Cyanobacteria (over 7,500 species) are photosynthetic organisms, typically microscopic and unicellular, although it’s not uncommon to see them in large colonial formations (as any reefer who has had to deal with an outbreak can tell you). Cyanobacteria exists almost anywhere there is water - in both fresh and saltwater. It has many forms and actually can appear in many different colors. Cyanobacteria was actually first named for the blue-green color (cyano-, from a Greek word meaning“blue”) of the first identified samples. But cyanobacteria appears in just about any color, depending on the species.

Cyanobacteria are actually quite beneficial in many ways, particularly in providing the main source of photosynthetic energy in many plants through a symbiotic relationship called endosymbiosis. Much like the zooxanthellae which live within the tissues of many corals and the mantles of clams, cyanobacteria exist within the tissues of many plant species, where it produces energyfor itself and the host plant by way of photosynthesis.

Now that we know a little bit about cyanobacteria, let’stalk about cyanobacteria in the aquarium. Cyano outbreaks in the aquarium are relatively common, almost always cause the reefer considerable grief, and are actually quite easy to diagnose and treat, if you have some common sense and a little patience.
Cyanobacteria is typically called “red slime algae” in the aquarium hobby, because a large colony typically resembles a velvety carpet or mat which will cover the sand and/or rockwork. The color ofthis growth is often a deep red or maroon, ranging to reddish purple or even brown. You may often  see fine bubbles of oxygen trapped in the filamentous surface of the colony. It’s often possible to peelor siphon the cyanobacteria out of the tank, but to your dismay, you’ll probably find that it grows back within hours.

The aquarist’s main objections to cyanobacteria are basically twofold. First, it is unsightly. It can coversand and rocks and is not particularly attractive. The other threat is that it can often smother corals,outcompeting them for both light and dissolved nutrients in the water column.

Cyanobacteria has three necessary ingredients: water, light and nutrients. If you take one of those away, a cyanobacteria outbreak will collapse and die, although it should be noted that small, microscopic traces of cyanobacteria are still almost certainly present in your aquarium. There just isn’t enough to pose a problem.
This is an aquarium we’re talking about, so you can’t remove the water. Water changes are a good idea in any case, but unless you feel up to doing significant daily water changes, this is not a long term solution. One thing to keep in mind, though, is that cyanobacteria colonies typically establish themselves in area of low water movement. While you may not be removing cyanobacteria from the system, you can at least keep it from forming large, unsightly and potentially damaging colonies by increasing the flow and circulation of water. Since we’ve determined that having aquariums precludes us from removing the water to get rid of cyano, we turn to light and nutrients.

If you don’t have any corals (many of which typically require at least some light), you can reduce or completely remove your lights (at least temporarily). You’ve probably noticed that in the morning when your lights come on, the cyano is mostly (or even all) gone, but as the day goes on, it spreads rapidly. It’s possible that aside from reducing your photoperiod, a bulb change is in order. Old bulbs shift their light spectra to a different wavelength, and this change can spur changes in algae and bacterial growth.

However, the best way to treat cyanobacteria is two fold: limiting the introduction of nutrients and encouraging nutrient export. You limit nutrients by feeding less. Cyanobacteria thrives on the nutrients produced by rotting food(especially flake food, which is often high in phosphates). Feed in very small quantities, and watch the fish closely. Stop feeding the moment any piece of food hits the bottom of the tank without a fisheating it. If you have food falling to the bottom of the tank, you’re using too much food (unless ofcourse the only fish you have are bottom feeders).

Nutrient export is achieved several ways. The most common is protein skimming. You can also use activated charcoal products like Boyd’s ChemiPure, though it should be noted that many peoples’experience with such products is that they should be used for short periods of time and removed,because the crushed media inside the filter bags provides a huge surface area for nitrifying bacteriato grow on, creating what’s known as a “nitrate factory.” Another way to export another nutrient isthe use of a phosphate reactor filled with phosphate removing media. While this will limit one crucialnutrient, it does nothing to remove nitrates.

Perhaps the best way to export nutrients is to install a refugium and grow any of the fast-growing macroalgae species in it. What happens is the macroalgae (plants) absorb the nitrates and phosphatesout of the water (nitrates and phosphates are the key ingredients in fertilizer and are more commonly known as plant food). As the plant grows, you clip some of it off and dispose of it (preferably toanother reefer in need.) It’s like a sponge - it soaks up nutrients, and then you take the plant (whichis full of those nutrients) out of the system (and take the nutrients with it). There are other benefits tohaving a planted refugium. The algae helps with oxygenation of the water, which can help to stabilizepH (if you run the lighting on a reverse photoperiod). The algae may be eaten by various residentsof your tank, ranging from crabs and shrimp to certain fish (depending on the type of algae you get to grow). The algae also provides a fertile breeding ground for amphipods and copepods, which aretypically very desirable as scavengers as well as food for a variety of fish (especially mandarins andthe other members of the dragonet family, which specialize in eating only copepods when found in the wild).

There are, of course, other methods of dealing with cyanobacteria; namely the use of medicationsand chemical treatments. Chemi-clean is one of the more popular brands. The manufacturer won’texplain exactly what it is, but it does seem to work with little adverse impact (other than dealing witha symptom, not the cause.) Some of the others are preparations of a common antibiotic called Erythromycin.Erythromycin is often very effective in killing bacteria, including cyanobacteria. Extremecaution is urged, however, when using Erythromycin or other anti-bacterial treatments in the aquarium-it’s important to recognize that the health of your aquarium depends very much on the establishmentand cultivation of a variety of nitrifying bacteria which lives in your live rock, sand, filter mediaand many other places within the aquarium system. These chemicals may be exceedingly effective in eliminating a colony of cyanobacteria... but may also kill the many beneficial types of bacteria thatkeep your tank’s inhabitants happy and healthy. It’s highly recommended, therefore, that chemicaladditives be avoided in favor of other means of treatment.

Finally, sometimes the best solution is to do nothing. Often, a tank will experience a cyanobacteria outbreak as a natural part of the maturation process. Siphon out excess cyano, keep up with regularwater changes, and eventually other algae will out-compete the cyanobacteria.