Micronutrient Cycling

For a high-level tour of how every element moves through the tank, start with Nutrient Cycling. This page covers the trace metals — molybdenum, zinc, copper, nickel, cobalt, and boron — that organisms need in vanishingly small amounts but cannot live without.

The shape of a trace nutrient

These six metals share an ecological shape. Each does one or two very specific biochemical jobs — usually sitting at the active site of a single enzyme — and none of them drives the large-scale redox or sediment chemistry that iron does. A cell needs them in tiny quantities, builds them into its machinery, and releases them again when it dies. Because their role is so focused, the simulator tracks each one simply: a single dissolved pool, a per-species body quota that says how much of the metal goes into each unit of new tissue, and bookkeeping that returns the metal to the water on respiration and death. Copper is the one exception — it carries enough toxicity and dosing nuance to be tracked in more detail, as described below.

The practical question for most of these is "could this ever limit my tank?" For most of them, in most tanks, the honest answer is no — ambient water already supplies more than enough. They are modelled anyway, both because mass balance demands it (a dying bloom has to release its trace metals somewhere) and because the few situations where they do bite — molybdenum in very soft water, zinc at high pH, copper toxicity to shrimp — are exactly the ones an aquarist needs warning about.

Molybdenum — the gatekeeper of nitrate use and nitrogen fixation

Molybdenum sits at the active site of two of the most important enzymes in the nitrogen cycle: nitrate reductase, which nearly every plant and alga uses to convert nitrate into a form it can build into protein, and nitrogenase, the enzyme by which cyanobacteria fix atmospheric nitrogen. Neither enzyme has a molybdenum-free substitute, so molybdenum scarcity shows up in two specific, testable ways: producers lean away from nitrate and onto ammonium, and cyanobacterial nitrogen fixation collapses — regardless of how much iron is present.

Despite that load-bearing biological role, molybdenum's chemistry is mercifully simple. It dissolves as molybdate, an anion that stays in solution across the whole pH and oxygen range of any aquarium — it doesn't precipitate, doesn't adsorb onto sediments, and doesn't participate in redox cycling. Ambient levels run from sub-microgram-per-litre in soft water to a few micrograms in tap water, and that is usually plenty. But because molybdenum cannot be scavenged from bound forms the way iron can, a very soft-water tank can hit a molybdenum ceiling on a cyanobacterial bloom even when iron has been dosed to abundance (Howarth & Cole 1985). Diatoms are the molybdenum-frugal group, equipped with high-affinity machinery that lets them thrive where molybdenum is scarce; cyanobacteria, carrying both nitrogenase and nitrate reductase, are the most molybdenum-hungry.

Zinc — the gatekeeper of the carbon-concentrating mechanism

Zinc sits at the active site of carbonic anhydrase, the enzyme that lets a cell convert bicarbonate into the CO₂ that photosynthesis actually fixes. This matters most at high pH, where free CO₂ is scarce and most of the dissolved inorganic carbon is locked up as bicarbonate. A cell with plenty of zinc can run its carbon-concentrating mechanism and tap that bicarbonate; a zinc-starved cell loses the ability and falls back on whatever dissolved CO₂ it can get, hitting carbon limitation much earlier as pH climbs.

The signature of zinc limitation is therefore subtle: zinc-starved producers slow down but do not collapse — they simply become carbon-limited sooner in hard, alkaline water (Sunda & Huntsman 1992). This is different from iron starvation, which strips a cell of pigment and kills it outright. Ambient freshwater carries a few micrograms of zinc per litre, and old galvanised plumbing can push that much higher, so zinc limitation is rare in practice. Diatoms, with their heavy commitment to the carbon-concentrating mechanism, need the most zinc; cyanobacteria can substitute cobalt or cadmium into the enzyme and so tolerate the least, giving them an edge in zinc-poor, high-pH water.

Copper — trace nutrient and shrimp-keeper's hazard

Copper is genuinely essential — it carries electrons in photosynthesis (plastocyanin) and respiration (cytochrome c oxidase), and it is the metal at the heart of haemocyanin, the blue, copper-based blood pigment that shrimp, daphnia, copepods, and snails use to carry oxygen. But copper scarcity is not what aquarists need to worry about: almost every alga can swap in an iron-based substitute when copper runs low and keep going. What matters with copper is the opposite problem — toxicity — and the form the copper is in.

