Despite its vocation as a potential source of biofuels, many challenges have hindered the development of biofuels technology from microalgae to become commercially viable.

Among them, and based on recent literature, we elect as the most important:

1. The selection of species must balance the requirements for biofuel production and extraction of valuable by-products (Ono and Cuello 2006);

2. Achieving greater photosynthetic efficiency through the continuous develop­ment of production systems (Pulz and Scheibenbogen 1998);

3. Developing techniques for growing a single species, reducing evaporation losses, and diffusion of CO2 (Ugwu et al. 2008);

4. Few commercial cultivating “farms,” so there is a lack of data on large-scale cultivation (Pulz 2001);

5. Impossibility of introducing flue gas at high concentrations, due to the pres­ence of toxic compounds such as NOx and SOx (Brown 1996);

6. Choosing algae strains that require freshwater to grow can be unsustainable for operations on a large-scale and exacerbate freshwater scarcity (Mcgraw 2009);

7. Current harvest and dewatering are still too energy intensive (Chen et al. 2009);

8. Some recent life cycle analyses (LCAs) project algae biofuels as having poor energy or greenhouse gas benefits (Benemann 2012; Clarens et al. 2010);

9. Depending on the processes, PBR systems can consume more energy than they produce (Slade and Bauen 2013);

10. Another disappointment that will likely arise is the scarcity of sites with favorable climate, land, water, and CO2 resources, all required in one place (Benemann 2012; Clarens et al. 2010; Slade and Bauen 2013);

11. CO2 supply is relatively expensive, due to high capital and operational costs for piping CO2 to, and transferring it into, the ponds (Benemann 2012).

12. Large-scale cultivation of algal biomass will require a lot of nitrogen and phosphorus; at a small-scale, recycling nutrients from wastewater could potentially provide some of the nutrients required (Slade and Bauen 2013).

Finally, to reach positive energy balance, it will be needed technological advances and highly optimized production systems. The amount of GHG decreases when the microalgae yield increases, primarily because CO2 is the main raw material utilized in photosynthesis during the growth of microalgae. Therefore, it is impor­tant to achieve high yields of biomass and oil in the cultivation plant. The miti­gation of environmental impacts, and in particular water management, presents both challenges and opportunities, many of which can only be resolved at the local level. Existing cost estimates need to be improved, and this will require empiri­cal data on the performance of systems designed specifically to produce biofuels (Slade and Bauen 2013).