Co-cultivation dynamics of the filamentous microorganisms Aspergillus niger and Streptomyces coelicolor in shake flasks

Abstract Background The co-cultivation of filamentous fungi and actinobacteria is challenging due to their complex growth interactions. This study investigates how key parameters, such as inoculation strategy, glutamic acid concentration, hydrodynamic stress, and dissolved oxygen, influence the growth dynamics between Aspergillus niger and Streptomyces coelicolor in shake flask co-cultures. Recognizing the crucial role of macromorphology in filamentous microorganisms, an automated image analysis pipeline was developed to quantitatively assess the heterogeneity and reproducibility of each population. Results Simultaneous growth was achieved when both microorganisms were inoculated in pelleted form, whereas spore inoculation led to complete A. niger dominance. At 1:2 and higher inoculation ratios (fungus to bacteria), S. coelicolor could compete effectively. While A. niger growth-maintained dominance at 136 and 250 rpm (1:1), S. coelicolor growth outcompeted the fungus at 60 rpm, a shift attributed to a reduced oxygen transfer rate. Notably, only the highest shear forces (250 rpm) produced homogeneous, reproducible fungal pellet populations. Overall, bottom-baffled flasks enhanced reproducibility compared to non-baffled flasks. Conclusion It is possible to regulate the growth of S. coelicolor and A. niger in a co-culture by the aforementioned parameters. Among these, the inoculation ratio is most important to achieve different dynamics. A quantitative analysis of morphology development while optimising inoculation strategies provides a foundation for designing co-culture experiments that achieve balanced and reproducible growth.