Pennate Diatom Community

This is the brown algae of new aquaria. In the first few weeks of a new freshwater tank, glass, sand, ceramic, and plant leaves develop a dusty, velvety brown coating that almost every hobbyist meets sooner or later — and almost everyone first mistakes for true brown algae (the seaweed group, Phaeophyta). It isn't. It is a film of pennate diatoms: elongate, boat-shaped cells with a golden-brown fucoxanthin pigment, taxa like Navicula, Nitzschia, Gomphonema, Cymbella, Achnanthes, and Cocconeis. They glue themselves to surfaces with mucilage stalks and pads, build up as a soft film, and then fade once dissolved silica draws down and the slower, silica-independent benthic green algae take over the surfaces they vacate.

The slow, persistent biofilm dweller

Where their centric cousins are fast-living water-column bloomers, pennate diatoms are K-strategists: slower-growing, deeply shade-tolerant, warmer-adapted, and persistent rather than boom-and-bust. In the aquarium this shows as a steadier, slower buildup of brown film that hangs on longer than the cloudy centric bloom in the open water. They are at home in dim, settled conditions — which is exactly why a young tank's shaded glass and substrate suit them so well.

A tighter grip on dilute silica

Both diatom types need silica, but pennates hold onto it better. They keep drawing silica down to lower concentrations than centrics can manage, which lets them carry on growing on the residual silica left after the bloom-forming centrics have crashed. This is why a pennate brown film can persist for months in an established tank even when the water tests near-zero for silica. The high-affinity uptake runs on the same specialised silicon-transporter proteins (SIT proteins) every diatom uses (Hildebrand et al. 1997), tuned here for scarcity. As with the centrics, dead cells return their silicon in two stages — a quick fraction back to the water at once, the rest as glass fragments dissolving over roughly ten days (Van Cappellen et al. 2002) — but because pennate films are persistent, that contribution is a steady trickle rather than a pulse. The Silicon Cycle page tells the whole silica story.

Champions of surface attachment

Pennate diatoms are the stickiest algae the model knows. They secrete thick polysaccharide stalks, pads, and tubes that cement cells to glass, sand grains, and even the filaments of other algae, so the overwhelming majority of their biomass lives attached rather than drifting. Once down, they stay down: their films resist resuspension, spread only slowly, and when cells die most of the debris stays in place as settled detritus rather than clouding the water. Many of the representative taxa are epipsammic (living on and between sand grains) or epilithic (on rock and glass) rather than planktonic. That heavy mucilage investment has a side effect: pennates leak more dissolved organic carbon than centrics, feeding the heterotrophic bacteria that help mature the biofilm around them.

Like the centrics, pennate diatoms run an iron- and molybdenum-frugal chemistry (Quigg 2003), scavenging nitrate at trace-metal levels that would throttle ordinary phytoplankton — another reason the pennate film persists after the bloomers have crashed. See Micronutrient Cycling.

Why the brown film outlasts the open water

Surface-attached pennate cells do not have to compete for the same dilute nitrogen the floating algae fight over. They grow inside a thin, still diffusion boundary layer against the surface, where nitrogen can be far richer than in the open water. The model captures this as an enriched perceived concentration for each surface, fed from three sources: settled detritus mineralizing on the surface and releasing ammonium locally; pore water proximity on sand or soil, where upward-diffusing ammonium is intercepted before it mixes away; and nitrification by nitrifying bacteria living in the same biofilm. Only the attached cells get this benefit — the floating fraction sees plain bulk water. Crucially, the enrichment raises only the nitrogen the cells perceive; their actual uptake still draws from the bulk pool, so nothing is created from nowhere (see biofilm enrichment).

This is the heart of the brown-film story. Bulk-water nitrogen falls fast as plants and competing algae strip it, but the pennate film keeps growing because its own microenvironment stays nitrogen-rich from detritus recycling and pore-water diffusion. The result is a long, stubborn brown phase that persists for weeks after the open-water nutrients have stabilised.

Every surface is its own world

The model doesn't lump all the brown film together — it grows each surface on its own terms, because each one offers a different microenvironment:

• Light. Each surface sits at its own depth and angle, so the light reaching it differs. Light is attenuated down through the water column (Beer-Lambert absorption by floating algae, refractory DOM, and background turbidity) before each surface takes its share — a deep sand bed gets far less than a glass wall near the top. Within a thick film, the cells self-shade one another.
• Nutrient enrichment. Each surface carries its own enrichment, set by the detritus, pore-water proximity, and nitrifier activity right there.
• Carrying capacity. Each surface holds only so much before crowding throttles growth (carrying capacity). Rough or porous surfaces such as ceramic and sand pack in more than smooth glass.

"Otos and nerites will clear it in a week"

Pennate diatom film is the favourite food of the benthic biofilm grazers: ostracods, bladder snails, Neocaridina shrimp, and many others. The common hobbyist advice that otocinclus catfish and nerite snails will clear a brown-algae outbreak in about a week is behaviourally accurate — the film is highly palatable and the mucilage scaffold is easily rasped off the glass. In nature the silica in frustules slightly lowers digestibility for some grazers; that fine detail isn't modelled, and pennate film is treated as good grazer food.

Pennate versus centric at a glance

The two diatom communities share one silicon physiology but live opposite lives:

The exact growth rates, light and silica half-saturations, temperature thresholds, and attachment rates behind this contrast are tabulated in the Parameter Reference.

Further reading

• Centric Diatom Community — the fast, free-floating water-column half of the diatom story
• Benthic Green Algae — the silica-independent film that inherits the surfaces when the brown phase fades
• Silicon Cycle — the silica boom-and-crash and the brown-to-green succession, week by week
• Biofilm Nutrient Enrichment — how the boundary layer keeps surface films growing after the open water runs lean
• Producers — how all the algae and plants fit together
• Parameter Reference — every rate, half-saturation, and ratio behind this page, with citations

Key references

• 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.
• Hoagland, K.D., Rosowski, J.R., Gretz, M.R. & Roemer, S.C. (1993). Diatom extracellular polymeric substances: function, fine structure, chemistry and physiology. Journal of Phycology 29, 537–566.
• Quigg, A. et al. (2003). The evolutionary inheritance of elemental stoichiometry in marine phytoplankton. Nature 425, 291–294.
• Reynolds, C.S. (1984). The Ecology of Freshwater Phytoplankton. Cambridge University Press.
• 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.