Reliable online measurement of population dynamics for filamentous co‐cultures

Understanding population dynamics is a key factor for optimizing co‐culture processes to produce valuable compounds. However, the measurement of independent population dynamics is difficult, especially for filamentous organisms and in presence of insoluble substrates like cellulose. We propose a workflow for fluorescence‐based online monitoring of individual population dynamics of two filamentous microorganisms. The fluorescent tagged target co‐culture is composed of the cellulolytic fungus Trichoderma reesei RUT‐C30—mCherry and the pigment‐producing bacterium Streptomyces coelicolor A3(2)—mNeonGreen (mNG) growing on insoluble cellulose as a substrate. To validate the system, the fluorescence‐to‐biomass and fluorescence‐to‐scattered‐light correlation of the two strains was characterized in depth under various conditions. Thereby, especially for complex filamentous microorganisms, microbial morphologies have to be considered. Another bias can arise from autofluorescence or pigments that can spectrally interfere with the fluorescence measurement. Green autofluorescence of both strains was uncoupled from different green fluorescent protein signals through a spectral unmixing approach, resulting in a specific signal only linked to the abundance of S. coelicolor A3(2)—mNG. As proof of principle, the population dynamics of the target co‐culture were measured at varying inoculation ratios in presence of insoluble cellulose particles. Thereby, the respective fluorescence signals reliably described the abundance of each partner, according to the variations in the inocula. With this method, conditions can be fine‐tuned for optimal growth of both partners along with natural product formation by the bacterium.