Research cooperations

Collaborative Research Center SFB987: Microbial Diversity in Environmental Signal Response

Within the framework of the Collaborative Research Centre, 15 microbiology-focused research teams working at the Philipps-Universität Marburg and the local Max Planck Institute for Terrestrial Microbiology jointly focus their research efforts on microbial diversity in environmental signal response. Within the framework of the chosen topic, the projects contribute to the following research areas: (1) sensing and adaptation to ecosystem changes, (2) sensing and adaptation to niche specific nutrients, and (3) sensing and responses to surface contact.
Period of funding: 07/01/2012 - 09/30/2020
Speaker: Erhard Bremer, Philipps-Universität Marburg
Participants from MPIterMic: Ralf Conrad, Regine Kahmann, Tobias Erb, Werner Liesack, Andreas Brune, Martin Thanbichler, Knut Drescher, Lotte Søgaard-Andersen

Collaborative Research Center TRR174: Spatiotemporal dynamics of bacterial cells

This DFG-funded collaborative research center comprises 16 research groups from the Marburg and Munich areas. Its goals are to (i) elucidate the molecular mechanisms that regulate the spatiotemporal dynamics of cellular components in bacteria; (ii) extract from the experimental data conserved design principles for spatiotemporally organized systems; and, (iii) mathematically model, design, and synthesize modules that spatially organize minimal cells or cell-free systems.

Period of funding: 01/01/2017 - 12/31/2020

Coordinator: Martin Thanbichler, Philipps-Universität Marburg
Participants from MPIterMic: Martin Thanbichler, Lotte Søgaard Andersen, Victor Sourjik

LOEWE Schwerpunkt „Diffusible Signals – Impact of diffusible signals at human cell-microbe interfaces“

The research project "Diffusible Signals" aims to investigate and modify a central basis of infection processes: the communication between bacteria and human inflammatory cells. Together, physicians, biologists and computer scientists are investigating the exchange of soluble (diffusible) signals at the interfaces between clinically important bacteria and inflammatory cells. New insights into infection processes can help develop new targeted therapies that strengthen human immune defenses and weaken bacterial attack.
Speaker: Bernd Schmeck, Philipps-Universität Marburg
Period of funding: 01/01/2021 - 12/31/2024
Participants from MPIterMic: Victor Sourjik, Knut Drescher

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Priority Programme (SPP 2141) “Much more than Defence: the Multiple Functions and Facets of CRISPR-Cas“

The discovery of the prokaryotic immune system CRISPR-Cas was one of the most exciting breakthroughs in biology in the last twenty years. Initially identified as defence mechanism, we now know that defence is just one of many functions of this molecular machine, and we have barely begun to understand the full biological potential of this system. The two major goals of this concerted Priority Programme are: (1) the identification and investigation of new CRISPR-Cas functions beyond viral defence using model representatives of archaea and bacteria; (2) the elucidation of the molecular mechanisms underlying these functions using state-of-the-art methods.
Period of funding: 11/01/2018 - 10/31/2021
Speaker: Anita Marchfelder, Universität Ulm
Participants from MPIterMic: Lennart Randau (Coordinating committee), Ulrike Endesfelder

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DFG-ANR grant “Deciphering and engineering of the molecular diversity of NRPS-derived azacyclic alkaloids in bacteria (NRPSBacAza)”

Nonribosomal peptide synthetases (NRPS) have recently been shown to reduce the virulence of the bacteria producing them towards the host. The details of the molecular mechanisms responsible for this biological activity and generation of chemical diversity are still unclear. Due to the often interesting pharmacological properties of corresponding aza cycles, these questions will be answered within the framework of NRPSBacAza. Based on the results obtained and in particular the structures and biochemical mechanisms of the enzymes involved, new alkaloids will then also be generated using synthetic biology methods. These may have new biological activities, e.g. as anti-virulence agents against Pseudomonas aeruginosa, an important human pathogenic bacterium.

