(Unedited version)
Originally appeared in the August 2006 issue of
Tropical Fish Hobbyist Magazine

Personally I find cyanobacteria one of the most annoying trouble makers in the aquarium. It's ugly, smells bad, smothers plants and seems to promote itself. It can be very difficult to get rid of. There are several methods people use to get rid of cyanobacteria and sometimes it takes several attempts to get it out of your aquarium. Some tanks tend to get it in reoccurring bouts, like it's always lurking in the corner trying to get back in, while some tanks never seem to have any propensity for it.

Until recent years cyanobacteria have been called blue-green algae. They do seem similar to algae on the surface, both can be annoying and unsightly green things that spring from no where and cover your tank. But cyanobacteria are quite different and much more primitive than algae.


As the name implies cyanobacteria are types of bacteria. Unlike most bacteria, cyanobacteria photosynthesize like algae and plants. Bacteria are different from other living things. They are one of the earliest life forms to evolve on earth. In fact some scientist believe that they've found fossils of cyanobacteria that are 3.8 billion years old. Early cyanobacteria became the dominant life form on earth and held that position for over 2 billion years. They were the early photosynthesizers and most likely responsible for first creating the oxygen atmosphere that allowed for the development of more advanced forms of life. Some early cyanobacteria created coral like reefs. These were large layered structures built over long periods of time. The structures are called stromatolites and some still live today.


Why are bacteria different than other cells and how is cyanobacteria different from the algae it resembles? Bacteria are single celled and their cells are different from those life forms that developed later, including our own. Bacterial cells are called prokaryotes, and those of later and more complex life forms are called eukaryotes.

Cells are the smallest living things. And though large living things like people or even smaller ones like the fish in our tanks, contain many, many cells, there are some organisms that have only one cell per individual. All cells have some basic characteristics; a cell membrane, cytoplasm, ribosomes and DNA. The main differences between the two cell types is the eukaryotes developed later, are more complex, including having special parts called organelles, have a nucleus around their DNA, are usually larger, and can be multicellular.

Most cyanobacteria photosynthesizes like algae and plants, making it's own food using water and energy from light, with a byproduct of oxygen. In fact it's now widely believed among many scientist that the photosynthesizing parts of a cyanobacteria cell are in the photosynthetic eukaryotic cells. These parts are called chloroplasts. There are several theories as to how this happened. The most commonly held is that an endosymbiotic relationship was formed between the two and later developments whittled down the cyanobacteria to just the chloroplasts. Cyanobacteria often form symbiotic relationships with other organisms, with fungus to create lichens, in sponges corals and the fresh water fern Azolla to name a few.

Cyanobacteria in the Aquarium

Cyanobacteria is often called blue green algae but it can come in a large variety of colors. Their color is determined by the chlorophyll and pigments in them. In fact the most dreaded cyanobacteria in the reef tank is a dark wine red color. Some cyanobacteria can even change their color to better utilize the light they are under.

Usually you will notice cyanobacteria in the aquarium in a colonial form when it grows in sheets. These can be quite large and cover pretty much all the surfaces in the tank, including over your plants, depriving them of light. Cyanobacteria also lives as a single cell, or can form other shapes, even hollow balls. Some cyanobacteria can even move by themselves, crawling along similar to a slug.

Though it can be annoying in the aquarium cyanobacteria does serve other important functions, the most important of course was in creating an oxygen atmosphere on our planet so higher life forms like us could develop. It's also important in nitrogen fixation. Nitrogen is important to plants and though there is a lot of it around, plants can't use it until it has been “fixed” converted to nitrate or ammonia. Cyanobacteria can fix nitrogen to make it usable by other plants. Some plants, like legumes even grow special nodules on their roots to house cyanobacteria. Nitrogen fixing cyanobacteria is necessary in the rice paddies to feed much of the world. Another cyanobacteria is a food in and of itself, spirulina, something you've probably fed your fish too.

