Silicon Cycle

For a high-level tour of how every element moves through the tank, start with Nutrient Cycling. Silicon is the element behind the brown-algae phase of every new tank — the boom-and-bust that arrives in the first weeks and then, just as suddenly, is gone for good.

Why silicon creates boom and bust

Silicon is the element that makes diatoms possible and decides when they have to stop. Diatoms build intricate glass shells — frustules — from dissolved silica, and unlike nitrogen or phosphorus, which are recycled fast through decomposition and bacteria, silicon stays locked inside those frustules for weeks after a diatom dies, dissolving back into the water with a half-life of about ten days. That slow return means a diatom bloom can strip the water of silica far faster than dead frustules can replenish it. When the dissolved silica runs out, diatom photosynthesis halts no matter how favorable the light, temperature, and other nutrients are. The bloom crashes, and the space it held opens up for silicon-independent competitors — green algae, periphyton, cyanobacteria — that were suppressed while diatoms dominated.

This boom-and-bust is not a failure mode; it is the normal diatom life cycle, and it drives one of the most important successional transitions in the model — the "brown algae" of a young aquarium giving way to green growth.

The one dissolved form

Silicon has a refreshingly simple chemistry compared with nitrogen. There is only one biologically available form — dissolved silica, the orthosilicic acid that diatoms take up and build into glass. There is no equivalent of the ammonium/nitrate split that complicates nitrogen, and no equivalent of phosphorus's web of organic pools. Silicon interacts with diatoms and almost nothing else: in a scenario with no diatoms, the dissolved silica simply sits at its starting value for the whole run.

Almost all of a tank's silicon arrives dissolved in the source water. Typical freshwater tap water carries somewhere in the single-digit to low-teens milligrams of silicon per litre, weathered out of silicate minerals in the catchment, and in a sealed system that starting stock is essentially the entire silicon budget — there is no ongoing external supply.

What returns silicon to the water

When diatoms die, their frustule silicon comes back in two stages — a fast trickle and a slow drip.

A small fraction dissolves almost immediately: the lightly silicified parts of the cell and the silicon held inside it release straight back to dissolved silica on cell death (Bidle & Azam 1999), giving a modest pulse that partly buffers the depletion left by a bloom. The great majority, though, enters a pool of intact and broken frustule fragments — amorphous opal — that dissolves only slowly. That slow dissolution follows first-order kinetics: the more biogenic silica is sitting in the tank, the faster it returns, scaled gently by temperature. Because it is a physical–chemical process rather than a biological one, it responds only weakly to warmth — bacteria accelerate frustule dissolution in nature but not in the model.

The roughly ten-day half-life sits in the middle of the freshwater literature range of five to twenty days (Ragueneau et al. 2000; Van Cappellen et al. 2002), and it has a major ecological consequence. After a bloom crashes, dissolved silica can stay depleted for one to three weeks while the frustules slowly recycle. During that window diatoms cannot regrow even from a trace inoculum — which is exactly why the succession from diatoms to silicon-independent periphyton is largely irreversible on aquarium timescales. The exact dissolution rate and its temperature sensitivity are tabulated in the Parameter Reference.

What removes silicon from the water

Diatom growth is the only silica sink. Silica goes into the frustule in lock-step with the nitrogen a diatom builds into new biomass — roughly one molecule of silicon per molecule of nitrogen, about two grams of silicon per gram of nitrogen (Brzezinski 1985) — and uptake is capped at whatever silica the water actually holds, so a diatom can never consume more than is there.

What makes silica limitation distinctive is how late it bites. Diatoms scavenge silica down to extraordinarily low concentrations using specialized silicon-transporter proteins (SITs; Hildebrand et al. 1997), so silica only begins to throttle photosynthesis once it falls below a couple of tenths of a milligram per litre. Above that, growth runs at full speed; below it, the limitation steepens quickly toward zero. The same limitation applies to every diatom in the tank, attached or planktonic, because dissolved silica is a well-mixed water-column resource. The half-saturation concentration at which this kicks in is given in the Parameter Reference; silica limitation throttles gross photosynthesis by Michaelis–Menten kinetics alongside the light, carbon, and nitrogen/phosphorus limitation factors.

How silicon moves between the pools

Silicon's cycle is the simplest of the major nutrients, passing through only three resting places — the dissolved pool, the living diatom, and the slowly dissolving fragments of dead frustules:

  Dissolved silica  ───►  Diatom frustule (built into the living cell)
        ▲                          │
        │                     cell death
        │                          │
        │                          ▼
        │        a fifth dissolves straight back, fast
        │        the rest becomes slow-dissolving glass fragments
        │                          │
        └──── slow dissolution ◄───┘
                 (half-life ~10 days)

During photosynthesis, diatoms pull silica from the water in proportion to the nitrogen they assimilate and lay it down in the frustule — silicon that is never tracked as a separate biomass pool, just carried implicitly in the diatom's chemistry. When the diatom dies — from age, temperature or pH stress, or grazing — the frustule silicon is released: the fast fifth straight back to the dissolved pool, the slow remainder into the fragment pool that dissolves over the following weeks.

Conservation

Silicon has no gaseous escape and no biological sink other than diatoms, so the total — dissolved silica, the frustule fragments, and the silicon held in living diatoms — is strictly conserved (mass balance) in both open and closed systems. In practice the dissolved-plus-fragment total dips during a growing bloom, as silicon moves into living cells, and recovers after the crash, as dead frustules dissolve; once the diatoms are gone and the frustules have fully dissolved, it returns to where it began. Silicon cycling also has no effect on alkalinity — neither the uptake of silica nor its release from dissolving frustules produces or consumes acid.