Period of Funding: 12/01/2020 - 11/30/2023

Participant from MPIterMic: Helge Bode (Speaker)

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BMBF Research Initiative Innovationsraum: Bioball - SynBioTech - Synergistische Entwicklung biotechnologischer und chemischer Verfahren zur Wertschöpfung von dezentralen C1-Stoffströmen

SynBioTech is part of the BioBall innovation area - BioBall derives from "Bioökonomie im Ballungsraum" (bioeconomy in the conurbation) as the BioBall innovation space was formed in the Frankfurt Rhine-Main metropolitan region. In the joint project SynBioTech, biogenic CO₂ is hydrogenated to methanol which is then converted into biomass for the feed industry or acid derivatives for the chemical industry, with the help of Methylorubrum extorquens strains. MPIterMic identifies alternative metabolic pathways for the production of (branched) acid derivatives, produces corresponding production strains of Methylobacterium and tests them under realistic production conditions.
Period of funding: 04/01/2020 - 03/31/2023

Speaker: Bastian Etzold, TU Darmstadt
Participant from MPIterMic: Tobias Erb

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**BMBF "Mikrobielle Biofabriken: PolyMore - Ein Paenibacillus-Polymyxa-Chassis für die chemische Produktion und neue Sporenprozesse"**

The funding program “Microbial Biofabrics for the Industrial Bioeconomy"of the Federal Ministry of Education and Research aims to identify previously not industrially used microorganisms and to optimize them in order to create new products or processes. The thematic priorities are (1) identification and characterization of new microorganisms for industrial production (2) further development of microorganisms into new platform organisms for use in industrial production 3) development of innovative process concepts and technologies for the cultivation of new platform organisms.
Period of funding: 02/01/2020 - 01/31/2023

Speaker: Johannes Kabisch, TU Darmstadt
Participant from MPI terMic: Tobias J. Erb

BMBF "Mikrobielle Biofabriken: RhabdoFerm – Photorhabdus und Xenorhabdus Bakterien als Produktionsstämme für biologisch aktive Naturstoffe mit Anwendung in Medizin, Landwirtschaft und Biotechnologie”

Many bacteria produce biologically active natural products or secondary metabolites, some of which are also used clinically, e.g. as antibiotics or against cancer. In the past, these natural products were mainly obtained from known natural product producers such as Streptomyces or Myxobacteria. However, recent work shows that many other bacterial genera are also capable of producing natural products, but their function and structure are mostly still unknown. The goal of RhabdoFerm is to uncover this treasure.
Period of funding: 02/01/2020 - 01/31/2023
Participant from MPIterMic: Helge Bode (Speaker)

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**BMBF „Mikrobielle Biofabriken: METAFOR – Entwicklung eines Ogataea polymorpha Plattformstamms für die Umsetzung von C1-Verbindungen in Wertprodukten”**

METAFOR develops a hybrid approach for the electrochemical CO₂ reduction to C1 compounds and the subsequent microbial conversion to important basic chemicals. For this purpose, the methylotrophic yeast Ogataea polymorpha is established as a platform organism for the conversion of the C1 compounds methanol and formate to valuable products. METAFOR combines the microbial process with an upstream chemical CO₂ reduction to formate. The chemical process is optimized to provide formate in a biocompatible aqueous solution that can be fed directly into the subsequent fermentation.
Period of Funding: 02/01/2020 - 01/31/2023
Participants from MPIterMic: Tobias J. Erb

BMBF German-French cooperation on antimicrobial resistance research, Project Grant “Transmission of antimicrobial resistance by gene transfer within bacterial biofilms”

The central goal of TARGET-Biofilms is to explore the fundamental and practical aspect of DNA conjugation within bacterial biofilms. The main objectives are (1) to provide a comprehensive understanding of the mechanisms, extent, and impact of bacterial conjugation within biofilms, and (2) to test the possibility to combine conjugation and CRISPR systems to perform in situ biofilm manipulation.
Period of funding: 09/01/2019 - 08/31/2022
Participant from MPIterMic: Knut Drescher (Speaker)

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BMBF (FNR/BMEL) "Entwicklung eines Verfahrens zur fermentativen Herstellung von redoxaktiven Substanzen aus Abfallströmen der Papierindustrie für den Einsatz in organischen Redox-Flow-Batterien - RasFerm"

The Project RasFerm contributes to the utilization of the large energy storage potential of redox flow batteries. Since redox flow batteries require large quantities of organic electrolyte, biogenic material flows - in the present project: waste flows from the paper industry containing xylose – are aimed to be used as a substrate for fermentation processes by microorganisms. In the subproject, various microorganisms are being identified for the biosynthesis of anthraquinones (AQs) and genetically optimized for xylose utilization.
Period of funding: 05/01/2019 - 04/30/2021
Speaker: Peter Czermak, TH Mittelhessen
Participation from MPIterMic: Helge Bode

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Priority Programme (SPP 1879) "Nucleotide Second Messenger Signaling in Bacteria"

