[Disclaimer, I am not a biologist or even a scientist of any sort. There are scientists on this board, and even some who specialize in bacteria. They may end up telling me that I have no idea what I am talking about as the information presented here, is for the most part a hypothesis, but one based upon research and experience. I have included at the end of this a list of sources that I took information from and I encourage you to do your own research as well.]
Cyanobacteria as a group are one of the most abundant bacterias on earth, and are arguably one of the most important life forms on the planet. Taxonomically they are a large group, forming a division of the bacteria kingdom. As such when speaking about cyanobacteria we are in reality talking about a very large and dynamic group that can be found in almost every habitat and ecological niche conceivable. As a group, they are credited with oxygenating the environment in the early days of Earth's history, and are beleived to have formed an endsymbiotic relationship with the chloroplasts in plants allowing for photosynthesis. There is even at least one theory that contends that they gave rise to mitochondria which are described as the "power house" in the nucleus of all cells including our own, but the validity of this theory is no longer widely held.
Cyanobacteria are unicellular organisms that often lives in colonies. Many types live in colonies that are visible to the eye forming filaments, hollow little balls or as is most often seen in our tanks in mats or sheets. They are capable of forming long filaments that break off from the main biomass, in order to establish new colonies.
Our main concern with cyabobacteria, is control in the tank environment. The species seen as problems in our tanks tend to be primarily, but not necessarily red in color and form mats that develop long filament like appendages. Once it grabs a foothold in the tank, it tends to spread and grow rather quickly and can be quite the nuisance. I have had cyanobacteria outbreaks so bad, that they start to cover and smother corals. It is a common problem that most, if not all, aquarists have had to deal with at one point or another, accordingly there is a lot of information, conjecture, personal experiences and advice to be found.
Methods of Control
There are a number of methods that are commonly prescribed in the various forums as a solution to cyanobacteria and/or a way to control its spread. The most often touted methods is to add more flow to the system, use of a additives, creating a low light environment, lowering the tank PH, and or nutrient control.
A commonly prescribed method to control a cyanobacteria outbreak is to increase flow to the effected area. I am not quite sure where this method originated, but it presumably comes from the fact that cyanobacteria seems to start in areas of low flow. As the cyanobacteria mats are fairly easy to dislodge, making it easy to siphon out, I would presume that the goal is to prevent the cyanobacteria from getting a foot hold. While this may be an effective method of preventing new cyanobacteria colonies from forming in the tank, it does little to alter the underlying causes for the uncontrolled growth of the cyanobacteria in the first place. Furthermore, in a tank that is quickly becoming overrun with cyanobacteria, high flow seems to do little but help it spread by blowing filaments and pieces of the mat around the tank. In fact, during large cyanobacteria outbreaks in my tank I have found it growing in my overflows and sump, areas that have some of the greatest amount of flow in my system.
It has been suggested that low PH is a method by which cyanobacteria can be controlled in our tanks. Studies have shown that cyanobacteria growth rates are optimal in PH range from 7.5 to 8.0 and as PH drops, growth rates slow down (http://jb.asm.org/cgi/reprint/149/1/237.pdf). As a result maintaining a low PH has been recommended to help control cyanobacteria outbreaks. While it is true that a low PH has been demonstrated to slow and even stop growth rates, the PH levels involved are far to low for our tanks. As indicated above the optimal PH range for growth of most cyanobacteria starts at 7.5 and rises. A PH of 7.5 is by most standards to low for our tanks, where some people become concerned when their PH falls below 8.0 (http://reefkeeping.com/issues/2004-05/rhf/index.php). In order to see a demonstrated decrease in growth of cyanobacteria a PH reading approaching 6.5 and even as low a 4.0 needs to be reached. Accordingly, I do not believe that lowering the PH of your tank is a sensible approach to cyanobacteria control.
Some people have had success using various substances marketed as red slime removers. I have never used them, but from my research on the subject it would appear that it is at most a temporary solution wherein the cyanobacteria returns in a few months time requiring another treatment. I would hazard to guess, that this is because the additive does nothing to address the underlying reason for the cyanobacteria in the first place, but rather addresses the symptoms of the underlying cause. Very few of these additives tell you exactly how they work, but it seems that there are two methods that they employ. The first type uses antibiotics and the second works by increasing the redox potential.
With cyanobacteria being a bacteria, and not an algae, the ability for an antibiotic to combat cyanobacteria should be fairly obvious. The problem with this, as I see it is two fold. First, it is combating the symptom (the cyanobacteria) without addressing the root cause (i.e. the reason behind the cyanobacteria), The second problem, is that antibiotics are somewhat indiscriminate and have the potential to disrupt the nitrogen cycle in your tank which uses bacteria to break down waste. A sudden increase in ammonia or nitrite could be extremely stressful if not fatal to your fish and inverts. In my opinion you are flirting with a potential problem, greater than the one you are trying to solve.
The second type increases the redox potential (ORP) in your tank, which aids in the breakdown of dissolved organic compounds (DOC). This is the same principal, by which Ozone works. This solution attempts to address the underlying cause of excess nutrients in your system, but leaves in place the shortfalls in husbandry that allowed an excess of organic compounds to accumulate in your system in the first place. Without a change in husbandry, it is inevitable that organic compounds will increase in the water column again, leading to another outbreak of cyanobacteria. There is some doubt about the ability of oxidzers, to truly affect the presence of DOC in your tank and further questions about what other process that may be inhibited or accelerated by their addition and I would suggest that you conduct further research into their use before trying them yourself (http://reefkeeping.com/issues/2003-12/rhf/feature/index.php) . That being said, people do report some success with their use but there are other more benign methods that will achieve the same result without the addition of chemicals to your tank.
