide always in anoxic pore
Detrital anoxia floor (max)	0.3	–	Hand-tuned sub-mm anoxic microzone fraction
K_detrital anoxia (C)	2.0e-4	mol C	Half-sat for detrital anoxia in settled C
f_local re-ox (max)	0.9	–	Hand-tuned ≥90% of sediment-reduced Fe trapped in oxic tanks
K_O2 (re-ox)	3.0e-5	mol/L	Same scale as Fe²⁺ oxidation affinity
k_pore re-ox	0.05 (t½ ≈ 14 h)	/h	Hand-tuned for pore Fe²⁺ steady-state
K_oxide (pore re-ox)	1.0e-5	mol	Hand-tuned (saturating in typical Walstad ~1e-3 mol oxide)
K_O2 (pore re-ox)	3.0e-5	mol/L	Mirrors Fe²⁺ oxidation affinity

Fe-P scavenging

Symbol	Value	Units	Source / Rationale
P:Fe scavenge ratio	0.05	mol P / mol Fe	Gunnars & Blomqvist 1997; Griffioen 1994 (range 0.03–0.10)
Adsorbed P (Fe-bound) fraction	1.0	–	Soil preset overrides (peat 0.10, walstad 0.60, volcanic 0.70)

Photoreduction

Symbol	Value	Units	Source / Rationale
k_photoreduction	0.02	/h	Barbeau 2006; Voelker & Sulzberger 1996; Emmenegger 2001 (1–5%/day in humic lakes)
K_light (photoreduction)	40.0	µmol/m²/s	Hand-tuned Michaelis half-sat (no photoinhibition at aquarium light)
K_DOM (photoreduction)	5.0e-6	mol C/L	Hand-tuned — trace DOM activates recycle

Iron dose release

First-order pH-modulated release of ligand-bound Fe from the iron:protected staging pool into FE_CHELATED; per-form parameter bundles for sulfate / gluconate / EDTA / DTPA / EDDHA.

Form / Parameter	Value	Units	Source / Rationale
Gluconate k_baseline	0.0578 (t½ ≈ 12 h)	/h	Microbial ligand stripping — hobbyist Flourish Iron timescale
EDTA k_baseline	0.00578 (t½ ≈ 5 d)	/h	Chaberek & Martell 1959 — Fe-EDTA stability
EDTA pH_break	6.5	pH	Chaberek & Martell 1959
EDTA k_breakdown (max)	0.06	/h	Hand-tuned breakdown
DTPA k_baseline	0.00289 (t½ ≈ 10 d)	/h	Chaberek & Martell 1959
DTPA pH_break	7.5	pH	DTPA holds to ~pH 7.5
DTPA k_breakdown (max)	0.06	/h	Hand-tuned
EDDHA k_baseline	0.00206 (t½ ≈ 14 d)	/h	Hamilton-Taylor et al. 2005 family — stable past pH 9
EDDHA pH_break	9.0	pH	EDDHA stability range
EDDHA k_breakdown (max)	0.06	/h	Hand-tuned
EDDHA pH_width	0.4	pH	Softer transition
Default pH_width	0.3	pH	Sigmoid width — sharp transition

Sulfur redox

Sulfate reduction (biology owns), water-column + cryptic-interface HS oxidation, FeS precipitation (mass-action), FeS re-oxidation, and pH-dependent H₂S speciation cache for gas exchange & toxicity.

Sulfate reduction (legacy — biology owns)

Symbol	Value	Units	Source / Rationale
k_SR	0.005	/h	Canfield 1991 freshwater rate scaled to aquarium T (legacy — biology owns SR now)
K_O2 (anoxia switch)	1.0e-5	mol/L	Mirrors IronRedox Hill-2 anoxia half-sat
K_detritus (settled, C)	5.0e-4	mol/L	Hand-tuned settled-detritus C half-sat

HS oxidation (water column + cryptic interface)

Symbol	Value	Units	Source / Rationale
k_so	10.0 (~6 min t½)	/h	Millero 1991 — water-column sulfide oxidation
K_O2 (so)	1.0e-5	mol/L	Hand-tuned — O2-saturated above 0.3 mg/L
f_pore re-ox (max)	0.7	–	Berner 1980; Jørgensen 1982 — looser than Fe trap (HS more diffusive)
K_O2 (pore re-ox)	3.0e-5	mol/L	Same scale as Fe cryptic trap

