Research Focus:
The research group Systems Biotechnology works in the core areas quantitative physiology and manipulation of redox balances with the overall aim of the sustainable production of chemicals and green energy carriers such as H2. We focus on several key classes of organisms: On the one hand we use photoautotrophic cyanobacteria (farmers) to provide redox power and organic carbon, on the other hand we employ metabolically engineered microbes (including heterotrophs) as production organisms (laborers). A third type of cell might come into play to stabilize synthetic consortia (balancers). We use pure cultures, co-cultures and synthetic consortia to achieve our goals for production. Applying Systems Metabolic Engineering to individual cell types following an iterative design-build-test-learn cycle, is a key approach to achieve our aims.
As a consequence, the group rests on four main pillars: (i) Modelling of metabolism (including metabolic flux analysis and genome scale modelling), (ii) analytics (metabolite fingerprinting, quantification, and isotope enrichments), (iii) in-depth physiology using mass-balanced culture techniques and ‘omics characterization, and last but not least (iv) microbial electrochemical technologies (MET) which allows the reversible conversion of electrical energy into biochemical energy to steer metabolism at the push of a button.
To address the diverse needs of the four pillars, the staff is organized in interdisciplinary research teams with a special focus on certain aspects of the pillars.
Group Leader:
Prof. Dr. Jens Krömer
Academic Staff:
Dr. Chandrakant Joshi
PhD-Students:
Laura Pause (jointly with BPV group)
Hans Schneider (jointly with BPV group)
Jianqi Yuan (jointly with BPV group)
Index:
You could use our publication index for further requests.
2024 (1)
- Pause, L., Weimer, A., Wirth, N.T., Nguyen, A.V., Lenz, C., Kohlstedt, M., Wittmann, C., Nikel, P.I., Lai, B., Krömer, J.O. (2024):
Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system
Microb. Biotechnol. 17 (1), e14375 10.1111/1751-7915.14375
2023 (4)
- Lai, B., Krömer, J., Aulenta, F., Wu, H., Nikel, P.I. (2023):
Exploiting synergies between microbial electrochemical technologies and synthetic biology
Microb. Biotechnol. 16 (3), 485 - 488 10.1111/1751-7915.14208 - Pan, M., Wang, Y., Krömer, J.O., Zhu, X, Lin, M.K.T.H., Angelidaki, I. (2023):
A coculture of photoautotrophs and hydrolytic heterotrophs enables efficient upcycling of starch from wastewater toward biomass-derived products: Synergistic interactions impacting metabolism of the consortium
Environ. Sci. Technol. 57 (41), 15523 - 15532 10.1021/acs.est.3c05321 - Schneider, H., Lai, B., Krömer, J. (2023):
Interference of electron transfer chain inhibitors in bioelectrochemical systems
Electrochem. Commun. 152 , art. 107527 10.1016/j.elecom.2023.107527 - Schneider, H., Lai, B., Krömer, J. (2023):
Utilizing cyanobacteria in biophotovoltaics: An emerging field in bioelectrochemistry
In: Bühler, K., Lindberg, P. (eds.)
Cyanobacteria in biotechnology. Applications and quantitative perspectives
Adv. Biochem. Eng. Biotechnol. 183
Springer Nature, p. 281 - 302 10.1007/10_2022_212
2022 (3)
- Brandenburg, F., Klähn, S., Schmid, A., Krömer, J.O. (2022):
Produktion von Aminosäurederivaten in Cyanobakterien. Production of amino acid derivatives in cyanobacteria
Biospektrum 28 (3), 341 - 343 10.1007/s12268-022-1756-z - Gemünde, A., Lai, B., Pause, L., Krömer, J., Holtmann, D. (2022):
Redox mediators in microbial electrochemical systems
ChemElectroChem 9 (13), e202200216 10.1002/celc.202200216 - Plan, M., Bongers, M., Bydder, S., Fabris, M., Hodson, M.P., Kelly, E., Krömer, J., Perez-Gil, J., Peng, B., Satta, A., Schrübbers, L.C., Vickers, C.E. (2022):
Analysing intracellular isoprenoid metabolites in diverse prokaryotic and eukaryotic microbes
In: Wurtzel, E.T. (ed.)
Carotenoids: Carotenoid and apocarotenoid analysis
Methods Enzymol. 670
Elsevier, p. 235 - 284 10.1016/bs.mie.2022.03.018
2021 (8)
- Brandenburg, F., Theodosiou, E., Bertelmann, C., Grund, M., Klähn, S., Schmid, A., Krömer, J.O. (2021):
Trans-4-hydroxy-L-proline production by the cyanobacterium Synechocystis sp. PCC 6803
Metab. Eng. Commun. 12 , e00155 10.1016/j.mec.2020.e00155 - Bühler, K., Bühler, B., Klähn, S., Krömer, J.O., Dusny, C., Schmid, A. (2021):
Biocatalytic production of white hydrogen from water using cyanobacteria
In: Rögner, M. (ed.)
