Glossary

Quick reference for scientific and technical terms used throughout the documentation. If you encounter an unfamiliar word in any of the docs, you will likely find it here.

A

Abiotic -- Not involving living organisms. Refers to purely physical or chemical processes such as UV photodegradation, mineral dissolution, or gas exchange.

Access fraction -- A value between 0 and 1 representing how much of a food source on a given surface a grazer can physically reach. Lower access means more of the prey is hidden in refugia.

Aerenchyma -- Air-filled channels inside plant roots and stems that transport gases (especially O2 and CO2) between above-water parts and submerged roots. Allows rooted macrophytes to access pore water CO2 directly.

Aerobic -- Requiring or occurring in the presence of dissolved oxygen. Aerobic respiration is the primary energy-generating process for most organisms.

Alkalinity -- A measure of water's capacity to neutralize acids, acting as a pH buffer. Higher alkalinity means pH changes less in response to the same amount of CO2 addition or removal. Also called total alkalinity (TA). See also buffering capacity.

Allelopathy -- Chemical warfare between organisms: one species releases secondary metabolites (allelochemicals) that suppress the growth, reproduction, or survival of competitors. Unlike resource competition (drawing down a shared nutrient), allelopathy is interference competition -- the producer actively poisons the niche. Modeled in EcoSym via two pure-C tracer pools (allelopathy:polyphenol and allelopathy:cyanotoxin) fed by macrophytes and cyanobacteria respectively, with Hill-2 suppression kernels on competing producers and on grazers (cyanotoxin only). The mechanism is one of the canonical drivers of alternative stable states in shallow lakes -- macrophyte-dominated clearwater systems are stabilised in part by polyphenol suppression of phytoplankton. See docs/chemistry/allelopathy.md for full details.

Allometric scaling -- The principle that biological rates (metabolism, feeding, respiration) change predictably with body size. Smaller organisms have higher mass-specific metabolic rates than larger ones.

Ammonium (NH4+) -- The ionized, relatively non-toxic form of dissolved nitrogen in water. Preferred nitrogen source for algae and the main excretion product of animals. Compare with unionized ammonia (NH3).

AMO (ammonia monooxygenase) -- The copper- and iron-containing enzyme that catalyzes the first step of nitrification, converting NH3 to hydroxylamine. AMO requires trace iron as a cofactor, so severe Fe depletion slows nitrifier growth even when NH4 and O2 are abundant.

Amorphous opal -- A non-crystalline form of silica (SiO2) that makes up diatom frustules. Dissolves slowly back into dissolved silica after diatom death.

Anaerobic -- Occurring without oxygen. Anaerobic decomposition is much slower than aerobic decomposition and uses alternative metabolic pathways such as fermentation.

Anoxia -- A condition where dissolved oxygen is at or near zero. Lethal for most aerobic organisms and dramatically slows decomposition. See also hypoxia.

Aragonite -- A crystalline form of calcium carbonate (CaCO3) about 39% more soluble than calcite. Found in crushed coral and oolithic sand substrates.

Assimilation efficiency -- The fraction of ingested food that a consumer actually absorbs into its body. The remainder is expelled as fecal pellets. Varies by food type (e.g., 50-65% for algae, 25-35% for detritus).

Attenuation coefficient -- A number describing how strongly a substance absorbs light per unit of concentration and depth. Higher values mean light is absorbed more quickly. See also Beer-Lambert law.

Autotroph -- An organism that produces its own food from inorganic substances, using light energy (photoautotroph) or chemical energy (chemoautotroph). Algae and plants are photoautotrophs.

B

Bacteriophage -- A virus that infects and kills bacteria. Bacteriophage-driven lysis is a major density-dependent mortality mechanism for bacteria in aquatic systems.

Bacterivore -- An organism that feeds primarily on bacteria. HNF and ciliates are the primary bacterivores in the model.

Beer-Lambert law -- A physics equation describing how light intensity decreases exponentially as it passes through an absorbing medium. Used to calculate how algae density, dissolved organic matter, and water depth reduce light availability.

Benthic -- Relating to the bottom of a body of water, or to submerged surfaces. Benthic organisms (snails, ostracods, shrimp) live on substrates rather than floating in the water column. Compare with planktonic.

BGE (bacterial growth efficiency) -- The fraction of consumed organic carbon that bacteria convert into new biomass, as opposed to respiring as CO2. In the model, BGE is 28% for labile DOM and 8% for refractory DOM.

Bicarbonate (HCO3-) -- The most abundant form of dissolved inorganic carbon at typical freshwater pH (6.5-8.5). Some algae and macrophytes can use bicarbonate for photosynthesis via carbon concentrating mechanisms.

Binary fission -- Asexual reproduction in which a single cell divides into two identical daughter cells. The reproduction method for bacteria, ciliates, and HNF.

Biofilm -- A community of microorganisms (bacteria, algae, etc.) attached to a surface and embedded in a self-produced matrix of sticky organic substances (EPS). Biofilms create nutrient-enriched microenvironments. Over months, biofilms develop structural complexity tracked by the biofilm maturity index.

Biofilm maturity index (M) -- A per-surface value (0 to 1) tracking the structural complexity of a biofilm. M = 0 is a bare surface; M = 1 is a fully mature biofilm with thick EPS scaffold, micro-channels, and trapped particulates. M integrates microbial activity history and determines habitat quality for benthic consumers, predation protection and light shielding for nitrifiers, and the effectiveness of refugia. See Biofilm Maturity.

Biogenic silica -- Silica (SiO2) incorporated into the glassy cell walls (frustules) of diatoms. Dissolves slowly after the diatom dies (half-life ~10 days), recycling silicon back into the water as dissolved silica.

Biomass -- The total mass of living organisms in a given area or volume, typically measured in milligrams of nitrogen (mg N) or carbon per liter.

Boron (B) -- A trace metalloid essential as a structural rather than catalytic cofactor. In vascular plants, boron crosslinks the rhamnogalacturonan-II domain of cell-wall pectin via two boron-diol ester bonds (O'Neill 2004) — the only metal-class plant cell-wall crosslinker known; B-deplete media collapses cell elongation in every vascular plant tested. In diatoms, boron stabilises the silica deposition vesicle during frustule construction and locks the mature frustule against premature dissolution (Loucaides 2008). In diazotrophic cyanobacteria, boron deposits into heterocyst-envelope glycolipids that maintain the O₂-diffusion barrier protecting nitrogenase (Bonilla 1990). Tracked as a single dissolved pool (boric acid B(OH)₃ + borate B(OH)₄⁻ lumped — they interconvert on millisecond timescales around pK_a ≈ 9.2 and biology absorbs both forms). Ambient freshwater B is 10–50 µg/L (Smedley 2002), an order of magnitude above cobalt and nickel — boron is genuinely abundant relative to other trace metals because its dominant source is silicate weathering rather than scavenged anthropogenic input. Seawater is ~4500 µg/L (the third-most abundant cation in the ocean after Na⁺ and Mg²⁺). No Monod gate on biology in V1 — at typical freshwater concentrations cellular K_B half-sats are saturated everywhere; B stoichiometry is held for mortality-delta reconciliation + respiration release so a future B-deficiency or boric-acid toxicity kernel has a clean mass-balance floor. Macrophytes override the universal anchor strongly upward (5 × 10⁻⁵ mol B / mol C, ~10× anchor) for cell-wall crosslinking; diatoms upward (1.5 × 10⁻⁵, ~3× anchor) for frustule integrity; diazotrophic cyanobacteria upward (2 × 10⁻⁵, ~4× anchor) for heterocyst envelopes. Conservative under water change; no sediment compartment, no speciation, no dosing plumbing. See micronutrient cycling.

Buoyancy regulation -- The ability of some planktonic cyanobacteria (Microcystis, Dolichospermum, Aphanizomenon) to adjust their vertical position in the water column using gas vesicles, letting them rise into high-light surface layers during calm conditions and sink to access nutrient-rich deep water. A major competitive advantage in stratified eutrophic lakes.

Buffering capacity -- The ability of water to resist changes in pH when acids or bases are added. Higher alkalinity means greater buffering capacity and more stable pH.

C

C3 plant -- A plant that uses the most common photosynthetic pathway, where CO2 is first fixed into a 3-carbon molecule. Most aquatic plants including Cryptocoryne, Salvinia, and duckweed are C3 plants.

C:N ratio (carbon-to-nitrogen ratio) -- The ratio of carbon to nitrogen in an organism or in organic matter. A key indicator of nutritional quality: low C:N means protein-rich; high C:N means carbon-rich. See also stoichiometry.

CaCO3 (calcium carbonate) -- A mineral compound used by snails and shrimp to build shells and exoskeletons. Its precipitation and dissolution affect both calcium concentration and alkalinity. See also calcite, aragonite.

Calcification -- The biological process of depositing calcium carbonate to build hard structures such as snail shells or shrimp exoskeletons.