FeS precipitation & re-oxidation

Symbol	Value	Units	Source / Rationale
k_FeS precipitation	1.0e6	(mol/L)⁻¹/h	Hand-set large (drives mass-action equilibrium)
k_FeS oxidation	0.005	/h	Berner 1981 — FeS persists for days under oxic
K_O2 (FeS ox)	3.0e-5	mol/L	Same scale as Fe pore re-oxidation

H₂S speciation & thermal

Symbol	Value	Units	Source / Rationale
pKa1 (H₂S)	7.05	pH	Millero 1986
Q10,S red	2.0	–	Standard microbial Q10
Q10,S ox	2.0	–	Stumm & Morgan family — abiotic kinetics

H₂S toxicity

Hill-2 acute mortality on consumers from undissociated H₂S (the only toxic species; pH-gated via SulfurRedox cache). Per-species K via the consumer K_H2S,tox.

Symbol	Value	Units	Source / Rationale
m_H2S,max (default)	0.05 (~70%/day)	/h	Matches Cu cap — 96-h kills near LC50 (Bagarinao 1992)
Hill n (default)	2.0	–	Bagarinao 1992 fig. 3 — well fit by Hill-2

Copper chelation

DOM-gated Cu²⁺ ⇌ Cu-DOM speciation equilibrium (no oxidation/reduction). Parallel to the Fe chelation kernel but ~10× stronger (Xue & Sigg 1993).

Symbol	Value	Units	Source / Rationale
k_chel (forward)	100.0 (~40 s timescale)	/h	Xue & Sigg 1993; Sunda & Huntsman 1995 — Cu binds DOM ~10× stronger than Fe
k_chel (back)	0.005	/h	Hand-tuned to match observed free-Cu²⁺ <1% of total dissolved
K_DOM (chelation)	3.0e-7 (~0.004 mg C/L)	mol C/L	Hand-tuned — saturated in DOM-bearing tanks
Q10,chelation	1.5	–	Mirrors IronRedox.Q10_chelation
T_ref	25	°C	Engine reference

Copper dose release

First-order pH-modulated release of ligand-bound Cu from copper:protected → CU_CHELATED. Cu-EDTA inverts polarity vs Fe-EDTA (breakdown at LOW pH, not HIGH).

Form / Parameter	Value	Units	Source / Rationale
Gluconate k_baseline	0.050 (t½ ≈ 14 h)	/h	Hand-tuned — Flourish day-scale observation
EDTA k_baseline	0.003 (t½ ≈ 10 d)	/h	Morel & Hering 1993 — Cu-EDTA log K=18.8
EDTA pH_break	4.0	pH	Outside aquarium range — kept for symmetry with Fe
EDTA k_breakdown (max)	0.030	/h	Hand-tuned
EDTA pH_width	0.4	pH	Sigmoid width
DTPA k_baseline	0.002 (t½ ≈ 14 d)	/h	Hand-tuned — DTPA effectively inert in aquarium pH
DTPA pH_break	5.5	pH	Off in normal tanks
DTPA k_breakdown (max)	0.050	/h	Hand-tuned
Default pH_width	0.3	pH	Sigmoid width

Copper toxicity

Hill-2 acute mortality + reproduction suppression on consumers driven by free Cu²⁺ (CU_FREE pool, not chelated). Per-species K via the consumer K_Cu,tox.

Symbol	Value	Units	Source / Rationale
m_Cu,max (default)	0.05 (~70%/day)	/h	Hand-tuned — 96-h kills near LC50 (Borgmann 1993, Lauer et al. 2012, EPA AWQC)
Hill n (mortality, default)	2.0	–	Reproduces observed shrimp dose-response (Lauer et al. 2012)
Hill n (repro suppression, default)	2.0	–	Complement of mortality curve at same K

Methanogenesis chemistry

Five-kernel CH₄ chemistry: settled-detritus methanogenesis (biology owns), water-column methanotrophy, cryptic-interface methanotrophy, ebullition. Closes the C book for anoxic substrate.