This DFG-funded priority programme centers on establishing the first systematic and comprehensive strategy ever to understand all fundamental aspects of second messenger signaling in bacteria at the molecular level. Biosynthesis, turnover and functions of “classical” second messengers as well as “newcomers” will be studied from molecular, cellular, physiological, systems-level and ecological perspectives. The research groups focus on (1) sensory inputs into second messenger signaling; (2) specific functions and “local” signaling of second messenger-producing and degrading enzymes (3) second messenger effector mechanisms and molecular targets; and, (4) novel physiological and ecological contexts as well as evolutionary aspects reflected in the molecular biology of second messenger signaling.
Period of funding: 09/01/2016 - 08/31/2022
Coordinator: Regine Hengge, Humboldt Universität zu Berlin
Participants from MPIterMic: Lotte Søgaard Andersen, Victor Sourjik

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Priority Programm (SPP 1927) "Iron-Sulfur for Life"

Iron-sulfur (FeS) centers are essential protein cofactors in all forms of life. In particular, FeS centers function as enzyme cofactors in catalysis and electron transfer, and as sensors of environmental conditions. Moreover, they are indispensable for the biosynthesis of other protein cofactors including complex metal-clusters. In the SPP it is planned to study novel enzyme mechanisms, innovative model complexes, and new biogenesis pathways in the context of metalloenzymes in living organisms, addressing (1) Assembly of FeS proteins as a starting point for versatile functionality; (2) Biosynthesis and crosstalk of complex metal cofactors by FeS proteins; (3) Catalysis and functions of complex FeS proteins for bio-applications, and (4) Disease-relevant roles of FeS proteins in cellular metal homeostasis. The program further aims at the development of future cellular systems for bioenergy production, fertilization and bio-applications.
Period of funding: 09/01/2016 - 05/31/2023
Speaker: Silke Leimkühler, University of Potsdam
Participant from MPIterMic: Seigo Shima

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Priority Porgramme (SPP 2002) „Small Proteins in Prokaryotes, an Unexplored World”

Modern genomics and transcriptomics technology have over the past decade discovered a wealth of hidden small genes containing short open reading frames (sORF) in many prokaryotic genomes. These sORF encode small proteins of ≤ 70 amino acids in length, and are typically missed by automated gene predictions. Recent studies have shown that these small proteins impact disparate cellular processes, running the gamut of energy generation, transport, virulence, symbiosis, sporulation, and photosynthesis. This Priority Programme aims to explore this emerging major class of prokaryotic gene products by unravelling the full repertoire of sORF, studying the functions and physiological roles as well as underlying molecular mechanisms of prokaryotic small proteins.

Period of funding: 01/01/2021 - 12/31/2023
Participant from MPIterMic: Jing Yuan more

MPG-FhG Project: “eBioCO2n” – Herstellung von Spezialchemikalien durch stromgetriebene CO2-Konversion

Crude oil remains the chemical industry’s most important raw material, from which plastics, paints and components of medicines are produced. The aim of the eBIOCO₂ Project is to replace at least a part of the fossil fuel with CO₂ for a circular economy that will reduce chemical production’s carbon footprint. For this they combine approaches from biochemistry, enzyme biology and synthetic biology, developing bio-electrodes to use electricity to drive enzymes that will work together to transform CO₂ into usable chemical substances. To bring the project to a close, they will build a demonstrator to produce the amino acids alanine, glycine and aspartate from CO₂ in order to prove the viability of electrically powered biocatalytic CO₂ conversion.
Period of funding: 04/01/2019 - 03/31/2023
Participant from MPIterMic: Tobias Erb

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Volkswagen LIFE Grant "BRILIANCE" - BRinging Inorganic carbon to LIfe with Artificial CO2-fixation in a minimal CEll

Life is the constant conversion of non-living to the living. In this project the research team aims at re-inventing this fundamental process in life. The group will re-program designer cells (so called 'minimal cells') to use a completely novel, artificial way for the capture and conversion of the inanimate gas CO₂. The project will explore new ways of harnessing CO₂ as sustainable source for the generation of organic compounds present in our everyday life as food, fuels and pharmaceuticals.
Period of funding: 01/01/2019 - 12/31/2023
Participant from MPIterMic: Tobias Erb (Speaker)

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FET OPEN Project "Gain4Crops"

The EC-funded project GAIN4CROPS is developing novel disruptive technologies to overcome one of the main constraints on photosynthetic efficiency: photorespiration, a process that reduces CO₂ assimilation efficiency, and thus biomass yield and agricultural productivity. The project aims to improve the efficiency of the C3 metabolism in plants, in a stepwise approach: (1) Enhancing C3 photosynthetic efficiency using a naturally occurring variation of photorespiratory metabolism, in particular C3-C4 intermediate photosynthesis; (2) Further optimization of the process by engineering new-to-nature metabolic pathways by innovative plant breeding techniques.
Period of funding: 05/01/2020 - 04/30/2025
Speaker: Andreas Weber, Heinrich-Heine-Universität Düsseldorf
Participant from MPIterMic: Tobias Erb