Calcite -- The most common and thermodynamically stable crystalline form of calcium carbonate. Its solubility product (Ksp) determines when precipitation or dissolution occurs.

Calcareous -- Containing or composed of calcium carbonate. Calcareous substrates (crushed coral, aragonite sand) can dissolve to replenish Ca2+ in the water.

Cobalt (Co) -- A trace metal essential as the active-site cofactor in vitamin B12 (cobalamin) -- the corrin-ring metallocoenzyme that powers methionine synthase (regenerating methionine from homocysteine, anchoring one-carbon metabolism) and methylmalonyl-CoA mutase. B12 is synthesised de novo only by certain bacteria and archaea; every eukaryotic alga, every animal, and every aquatic fungus is auxotrophic for the vitamin and acquires it from the bacterial pool. A second smaller role is Co-substituted carbonic anhydrase in cyanobacteria when zinc is depleted (Saito 2002). Tracked as a single dissolved pool (free Co²⁺ + organic complexes lumped) at sub-µg/L concentrations across all freshwater types -- the rarest of the tracked trace metals because most cells acquire B12 from the bacterial pool rather than concentrating free Co²⁺. No Monod gate on biology in V1 -- B12 itself is not modelled as a distinct dissolved currency from free Co, so a Co_B12 half-sat would have no physiological surface to gate; Co stoichiometry is held for mortality-delta reconciliation + respiration release so a future B12-cycling process or Co-CA substitution kernel has a clean mass-balance floor. Cyanobacteria override the universal anchor upward (3 × 10⁻⁸ mol Co / mol C) for B12 biosynthesis + Co-CA; consumers slightly above (1 × 10⁻⁸) for the animal-tissue cobalamin pool. Conservative under water change; no sediment compartment, no speciation, no dosing plumbing. See micronutrient cycling.

Carbonic anhydrase (CA) -- A zinc-dependent enzyme that speeds up the conversion between CO2 and bicarbonate. Some aquatic plants (like hornwort) produce it externally to help access bicarbonate from the water. Because CA is a zinc metalloenzyme, severe Zn limitation throttles HCO₃⁻ use and forces cells to rely on diffusional CO₂ uptake — an important gate at high pH where free CO₂ is scarce. Some cyanobacteria substitute Co²⁺ or Cd²⁺ for Zn²⁺ at the CA active site, letting them tolerate Zn-poor water better than eukaryotic algae.

Carbon concentrating mechanism (CCM) -- Cellular machinery that allows some algae and aquatic plants to actively pump bicarbonate into their cells and convert it to CO2 internally. An advantage at high pH where free CO2 is scarce.

Carbonate (CO3 2-) -- The most fully deprotonated form of dissolved inorganic carbon. Becomes significant only at high pH (above ~9) and is important for CaCO3 precipitation.

Carbonate system -- The set of chemical equilibria governing how dissolved CO2, bicarbonate, and carbonate interconvert in water. Controls pH and buffering capacity.

Carrying capacity -- The maximum population or biomass density that a given environment or surface can support, determined by available resources (space, food, light, nutrients).

Cell quota (Q) -- The internal cellular concentration of a limiting nutrient, expressed as mol element per mol biomass C. The quota distinguishes structural nutrient (built into proteins, DNA, membranes) from luxury-stored nutrient (kept in polyphosphate granules, cyanophycin, or vacuolar pools). In Droop kinetics the quota gates growth via (1 − Q_min/Q). Q_min is the minimum needed for any division (typically 0.005 for P, 0.020 for N, mol/mol C); Q_max is the saturation ceiling — diatoms reach Q_P_max ≈ 0.05, cyanobacteria reach Q_N_max ≈ 0.25.

Centric diatom -- A diatom with radial symmetry (circular, drum-shaped valve), as opposed to pennate diatoms which are bilaterally symmetrical. Most centric diatoms are planktonic free-floaters -- the classic "spring bloom" specialists of temperate lakes, including Cyclotella, Asterionella, Fragilaria, and Synedra. In EcoSym modeled as diatom_centric, a fast-growing r-strategist subcommunity.

Charge balance -- The principle that total positive charges in solution must equal total negative charges. The model uses this equation to solve for pH given current DIC and alkalinity values.

Chemoautotroph -- An organism that obtains energy by oxidizing inorganic chemicals (rather than from light) and uses that energy to fix CO2 into organic carbon. Nitrifying bacteria are chemoautotrophs.

Chitin -- A tough, flexible polysaccharide that forms the structural material of arthropod exoskeletons (including shrimp) and fungal cell walls. In consumer species, the chitin fraction is simplified as CaCO3. In fungi, chitin cell wall fragments are routed to refractory DOM upon death.

Chytrid -- A small, often unicellular aquatic fungus that reproduces by releasing motile zoospores. Chytrids are the grazeable component of the aquatic fungi functional group -- their zoospores (2-10 um) are consumed by ciliates and HNF via the mycoloop.

Ciliate -- A single-celled organism (protist) covered in cilia (tiny hair-like structures). Ciliates are primarily bacterivores that bridge the size gap between bacteria and larger grazers in the microbial loop.

Cilia -- Tiny hair-like structures on the surface of cells, used for swimming or creating water currents to sweep food particles toward the mouth.

Cladoceran -- A group of small crustaceans commonly known as water fleas, including Daphnia. They have a bivalved carapace and reproduce by parthenogenesis.

Clearance rate -- The volume of water a filter feeder can process per unit time to extract food particles.

Co-limitation -- When two or more nutrients or resources simultaneously limit an organism's growth. For diatoms, silica is a co-limiting factor alongside nitrogen, phosphorus, CO2, and light.

Competitive exclusion -- The ecological principle that two species competing for the same limited resource cannot coexist indefinitely; one will eventually outcompete the other.

Conservative pool -- A dissolved substance tracked by the model that has no biological sinks or sources. Magnesium is currently a conservative pool.

Copepod -- A small crustacean (0.5-2 mm) common in freshwater and marine environments. The copepod species in the model uses cyclopoid parameters — a raptorial omnivore and the apex predator that links the microbial loop to the broader food web.

Copepodite -- A juvenile developmental stage of a copepod, intermediate between nauplius and adult.

Corona -- The crown of cilia around a rotifer's mouth, used to create water currents that sweep food particles in.

Coupled nitrification-denitrification -- A process in sediments where ammonium is first oxidized to nitrate (nitrification) in the aerobic layer, then the nitrate diffuses to the anoxic layer where it is converted to nitrogen gas (denitrification) and lost from the system.

Crowding mortality -- Extra mortality at high population densities due to competition for space, waste buildup, and increased disease transmission. A density-dependent population control mechanism.

Cyanophycin -- A non-ribosomal co-polymer of arginine and aspartate stored as dense intracellular granules in essentially every cyanobacterium (Simon 1971; Allen 1984). The luxury reservoir for Droop nitrogen dynamics in cyanobacteria, and the destination for nitrogen freshly fixed by nitrogenase in heterocyst-bearing genera. Cyanophycin can store ~25 % of cellular C as nitrogen — the largest luxury-N reservoir of any algal class (Q_N_max ≈ 0.25 mol N / mol C, vs ~0.15 for greens and ~0.18 for diatoms). The size of the cyanophycin pool also gates nitrogenase repression: cells with full granules suppress fixation; cells whose granules have drained activate it. This internal sensing pathway (NtcA / 2-oxoglutarate) explains why cyanobacteria continue fixing N₂ for several days into a post-bloom DIN crash even after external NH4 + NO3 are zero. See also luxury uptake, polyphosphate, cell quota.

Cyanotoxin -- Toxic secondary metabolites produced by some cyanobacteria (microcystin, anatoxin-a, cylindrospermopsin, saxitoxin). Responsible for most freshwater harmful algal blooms with significant impacts on drinking water, livestock, and wildlife. Primarily associated with bloom-forming planktonic genera (Microcystis, Dolichospermum, Aphanizomenon) and some benthic mat formers (Phormidium, Lyngbya). Not explicitly modeled in EcoSym but reflected implicitly in low consumer grazing preferences.

D

Dactylus -- The claw-like tip of a crustacean leg, used for gripping surfaces.

Decapod -- An order of crustaceans with ten legs, including shrimp, crabs, and lobsters.

Denitrification -- An anaerobic microbial process that converts nitrate (NO3-) to nitrogen gas (N2), which escapes the water. Permanently removes nitrogen from the ecosystem and increases alkalinity. See also coupled nitrification-denitrification.

Density-dependent -- A process whose rate changes with population density. Examples include crowding mortality, viral lysis, and cannibalism, all of which intensify as populations grow.

Detachment rate -- The rate at which biofilm or attached algae naturally slough off a surface and re-enter the water column. Smooth surfaces shed biofilm faster than rough ones.

Detritivore -- An organism that feeds on detritus (dead organic matter). Cherry shrimp and ostracods are the primary detritivores in the model.

