Generalized Morphology Modeling of Aggregating, Filamentous Microorganisms

Widely used in industrial biotechnology, filamentous fungi produce chemicals, enzymes, acids, antibiotics, and further lifesaving pharmaceuticals. Due to a strong relation between fungal morphology, process conditions, and productivity, targeted morphology engineering techniques aim to improve fungal morphology in terms of process behavior and productivity. However, the exact impact of such genetic and process modification methods are often unknown. The reason for this is the lack of appropriate analytical methods and models that correlate the fungal morphology to substrate supply. In this chapter, we present a method based on X-ray micro-computed tomography and image processing for detailed analysis of three-dimensional fungal morphology. This method has been extended in terms of sample throughput and, in combination with an additionally developed 2D image analysis method, allows the description of the micro- and macro-morphological development of complete fungal cultures. Furthermore, we used Monte Carlo growth simulations to expand the database of experimentally 3D-imaged fungal pellets by 3125 in-silico generated, morphologically different fungal structures. This database was used to perform diffusion computations through the 3D images, revealing a universal correlation between the structure and diffusivity through hyphal networks. The developed methods and results eventually contribute to targeted morphology engineering and improved control of filamentous fungal bioprocesses, leading to increased productivity.