This is why the model tracks copper more richly than the other trace metals, splitting it into a free, bioavailable form and a protected, chelated form. Free copper is acutely toxic to invertebrates: it disrupts the ion regulation at their gills and interferes with their copper-based blood pigment, with lethal concentrations in the range of roughly 5–30 µg/L for crustaceans and 20–50 µg/L for snails (Grosell 2012) — ten times lower than for fish, and orders of magnitude below anything that troubles algae or bacteria. Chelated copper, bound to organic molecules, is effectively non-toxic while remaining available to plants.

That distinction is exactly why aquarium fertilizers deliver copper in chelated form (gluconate in Seachem Flourish; EDTA or DTPA in dry trace mixes and Tropica) — so that free copper never reaches the shrimp — while copper sulfate is reserved for algicide and snail or parasite treatments precisely because it releases free copper. The model reproduces this faithfully: dose chelated copper and it stays in the protected form, equilibrating against the tank's organic matter and leaving invertebrates unharmed; dose copper sulfate and it enters as free copper, triggering invertebrate mortality (and, below the lethal threshold, suppressing shrimp breeding — neocaridina stop berrying well before copper reaches a lethal level). In a tank rich in dissolved organics, copper binds organic ligands so strongly that free copper is typically well under 1% of the total (Xue & Sigg 1993), which is why an established, tea-stained tank tolerates copper that would devastate a sterile one. The per-species toxicity thresholds and the release timescales of each chelated form are tabulated in the Parameter Reference.

Among the producers, cyanobacteria and the nitrifying bacteria carry the most copper (obligate plastocyanin, and the copper-based ammonia-oxidizing enzyme respectively), so a cyanobacterial crash or a nitrifier die-off releases a small pulse of copper back into the water — which the mass-balance diagnostics will show.

Nickel, cobalt, and boron — tracked, rarely limiting

The last three trace metals are accounted for in full — every organism carries a body quota and releases the metal on death, so mass balance stays closed — but at realistic aquarium concentrations none of them limits growth, so the model does not throttle any process on them. They are worth knowing about for the biology they represent:

Nickel is the metal in urease, the enzyme that lets nearly every bacterium and alga salvage nitrogen from urea, and in the hydrogenase that nitrogen-fixing cyanobacteria use to recycle the hydrogen their fixation machinery wastes. A nickel-starved cyanobacterium doesn't lose the ability to fix nitrogen — it just pays a higher energy price for it. Tap water typically supplies a microgram or two per litre, more from steel or plated plumbing, which is ample.

Cobalt is the metal at the heart of vitamin B12. Only certain bacteria can build B12 from scratch; every alga, animal, and fungus has to acquire it from that bacterial supply. So cobalt quietly couples the bacterial community to the rest of the food web through a shared vitamin currency. Cobalt is the rarest of the tracked trace metals in both water and tissue, which fits its role — most cells get their B12 secondhand from bacteria rather than concentrating cobalt themselves. Cyanobacteria, the principal B12 makers, carry the most.

Boron is unusual in that its role is structural rather than catalytic. It crosslinks the cell walls of vascular plants — the only metal known to do so, and the reason rooted, floating, and submerged macrophytes all carry far more boron than algae do — and it stiffens diatom shells and the protective envelopes of nitrogen-fixing cyanobacteria. Freshwater carries more than enough boron to saturate all of these needs; a deficiency would only appear in a pure-RO tank with no supplementation, and toxicity only from badly over-aggressive dosing.

How a trace metal moves through the tank

The path is the same for all six. A growing cell draws its trace metals from the water in proportion to the carbon it fixes, building them into tissue at its species-specific quota. Maintenance respiration returns a share to the water continuously. When organic matter decomposes — through bacterial decay, sunlight, the anaerobic nitrate pathways, or soil mineralization — it releases its trace metals back to dissolved form. And when a cell dies, any metal it had concentrated above the average tissue content is released in a pulse (a metal-rich species like a copper-heavy cyanobacterium or a zinc-hungry diatom spills its surplus on death). All of this is conservative: apart from dilution by water changes, the total amount of each metal in the tank stays fixed, and the mass-balance diagnostics track every one of them as a first-class element. Per-species body quotas and their literature sources are listed in the Parameter Reference.

What the model deliberately leaves out

A few reasonable-sounding couplings are intentionally out of scope, because they would add complexity without changing any realistic aquarium outcome: there is no sulfide-driven precipitation of these metals (which would require conditions an aquarium doesn't reach), no sediment or pore-water compartment for copper, and no phosphate coupling for any of them — only iron drags phosphorus around. The trace metals also don't get the dosing machinery copper has, because ordinary molybdenum, zinc, and nickel supplements dissolve in seconds and need no staging. If a future scenario genuinely needs one of these couplings, it can be added without disturbing the rest of the model.