Detritus -- Dead organic matter, including dead organisms, fecal pellets, and other organic debris. Tracked as suspended (floating in the water column) and settled (sunk to the bottom).

Diatom -- A type of microalga with a siliceous cell wall called a frustule. Diatoms are cool-adapted, shade-tolerant, and bloom early in aquarium setups before crashing when dissolved silica runs out. EcoSym splits the diatom functional type into two subcommunities: centric diatoms (fast planktonic bloomers) and pennate diatoms (slow benthic biofilm dwellers, the "brown algae" of new aquaria).

DIC (dissolved inorganic carbon) -- The total of all inorganic carbon dissolved in water: CO2(aq) + bicarbonate (HCO3-) + carbonate (CO3 2-). Its balance with alkalinity determines pH.

Diffusion boundary layer -- A thin layer of slow-moving water (tens to hundreds of micrometers thick) clinging to every submerged surface. Nutrients released within this layer linger long enough for attached organisms to intercept them before they disperse into the bulk water.

Diffusivity -- A physical property describing how fast a dissolved substance spreads through water by random molecular motion. Each solute has its own diffusivity value.

DIN (dissolved inorganic nitrogen) -- The sum of ammonium (NH4+) and nitrate (NO3-) dissolved in the water. The total nitrogen available for biological uptake.

Dispersal fraction -- The proportion of new algal growth on a surface that is redistributed to other surfaces (via fragments, daughter cells, or spores) rather than staying where it was produced.

Dissolution enthalpy -- The heat energy associated with a gas dissolving in water. Used in the van't Hoff equation to calculate how gas solubility changes with temperature.

Dissolved silica (DSi) -- Silicic acid (H4SiO4) dissolved in water -- the only form of silicon that diatoms can use to build their frustules. Typically starts at about 8 mg Si/L in freshwater.

Dissolved organic matter (DOM) -- Organic molecules dissolved in the water rather than existing as solid particles. Split into labile (easily consumed) and refractory (resistant to breakdown) fractions.

Labile DOM -- The fast-turnover dissolved organic matter pool: fresh low-molecular-weight exudates (amino acids, sugars, organic acids) from algae, epiphytes, and cell lysis. Bacteria consume it rapidly with ~28% bacterial growth efficiency. Half-saturation ~ 0.1 mg C/L. See DOM and refractory DOM.

Refractory DOM -- The slow-turnover dissolved organic matter pool: humic and fulvic-like polymers that accumulate slowly. Bacteria consume it at about one-tenth the rate of labile DOM and with much lower bacterial growth efficiency (~8%). Absorbs light in the water column (k ~ 50 L mol⁻¹ m⁻¹) and progressively darkens aged water.

Diurnal -- Recurring on a daily cycle. Diurnal oscillations in O2 and pH are caused by the day/night cycle of photosynthesis and respiration.

DNRA (dissimilatory nitrate reduction to ammonium) -- An anaerobic microbial pathway that converts nitrate to ammonium, conserving nitrogen within the system. Unlike denitrification, DNRA keeps nitrogen available. Favored when organic carbon is abundant relative to nitrate. Modelled as the DNRA biology guild (species/bacteria/dnra.py) — fermentative anaerobes (typical genera: Clostridium, Citrobacter, Wolinella) that share the NO3 rung of the diagenetic ladder with the denitrifier and compete for the same pore-DOM substrate. The reaction 2 CH₂O + NO3⁻ + 2 H⁺ → NH4⁺ + 2 CO₂ + H₂O is more electron-efficient per NO3 than denitrification (8 e⁻ → NH4 vs 5 e⁻ → N2), so DNRA wins under high-C / low-NO3; denitrifiers' faster μ_max wins at the opposite end. Niche partition is emergent from per-NO3 stoichiometry, not a hardcoded sigmoid switch.

Doubling time -- The time it takes for a population to double in size under ideal conditions. A measure of maximum growth speed.

Droop kinetics -- A mathematical model of algal growth in which uptake of a limiting nutrient and growth on that nutrient are decoupled. Cells maintain an internal cell quota Q (mol of element per mol of biomass C) by drawing nutrient from the water into a luxury reservoir, and growth is gated by the Droop factor (1 − Q_min/Q). Below Q_min the cell cannot divide; above Q_min growth ramps smoothly up to its asymptote near Q_max. Introduced by M.R. Droop (1968, 1974) for B12-limited Monochrysis and Caperon (1968) for nitrate-limited Isochrysis. Replaces single-Monod kinetics, which couple uptake and growth in the same time step. See also luxury uptake, polyphosphate, cyanophycin.

Dynamic surface -- A colonizable surface whose area is a function of the simulation state, recomputed each integration step. The model's only dynamic surface is macrophyte_leaf_surface, whose area = Σ (SLA_cm2_per_mg_C × shoot/stem/frond C) across all macrophyte instances. Contrast with static surface.

E

Ecological succession -- The process by which species composition changes over time. In new aquaria, the classic example is diatoms giving way to green algae as dissolved silica is depleted.

Effective diffusivity -- The actual rate at which a dissolved substance moves through a porous medium (like sediment), reduced from the free-water diffusivity by porosity and tortuosity.

Egestion -- The expulsion of undigested food as fecal pellets. Distinguished from excretion, which is the release of metabolic waste products like NH4+ and PO4.

Electron acceptor -- A chemical that receives electrons during metabolic reactions. Oxygen is the primary electron acceptor in aerobic respiration; nitrate and sulfate serve as alternatives under anaerobic conditions.

Epilithic -- Growing on rock or stone surfaces.

Epipsammic -- Growing on or among sand grains.

Epiphytic -- Growing on the surface of another plant or alga, without being parasitic.

EPS (extracellular polymeric substances) -- A matrix of sticky organic molecules (polysaccharides, proteins) produced by biofilm organisms to anchor themselves to surfaces and resist detachment.

Equilibrium constant -- A number describing the balance point of a reversible chemical reaction. For the carbonate system, K1 and K2 govern how DIC is distributed among CO2, bicarbonate, and carbonate at a given pH.

Estivate -- To enter a state of dormancy during unfavorable conditions (like low oxygen).

Euryhaline -- Able to tolerate a wide range of salinities.

Eutrophic -- Rich in nutrients, often leading to excessive plant or algal growth, turbid water, and oxygen depletion.

Exoskeleton -- A hard external covering providing structural support, found in arthropods like shrimp. Must be periodically shed (molted) to allow growth and requires calcium to rebuild.

Exudation -- The release of dissolved organic compounds (sugars, amino acids, organic acids) by living algae during normal metabolism, typically 5-10% of fixed carbon. Feeds the microbial loop.

Exuviae -- The cast-off exoskeleton left behind after a crustacean molts. In the model, exuviae enter the CaCO3 substrate pool.

Extinction threshold -- The minimum biomass below which a species can no longer sustain itself; growth is disabled and the population can only decline toward zero.

F

Facultative anaerobe -- An organism that can survive and grow in both the presence and absence of oxygen, switching between aerobic and anaerobic metabolism.

Fecal pellet -- A compact package of undigested food excreted by a consumer. Fecal pellets become detritus and vary in sinking rate by species.

Fermentation -- An anaerobic metabolic pathway that breaks down organic matter without using oxygen. Produces less energy than aerobic respiration.

Ferredoxin -- A small iron-sulfur protein that shuttles electrons inside photosynthesizing and nitrogen-fixing cells. Because each ferredoxin holds 2–4 Fe atoms, organisms with heavy electron-transport demand (cyanobacteria during N2 fixation, dense algal blooms) need more iron per unit biomass than quieter cells.

Ferrihydrite -- A poorly crystalline Fe(III) oxyhydroxide that forms when dissolved Fe(II) is oxidized in oxic water. Freshly precipitated ferrihydrite is highly sorptive — it co-precipitates phosphate and traps it at the sediment surface. Under anoxic conditions microbes reduce ferrihydrite back to Fe(II), releasing the bound P (see internal P-loading).

Fickian diffusion -- Diffusion described by Fick's law, where the flux of a dissolved substance is proportional to its concentration gradient. Used to model nutrient transport from pore water through the substrate (soil matrix, sand cap, and diffusive boundary layer) to the water column.

Filamentous -- Having a thread-like form made of cells arranged in a chain. Some cyanobacteria (e.g., Anabaena) grow as filaments.

Filter feeder -- An organism that feeds by straining food particles from water using a fine mesh or similar structure. Daphnia and rotifers are filter feeders. Compare with raptorial.

First-order kinetics -- A rate law where the reaction rate is proportional to the concentration of the substance being consumed. Decomposition and frustule dissolution follow first-order kinetics.

First-order relaxation -- A process where a quantity (such as headspace gas composition) gradually approaches a target value at a rate proportional to the current difference.

