Even though the optimistic outlook on microalgae-based biofuels has driven microalgal research forward, we are still far from understanding the molecular networks underlying the complex metabolic flexibility and physiological adaptations to environmental cues of photosynthetic microalgae. Elucidation of molecular mechanisms of favorable traits such as stress-induced oil accumulation and anaerobic fermentation capability is of fundamental importance to the basic biology and of practical importance to algal biotechnology. The recent efforts in sequencing algal genome sequences have facilitated isolation of genes involved in lipid biosynthesis, photosynthesis, anaerobic adaptation, and stress regulation. The utiliza­tion of reverse genetics techniques has allowed functional characterization of some of the isolated genes. Furthermore, integrated omics approaches have started to reveal novel insights into the gene regulatory networks and cellular responses associated with metabolic features for fuel production. The accumulated knowledge has generated testable hypotheses and provided strategies to increase biomass and improve fuel production. However, the mo­lecular toolbox required for reliable genetic manipulation of microalgae remains limited to only a few species (e. g., C. reinhardtii, Volvox carteri, Nannochloropsis sp., and the diatom Phaeodactylum tricornutum) (Kilian et al., 2011; Leon and Fernandez, 2007; Schiedlmeier et al., 1994; Schroda, 2006; Siaut et al., 2007). For other species, genetic transformations have been documented sporadically but have not been robustly applied to routine genetic modi­fications. Lack of a reliable toolkit makes hypothesis-driven functional studies and practical manipulation in oleaginous species impossible. Development of custom-made molecular toolkits for the chosen oleaginous algal species will be essential for metabolic engineering. Because genomic sequencing projects of various microalgae are in progress, the development of toolkits will accelerate in the coming years and shape the future of microalgal biotechnology.

The recent advances in developing innovative technologies are aimed at improving the economics of microalgae-based biofuels. However, the practical application of the current technology is still in its infancy, and most of the work has only been demonstrated at the laboratory scale level. For instance, the proposed metabolic engineering strategies to improve biodiesel production are designed to increase oil content at the per-cell level. Crucial to overall yield relies on oil content at the per-culture basis. It is not clear whether small-scale experimental concepts can be directly translated into large-scale industrial setups. If not, what factors need to be considered and modified to allow laboratory oil producers to scale up to industrial-level production? Until now, accurate assessment of energy balance and carbon reduction potential based on industrial-scale data spanning continuous seasons remains lim­ited. It is therefore difficult to assess the overall yield, energy balance, carbon mitigation, and environmental impacts of the yet-to-be-refined technology. Moreover, other interference factors such as parasite contamination, temperature fluctuation, weather influence, and light penetration that can potentially affect the productivity of the energy crop also need to be con­sidered during such an assessment. To make microalgae-based fuels a realistic industrial commodity, multidisciplinary principles need to be integrated into current research strategies to establish production platforms. In particular, integration of engineering and biology, followed by life-cycle-based long-term feedback evaluation/adjustment analyses of produc­tion pipelines, will be crucial to establishing solutions and optimizing protocols for energy production from microalgae.

Currently, the algal products (mostly food supplements and cosmetics products) on the market cost approximately two orders of magnitude more than the current cost for biodiesel production derived from oleaginous crops (Wijffels and Barbosa, 2010; Wijffels et al., 2010). Therefore, the practicality of producing microalgae-based fuels using the current technology is still questionable (Chisti, 2008; Reijnders, 2008). Before the microalgae-to-fuels technology is in place, incorporating the existing high-valued commodities into fuel production pipelines may provide a sustainable business model for microalgal biotechnology.

Acknowledgment

I am grateful to Dr. Lu-Shiun Her for his valuable comments on and suggestions regarding this chapter.