Cyanobacteria: the “algae” that is really a bacterium

Cyanobacteria — “blue-green algae,” or BGA — is the slimy, blue-green sheet that spreads across substrate, silicone and slow-growing plants, peels off in one gelatinous piece, and gives off an unmistakable musty, earthy smell. It is one of the more disheartening things to find in a tank, but it is also one of the more beatable, once you understand what it is.

Not an alga at all

Despite the name, cyanobacteria are bacteria — prokaryotes, with no nucleus and none of the internal machinery of true algae or plant cells. They are, in fact, among the oldest organisms on Earth, and, through an ancient symbiosis, the lineage from which the chloroplasts inside every plant are descended. They photosynthesise using chlorophyll plus a blue pigment called phycocyanin, which is where the blue-green colour comes from (BGA can also appear dark green, black, or even reddish).

Two consequences of being a bacterium matter in the tank. First, many cyanobacteria can fix nitrogen straight from the atmosphere — they can make their own nitrogen when the water is short of it, an advantage no true alga or plant in your tank has. Second, because it is a bacterium, it is vulnerable to an antibiotic — which is both a genuine treatment option and a trap, as we will see.

The musty smell is real chemistry, not imagination: cyanobacteria release geosmin and a related compound (2-methylisoborneol), the same molecules that give beetroot and rain-on-dry-earth their scent (Jüttner & Watson, 2007). If your “algae” smells earthy, that alone strongly points to cyanobacteria.

Stagnation, organics, and lean nitrogen

Cyanobacteria tend to take hold where a few conditions combine. None is a proven single cause, but the pattern is consistent enough to act on:

• Poor flow and dead spots. BGA thrives in low-circulation corners, along the substrate surface and in shaded areas where water barely moves and organic debris settles. Improving circulation is one of the most reliable preventives, since good flow and circulation leave no dead corners for it.
• Accumulated organic waste. Detritus in the substrate, an under-maintained tank, mulm and uneaten food all favour it: letting dissolved organics build up shifts the whole tank in a microbial direction.
• Very low nitrate. Because many cyanobacteria fix their own nitrogen, they hold an advantage when the water column is short of it while other plants and algae struggle. A tank dosed extremely lean on nitrogen is a common setting for BGA. This link is well observed and mechanistically plausible, though it is not the whole story — plenty of BGA appears in tanks with adequate nitrate, where stagnation and organics carry the blame.

What works, and why

Because cyanobacteria are photosynthetic bacteria rather than tough attached algae, two approaches work on them that do little for other algae:

The blackout

A total blackout — three to four days of complete darkness (cover the tank so no light gets in at all) — is strikingly effective against BGA and much less so against most true algae. As a photosynthesiser without the resilience of established green algae, cyanobacteria collapse quickly without light. The method: manually remove and siphon out as much as you can first, do a decent water change, then black the tank out fully for three to four days. Keep the filter running and, ideally, add an airstone, because the die-off consumes oxygen. Your plants will shrug off a few days of dark; the BGA will not.

Erythromycin — effective, but handle with care

Because cyanobacteria are bacteria, the antibiotic erythromycin (the active ingredient in several “blue-green remover” products) kills them, often dramatically. But this is a treatment to use thoughtfully, not a first reach:

One frequently-suggested tweak has a logic to it: if your nitrate is genuinely near zero, raising it modestly (dosing to a few ppm) removes the nitrogen-fixers’ advantage and, alongside the physical measures, helps the plants compete. It is not a standalone cure, but it addresses the lean-nitrogen part of the picture.

Keeping it away

BGA rarely returns to a tank that is well circulated and well kept:

• Circulation everywhere. Eliminate dead spots; make sure flow reaches the substrate surface and the back corners.
• Stay on top of organics. Regular water changes, gentle substrate maintenance, sensible feeding, and not letting mulm pile up.
• Don’t starve nitrogen to zero. Keep a small, steady amount of nitrate present rather than dosing so lean the water column bottoms out.
• Keep plants dense and growing. As with every algae, healthy competitive plants are the best long-term defence.

1. Jüttner, F. & Watson, S.B. (2007). Biochemical and ecological control of geosmin and 2-methylisoborneol in source waters. Applied and Environmental Microbiology, 73(14), 4395–4404.