Microalgal cultures are susceptible to contamination by different species of microalgae, bacteria, viruses, fungi, protozoa, and rotifers. The contamination by other microorganisms can cause changes in the cell structure and reduce the concentration and microalgal yield in just a few days (Park et al., 2011). These are controlled in open ponds by effectively operating the system as a batch culture and restarting the culture at regular intervals with fresh water and unialgal inoculum. Other contaminants include insects, leaves, and airborne material. It is essential to control this contaminants within acceptable limits. In open ponds, large con­taminants can be removed regularly by placing a suitably sized screen in the water flow. This can be done manually or it can be automated.

Some characteristics can make cultures more susceptible to contamination, such as cultures in continuous mode. According to the characteristics of the microalgal species used, one can apply techniques to maintain an axenic culture. Some of these techniques are maintaining the process of cultivation at an alkaline pH (9.0 to 11.0), using high concentrations of nutrients or salinity, and using antibiotics. The photobioreactor must be periodically cleaned to minimize the chances of contamination (Wang et al., 2012).

If the microalgal biomass is applied to products such as biofuels, waste treatment, biofertilizers, or biofixation of CO2, impurities are acceptable in the microalgal cultivation. However, for bioproducts such as drugs and food, crops must be kept in axenic cultures (Wang et al., 2012).