Floating macrophyte -- An aquatic plant that floats at the water surface (e.g., Salvinia, duckweed). Floating macrophytes shade the water column below and compete with each other for surface area.

Formation factor -- The combined effect of porosity and tortuosity on diffusion through a porous medium. Each substrate layer has its own formation factor: ~0.19 for coarse aquarium sand (porosity 0.38 × tortuosity 0.5) and ~0.11 for typical soil (porosity 0.38 × tortuosity 0.3). Multiplied by the free-water diffusivity to get the effective diffusivity through that layer.

Frustule -- The intricate glassy cell wall of a diatom, made of biogenic silica (amorphous opal). Dissolves slowly after the diatom dies, recycling silicon as dissolved silica.

Fucoxanthin -- A golden-brown photosynthetic pigment found in diatoms. Gives the characteristic brown color to diatom blooms in new aquaria.

Fulvic acid -- A class of complex organic molecules found in dissolved organic matter. Part of the refractory DOM fraction; absorbs light and stains water yellow-brown. See also humic substances.

Functional response -- The mathematical relationship between food availability and a consumer's feeding rate. The model uses the Holling Type II functional response.

Functional type -- A grouping of ecologically similar species that share key traits, modeled together as one entity (e.g., "planktonic green algae" represents Scenedesmus, Chlorella, etc.).

Fungal conditioning -- The process by which aquatic fungi convert refractory organic matter into labile dissolved organic matter through extracellular enzyme activity (cellulases, laccases, peroxidases). About 20% of the refractory carbon that fungi process is released as bioavailable molecules (amino acids, sugars, organic acids) rather than respired as CO2, making it immediately accessible to heterotrophic bacteria. This handoff drives the fungal-to-bacterial decomposition succession observed in Walstad-style substrates.

Hyphomycete -- A filamentous aquatic fungus that grows as a branching hyphal network on submerged solid substrates (leaf litter, detritus, soil). Hyphomycetes are the dominant biomass component of the aquatic fungi functional group in the model. Their substrate-embedded hyphae (50-500 um) are largely inaccessible to microzooplankton grazing.

Mycoloop -- A trophic pathway in which aquatic fungi (primarily chytrids) produce motile zoospores that are consumed by microzooplankton (ciliates, HNF), channeling energy from refractory organic matter into the food web. Runs in parallel with the microbial loop. Named by Kagami et al. (2007).

G

Gas-phase resistance -- The resistance to gas transfer caused by the stagnant air boundary layer at the water surface. Negligible for sparingly soluble gases like O2 and CO2, but dominant for highly soluble gases like NH3. See two-film model.

Gastropod -- A class of mollusks that includes snails and slugs. Bladder snails are freshwater gastropods.

Gaussian response -- A bell-curve-shaped function used to model how an organism's growth rate varies with an environmental parameter (like salinity), peaking at the optimal value and declining symmetrically on either side.

General hardness (GH) -- A measure of the concentration of divalent cations (primarily calcium and magnesium) in water, expressed in degrees of German hardness (dGH). Important for shell-building organisms. Distinct from alkalinity.

Glycerol -- A sugar alcohol produced internally by some halophilic algae to balance osmotic pressure in extremely salty water. Some leaks out as dissolved organic carbon.

Glycolate pathway -- A metabolic pathway that recovers some carbon lost during photorespiration. Consumes energy and O2, making photorespiration a wasteful process.

Gross photosynthesis -- The total amount of carbon fixed by photosynthesis before subtracting losses to respiration, photorespiration, and exudation. Compare with net photosynthesis.

Growth Rate Hypothesis -- The ecological theory that fast-growing organisms have higher phosphorus content (lower N:P ratio) because rapid growth requires abundant ribosomal RNA, which is phosphorus-rich.

H

Haemoglobin -- An oxygen-carrying protein in blood. Daphnia upregulate haemoglobin under low-oxygen conditions to improve oxygen uptake, turning visibly red in hypoxic water.

Habitat factor -- A multiplier (0 to 1) on a benthic consumer's maximum ingestion rate, derived from the area-weighted average biofilm maturity index raised to a species-specific exponent. Represents the dependence of shelter and brooding habitat on structural biofilm complexity, independent of food availability. See Biofilm Maturity.

Half-life (t1/2) -- The time required for half of a substance to undergo a process like dissolution or decay. Biogenic silica has a dissolution half-life of about 10 days at 20 degrees C.

Half-saturation constant (K) -- In Monod or Michaelis-Menten kinetics, the substrate concentration at which a rate reaches exactly half of its maximum. A lower K means the organism is more efficient at low concentrations.

Halophile -- An organism that thrives in high-salt environments. The freshwater V1 product does not include halophilic species.

Halotolerant -- Able to survive in salty conditions, though not necessarily requiring them. Distinct from halophile.

Headspace -- The volume of gas (air) above the water surface in a container. In a sealed system, the headspace acts as a finite reservoir of O2 and CO2 that buffers dissolved gas concentrations.

Headspace leak rate -- A parameter controlling how quickly gas in the headspace exchanges with the outside atmosphere. Zero means fully sealed; high values simulate an open-top container.

Henry's law -- A physical law stating that at equilibrium, the concentration of a dissolved gas is proportional to its partial pressure in the gas phase above the liquid. Governs O2 and CO2 exchange between water and headspace.

Hermaphroditic -- Having both male and female reproductive organs. Bladder snails are hermaphroditic, enabling rapid population growth from a single individual.

Heterocyst -- A specialized, thick-walled cell in certain cyanobacteria (like Anabaena) where nitrogen fixation occurs. Provides a low-oxygen environment to protect the oxygen-sensitive nitrogenase enzyme.

Heterotroph -- An organism that obtains energy by consuming organic matter produced by other organisms. All consumers, heterotrophic bacteria, ciliates, and HNF are heterotrophs. Compare with autotroph.

HNF (heterotrophic nanoflagellate) -- Very small (2-20 micrometer) single-celled protist consumers that feed primarily on bacteria. The first link in the microbial loop, bridging bacteria to ciliates.

Holdfast -- A structure by which an alga attaches to a surface. Filamentous algae have strong holdfasts; unicellular green algae lack them and attach poorly.

Holling Type II functional response -- A mathematical model of predator feeding where the feeding rate increases with prey density but levels off at a maximum, forming a saturation curve. The leveling off represents handling time limitations.

Humic substances -- Large, complex organic molecules formed from the partial decomposition of plant and animal matter. They resist further decomposition, absorb light (causing water discoloration), and are the main component of refractory DOM. See also fulvic acid.

Hydrolysis -- The chemical breakdown of a compound by reaction with water. Extracellular enzymes from bacteria stimulate hydrolysis of soil organic matter.

Hypersaline -- Having salinity much higher than normal seawater (>35 PSU).

Hypoxia -- A condition of low dissolved oxygen, typically below about 2 mg/L. Stresses aerobic organisms, reduces feeding rates, and can lead to mortality. Compare with anoxia.

I

Ideal gas law -- The equation PV = nRT relating the pressure, volume, temperature, and number of moles of a gas. Used to calculate partial pressures in the headspace.

Immobilization -- The uptake and incorporation of dissolved inorganic nutrients into microbial biomass, temporarily making them unavailable to other organisms.

Ingestion rate -- The rate at which a consumer takes in food, typically expressed per unit body mass per unit time. Limited by a maximum rate even when food is abundant.

Internal P-loading -- Release of previously buried phosphate back into the water column from the sediment, driven by microbial reduction of ferrihydrite under anoxic conditions. Adsorbed P rides down on Fe(III) oxides during oxic periods and is liberated when those oxides dissolve, so a tank with periodic sediment anoxia keeps re-fertilising itself even without new external P input.

Iron (Fe) -- A trace metal essential as an enzyme cofactor for photosynthesis (ferredoxins, cytochromes), nitrogen fixation (nitrogenase), nitrification (AMO), and denitrification (nitrate reductase). Cycles rapidly between dissolved Fe(II) and solid Fe(III)-ferrihydrite depending on O2 and pH, and governs internal P-loading through co-precipitation with phosphate. See iron cycle.

Iron plaque -- The reddish-brown ferric oxyhydroxide crust that forms on the surface of submerged-macrophyte and rice roots when pore-water Fe²⁺ encounters the oxic micro-zone produced by radial oxygen loss. Fresh ferrihydrite scavenges dissolved phosphate as it precipitates, locking soluble P onto an effectively-immobile sediment surface — a major P sink in heavily-planted Walstad-style tanks that partly counter-balances the rice-paddy "internal P-loading" mechanism that root rhizosphere reduction drives in the opposite direction. Visible to the naked eye on healthy mature root systems. References: Christensen & Sand-Jensen (1998); Hansel et al. (2001).