Methanogenic source (legacy — biology owns)

Symbol	Value	Units	Source / Rationale
k_methanogenesis	1.0e-3	/h	Bastviken 2004 freshwater sediment rate scaled to aquarium T (legacy — biology owns)
K_O2 (anoxia switch)	1.0e-5	mol/L	Mirrors IronRedox / SulfurRedox
K_detritus (settled, C)	5.0e-4	mol/L	Hand-tuned — sterile substrate has no methanogens
K_NO3 (methanogenesis)	5.0e-6 (~0.07 mg N/L)	mol/L	Terminal-acceptor ladder ordering
K_pore SO4 (methanogenesis)	1.0e-5 (~0.32 mg S/L)	mol/L	Ladder ordering

Methanotrophy (water column + cryptic interface)

Symbol	Value	Units	Source / Rationale
k_mox	0.05 (~14 h t½)	/h	Bastviken 2004; Hanson & Hanson 1996
K_O2 (mox)	1.5e-5 (~0.5 mg/L)	mol/L	Hand-tuned — methanotrophs microaerophilic
f_pore oxidation (max)	0.5	–	Hand-tuned — looser than Fe (0.9) and S (0.7) because CH4 bubbles bypass dissolved-phase oxidation
K_O2 (pore oxidation)	3.0e-5	mol/L	Same scale as Fe / S cryptic traps

Ebullition & solubility

Symbol	Value	Units	Source / Rationale
k_ebullition	0.2	/h	Hand-tuned/calibrated for LSODA stiffness — reduced 5× from 1.0 (May 2026)
CH4 saturation	1.4e-3	mol/L	Henry's law at 1 atm, 25 °C (Sander 2015)
Q10,methanogenesis	4.0	–	Bastviken 2004 — methanogens more T-sensitive than other anaerobes
Q10,mox	2.0	–	Standard abiotic-kinetics family

Silicon cycling

First-order dissolution of biogenic opal (diatom frustules) back to dissolved silica with weak Q10.

Symbol	Value	Units	Source / Rationale
k_dissolution	0.003/24 (t½ ≈ 10 d)	/h	Ragueneau et al. 2000; Van Cappellen et al. 2002 (5–20 d range)
Q10,dissolution	1.5	–	Physical-chemical process — weaker than metabolic
T_ref	25	°C	Engine reference

CaCO₃ equilibrium

First-order saturation-state-driven CaCO₃ precipitation (Ω > 1) and dissolution (Ω < 1 with calcareous substrate present); calcite or aragonite phase.

Symbol	Value	Units	Source / Rationale
k_precipitation	0.005	/h per unit Ω excess	Hand-tuned slow abiotic kinetics (Morse & Arvidson 2002 family)
k_dissolution	0.002	/h per unit Ω deficit	Morse & Arvidson 2002 — dissolution slower than precip
CaCO3 substrate	0.0 (disabled)	mol	Set per scenario; Plummer & Busenberg 1982 for Ksp(T)
Mineral phase	"calcite"	str	Plummer & Busenberg 1982 (calcite); aragonite Ksp ~39% higher

DOM photodegradation

Light-saturated photochemical breakdown of labile and refractory DOM to DIC + NH₄ + PO₄, with refractory humics 1.5× more photoreactive.

Symbol	Value	Units	Source / Rationale
k_photo	0.03/24 (~3%/day max)	/h	Cory et al. 2014; Bertilsson & Tranvik 2000 — brown-water lake range
Photo (refractory) multiplier	1.5	–	Zepp & Schlotzhauer 1981; Bertilsson & Tranvik 2000 — humic aromatic UV absorption
K_light	150.0	µmol/m²/s	Tranvik & Bertilsson 2001 — saturation above ~0.4 W/m²
Fraction mineralized	0.40	–	Moran & Zepp 1997 — 30–50% literature range
Q10,photo	1.3	–	Photochemistry — weak T-dependence
T_ref	25	°C	Engine reference

Allelopathy decay

First-order decay of polyphenol (light-gated photodegradation) and cyanotoxin (T-gated microbial breakdown) allelochemical tracer pools back to DIC. Also provides pure-function Hill-2 suppression / mortality kernels consumed by producer / consumer flux().

