The goal is to explore the impact of various abiotic stress conditions in the microbial communities of the Chlorella cultivation medium. The cultivation was a two-stage process. In the first stage, Chlorella was cultivated under optimum conditions in two pilot-scale photobioreactors. One reactor had a natural air supply, and the other had natural air mixed with an additional CO2 supply. In the second stage, in the reactor with additional CO2, depleted nitrogen with optimum phosphorus, depleted nitrogen with excessive phosphorus, and periodic cold shock were applied. Samples were collected on the last day of cultivation from each stage.