Iron-reducing bacteria -- Heterotrophic anaerobes (typical genera: Geobacter, Shewanella) that reduce buried Fe(III)-ferrihydrite back to dissolved Fe²⁺ once nitrate is drained. The reaction 4 Fe(OH)₃ + CH₂O + 8 H⁺ → 4 Fe²⁺ + CO₂ + 11 H₂O uses pore-water labile DOM as the electron donor; per mol of carbon oxidised, four mol of Fe(III) are reduced. Iron-reducers drive internal P-loading by releasing the phosphate that fresh ferrihydrite was scavenging, and supply Fe²⁺ to macrophyte roots and (via upward diffusion) the water column. Geobacter cells carry an unusually heavy load of c-type cytochromes (extracellular nanowires that shuttle electrons to Fe(III) surfaces). One rung below the denitrifier on the diagenetic ladder.

Diagenetic ladder -- The textbook ordering of microbial respiration in anoxic sediment by terminal electron acceptor: O₂ ▶ NO₃ ▶ Mn(IV) ▶ Fe(III) ▶ SO₄ ▶ CO₂. Each rung yields less ATP per electron than the rung above, so guilds with access to a higher-energy acceptor outcompete those below — the denitrifier draws down NO₃ before iron-reducing bacteria can claim Fe(III), Fe-reducers consume buried oxide before sulfate reduction becomes competitive, and methanogens fire only after pore SO₄ is depleted. The ladder runs as a temporal succession in a fresh substrate (denitrification → Fe reduction → sulfate reduction → methanogenesis over months) rather than in parallel. Reddy & DeLaune (2008, ch. 5); Berner (1980).

K

kLa (mass transfer coefficient) -- The volumetric mass transfer coefficient describing how fast a gas crosses the water-air interface. Strictly, kLa refers to the liquid-side coefficient; the model applies a two-film correction to obtain the overall KLa that accounts for gas-phase resistance as well. For O2 and CO2, the correction is negligible; for NH3, it reduces the effective rate by roughly 15x. Higher KLa means faster equilibration between dissolved gas and the headspace or atmosphere.

Ksp (solubility product constant) -- The equilibrium constant for the dissolution of a sparingly soluble mineral. For calcite, if the ion product exceeds Ksp, the mineral tends to precipitate; if below, it tends to dissolve.

K-strategist -- An organism with a slow-growth, persistent life history adapted to stable environments near carrying capacity (K). Low reproductive rate, long-lived individuals, high investment in each unit of biomass, strong competitive ability. In EcoSym, pennate diatoms and benthic cyanobacteria are K-strategists. Contrast with r-strategists.

L

Labile -- Easily decomposed or consumed by microorganisms. Labile DOM consists of simple molecules (amino acids, sugars, organic acids) that turn over in days to weeks. Contrast with refractory.

Lentic -- Referring to still or slow-moving freshwater habitats like lakes and ponds.

Liebig's law of the minimum -- The principle that growth is limited by whichever essential resource is in shortest supply, regardless of the abundance of other resources.

Lignin -- A complex organic polymer found in plant cell walls that is highly resistant to microbial decomposition. A major component of refractory soil organic matter.

Lysis -- The rupture and destruction of a cell, releasing its contents. Can be caused by viruses (viral lysis) or physical/chemical damage.

Luxury uptake -- Uptake of a nutrient in excess of immediate growth needs, stored in a cellular reservoir for later use. The classical algal example is the post-bloom phosphorus crash: cells continue scavenging PO4 down to nM levels long after dissolved P has dropped below the level that would activate growth, packing the captured phosphate into polyphosphate granules. The same dynamic operates for nitrogen, with greens accumulating free amino acids, diatoms accumulating vacuolar nitrate, and cyanobacteria accumulating cyanophycin. Luxury uptake is what allows cells to keep growing for days after their substrate has crashed in the surrounding water — the canonical "post-bloom water clarity" effect. Implemented in EcoSym via Droop kinetics on every algal class.

M

Macrophyte -- A large aquatic plant visible to the naked eye, as opposed to microscopic algae. Includes rooted plants, floating plants, and submerged plants.

Maintenance respiration -- The baseline rate of oxygen consumption needed to sustain basic life functions (cell maintenance, swimming, osmoregulation) independent of growth or feeding.

Mass balance -- The accounting principle that matter is neither created nor destroyed: the total amount of each element (N, C, P) in the system must be accounted for at all times across all pools.

Mechanical interference -- Physical disruption of one species by another's activity, distinct from predation. Large Daphnia populations generate filtering currents that damage or dislodge smaller rotifers.

Meiofauna -- Small animals (roughly 0.1-1 mm) living on or near the bottom substrate.

Methanogenesis -- The microbial production of methane (CH4) from organic matter under strictly anaerobic conditions. One of the slowest and least efficient decomposition pathways.

Michaelis-Menten kinetics -- A mathematical model describing how a reaction rate increases with substrate concentration and saturates at a maximum: rate = Vmax x [S] / (Km + [S]). Functionally equivalent to Monod kinetics but applied to enzyme reactions.

Microbial loop -- The ecological pathway where dissolved organic matter is consumed by bacteria, which are eaten by HNF, which are eaten by ciliates, which are eaten by larger consumers -- recycling dissolved nutrients back into the food web.

Microbial mat -- A cohesive, layered community of microorganisms (dominated by cyanobacteria, with embedded bacteria, diatoms, and protists) bound together by EPS into a thick biofilm, usually millimeter to centimeter scale. Found in hot springs, polar ponds, intertidal flats, hypersaline lagoons, and as the "BGA" pest of planted aquaria. Mats typically show vertical gradients in light, oxygen, and redox, with anoxic interiors that enable nitrogen fixation even in oxygenated surface waters.

Microzooplankton -- Very small animal-like plankton (roughly 10-200 micrometers), primarily ciliates and HNF, that feed on bacteria and small algae.

Mineralization -- The conversion of organic matter into inorganic nutrients (CO2, NH4+, PO4) through decomposition or metabolism. The process by which nutrients locked in dead matter become available to producers again. Also called remineralization.

Potassium (K) -- A macronutrient and the dominant intracellular cation in every living cell. Acts as an osmotic regulator (controls cell turgor and volume), as a charge-balancer for ammonium and nitrate uptake at the cell membrane, and as a cofactor for over sixty enzymes (pyruvate kinase, phosphofructokinase, ribosome assembly). Tissue K:C ratios sit at ~2.5 × 10⁻² mol K / mol C in microbes and algae, ~5 × 10⁻² for vascular plants — three orders of magnitude above iron. Tracked as a single dissolved water-column pool (K_AQ, mg K/L) plus an optional pore-water compartment (soil_pore:k) for substrate scenarios. Biogeochemistry is simple — no redox, no precipitation, no gas exchange — but biology is large: every producer carries a Monod growth gate on K, and macrophytes are particularly K-demanding (the planted-tank Estimative Index workflow exists precisely to keep K replete). Dosed via the formless potassium_dosing block (K2SO4 / KCl / KNO3 all land in the same K_AQ pool). Conservative under water change with tap-water refill at ~5 mg K/L; no clay CEC binding modelled yet, so aquasoil scenarios may overstate the speed of dose decay. See potassium cycle.

Molybdenum (Mo) -- A trace metal essential as the active-site cofactor in assimilatory nitrate reductase (used by every producer that takes up NO₃⁻) and in the FeMo-cofactor of nitrogenase (cyanobacterial N₂ fixation). Tracked as a single dissolved pool (MoO₄²⁻, molybdate) at sub-µg/L to low-µg/L concentrations. Mo limitation does not zero photosynthesis -- it throttles the NO₃⁻ uptake weight (shifting N-source preference toward NH₄⁺) and caps N₂ fixation independently of iron availability. Conservative under water change; no sediment compartment, no speciation, no redox cycling on simulation timescales. See molybdenum cycle.

Zinc (Zn) -- A trace metal essential as the active-site cofactor of carbonic anhydrase, the enzyme that interconverts CO₂ and HCO₃⁻ and underpins every carbon-concentrating mechanism. Zn also cofactors hundreds of Zn-finger transcription factors, matrix metalloproteinases, and Cu/Zn-SOD in animal tissue. Tracked as a single dissolved pool (total Zn²⁺ + organic complexes) at single-digit to tens of µg/L concentrations — higher than Mo because CA is a bulk enzyme and animal tissue is Zn-rich. Zn limitation does not zero photosynthesis -- it throttles the HCO₃⁻ contribution to C uptake, forcing cells to rely on diffusional CO₂, which bites hardest at high pH. Conservative under water change; no sediment compartment, no speciation, no redox cycling on simulation timescales. See zinc cycle.