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Horizon 2020 Project "BioRoboost"

Synthetic biology (SynBio) is a multidisciplinary, emergent field, evolving so fast that it still lacks a consensus definition, and its outstanding success in the last years should not hide the difficulties in defining and adopting biological standards. However, the benefits of standardisation of biological systems are overwhelming. The main goal is to set universal standards in synthetic biology in a holistic, systematic way: from the biological part to the experimental procedure.
Period of funding: 01/01/2018 - 09/30/2021
Speaker: Manuel Porcar, Valencia
Participant from MPIterMic: Tobias Erb

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**Heineman Project Grant “Interaction mechanisms of Vibrio cholerae biofilms and macrophages“**

The Minna-James-Heineman-Stiftung allocates research grants to young, highly qualified and talented scientists in the areas of biology, medicine and biomedical research. In this project, the labs of Knut Drescher and Roi Avraham (Weizmann Institute of Science, Israel) jointly investigate how Vibrio cholerae interacts with human leukocytes, and which mechanisms determine the interaction.
Period of funding: 06/01/2019 - 12/31/2022
Participant from MPIterMic: Knut Drescher

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LOEWE Research Cluster "Dynamics of Membranes. Molecular basics and theoretical description: DynaMem"

DynaMem combines research approaches of the basic behavior of biological membranes, the dynamics of membranes, membrane systems, and organelles in cellular, supra-cellular context and also at level of organisms to understand basic principles of dynamics and their significance in a cellular context in a long term run. Detailed analyses of new aspects of membrane dynamics will lead to knowledge which leads to new strategies for the development of therapeutically approaches. According to this scientific concept DynaMem is focuses on three key aspects: (A) Manipulation of membrane functions, (B) Cellular manipulation of membrane dynamics, (C) Dynamics of membrane systems and organelles.
Period of funding: 01/01/2018 - 12/31/2021
Speaker: Enrico Schleiff, Goethe University Frankfurt
Participant from MPIterMic: Helge Bode

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LOEWE-Center "Translational Biodiversity Genomics (TBG)"

Biodiversity is the result of 3.5 billion years of evolution and one of the most complex phenomena on earth. The LOEWE Centre for Translational Biodiversity Genomics focusses on the genetic basis of biological diversity to make it accessible for basic and applied research. We sequence and study genomic variation across the tree of life to comprehend the origin and functional adaptations of diversity from genes to ecosystems (Comparative Genomics). The data addresses societal knowledge demands in applied fields, such as the genomic basis of biologically active substances (Natural Products Genomics), and the sustainable use and management of biological resources (Genomic Biomonitoring; Functional Environmental Genomics).

Period of funding: 01/01/2018 - 12/31/2021

Speaker: Axel Janke, Senckenberg Research Institute, Frankfurt
Participant from MPIterMic: Helge Bode

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LOEWE Center for Synthetic Microbiology (SYNMIKRO)

The LOEWE program is an excellence initiative of the state of Hesse to promote excellent research at Hessian universities and other research institutions. SYNMIKRO, the LOEWE Center for Synthetic Microbiology, was founded in 2010 as a cooperation center between Philipps University Marburg and the Max Planck Institute for Terrestrial Microbiology. To this end, more than 50 million euros in funding was received from 2010 to 2018. Since then, the center has grown steadily and has become a center of attraction for young and more experienced scientists from all over the world. In SYNMIKRO, Biologists, biochemists, physicists, mathematicians, bioinformaticians and bioethicists work together in - the research collaboration that is unique for Germany offers completely new opportunities to expand our understanding of the molecular basis and potential uses of microorganisms and to open up new applications. The Marburg researchers aim to design synthetic cells with tailored properties from standardized building blocks. These cells could be used, for example, to produce new drugs, chemicals, biofuels and food additives efficiently, cost-effectively and in an environmentally compatible manner.

International Max Planck Research School for Environmental, Cellular and Molecular Microbiology

Research in the graduate school aims at understanding how microorganisms compete, adapt, and differentiate in response to changes in the environment. To reach this aim, microbial ecology is tightly integrated with molecular and cellular microbiology and microbial physiology and biochemistry. The faculty members of the graduate school are from the Max Planck Institute or the Philipps-Universität.