Symbol	Value	Units	Source / Rationale
Hill n (default)	2.0	–	Mirrors Cu toxicity Hill exponent
m_allelo,max (default)	0.04 (~60%/day)	/h	Rohrlack 2003 (daphnia 24 h 50% at 5 µg MC-LR/L)
k_polyphenol decay	5.0e-3 (~6 d t½)	/h	Wetzel 1992 (phenolic-OH more UV-absorbing than bulk DOM)
k_cyanotoxin decay	2.0e-3 (~14 d t½)	/h	Edwards & Lawton 2009 — adapted-community bioremediation
K_light	150.0	µmol/m²/s	Same scale as DOMPhotodegradation
Q10,cyanotoxin decay	2.0	–	Edwards & Lawton 2009 — standard microbial Q10
T_ref	25	°C	Engine reference

Biofilm maturity

Per-surface EPS-scaffold maturity index M (0–1) integrating activity history (bacteria + fungi + detritus + nitrifier Monod terms) against decay + grazer-damage; gates late-coloniser exposure, nitrifier protection, grazer access.

Maturation kinetics

Symbol	Value	Units	Source / Rationale
k_mature	0.040/24	/h	Battin et al. 2016 — stream biofilms reach maturity in 2–6 months; hand-tuned to t½ ≈ 4 mo at full activity
k_decay	0.001/24	/h	Hand-tuned — biofilms persist after activity drops
k_graze damage	0.012/24	/h	Feminella & Hawkins 1995; Dillon 2000 — radula physically strips EPS (raised from 0.002/24)
K_graze damage	5.0e-7	mol C/L	Hand-tuned (~6 µg C/L, few mg grazers in 30 L tank)
Q10,maturation	2.0	–	Flemming & Wingender 2010 — enzymatic EPS secretion
Q10,decay	2.0	–	Besemer 2015 — extracellular hydrolase Q10
T_ref	25	°C	Engine reference

Activity-signal weights & half-sats

Symbol	Value	Units	Source / Rationale
w_bacteria	0.35	–	Hand-tuned activity-signal weight
w_fungi	0.25	–	Hand-tuned activity-signal weight
w_detritus	0.25	–	Hand-tuned activity-signal weight
w_nitrifier	0.15	–	Hand-tuned activity-signal weight
K_bacteria	5.0e-5 (~0.6 mg C/L)	mol C/L	Hand-tuned to keep Monod responsive across realistic biomass
K_fungi	5.0e-6	mol C/L	Hand-tuned
K_detritus	2.0e-5	mol C/L	Hand-tuned
K_nitrifier	1.0e-5	mol C/L	Hand-tuned

Per-grazer damage coefficients

Symbol	Value	Units	Source / Rationale
Bladder snail	1.0	–	Hand-tuned (radula scraper — Dillon 2000)
Neocaridina	0.7	–	Hand-tuned (thoracic scraper)
Ostracod	0.3	–	Hand-tuned (browser/picker)
Daphnia / Copepod / Rotifer	0.0	–	No biofilm contact (planktonic)
Ciliate	0.05	–	Hand-tuned (minimal structural damage)
Nanoflagellate	0.02	–	Hand-tuned (negligible)

Bioturbation

FeS re-exposure (gallery-fauna only) and settled-detritus resuspension driven by burrowing-fauna intensity published into env._bioturbation_intensity. Bioirrigation lives as a multiplier in PoreWaterDiffusion.

Symbol	Value	Units	Source / Rationale
k_FeS bioturbation	0.02 (~35 h t½ at intensity=1)	/h	Mermillod-Blondin 2011 — paced ~4× faster than SulfurRedox.k_fes_ox_per_h (bypass of O2 penetration limit)
k_resuspension bioturbation	3.0e-4 (~0.7%/day)	/h	Hand-tuned ≈0.5× Decomposition baseline
Resuspension weight (gallery)	1.0	–	Hand-tuned (parameter for future asymmetric tuning)
Resuspension weight (biodiffusor)	1.0	–	Hand-tuned
Q10,chem	2.0	–	Standard chemical Q10
T_ref	25	°C	Engine reference