Copper (Cu) -- A trace metal essential as the active-site cofactor in plastocyanin (the mobile Cu-electron carrier between cytochrome b6f and Photosystem I in oxygenic photosynthesis), cytochrome c oxidase (respiratory complex IV in every aerobic cell), and Cu/Zn superoxide dismutase. In crustaceans and molluscs, Cu is the metal centre of haemocyanin, the Cu-based blood oxygen carrier (so shrimp / daphnia / snail haemolymph is meaningfully Cu-rich). Tracked with a free/chelated speciation split (Tier B) because aquarium fertilizers deliver Cu in chelated form (Seachem Flourish gluconate; CSM+B / Tropica EDTA / DTPA — effectively non-toxic) while Cu sulfate algicide dumps unprotected Cu²⁺ that is acutely toxic to shrimp and snails above ≈5–10 µg/L. Free Cu²⁺ is typically < 1% of total dissolved Cu in a DOM-rich freshwater tank; CopperChelation runs the equilibrium. Dose forms stage through copper:protected and drain to CU_CHELATED at form- and pH-specific rates via CopperDoseRelease. No Monod gate on biology: plastocyanin has a cytochrome c₆ substitute in almost every eukaryotic alga and many cyanobacteria, so Cu scarcity softens rather than caps photosynthesis. The dominant Cu signal at aquarium scales is toxicity: processes/copper_toxicity.py reads CU_FREE alone to apply Hill-2 acute mortality to sensitive invertebrates (daphnia, copepod, neocaridina, ostracod, bladder_snail) above per-species thresholds (element_half_sat["Cu_tox"]), plus complementary reproduction suppression on neocaridina well below the lethal level. See copper cycle.

Plastocyanin -- A small soluble copper-containing electron-transport protein in the thylakoid lumen of chloroplasts and the periplasm of cyanobacteria. It shuttles electrons from the cytochrome b6f complex to Photosystem I during oxygenic photosynthesis. Most eukaryotic algae and many cyanobacteria can substitute cytochrome c₆ (an Fe-based electron carrier) for plastocyanin under Cu limitation — this is why the simulator applies no Monod gate on Cu despite the essential role of plastocyanin. Some cyanobacterial lineages carry obligate plastocyanin without the c₆ fallback, which is why the cyanobacteria Cu:C ratio sits meaningfully above the universal detritus anchor.

Haemocyanin -- The copper-based blood oxygen carrier used by crustaceans (shrimp, daphnia, copepods, ostracods) and molluscs (snails). Each haemocyanin molecule carries a pair of Cu atoms at its oxygen-binding site; oxygenated haemocyanin is blue (not red like haemoglobin). The simulator does not simulate haemolymph explicitly, but consumer Cu:C is elevated above the universal detritus anchor to account for the Cu locked in haemocyanin — mortality-delta reconciliation releases this Cu to dissolved when a consumer dies.

Molting -- The periodic shedding of an exoskeleton by crustaceans to allow growth. The animal is soft and vulnerable immediately after molting. Requires adequate dissolved calcium.

Monod kinetics -- A mathematical model relating microbial growth rate to substrate concentration, following a saturation curve: rate = mu_max x [S] / (Ks + [S]). Functionally identical to Michaelis-Menten kinetics.

Mortality ramp -- A linear increase in death rate between a stress threshold and a lethal threshold for a given environmental factor (temperature, pH, salinity, etc.).

Mucilage -- A thick, slimy substance secreted by some organisms for adhesion or protection. Diatom mucilage improves surface adhesion; cyanobacterial mucilage sheaths reduce grazer access.

N

N:P ratio (nitrogen-to-phosphorus ratio) -- The molar ratio of nitrogen to phosphorus in an organism's body. Determines how much of each nutrient is needed for growth. The Redfield ratio of 16:1 is a common reference.

N2 fixation (nitrogen fixation) -- The biological conversion of atmospheric nitrogen gas (N2) into ammonium, performed by cyanobacteria using the nitrogenase enzyme. The only process that adds new nitrogen to the ecosystem. Energetically expensive and inhibited by oxygen.

NADPH -- Nicotinamide adenine dinucleotide phosphate. A molecule produced by the light reactions of photosynthesis that provides reducing power for fixing CO2 into organic carbon and for reducing nitrate inside cells.

Nauplius (pl. nauplii) -- The earliest larval stage of crustaceans such as copepods. Very small and vulnerable to cannibalism by adults.

Net photosynthesis -- The actual carbon gain after subtracting respiration, photorespiration, and exudation from gross photosynthesis.

Niche -- The specific role, habitat, and set of environmental conditions that a species occupies in an ecosystem.

nifH -- The gene encoding the nitrogenase enzyme subunit. Its expression is suppressed when dissolved inorganic nitrogen is abundant.

Nitrate reductase -- An enzyme that converts nitrate (NO3-) to a usable form inside cells. Requires light-derived energy (NADPH), which is why algae prefer ammonium in dark conditions. The active site carries a molybdenum cofactor, so severe Mo depletion also throttles the NO₃⁻ half-cell independently of light — the NH₄/NO₃ partitioning shifts toward NH₄⁺ even in full daylight.

Nickel (Ni) -- A trace metal essential as the active-site cofactor in urease (the enzyme that hydrolyses urea to two ammonia molecules and CO₂, carried by nearly every cultivable freshwater heterotroph and by most photosynthetic algae) and in the [NiFe]-uptake-hydrogenase that diazotrophic cyanobacteria use to recycle the H₂ produced as an obligate side-product of nitrogenase activity. Tracked as a single dissolved pool (free Ni²⁺ + organic complexes lumped) at sub-µg/L pristine to low-µg/L tap-water concentrations (steel / Ni-plated plumbing pushes 10+ µg/L). No Monod gate on biology in V1 — urea is bundled into DON within labile DOM rather than tracked as a distinct sub-pool, so a Ni_urease half-sat would have no physiological surface to gate; Ni stoichiometry is held for mortality-delta reconciliation + respiration release so a future urea-metabolism process or a refinement of the cyano N₂-fix H₂-recycling kernel has a clean mass-balance floor. Cyanobacteria override the universal anchor upward (3 × 10⁻⁷ mol Ni / mol C) for hydrogenase + urease; consumers slightly above (2 × 10⁻⁷). Conservative under water change; no sediment compartment, no speciation, no redox cycling on simulation timescales. See micronutrient cycling.

Nitrification -- The bacterial oxidation of ammonium (NH4+) to nitrate (NO3-), carried out by nitrifying bacteria. Consumes oxygen and decreases alkalinity.

Nitrifying bacteria -- Chemoautotrophic bacteria that obtain energy by oxidizing ammonium to nitrate. Predominantly surface-attached in aquaria and suppressed by light and low oxygen.

Nitrogenase -- The enzyme complex used by cyanobacteria to fix atmospheric N2 into ammonium. Irreversibly damaged by oxygen, which is why nitrogen fixation is suppressed under high O2. The active site is the FeMo-cofactor — an iron-sulfur cluster with a single molybdenum atom at which N₂ binds — so fixation is co-limited by both Fe and Mo availability in series with the light, O₂, DIN, and P gates.

Nucleocytoviricota -- A group of giant viruses that infect eukaryotic cells, including ciliates and HNF. Cause density-dependent lysis mortality.

O

ODE (ordinary differential equation) -- A mathematical equation describing how a quantity changes over time. The simulator solves a system of ODEs to track how every pool changes each timestep.

Oolithic -- Formed from small rounded grains typically composed of calcium carbonate. Oolithic sand is a type of aragonite marine sand used as aquarium substrate.

Optical depth -- A dimensionless measure of how opaque a medium is to light. Calculated as attenuation coefficient times concentration times physical depth.

Osmoregulation -- The biological process by which an organism maintains its internal salt and water balance. Costs extra energy when the external salinity deviates from the organism's optimum.

Osmolyte -- A substance produced by cells to balance internal osmotic pressure with the external environment. Some halophilic algae use glycerol as an osmolyte in salty water.

P

P_max -- The maximum photosynthetic rate of a species under ideal conditions (optimal temperature, saturating light, abundant CO2 and nutrients).

PAR (photosynthetically active radiation) -- The wavelengths of light (roughly 400-700 nm) that plants and algae can use for photosynthesis, measured in micromoles of photons per square meter per second.

Partial pressure -- The pressure exerted by a single gas in a mixture, proportional to its fraction of the total gas. Used in Henry's law to determine how much gas dissolves.

Parthenogenesis -- Asexual reproduction where females produce offspring from unfertilized eggs. Allows very rapid population growth. Used by Daphnia, rotifers, and ostracods.

Partition coefficient (K_aw) -- The dimensionless air-water partition coefficient: the ratio of gas-phase concentration to dissolved concentration at equilibrium. High K_aw (like O2 ≈ 31) means the gas prefers the air phase; low K_aw (like NH3 ≈ 0.0007) means it strongly prefers water. Determines which film resistance dominates in the two-film model.

Pellicle -- A thin, flexible outer covering of certain protist cells (like ciliates), providing structural support.

Pennate diatom -- A diatom with bilateral symmetry (elongated, boat-shaped valve), as opposed to centric diatoms which are radially symmetrical. Many pennate diatoms are benthic surface-dwellers.

