Certain embodiments and aspects of the present invention relate to a photobioreactor including covered photobioreactor units through which a liquid medium stream and a gas stream flow. The liquid medium comprises at least one species of phototrophic organism therein. Certain methods of using the photobioreactor system as part of fuel generation system and/or a gas-treatment process or system at least partially remove certain undesirable pollutants from a gas stream. In certain embodiments, a portion of the liquid medium is diverted from a photobioreactor unit and reintroduced upstream of the diversion position. In certain embodiments, the disclosed photobioreactor system, methods of using such systems, and/or gas treatment apparatus and methods provided herein can be used as part of an integrated combustion method and system, wherein photosynthetic organisms used within the photobioreactor are harvested from the photobioreactor, processed, and used as a fuel source for a combustion system such as an electric power plant.