One of these methods is cutting your tank off from all light sources for a few days, without a light source the bacteria will start to die off. People are often concerned with the effect, if any, that this will have on their high light corals. In my experience, this is not a particular concern. During one particularly bad outbreak that I went through, I ended up turning the lights off for almost a week without any adverse effect in my SPS dominated tank. As with the other methods discussed above, this does not address the underlying problem in the tank, but rather addresses the symptoms. The benefit of this method, is that it addresses the symptoms without the addition of chemicals or otherwise screwing with your tank's chemistry.
The only way to address the underlying cause of a cyanobacteria outbreak, and to prevent it from coming back is through nutrient control. Nutrient control attempts to limit the amount of nutrients available to the cyanobacteria in order to prevent its spread throughout the tank. Nutrient control is generally important, and will not only help prevent the spread of cyanobacteria but will also assist in controlling nuisance algae. Nutrients are added to the system through water changes, the addition of top off water and the feeding of your tanks inhabitants. The importance of a quality RO/DI system can not be overstated as this is the primary method by which nutrients and other contaminants are removed from your top off water and water used for water changes.
Currently cyanobacteria is farmed as a fertilizer on an industrial scale, and research is ongoing to farm them as a food source and as an alternative energy source. The fact that cyanobacteria is farmed as fertilizer source can give us a clue as to what is fueling them in our tanks. There are three main elements that are needed to support plant growth, nitrogen, phosphorus and potassium and they will be found in abundance in any good fertilizer (http://en.wikipedia.org/wiki/Fertilizer). Deductively, it would make sense to limit those elements if we where trying to control the growth of a bacteria that is grown to be used as a fertilizer. From experience I believe that excess potassium in our systems is less of a concern, but I could be absolutely wrong. To anyone who has kept reef tanks for a significant period of time the limitation of nitrogen and phosphorus will strike a cord, as it is a commonly held concept that the limitation of nitrate and phosphate within our systems is an important part of good husbandry.
It should be noted that different species of cyanobacteria may behave differently and as such any information found on cyanobacteria can not be universally applied by the average hobbyist to the cyanobacteria found in ones tank. At least one study (http://cat.inist.fr/?aModele=afficheN&cpsidt=14117854) involving coral reefs, have shown that specific types of cyanobacteria growth can be enhanced by the addition of phosphate, which was used to show that the availability of phosphate was a limiting factor in the growth of cyanobacteria. Another study (http://www.springerlink.com/content/41207667128003ur/) indicated that cyanobacteria mats where accumulating nitrogen from the marine environment, and to a proportional but lesser degree phosphates. A study performed on freshwater cyanobacteria (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1151820) found that high concentration of phosphate slowed the growth of one species while high levels of phosphate encouraged the growth a related species. Cyanobacteria cultivation has been suggested as a method to remove nitrates from ground water, although it is indicated that phosphate was a needed addition suggesting that phosphate was the limiting factor in this scenario. (http://aem.asm.org/cgi/content/abstract/66/1/133)
Although these studies may not have been performed on the specific strains of cyanobacteria in our tanks, they do show that control of nitrate and phosphates in our system is essential to controlling the outbreak of cyanobacteria in our system. This is basic husbandry, and for me at least, consists of routine water changes with RO/DI water, a proper skimmer, using GFO in a reactor, and being particular about what I feed my tank inhabitants.
What I Do When I Have a Cyanobacteria Problem.
In the eight years or so that I have been keeping reef tanks, I have found that most tanks go through a period wherein cyanobacteria becomes a problem during the first year after they are set up while the tank is becoming established. Having set up four personal systems, and having assisted others setting up their tanks, I have dealt with cyanobacteria many times and have been able to successfully address the problem in each instance.
Once a cyanobacteria problem has arrived in my tanks, I will generally let it grow unmolested for a brief period of time. My thinking on this is that there is a food source in the tank for the cyanobacteria and as it grows and spreads it will use up this food source, removing it from the water column. I then will siphon as much of the cyanobacteria out of the tank as possible. I filter this water through filter socks (as opposed to doing a water change in conjunction), as I do not want to add any new water into the system at this time as adding new water has the potential for adding more nutrients into this system. By siphoning out the cyanobacteria, I am removing the excess nutrients from my system that the cyanobacteria has already used. I will repeat this step two or three times over a week, allowing a day or two in between for the cyanobacteria to regrow, using up more nutrients in the system which are then removed by siphoning. Once this step is complete, I will turn the lights off of my system for at least three days, sometimes as long as five days. If there is any visible cyanobacteria still in your system after the siphoning you will see it start to die back. Before I put the lights back on, I will do one or two large water changes and I will start to aggressively run carbon and GFO. The cyanobacteria that has died off in the tank, will release nutrients back into the water column which needs to be removed. In extreme cases, I have had to repeat this process a second time, usually a week later but I have never had to repeat the process three times.
It is important to realize that this in itself is not a solution to the problem, this must be followed up with good husbandry. Routine water changes are (IMO) essential, and I wouldn't think of running a tank without using GFO. Without basic tank maintenance, your water quality will degrade overtime until you reach a point where either cyanobacteria or nuisance algae will gain a foothold and become another problem that must be dealt with.