Perceived concentration -- The effective nutrient concentration that a surface-attached organism "sees" due to biofilm enrichment -- higher than the actual bulk water concentration. Used only for growth rate calculations; actual nutrient uptake still comes from bulk pools.

Periphyton -- A community of algae, bacteria, and other microorganisms growing attached to submerged surfaces, forming a biofilm. In the model, specifically refers to benthic green algae.

Phagocytosis -- The process by which a cell engulfs and ingests another cell or particle. The feeding mechanism of protist consumers like ciliates and HNF.

Phloem translocation -- The transport of sugars and other organic compounds through a plant's phloem tissue from leaves (source) to roots (sink).

Photodegradation -- The breakdown of dissolved organic matter by sunlight (especially UV light) through purely chemical reactions. Releases CO2, NH4+, and PO4 without requiring biological activity.

Photoinhibition -- Suppression of a biological process by light. Nitrifying bacteria are photoinhibited at bright intensities (roughly daylight levels), with the nitrite oxidisers more sensitive than the ammonia oxidisers -- they shrug off the dim light of a shaded substrate but are throttled in the brightly-lit water column, giving them an advantage as surface- and crevice-dwellers.

Photoperiod -- The number of hours per day during which the light is on. Controls the duration of photosynthesis and the length of the dark respiration period.

Photophosphorylation -- The process in photosynthesis where light energy is used to produce ATP (cellular energy currency). Cyanobacteria need ATP from photophosphorylation to power nitrogenase for nitrogen fixation.

Photorespiration -- A wasteful metabolic process where RuBisCO binds oxygen instead of CO2, consuming energy without producing useful carbon. Becomes significant when O2 is high relative to CO2. Acts as a natural brake on oxygen accumulation.

Photosynthetic quotient (PQ) -- The ratio of O2 produced to CO2 fixed during photosynthesis. Normally 1:1, but increases when algae assimilate nitrate (which requires extra electrons from water splitting).

Phycocyanin -- A blue-green photosynthetic pigment characteristic of cyanobacteria.

Phytoplankton -- Microscopic primary producers suspended in the water column, including planktonic algae (diatoms, green algae) and cyanobacteria. The base of pelagic food webs.

pKa -- The negative logarithm of an equilibrium constant. For ammonia, pKa ~9.25 at 25 degrees C means at pH 9.25, exactly half the ammonia is in the toxic NH3 form and half is NH4+.

Planktonic -- Free-floating in the water column, as opposed to attached to a surface. Planktonic organisms are carried by water currents. Compare with benthic.

Pore water -- Water trapped in the spaces between soil or sediment particles. Accumulates nutrients from soil decomposition and has different chemistry (especially much higher CO2) than the overlying water column. Also called interstitial water.

Porosity -- The fraction of a sediment's volume that is water-filled pore space rather than solid particles. Aquarium sand has a porosity of about 0.38.

Polyphosphate -- An inorganic polymer of phosphate residues stored as dense intracellular granules in essentially every algal class — green, diatom, and cyanobacterium. The luxury reservoir for Droop phosphorus dynamics: when external PO4 is abundant, cells fill polyphosphate granules above their immediate growth need; when PO4 crashes, cells continue growing for several days on the granule pool before the cell quota Q_P drains back to Q_P_min and division halts. Diatoms hold the largest polyphosphate reservoirs (Q_P_max ≈ 0.05 mol P / mol C); greens and cyanobacteria hold ~0.03–0.04. The granules are visible in electron micrographs and stain with toluidine blue. See also luxury uptake, cyanophycin.

Primary producer -- An organism at the base of the food web that converts inorganic nutrients and light energy into organic matter through photosynthesis. Algae and aquatic plants are primary producers.

Prokaryote -- An organism whose cells lack a membrane-bound nucleus (bacteria and archaea). Cyanobacteria are prokaryotic despite performing plant-like photosynthesis.

Protist -- A single-celled eukaryotic organism, such as a ciliate, nanoflagellate, or amoeba. Not a plant, animal, or fungus.

PSU (practical salinity units) -- A unit for measuring salinity in water. Roughly equivalent to parts per thousand of dissolved salt. Freshwater is near 0 PSU; seawater is about 35 PSU.

Q

Q10 -- A factor describing how much a biological or chemical rate increases for every 10 degrees C rise in temperature. A Q10 of 2.0 means the rate doubles per 10 degrees C warming.

R

Radial oxygen loss (ROL) -- The transport of photosynthetically-produced O₂ from leaves down through hollow internal channels (aerenchyma) of stems and rhizomes into the rhizosphere of submerged rooted plants. ROL produces a thin oxic film on the surface of every root in an otherwise anoxic substrate. This film drives a tightly-coupled cluster of fast oxidation reactions (NH₄ → NO₃, HS⁻ → SO₄²⁻, CH₄ → CO₂, Fe²⁺ → root iron plaque) that together make heavily-rooted Walstad-style sealed substrates function: coupled nitrification-denitrification drives a major N-loss path, sulfide is detoxified before it can damage roots, and Fe-P plaque locks soluble P onto a sediment surface. Submerged macrophytes typically ship 1–8% of gross photosynthetic O₂ down their aerenchyma; emergent species ship more (10–25%). Modelled in processes/rhizosphere_oxidation.py. References: Sand-Jensen et al. (1982); Caffrey & Kemp (1991); Reddy et al. (1989).

Radula -- A tongue-like organ covered with tiny teeth, used by snails to scrape biofilm and algae from surfaces.

Raptorial -- A predatory feeding strategy involving actively detecting, pursuing, and capturing individual prey items. Cyclopoid copepods are raptorial hunters. Compare with filter feeder.

Redfield ratio -- The characteristic elemental ratio of C:N:P (approximately 106:16:1) found in marine plankton. Used as a reference stoichiometry for organic matter.

Redox state -- The electron-availability regime of a water or sediment parcel, ranging from strongly oxidising (O2 plentiful, iron as Fe(III), nitrogen as NO3-) to strongly reducing (no O2, iron as Fe(II), nitrogen as NH4+, eventually methanogenic). Redox state sets which microbial metabolisms can run and which mineral phases are stable; thin redox gradients at the sediment surface drive coupled nitrification-denitrification and internal P-loading.

Refractory -- Resistant to decomposition or microbial consumption. Refractory DOM (humic/fulvic polymers) turns over very slowly and absorbs light, darkening the water. Contrast with labile.

Refugia -- Physical hiding places (crevices, pores, interstitial spaces) where prey organisms are protected from grazing. Refugia prevent total prey extinction and stabilize predator-prey dynamics.

Reproduction suppression -- A biological response in which organisms stop breeding under adverse environmental conditions without increased mortality. Cherry shrimp exhibit this under poor water quality.

r-strategist -- An organism with a fast-growth, boom-bust life history adapted to disturbed or resource-pulse environments. High reproductive rate, short-lived individuals, low per-unit investment, strong colonization of empty space. In EcoSym, centric diatoms and planktonic cyanobacteria are r-strategists. Contrast with K-strategists.

Respiration -- The metabolic process by which organisms break down organic matter using oxygen to release energy, producing CO2 as waste. Occurs continuously (day and night), unlike photosynthesis which requires light.

Respiratory quotient (RQ) -- The ratio of CO2 produced to O2 consumed during respiration. Depends on the substrate being metabolized: 1.0 for carbohydrates, ~0.8 for protein, ~0.7 for lipid.

Resuspension -- The process by which settled material on the bottom is stirred back up into the water column by physical forces.

Rhizome -- A horizontal underground stem that stores nutrients and produces new roots and shoots. Found in rooted macrophytes like Cryptocoryne and Vallisneria.

Rosette plant -- A plant whose leaves radiate outward from a central point at the base. Cryptocoryne and Vallisneria are rosette plants.

RuBisCO -- Ribulose-1,5-bisphosphate carboxylase/oxygenase, the enzyme responsible for fixing CO2 during photosynthesis. Also binds O2 (causing photorespiration). The most abundant protein on Earth.

RuBisCO specificity factor -- A number describing how strongly a species' RuBisCO prefers CO2 over O2. Higher values mean less photorespiration. Ranges from ~80 (green algae) to 120 (cyanobacteria) in the model.

S

Salting out -- The phenomenon where dissolved salts reduce the solubility of gases in water. Saltwater holds less dissolved O2 and CO2 than freshwater at the same temperature.

Saturation kinetics -- A mathematical relationship where a rate increases with substrate concentration but approaches a maximum asymptotically. The generic shape underlying Monod, Michaelis-Menten, and Holling Type II formulations.

Schmidt number -- A dimensionless number characterizing the ratio of momentum diffusivity (viscosity) to mass diffusivity for a gas in a fluid. Used to scale gas transfer coefficients between different gases.

SDA (specific dynamic action) -- The metabolic cost of digesting and processing food, expressed as a fraction of assimilated carbon. Sometimes called the "heat increment of feeding."

