PBRs can be operated in batch or continuous mode. There are several advantages when using them in continuous mode. Firstly, continuous culture provides a higher control than batch mode. Secondly, growth rates can be regulated and keep in a steady state for long periods, and the biomass concentration can be modulated by dilution rate control. In addition, results are more reliable and reproducible owing to the steady state of continuous reactors, and the system yields better quality production (Molina et al., 2001).

However, there are limitations that can make the continuous process unsuitable for some cases. One of these limitations is the difficulty in controlling the production of some non­growth-related products. For instance, the system often requires feed-batch culturing and continuous nutrient supply that can lead to wash-out. Filamentous organisms can be difficult to grow in continuous PBRs because of the viscosity and heterogeneity of the culture medium. Another problem is that the original strain can be lost if it is displaced by a faster-growing contaminant. The contamination risk and loss of reliability of the bioreactor becomes more relevant when long incubation periods are needed, so the potential initial investment in necessary better quality equipment could rise and hamper the economic viability of the production unit (Mata et al., 2010).

The possible coproduction of high value chemicals could lead to the solution of the above problems, but it implies taking multiple parameters and options into consideration. The microalgae production units will suffer drastic changes, both in the operational aspect (temperature, insolation, wind, microalgal and bacterial or fungical contaminations etc.) and in the commercial one (oscillations in value of by-products, improvements in centrifugation or extraction strategies or development of non-algal biofuels, etc). Taking into consideration all the above mentioned parameters, it can be ascertained that any microalgae-based biodiesel project is unique. Hence, such projects must be designed by thinking in terms of a flexible or even multipurpose and adaptable installation (Richmond, 2010).