Abstract Artificial, non-sterile, microalgal biofilms present a promising biotechnological avenue for the production of valuable biomass, biofuels and biochemicals while simultaneously engaging in photosynthetic carbon capture. Here we use a psbA amplicon library and high-throughput 16S and 18S rRNA gene sequencing to investigate the effects of time and CO2 concentration on the composition and community dynamics of photoautotrophically grown microalgal biofilms pre-conditioned with wastewater and heavily seeded with the green alga Scenedesmus obliquus. While biomass increased in a stable, linear manner, our analysis revealed that the photoautotrophic community dramatically changed over time. Photoautotrophs such as Chorella and the cyanobacterium Leptolyngbya, presumably seeded from the wastewater, rapidly established as constituents of the biofilm while the seed species was far less dominant than anticipated. With time, photoautotrophic diatoms and dinoflagellates also established themselves as constituents of the biofilm. Low CO2 (0.04% v/v) favoured the early proliferation of cyanobacteria while high CO2 (12%) delayed, but did not prevent the proliferation. In addition, a phylogenetically diverse array of heterotrophic α-, β- and γ-proteobacteria, Bacteriodetes along with a selection of eukaryotic microorganisms inhabited the biofilms. Principal coordinate analyses reveal unique clustering patterns indicating that the composition of the initial and the final microbial communities were distinctly different from one another. Alpha diversity measures indicated that the 16S (prokaryotic) community peaked around day 10 / 11 at both 0.04% and 12% CO2. However, unlike the 18S (eukaryotic) community where diversity was at a maximum at the end of the 26-day time-course, prokaryotic diversity achieved minimum values, particularly for biofilms grown at 0.04% CO2, where the cyanobacteria proliferated. In spite of the planned experimental design bias toward S. obliquus biofilm growth, the collective data suggest that selection against undesirable microorganism also needs to be incorporated as an essential feature of biofilm photobioreactor design and operation.

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