BiotechnologyJournalDOI 10.1002/biot.201000129 Biotechnol. J. 2010, 5, 660–670660 © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim1 IntroductionThe use of microorganisms to produce compoundsof commercial value enjoys a rich history. Of recentinterest is the use of algae for the synthesis of nu-traceuticals and biofuels. For example, high-valuemolecules are extracted from microalgae, such ascarotenoid pigments and docosahexaenoic acid(DHA), an ω3 fatty acid [1]. Polysaccharides, sterols,and polyunsaturated fatty acids are all nutraceuti-cal compounds extracted from algae [2]. Large-scale commercial culture of strains of Chlorella andArthospira as a nutritious food date back to the1960s and 1970s, respectively [1].Table 1 lists a fewof the well-defined molecules of commercial valuethat are purified from algal sources.Microalgae hold promise as a source of renew-able energy. Algae-derived hydrogen, methane, tri-acylglycerols, and ethanol all serve as potential ma-terials for biofuels [3–6]. For example, dependingon production conditions, Schizochytrium sp. andBotryococcus braunii may yield 50–77% and 25–75%oil by mass, respectively [3]. Algae oils are rich inthe triacylglycerols that serve as material for con-version to biodiesel [3]. Some species of microal-gae, such as Chlamydomonas reinhardtii, may pro-ReviewMetabolic systems analysis to advance algal biotechnologyBrian J. Schmidt1**, Xiefan Lin-Schmidt1, Austin Chamberlin1, Kourosh Salehi-Ashtiani2* and Jason A. Papin11Department of Biomedical Engineering, University of Virginia, Health System, Charlottesville, VA, USA2Center for Cancer Systems Biology (CCSB), Department of Cancer Biology and Dana-Farber Cancer Institute, and Departmentof Genetics, Harvard Medical School, Boston, MA, USAAlgal fuel sources promise unsurpassed yields in a carbon neutral manner that minimizes resourcecompetition between agriculture and fuel crops. Many challenges must be addressed before algalbiofuels can be accepted as a component of the fossil fuel replacement strategy. One significantchallenge is that the cost of algal fuel production must become competitive with existing fuel al-ternatives. Algal biofuel production presents the opportunity to fine-tune microbial metabolic ma-chinery for an optimal blend of biomass constituents and desired fuel molecules. Genome-scalemodel-driven algal metabolic design promises to facilitate both goals by directing the utilizationof metabolites in the complex, interconnected metabolic networks to optimize production of thecompounds of interest. Network analysis can direct microbial development efforts towards suc-cessful strategies and enable quantitative fine-tuning of the network for optimal product yieldswhile maintaining the robustness of the production microbe. Metabolic modeling yields insightsinto microbial function, guides experiments by generating testable hypotheses, and enables therefinement of knowledge on the specific organism. While the application of such analytical ap-proaches to algal systems is limited to date, metabolic network analysis can improve understand-ing of algal metabolic systems and play an important role in expediting the adoption of new bio-fuel technologies.Keywords: Algae · Biofuels · Chlamydomonas reinhardtii · Flux balance analysis · Metabolic networkCorrespondence: Dr. Jason A. Papin, Department of BiomedicalEngineering, University of Virginia, Box 800759, Health System,Charlottesville, VA 22908, USAE-mail: [email protected]: FBA, flux balance analysis** Additional corresponding author: Dr. Kourosh Salehi-AshtianiE-mail: [email protected]** Current address: Entelos, Foster City, CA 94404, USAReceived 12 April 2010Revised 9 June 2010Accepted 10 June 2010Supporting information available online© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 661Biotechnol. J. 2010, 5, 660–670 www.biotechnology-journal.comduce hydrogen directly [4, 7]. Additionally, the dou-bling time of microalgae in the exponential growthphase is as short as 3.5 h, and they are efficient atutilizing light to produce biomass, facilitating rapidfuel production [4]. Although some algae may becapable of utilizing biomass feedstocks as other mi-crobes do, utilizing the photosynthetic route willarguably be the most efficient means of biofuelproduction [5].Microalgal biofuel cultivation promises to behighly sustainable. Importantly, microalgae aremuch more distant from the human food chainthan plant crops, avoiding competition betweenagricultural and biofuel resources [3]. As shown inTable 2, biodiesel produced from photosyntheticmicroalgae have a much higher yield than currentbiofuels and can be cultured on marginal land, fur-ther reducing the diversion of agricultural re-sources. Additionally, some algae can be culturedwith saltwater or wastewater, avoiding use of fresh-water resources [5]. Since microalgal fuel yields onan area basis are higher than currently possiblewith crops, they are more capable of meeting fueldemand [3]. Furthermore, microalgae cultureshave been demonstrated to fix carbon dioxide, andmay be utilized in the bioremediation of industrialflue gases [8–10]. Algal fuels are therefore carbonneutral, or carbon negative in the case of hydrogen.Despite the advantages of algae as a source ofbiofuels, there are still significant challenges thatmust be addressed before algal biofuels can bewidely adopted. Although compatible with the ex-isting fuel infrastructure, biodiesel from algae isnot yet economically competitive with fossil fuelsor corn ethanol (Table 2). For algae biodiesel pro-duction, an additional challenge will be altering theselected algae to produce triacylglycerol fatty acidconstituents with the optimal length and hydrocar-bon saturation [5]. In this review article, we de-scribe a systems level metabolic modeling ap-proach that enables the generation of hypothesesto modify algal metabolism towards more efficientTable 1. Selected molecularly defined products currently isolated from microalgaeName or family Structure Companies Commercialized speciesAstaxanthin Cyanotech [1] Haematococcus (food colorant, Mera Pharmaceuticals [1] pluvialis [1]antioxidant [1]) Bioreal [1]Parry’s Pharmaceuticals [1]Algatech [1]Docosahexaenoic acid Seambiotic Crypthecodinium (ω3 fatty acid, Martek Biosciences Corporation [1] conhii [1]cardiovascular health, OmegaTech [1] Shizochtrium sp. [1]brain development [1]) Nutrinova [1] Ulkenia sp. [1]Ethanol