Daniel's research focuses on the metabolic engineering of Pseudomonas putida for C1 assimilation and lignin valorization

​Current biotechnological processes for the production of fine and bulk chemicals rely on substrates like refined sugars (e.g., glucose, fructose, etc.) leading to a competition with the global food industry. With the growing world population, it is expected that the overall food demand for the global nutrition will increase by 70% by 2050. To eliminate the competition for common substrates, Daniel works on the metabolic engineering of Pseudomonas putida for the utilization of lignin as an alternative feedstock for the biotechnological industry. Lignin is one of the most abundant biomolecules worldwide and a major waste product of the current paper industry. As hydrophobic fraction of plant cell walls, it is a CO2-derived renewable component making it a promising sustainable substrate for the biotechnological production of precursor molecules for several industrial branches. However, the utilization of lignin brings its limitations due to the release of toxic side products and toxic intermediate metabolites. Daniel's research aims to overcome these limitations by model-based computational comparison of different metabolic pathways for the assimilation of toxic components and the subsequent introduction of the best-performing pathways into P. putida. By engineering a whole-cell biocatalyst tolerant to the utilization of lignin as sole carbon source, his research contributes to the ongoing efforts for a transition towards a circular bioeconomy.

​Before starting his PhD at the AIBN in April 2022, Daniel graduated with a B.Sc. (2018) and a M.Sc. (2021) degree in Molecular Biotechnology from the Bielefeld University, Germany. After his participation in the international Genetically Engineered Machines competition (iGEM) in 2017, an industrial internship at Evonik Industries, Germany (2018), and an external research stay at the Massachusetts Institute of Technology, USA in 2019, Daniel got fascinated with the concepts of synthetic biology and metabolic engineering, while he also got aware of their limitations. Therefore, he decided to familiarize himself with FBA-based metabolic modeling by supporting work on synthetic microbial co-cultures during his master's thesis at the Research Center Jülich, Germany (Helmholtz Society, 2020-2021). In addition, he learned crucial techniques in metabolomics while studying the phosphoregulation of the central carbon metabolism in E. coli during a research internship at ETH Zürich, Switzerland (2021-2022). As part of a joint supervision program between the University of Queensland and the Technical University of Denmark, Daniel is now pursuing his Ph.D. under the supervision of Dr. Birgitta Ebert (AIBN), Dr. Esteban Marcellin (AIBN), and Dr. Pablo I. Nikel (Center for Biosustainability, Denmark).


​In 2018, Daniel worked as an intern at the Nutrition and Health branch of Evonik Industries AG in Künsebeck, Germany. Under the supervision of Dr. Frank Schneider and Dr. Kay Marin, he established alternative regulation mechanisms on the transcriptional and translational level in Corynebacterium glutamicum based on CRISPR interference and sRNA.


​Daniel works together with the Systems Environmental Microbiology (SEM) Group led by Dr Pablo I. Nikel (Center for Biosustainability, DTU, Denmark). Besides the development of novel genetic engineering tools in Pseudomonas putida, the SEM group works on the establishment of synthetic C1 assimilation pathways for the biological fixation of CO2 emissions. With their expertise, pathways for the efficient assimilation of toxic side effects of the lignin degradation pathway will be identified and introduced into developed lignin-utilization strains.
In collaboration with the Laboratory for Process Systems Engineering (Prof. Alexander Mitsos) at RWTH Aachen, Germany, beneficial gene knockouts will be identified based on genome-scale models Daniel developed for his lignin- utilization strains. The work is carried out together with Anita Ziegler.

Key Publications

  1. ​Simone Schito, Rico Zuchowski, Daniel Bergen, Daniel Strohmeier, Bastian Wollenhaupt, Philipp Menke, Johannes Seiffarth, Katharina Nöh, Dietrich Kohlheyer, Michael Bott, Wolfgang Wiechert, Meike Baumgart, Stephan Noack. Communities of Niche-optimized Strains (CoNoS) - Design and creation of stable, genome-reduced co-cultures. Metabolic Engineering 73,91-103 (2022). https://doi.org/10.1016/j.ymben.2022.06.004
  2. Lennard Karsten, Daniel Bergen, Christina Drake, Saskia Dymek, Maximillian Edich, Markus Haak, Denise Kerkhoff, Yannic Kerkhoff, Michelle Liebers, Camilla März, Laura Schlüter, Olga Schmidt, Svenja Vinke, Christopher Whitford, Boas Pucker, Julian Droste, Christian Rückert, Kristian Müller, Jörn Kalinowski. Expanding the Genetic Code. Conference: iGEM 2017, Boston. (2017). https://doi.org/10.13140/RG.2.2.20342.91203