AimsTo achieve the functional specialization of a microalgae community through operational tuning of an open photobioreactor used for biogas upgrading under alkaline conditions. Methods and ResultsAn open photobioreactor was inoculated with an indigenous microalgae sample from the Texcoco Soda Lake. A microalgae community was adapted to fix CO2 from synthetic biogas through different culture conditions reaching a maximum of 220mg CO(2)l(-1) per day. Picochlorum sp. and Scenedesmus sp. were identified as the prominent microalgae genera by molecular fingerprinting (partial sequencing of 16S rRNA and 18S rRNA genes) but only the first was detected by microscopy screening. Changes in the microalgae community profile were monitored by a range-weighted richness index, reaching the lowest value when biogas was upgraded. ConclusionsA robust microalgae community in the open photobioreactor was obtained after different culture conditions. The specialization of microalgae community for CO2 fixation under H2S presence was driven by biogas upgrading conditions. Significance and Impact of the StudyThe alkaline conditions enhance the CO2 absorption from biogas and could optimize specialized microalgae communities in the open photobioreactor. Denaturing gradient gel electrophoresis fingerprinting and richness index comparison are useful methods for the evaluation of microalgae community shifts and photosynthetic activity performance, particularly in systems intended for CO2 removal from biogas where the CO2 assimilation potential can be related to the microbial richness.