Battling the Cyano Beast

Now that we've taken a little time to appreciate our foe, let's look at ways to try to get it out of the aquarium. Traditional methods of dealing with cyanobacteria have been using water changes, black outs, and bacterial medications. Newer methods include increasing CO2 and fertilizers.

Water Changes

I believe that usually best first method to deal with any aquarium problem is to step on the water changes. There are some methods that discourage water changes, but in my experience when dealing with multiple tanks, those that get regular water changes are more healthy.

A tank that I kept expecting to have problems with was the one at the school, where the kids do most of the maintenance and I just sit back and direct. I was particularly worried when in the middle of the year we switched fish from a nice group of livebearers to a group of blood red jewels (Hemichromis lifalili). There was a small problem of diatoms but the addition of a Plecostomus took care of that. I think the school set up continues to work because of the weekly water changes. We do about a 10% to 20% water change every week and it's been about the most trouble free tank I've ever worked with regardless of the mix of fish we've had in it. The second smaller tank we set up this year has been equally as trouble free.


Aquarium black outs are an attempt to kill the cyanobacteria with a lack of light, that will hopefully get rid of it before overly damaging the plants. Basically you turn off the lights and cover the tank, black construction paper is particularly effective. You should be careful when using this method. The dying cyanobacteria are going to pollute your tank. If you have a bad infection that dies off suddenly it can have some pretty catastrophic effects on your tank. Bad bacteria multiply, your tank gets stinky, there's a lack of oxygen, it starts to kill your plants and fish and gets worse until there's not much, if anything left. To prevent this sort of calamity and still use the blackout methods, make sure your filter is working properly and has good flow. Aeration is helpful too, even if you don't usually run an air stone in your tank, this may be a good time to run one at least temporarily. Check your tank regularly and do water changes, daily is not a bad idea if you have a bad infestation. Be sure to vacuum any detritus from the bottom of the tank when doing your water changes.


Since cyanobacteria is a bacteria, fish medications can be an affective way to kill it. Find a medication containing erythromycin. Check at your local fish store, look on the backs of the bottles of anti-bacterial medications and find one that has erythromycin. Dose as directed. This will usually kill your cyanobacteria. It starts slowly disappearing after a day or two and then keeps fading away. Erythromycin will also kill other bacteria in your tank so don't use it lightly. You'll need to carefully watch your tank when using it to make sure the whole thing doesn't start going way down hill. Do as many water changes as the medication allows and when your all done do some more. You'll have to watch your tank carefully for several weeks after using an anti bacterial in case you start to get other problems from the loss of the rest of your tank bacteria.

CO2 and Fertilizers

Another more recent method used to combat cyanobacteria is the increased use of CO2 and nitrates. There are mixed ideas as to why this method is effective, since the cyanobacteria would also use the CO2 and nitrates, but many people have claimed it has been effective in ridding their tanks of unwanted cyanobacteria. As with other methods when using this one be sure to do those water changes, and make sure to clean out any excess detritus that may be hidden in the tank.

A Necessary Evil

Cyanobacteria are found all over the world, everywhere. They live in fresh and salt water, in the soil and even in extreme places where most other life can't survive. They can be an annoyance in the aquarium and we strive to eliminate visible colonies in our tanks, but they are essential to life as we know it.

Questions or Comments?

If you have questions or Comments about this column, join the Natural Aquariums Forum and post them here.

Welcome to the Jungle | Into The Forest | The Creepy Crawlies | A Clearing in the Thicket | Algae Eaters for the Planted Aquarium
North American Natives | Why things go wrong Pt 1 | Why things go wrong Pt 2 (Algae) | Algae Eating Shrimp | Lo-Tech Tanks
Welcome to the Fish Room | The Stemmed Plants | Mosses | A Livebearer Biotope | Planted Tank Social | The Genus Hygrophila | Cyanobacteria
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