The diatom bloom-and-crash, week by week

The silicon cycle drives the brown-algae succession that nearly every new freshwater aquarium goes through:

1. Early colonization (weeks 1–4). Diatoms move onto surfaces fast. Silica is abundant from the tap water, and diatoms are shade-tolerant and cold-adapted, which gives them the edge over green algae in a newly set-up tank.
2. Bloom peak (weeks 3–6). Diatom biomass tops out. Silica is now being consumed faster than frustule dissolution can replenish it.
3. Silica runs low. As dissolved silica falls past the limiting threshold, photosynthesis is throttled and growth can no longer keep pace with mortality.
4. The crash (weeks 6–10). Diatom biomass falls away. Dead cells release their frustule silicon — the fast fifth at once, the rest into the slowly dissolving fragment pool.
5. The dissolution lag (weeks 8–12). Even after the crash, silica stays low because the fragments take about ten days to give it back. That extended depletion blocks any diatom recovery.
6. Periphyton takes over. Silicon-independent growth — benthic green algae, cyanobacteria — fills the vacated surfaces, and by the time silica recovers the new community is entrenched and diatoms cannot reclaim it (see competitive exclusion).

This succession is largely one-way on aquarium timescales: once established, the periphyton holds its advantage through faster growth in warm, bright conditions and its freedom from silica limitation, reinforced by biofilm nutrient enrichment on the surfaces it occupies.

When does silica actually become limiting? The Si:N ratio

The whole boom-and-crash only happens when there is enough nitrogen to fuel a diatom bloom big enough to strip the silica pool — and that is not always the case.

Because diatoms consume silicon and nitrogen at a roughly one-to-one molar ratio, while other algae compete for the nitrogen but not the silicon, the key predictor is the molar silicon-to-nitrogen ratio of the water. When there is more nitrogen than silicon (a low Si:N), diatoms can keep growing until the silica runs out — the classic bloom-and-crash. When there is more silicon than nitrogen (a high Si:N), nitrogen runs out first; the diatoms simply fade from nitrogen starvation alongside everything else, and no dramatic succession occurs.

Most freshwater tap water has a silicon-to-nitrogen ratio well above one. A typical tap supply might carry several times more silicon than nitrogen in molar terms — so even if every atom of nitrogen went to diatoms, they would use only a fraction of the silica, nowhere near the limiting threshold. In real aquaria the diatom bloom happens because fish waste and feeding add nitrogen continuously. A stocked tank accumulates nitrogen from food and waste while silica stays at whatever came in with the tap water, and as nitrogen climbs the ratio tips below one and silica depletion becomes inevitable during a healthy bloom. This is why a fed, stocked tank gets its brown-algae phase in the first weeks and a bare jar of tap water does not.

The practical implication for scenario design: to see the diatom succession, the scenario has to supply enough nitrogen — through elevated starting nitrogen, organic loading from detritus or soil, feeding, or nutrient-replenishing water changes. A tank with only tap-water nutrients will show diatoms fading from general starvation, not the dramatic silica-specific crash.

How silicon interacts with the other cycles

• Nitrogen and phosphorus. Silica limitation caps diatom growth, which in turn limits how much nitrogen and phosphorus the diatoms draw down — leaving the surplus for silicon-independent algae. After a crash, the nitrogen and phosphorus locked in dead diatom biomass are released by decomposition, a nutrient pulse that benefits the succeeding periphyton. See Nitrogen Cycle and Phosphorus Cycle.
• Carbon. Silica limitation cuts diatom carbon fixation, reducing both oxygen production and CO₂ drawdown. In a full silica crash, diatoms contribute essentially nothing to primary production. See Carbon Cycle.
• Oxygen. The diatom bloom is often the dominant oxygen source in a new tank's first weeks; when it crashes, oxygen production shifts to green algae and macrophytes, and the decomposition of the dead diatoms can carve a brief oxygen dip during the crash itself.

How silicon differs from the other nutrients

Further reading

• Biofilm Nutrient Enrichment — how surface enrichment drives the diatom bloom that consumes silica
• Algae Settlement and Surface Dynamics — surface colonization and the diatom-to-periphyton succession
• Death and Decomposition — frustule dissolution after diatom mortality
• Nitrogen Cycle — how silica depletion leaves excess nitrogen and phosphorus for other producers
• Parameter Reference — the dissolution rate, the silica half-saturation, and the Si:N uptake ratio behind this page, with citations

Key references

• Bidle, K.D. & Azam, F. (1999). Accelerated dissolution of diatom silica by marine bacterial assemblages. Nature 397, 508–512.
• Brzezinski, M.A. (1985). The Si:C:N ratio of marine diatoms: interspecific variability and the effect of some environmental variables. Journal of Phycology 21, 347–357.
• Hildebrand, M., Dahlin, K. & Volcani, B.E. (1997). Characterization of a silicon transporter gene family in Cylindrotheca fusiformis. Molecular and General Genetics 260, 480–486.
• Ragueneau, O. et al. (2000). A review of the Si cycle in the modern ocean. Global and Planetary Change 26, 317–365.
• Sommer, U. (1986). Phytoplankton competition along a gradient of dilution rates. Oecologia 68, 503–506.
• Van Cappellen, P. et al. (2002). Dissolution kinetics of biogenic silica in marine sediments. Geochimica et Cosmochimica Acta 66, 1149–1158.
• Werner, D. (ed.) (1977). The Biology of Diatoms. Blackwell, Oxford.