Photosynthesis: Biotechnological applications with microalgae
De Gruyter, Berlin ; Boston, p. 279 - 306 10.1515/9783110716979-011 - Bühler, K., Krömer, J.O., Klähn, S., Bühler, B., Dusny, C., Schmid, A. (2021):
Weißer Wasserstoff made in Leipzig
Biospektrum 27 (3), 335 10.1007/s12268-021-1572-x - Krömer, J.O. (2021):
Buchrezension zu: Industrial Microbiology
Biospektrum 27 (4), 452 10.1007/s12268-021-1581-9 - Lai, B., Schneider, H., Tschörtner, J., Schmid, A., Krömer, J.O. (2021):
Technical-scale biophotovoltaics for long-term photo-current generation from Synechocystis sp. PCC6803
Biotechnol. Bioeng. 118 (7), 2637 - 2648 10.1002/bit.27784 - Lai, B., Schneider, H., Tschörtner, J., Schmid, A., Krömer, J.O. (2021):
Inside front cover image, Volume 118, Number 7, July 2021
Biotechnol. Bioeng. 118 (7), ii - ii 10.1002/bit.27411 - Nguyen, A.V., Lai, B., Adrian, L., Krömer, J.O. (2021):
The anoxic electrode-driven fructose catabolism of Pseudomonas putida KT2440
Microb. Biotechnol. 14 (4), 1784 - 1796 10.1111/1751-7915.13862 - Welter, E.S., Kött, S., Brandenburg, F., Krömer, J.O., Goepel, M., Schmid, A., Gläser, R. (2021):
Figures of merit for photocatalysis: Comparison of NiO/La-NaTaO3 and Synechocystis sp. PCC 6803 as a semiconductor and a bio-photocatalyst for water splitting
Catalysts 11 (11), art. 1415 10.3390/catal11111415
2020 (4)
- Babel, H., Krömer, J.O. (2020):
Evolutionary engineering of E. coli MG1655 for tolerance against isoprenol
Biotechnol. Biofuels 13 , art. 183 10.1186/s13068-020-01825-6 - Krömer, J.O., Ferreira, R.G., Petrides, D., Kohlheb, N. (2020):
Economic process evaluation and environmental life-cycle assessment of bio-aromatics production
Front. Bioeng. Biotechnol. 8 , art. 403 10.3389/fbioe.2020.00403 - Lai, B., Bernhardt, P.V., Krömer, J.O. (2020):
Cytochrome c reductase is a key enzyme involved in the extracellular electron transfer pathway towards transition metal complexes in Pseudomonas putida
ChemSusChem 13 (19), 5308 - 5317 10.1002/cssc.202001645 - Lai, B., Krömer, J.O. (2020):
Steering redox metabolism in Pseudomonas putida with microbial electrochemical technologies
In: Tiquia-Arashiro, S.M., Pant, D. (eds.)
Microbial Electrochemical Technologies
CRC Press, Boca Raton, FL, p. 59 - 75 10.1201/9780429487118
2019 (3)
- Lai, B., Nguyen, A.V., Krömer, J.O. (2019):
Characterizing the anoxic phenotype of Pseudomonas putida using a bioelectrochemical system
Methods Protoc. 2 (2), art. 26 10.3390/mps2020026 - Tschörtner, J., Lai, B., Krömer, J.O. (2019):
Biophotovoltaics: green power generation from sunlight and water
Front. Microbiol. 10 , art. 866 10.3389/fmicb.2019.00866 - Vassilev, I., Kracke, F., Freguia, S., Keller, J., Krömer, J.O., Ledezma, P., Virdis, B. (2019):
Microbial electrosynthesis system with dual biocathode arrangement for simultaneous acetogenesis, solventogenesis and carbon chain elongation
Chem. Commun. 55 (30), 4351 - 4354 10.1039/c9cc00208a
2018 (8)
- Averesch, N.J.H., Krömer, J.O. (2018):
Metabolic engineering of the shikimate pathway for production of aromatics and derived compounds – present and future strain construction strategies
Front. Bioeng. Biotechnol. 6 , art. 32 10.3389/fbioe.2018.00032 - Averesch, N.J.H., Martínez, V.S., Nielsen, L.K., Krömer, J.O. (2018):
Toward synthetic biology strategies for adipic acid production: An in silico tool for combined thermodynamics and stoichiometric analysis of metabolic networks
ACS Synth. Biol. 7 (2), 490 - 509 10.1021/acssynbio.7b00304 - Kracke, F., Lai, B., Yu, S., Krömer, J.O. (2018):
Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation – A chance for metabolic engineering
Metab. Eng. 45 , 109 - 120 10.1016/j.ymben.2017.12.003 - Krieg, T., Phan, L.M.P., Wood, J.A., Sydow, A., Vassilev, I., Krömer, J.O., Mangold, K.-M., Holtmann, D. (2018):
