Filamentous co-cultures: from screening to bioprocess development (Co-Pilot)

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The co-cultivation of cellulolytic filamentous fungi and filamentous soilbacteria on cellulosic substrates represents a promising approach forthe discovery and production of natural products. Due to thecomplexity, filamentous co-cultures are poorly studied andcharacterized. In the proposed project, the cellulose degraderTrichoderma reesei is partnered with various Streptomyces strains tosystematically unlock the production of novel natural products in thelatter genus. The work is based on our experience with a model cocultureof T. reesei and Streptomyces coelicolor, which is well knownto produce pigments and antibiotics. For this co-culture, weestablished a fluorescence-based method to follow populationdynamics and non-invasive methods for analysis of metabolism andpigment formation. To enable the screening of population dynamics ofmany different co-cultures using non-tagged Streptomyces strains, amethod based on autofluorescence profiling in combination withfluorescently-tagged T. reesei will be established. By meta-analysis ofaxenic and co-cultures of different Streptomyces strains, correlationsbetween the axenic performance indicators (e.g. growth rate) and coculturebehavior can be established. Thereby, we especially expectgreat performance differences depending on morphology. Tosystematically analyze the influence of morphology, co-cultures of adispersed growing knockout strain of our model bacterium S.coelicolor will be compared to our established co-culture of the pelletgrowing wildtype strain of S. coelicolor. Thereby, population stability,product formation, morphology, and rheology will be monitored andcorrelated to the different morphology:performance results of theStreptomyces screening. This will allow to estimate to what extentStreptomyces co-culture behavior can be generalized and predicted,which will aid in future design of filamentous co-cultures.Subsequently, a systematic up-scaling from microtiter plate to stirredfermenter will be performed for the most promising co-cultivationsdiscovered during the screening. Due to the morphologicalcomplexity, the co-culture morphology and performance is assumed to be sensitive towards changes in fluid dynamics. Therefore, scaleupwill be compared based on maximum local and average volumetricpower input by assessment of different impellers under closeinvestigation of morphology and rheology. All measurementtechniques already applied in small scale will be used to study howthe biosynthetic performance of filamentous co-cultures changeacross scales. With this information, we will be able to steer theinteractions of co-culture partners and enable a straightforwardmorphology-based scale-up to the pilot scale.