Self-shading -- The process by which dense populations of algae or plants block light from reaching their own deeper layers, reducing average light availability. A self-regulating feedback mechanism.

Senescence -- The natural aging and deterioration of plant tissue, leading to cell death. Shoot senescence in macrophytes produces detritus.

Sessile -- Permanently attached to a surface and unable to move.

Settlement rate -- The speed at which planktonic organisms or particles sink to and attach to surfaces. Influenced by cell density, mucilage production, and surface roughness.

Sigmoid function -- An S-shaped mathematical curve that transitions smoothly between two extreme values. Used in the model to partition nitrate reduction between DNRA and denitrification.

SIT proteins (silicon transporters) -- Specialized membrane proteins in diatoms that actively transport dissolved silica into the cell for frustule construction. Enable efficient uptake even at very low silica concentrations.

Sloppy feeding -- Food material lost during the capture and handling process by a consumer, released as dissolved organic matter rather than being ingested.

Soft water -- Water with low concentrations of dissolved calcium and magnesium (low GH). Shell-building organisms (snails, shrimp) may experience stress in soft water.

Soil organic matter -- Organic material buried in the substrate layer of a planted aquarium. Split into labile and refractory fractions. Acts as a long-term nutrient reservoir in Walstad-style tanks.

Speciation (chemical) -- The distribution of a dissolved substance among its different chemical forms. For example, DIC speciation is the breakdown into CO2, bicarbonate, and carbonate based on pH.

State vector -- The complete set of numerical values describing the current state of the simulated ecosystem at any point in time, including all biomass pools, nutrient concentrations, and gas amounts.

Static surface -- A colonizable surface with a fixed area set at scenario load (e.g. glass, ceramic, sand, gravel). Contrast with dynamic surface.

Stoichiometry -- The quantitative relationship between elements in chemical reactions or biological processes. In ecology, refers to the fixed elemental ratios (C:N:P) in organisms and organic matter.

Stoichiometric homeostasis -- The maintenance of a fixed body composition (C:N:P ratio) by consumers, regardless of what they eat. Excess elements are excreted; deficit elements limit growth.

Stolon -- A horizontal stem growing along the substrate surface, producing new plants at its nodes. Vallisneria spreads by stolons.

Substrate -- (1) The physical bottom material in an aquarium (sand, gravel, soil). (2) In biochemistry, the molecule acted upon by an enzyme or consumed by a microorganism.

Succession -- See ecological succession.

Sulfate reduction -- An anaerobic metabolic pathway in which bacteria use sulfate as an electron acceptor instead of oxygen. Occurs in oxygen-depleted sediments. Produces sulfide (HS-), which precipitates as iron monosulfide (FeS) in iron-rich sediments and otherwise leaks upward into the water column. See Sulfur Cycle.

Sulfide (HS-, H2S) -- The reduced form of dissolved sulfur, produced by sulfate reduction. pH-gated speciation: above pKa1 = 7.05 the bisulfide ion HS- dominates, below it the undissociated H2S form dominates. Only the H2S form is volatile (degasses into the headspace) and acutely toxic to invertebrates -- shrimp like Neocaridina crash at 10-30 µg H2S/L. See Sulfur Cycle.

Iron monosulfide (FeS) -- The black mineral that precipitates instantaneously when pore-water Fe2+ meets sulfide. The model's representation of "black-substrate" / old-tank-syndrome buffering: as long as substrate Fe is plentiful, sulfide produced by sulfate reduction is captured into FeS rather than escaping into the water column. When the substrate Fe inventory saturates, sulfide leaks upward and a sulfide event begins. See the FeS Coupling section of the iron cycle docs.

Old tank syndrome -- The hobbyist term for the slow drift of an established but neglected aquarium toward a sulfidic black-substrate steady state, characterised by H2S smell, dying shrimp, and a black layer in the gravel. In the model this is what happens when sulfate reduction outruns the substrate Fe buffer described under iron monosulfide.

Supersaturation -- A state where a dissolved substance exceeds its equilibrium solubility. For calcite, supersaturation ([omega] > 1) means CaCO3 tends to precipitate.

Surface-renewal model -- A physical model of gas transfer across the water-air interface, used to derive the CO2 transfer coefficient from the O2 coefficient using the square root of their Schmidt number ratio.

T

Thallus -- The body of a plant or alga that is not differentiated into distinct stems, leaves, and roots. Duckweed's entire body is a thallus.

Thermal optimum -- The temperature at which a biological rate (especially photosynthesis) reaches its maximum value. Below this temperature, rates increase with warming; above it, rates decline.

Tortuosity -- A measure of how winding the path is through a porous medium compared to a straight line. Higher tortuosity reduces effective diffusivity.

Total alkalinity (TA) -- The formal measure of water's acid-buffering capacity, defined as [HCO3-] + 2[CO3 2-] + [OH-] - [H+]. Changed by nitrification (decreases), denitrification (increases), and calcification (decreases). See also alkalinity.

Transmittance -- The fraction of light that passes through a medium (such as a floating plant canopy) without being absorbed. A transmittance of 0.05 means only 5% of light gets through.

Trophic cascade -- An indirect ecological effect that ripples through multiple levels of the food web. For example, removing copepods allows ciliates to bloom, which suppresses bacteria, which slows decomposition.

Two-film model -- A model for gas exchange across the water-air interface (Whitman 1923, Liss & Slater 1974). Gas molecules must diffuse through two stagnant boundary layers: a liquid film and a gas film. The total resistance is the sum of both film resistances. For sparingly soluble gases (O2, CO2) the liquid film dominates; for highly soluble gases (NH3) the gas film dominates, dramatically reducing the effective transfer rate. See Dissolved Gases and Gas Exchange.

Trophic level -- A position in the food web hierarchy: primary producers (level 1), primary consumers/herbivores (level 2), secondary consumers/predators (level 3), etc.

Turion -- A specialized dormant bud formed by some aquatic plants (like duckweed) to survive winter or unfavorable conditions. Sinks to the bottom and regenerates when conditions improve.

U

Unionized ammonia (NH3) -- The uncharged, toxic form of ammonia that can pass through cell membranes and damage organisms. Its fraction increases with pH and temperature. Distinct from ammonium (NH4+), which is relatively harmless.

Urease -- A nickel-dependent enzyme that hydrolyses urea (CO(NH₂)₂) to two ammonia molecules and CO₂. It is one of the oldest enzymes in the biosphere (the first enzyme ever crystallised, by Sumner in 1926, demonstrating that enzymes are proteins) and is carried by nearly every cultivable freshwater heterotroph plus most photosynthetic algae as an organic-N salvage pathway. EcoSym does not currently model urea as a distinct DON sub-pool — it is bundled into the labile DOM fraction — so urease's biological surface is implicit; Ni stoichiometry is tracked through every C-flux callsite so a future urea-metabolism process can wire onto the existing state variable without touching the species files.

V

Van't Hoff equation -- A thermodynamic equation used to calculate how an equilibrium constant changes with temperature, based on the enthalpy of the process.

Vapor pressure deficit -- The difference between the actual moisture content of the air and the maximum it could hold at that temperature. Drives evaporation rate in open-top containers.

Vascular plant -- A plant with specialized conducting tissues (xylem and phloem) for transporting water and nutrients. Macrophytes are vascular plants; algae are not.

Viral lysis -- The killing of a cell by a virus replicating inside it until it bursts, releasing its contents as DOM. A major density-dependent mortality source for bacteria, protists, and planktonic phytoplankton (cyanobacteria, green algae, diatoms). For phytoplankton it is frequently the primary bloom-termination mechanism — cyanophages routinely drive Microcystis / Synechococcus crashes faster than grazing or nutrient depletion would.

Viral shunt -- The rapid recycling loop where viral lysis releases cell contents (from bacteria or planktonic phytoplankton) as DOM, which is immediately consumed by other bacteria, keeping nutrients cycling within the microbial community without reaching higher trophic levels. On phytoplankton, the shunt diverts a substantial fraction of fixed carbon away from grazers and into the bacterial loop — a major reason why apparent "primary production" in real lakes does not all reach the food web.

Volatilization -- The process by which a dissolved substance (particularly NH3) escapes from water into the gas phase. Rate depends on pH, temperature, and gas exchange conditions. For NH3, the rate is strongly limited by gas-phase resistance in the two-film model.

W

Walstad method -- A low-tech planted aquarium approach using a layer of organic soil capped with sand or gravel, relying on plants and natural processes rather than external filtration or fertilization. Named after Diana Walstad.

Z

Zooplankton -- Small animals that drift or swim weakly in the water column, including cladocerans (Daphnia), rotifers, and copepods.

Zoospore -- A motile, flagellated reproductive cell produced by chytrid fungi. Zoospores (2-10 um) are the grazeable fraction of aquatic fungal biomass, consumed by ciliates and HNF via the mycoloop.