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Utilization of renewable sources for energy is becoming an increasing necessity, due to the impending depletion of fossil fuels and consequently the search for alternative sources. Special emphasis on sustainability and environmental compatibility is the catalyst motivating today’s bioenergy science. In this respect, hydrogen is a potential candidate for development, considering its advantages as an energy carrier and that its production can be accomplished, using chemical and/or biological processes. Keeping the environment in mind as the keystone for future energy routes, biological hydrogen production is a vital topic for research. Compared to the other microorganisms, the ability of some strains of microalgae to produce hydrogen under defined culture conditions is getting more attention, due to the clean and sustainable nature of their biological processes. Among microalgae that one should highlight is Chlamydomonas reinhardtii, which is well studied both under laboratory and outdoor conditions. Reaching the ultimate goal of a commercial system will require understanding the overall biological process, from the single cell to the complex environmental interaction level. Within this context, this chapter discusses step-by-step the hydrogen-production process by microalgae with a specific focus on C. reinhardtii, considering key environmental factors such as light, temperature, pH, and fluid dynamics.

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