Characterization of a membrane-separated and a membrane-less electrobioreactor for bioelectrochemical syntheses
Biotechnol. Bioeng. 115 (7), 1705 - 1716 10.1002/bit.26600 - Varela, C., Schmidt, S.A., Borneman, A.R., Pang, C.N.I., Krömer, J.O., Khan, A., Song, X., Hodson, M.P., Solomon, M., Mayr, C.M., Hines, W., Pretorius, I.S., Baker, M.S., Roessner, U., Mercurio, M., Henschke, P.A., Wilkins, M.R., Chambers, P.J. (2018):
Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains
Metab. Eng. 49 , 178 - 191 10.1016/j.ymben.2018.08.006 - Vassilev, I., Gießelmann, G., Schwechheimer, S.K., Wittmann, C., Virdis, B., Krömer, J.O. (2018):
Anodic electro-fermentation: Anaerobic production of L-Lysine by recombinant Corynebacterium glutamicum
Biotechnol. Bioeng. 115 (6), 1499 - 1508 10.1002/bit.26562 - Vassilev, I., Hernandez, P.A., Batlle-Vilanova, P., Freguia, S., Krömer, J.O., Keller, J., Ledezma, P., Virdis, B. (2018):
Microbial electrosynthesis of isobutyric, butyric, caproic acids, and corresponding alcohols from carbon dioxide
ACS Sustain. Chem. Eng. 6 (7), 8485 - 8493 10.1021/acssuschemeng.8b00739 - Yu, S., Lai, B., Plan, M.R., Hodson, M.P., Lestari, E.A., Song, H., Krömer, J.O. (2018):
Improved performance of Pseudomonas putida in a bioelectrochemical system through overexpression of periplasmic glucose dehydrogenase
Biotechnol. Bioeng. 115 (1), 145 - 155 10.1002/bit.26433
2017 (4)
- Averesch, N.J.H., Prima, A., Krömer, J.O. (2017):
Enhanced production of para-hydroxybenzoic acid by genetically engineered Saccharomyces cerevisiae
Bioprocess. Biosyst. Eng. 40 (8), 1283 - 1289 10.1007/s00449-017-1785-z - Gold, D.A., O'Reilly, S.S., Watson, J., Degnan, B.M., Degnan, S.M., Krömer, J.O., Summons, R.E. (2017):
Lipidomics of the sea sponge Amphimedon queenslandica and implication for biomarker geochemistry
Geobiology 15 (6), 836 - 843 10.1111/gbi.12253 - Koch, C., Kuchenbuch, A., Kracke, F., Bernhardt, P.V., Krömer, J.O., Harnisch, F. (2017):
Predicting and experimental evaluating bio-electrochemical synthesis — A case study with Clostridium kluyveri
Bioelectrochemistry 118 , 114 - 122 10.1016/j.bioelechem.2017.07.009 - Watson, J.R., Krömer, J.O., Degnan, B.M., Degnan, S.M. (2017):
Seasonal changes in environmental nutrient availability and biomass composition in a coral reef sponge
Mar. Biol. 164 (6), art. 135 10.1007/s00227-017-3167-0
New concepts for an integrative bio economy: Sustainable Valorization of CO2 and sunlight
This project aims to generate a sustainable resource platform on the basis of CO2 driven by light energy from sunlight. Several target compounds and reactor platforms are considered and a comparison of state of the art biotechnological- and heterogeneous catalysis is performed. Target molecules include 4-Hydroxyprolin, methane, methanol, oxalic and tartaric acid.
Diese Maßnahme wird mitfinanziert mit Steuermitteln auf Grundlage des von den Abgeordneten des Sächsischen Landtags beschlossenen Haushalts.
(This project is co-financed by means of taxation based on the budget adopted by the representatives of the Landtag of Saxony.)
How do sponges and bacteria together maintain productivity on coral reefs?
Integrating invertebrate biology, microbiology, genomics and metabolomics, this project aims to listen in on conversations between a Great Barrier Reef sponge and its bacterial symbionts. Coral reefs thrive in nutrient-poor tropical seas by relying on efficient retention and recycling of essential elements, and marine sponges are proving critically important in this role. They achieve this by cooperating with metabolically diverse bacterial symbionts via mechanisms that are largely unknown. Using the first and most advanced genome-enabled sponge in the world, this project seeks to reveal genomic and metabolic details of the partnership, with potential to inform environmental restoration, pharmaceuticals and biotechnology.
