Contamination of cultures by “weed” microalgae or predators is emerging as a major issue in large-scale cultivation of microalgae (Kazamia et al. 2012; Shurin et al. 2013). Although little is known about dispersal strategies of microorganisms, it is likely that wastewater contains spores of weed microalgae and predators. Contamination will therefore be more difficult to avoid when wastewater is used as a source of nutrients than when a pure culture medium is used. The risk of contamination can be limited by sterilizing the wastewater by micro — or ultrafiltration or by chemical disinfection. The cost of disinfection, however, will probably be too high when microalgae are pro­duced for low-value products such as fuel or animal feed (Wang et al. 2013). Wastewater will likely contain spores or dispersal stages of herbivores of microalgae such as microcrustaceans, rotifers, or ciliates. The microcrustacean Daphnia or the water flea is often an important herbivore in microalgae-based wastewater treatment systems. If Daphnia invades the system, it can reduce microalgal biomass by two orders of magnitude within a few days (Cauchie et al. 2000). Due to its large size, Daphnia can be relatively easily removed by simple screening using a nylon mesh (Borowitzka et al. 1985). Smaller herbivores like rotifers or ciliates can also decimate microalgal biomass within a few days once they have invaded the culture (Schltiter et al. 1987; Moreno-Garrido and Canavate 2001). However, these smaller herbivores cannot be so easily controlled by simple screening.

Some authors have proposed to use a wild consortium of microalgae rather than monospecific cultures for biofuel production. Today, most microalgae-based wastewater treatment systems use such wild consortia rather than monospecific microalgal cultures. Consortia of microalgae may be more resistant to the impact of small herbivores than monospecific microalgal cultures. If a small herbivore invades the culture, small microalgae will be consumed by large microalgal species that cannot be ingested by the herbivore may take over the culture and maintain a high productivity (Shurin et al. 2013). Consortia of microalgae are not only more resistant to herbivores, but may also be more efficient converting nutrients into biomass than monospecific cultures (Ptacnik et al. 2008; Kazamia et al. 2012; Shurin et al. 2013). However, the use of consortia rather than pure algal cultures may pose a problem for the valorization of the resultant biomass. First, if the consortia contain toxic species such as cyanobacteria, the biomass cannot be used for food or animal feed. Second, it is more difficult to control the biochemical composition of the biomass in mixed consortia than in pure cultures. Some species in the consortium may produce carbohydrates, for instance, while others produce lipids. The consortia that occur in wastewater treatment systems are often domi­nated by a few freshwater microalgal species, very often chlorophytes (Chlorella, Scenedesmus, Micractinium, Pediastrum) (Pittman et al. 2011). Some control over community composition is possible by recycling part of the harvested biomass. In a long-term study in a HRAP, recycling of the harvested biomass resulted in a 90 % dominance of the community by the large species Pediastrum, which improved the harvestability of the biomass (Park et al. 2011b).