The project is a collaboration with the Degnan labs at the University of Queensland (Brisbane, Australia) and funded through the Australian Research Council (DP170102353).
Fluxomics – Quantifying the metabolic phenotype (Higrade 2018)
With the rise of Systems Biology tools in many areas of the life sciences, data on gene expression, protein abundance and metabolite concentrations become readily available, yet the quantification of intracellular reaction rates (fluxes) is still a non-trivial task for many researchers. This course introduces different concepts of metabolic flux analysis in a hands-on format and enable researchers to develop a quantitative description of their organism or consortium of study.
Masterstudiengang Biochemie, Universität Leipzig (Sommersemester)
Modul: "Quantitative Biologie für eine nachhaltige Umwelt- und industrielle Biotechnologie"
Erwerb von Fertigkeiten in der quantitativen Beschreibung biologischer Prozesse. Nachweis der Lernkompetenz durch Berechnung von maximal möglichen Ausbeuten sowohl in Produktionssystemen als auch bei Abbauprozessen und durch Verfolgung von Stoffflüssen. Dies legt die Grundlage zur Beschreibung der Nachhaltigkeit biologischer Systeme.
Hierbei kommen biologische Datensätze und Modellierungsansätze der Systembiologie zum Einsatz. Die Absolventen erlernen sowohl das Erstellen von Modellen einerseits und die Prozessierung der Daten andererseits. Es werden sowohl stöchiometrische als auch thermodynamische Ansätze verfolgt, um unterschiedliche Prozesse in den Bereichen weiße Biotechnologie und Umweltbiotechnologie zu beschreiben.
LC-MS/MS based proteomics analysis of Synechocystis sp. PCC6803 phenotype in biophotovoltaics
Understanding how Synechocystis behaviours exposing to anodic electron sink plays a central role in quantitative biophotovoltaics research and subsequent rational system engineering. The project aims to apply the lab-established LC-MS/MS methods to quantitatively address the proteome changes steered by the electrode. Two objectives will be focused on in this project, with each of them corresponding to an individual master thesis:
- Global proteome analysis focusing on cellular metabolism in response to different working conditions (e.g. light, working electrode potential, etc);
- Membrane proteome analysis with the target to identify key redox proteins involved in extracellular electron transfer or transporters responsible for mediator transportation.
CRISPR-based interrupting system (CRISPRi) for Synechocystis sp. PCC6803
This project is aiming to develop the CRISPRi system to targeted interrupt specific protein(s) of Synechocystis to identity its (their) functions involved in the performance of the microorganism in a biophotovoltaics system. The work will be based on a well-established system developed in KTH Sweden (Yao, L., et al. (2016). ACS Synthetic Biology 5(3): 207-212; Yao, L., et al. (2020). Nature Communications 11(1): 1666) and localize it into our lab. Essential strains and plasmids were kindly provided by Prof. Hudson. As a proof-of-concept study, the initial target will be to create a Synechocystis mutant with inducible inhibition of the photosystem II (PSII) protein complex. Different subunits of PSII should be tested and the time-course PSII activity (based on O2 evolution rate and PAM measurement) should be traced after induction.
Gas composition analysis using membrane-inlet mass spectrometry
This project aims for developing a quantitative protocol to trace the gas composition of the medium in BPV reactor. A membrane-inlet mass spectrometry will be used, and oxygen and CO2 are of particular interest in this project. Oxygen evolution rate and CO2 assimilation rate are the key parameters to be determined. The research question involved in this project is how the photosynthetic and carbon assimilation activities of Synechocystis sp PCC6803 are impacted by the anodic electron sink in BPV system.
Quantitative physiology of Synechocystis sp PCC6803 in response to light availability
Synechocystis is an important model organism for Cyanobacteria, which are considered as phototrophic platform organisms in biotechnology. This thesis aims at quantifying intracellular metabolite concentrations in response to light. These metabolites are the building blocks for biotechnological processes based on CO2. It will involve cultivation of microbes, sampling and mass spectrometry. Knowledge in microbial metabolism and a strong interest in quantitative work are desired.
Fluxomics of Cyanobacteria using 13C tracers
This project aims to determine uptake kinetics of isotopic tracers into the metabolism of Synechocystis sp. PCC6803. It will involve cultivation of microbes, sampling and mass spectrometry. A fundamental interest in microbiology and analytics is desired.
Photolysis of water in a bioelectrochemical system as a path to hydrogenporoduction
Hydrogen is considered a key energy carrier of the future. Splitting water into oxygen and hydrogen is a great way to generate H2. In this project we explore the capability of Cyanobacteria to catalyse this process and use an electrochemical system to separate H2. Being a fundamental research project, creativity and interest in electrochemical technology as well as microbiology are paramount.