Doctoral Researchers

 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Bio Pilot Plant
PhD Project:

Exploiting the metagenome of microbial communities on a microfluidic platform

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Abstract: In the course of this dissertation a surfactant-based microfluidic platform is employed to discover new bioactive natural products. Due to the failure of the recently predominant...
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... target-oriented screening approaches we intend to use a whole-cell-based screening method. To test for the synthesis of natural products within the droplets, we utilize reporter cells that ideally indicate antimicrobial activity, using constitutive or stress-inducible promoters. Three different strategies are envisaged. In one approach, we plan to exploit complex mixtures of antibiotic producers derived from different habitats like soil and sea water with laying the focus on yet uncultivated or slow growing actinomycetes. Second, the system can be applied in the research of silent gene clusters revealed by genome mining of characterized bacterial strains. This will be realized by cultivating a single strain of Actinobacteria under highly variable culture conditions implemented by media gradients during droplet generation. A third envisioned approach is to screen a combinatorial library of oligopeptides with putative antimicrobial activity (provided by Prof. Dr. Wiesmüller EMC microcollections GmbH, Tübingen). After detection of droplets with inhibited reporter strains the respective amino acid sequence can be elucidated by mass spectrometry analysis.
 
 
Mamerow, Svenja Katharina

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Institute/Dep.
PhD Project:

Development and Evaluation of Influenza A Virus Live Attenuated Vaccines in Swine

 
 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
ZIK Septomics
Research Group Fungal Septomics
PhD Project:

Characterizing innate immune cell activation by fungal pathogens using Live Cell Imaging

 
 
Märten, Arno

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Geosciences
Applied Geology
PhD Project:

How do microbes influence the bioavailability of metals? A bioremediation study

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Abstract: This project aims at investigating the microbial impact on bioremediation of acidic, heavy metal contaminated and nutrient-deficient soils. Large areas within Europe are affected by...
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... former and actual mining activies often leading to metal contamination of surface water and groundwater. Since conventional clean-up technologies such as “dig and drop” are by far to expensive, cost-effective methods for remediation are needed. A promising and emerging technology for this is bioremediation, that is the use of plants and microbes for either extracting metals from the soil (phytoextraction) or stabilising them in the soil (phytostabilisation) to decrease mobility, bioavailability and therefore toxicity of the metals. Typically, fast-growing plants are used for bioremediation (then called phytroremediation) since they form high biomass and are therefore either able to extract large amount of metals or to protect soil from erosion and leaching of metals to groundwater. However, speciation, mobility and toxicity of metals are strongly influenced by microbial actions such as exudation of chelating agents, acidification, biomineralisation, biosorption, or uptake of metals. Thus, the focus of this project is on interaction of microbes with the environment by influencing speciation and by this bioavailability of metals. The research will be situated in the former Uranium mining area of Eastern Thuringia. Mining was terminated in 1990 and since then, billions of Euros were spent by the German Government for remediation of the area. In this area the Friedrich-Schiller university has established a test field site where phytoremediation is investigated at the field scale.” Microbes will be isolated from soil, from secondary minerals formed within the soils and directly from plant roots. They will be identified and characterized for their plant growth promoting properties and for their metal tolerance. Since it is well known that microbial communities perform different from the single strains alone, microbial communities will be identified that are promising to phytoremediation. To investigate how these microbial communities interact with their environment, experiments with shallow groundwater lysimeters will be set up. Lysimeters filled with homogenized contaminated substrate, planted with e.g. Festucra rubra (red fescue), Trifolium pretense (red clover) or Helianthus annuus (sunflower) and inoculated with promising microbial communities will be studied for plant performance. Redox potential, water tension, evaporation, soil water chemistry and the formation of secondary minerals will be monitored. To obtain a closer insight into the relevant processes, rare earth elements will be used as tracers to visualize processes such as dissolution, precipitation, sorption and uptake of metals in the system soil-water-biota. This project links Geology and Geochemistry with Microbiology. It is embedded in two large research groups (Georg Büchel/Dirk Merten, Applied Geology and Erika Kothe, Microbial Communication) with both groups already collaborating in various third-party funded projects.
 
 
Martin, Marivic

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Junior Research Group Terrestrial Biofilms
PhD Project:

Phenotypic heterogeneity and population dynamics in biofilms

 
 
Marx, Carina

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Institute/Dep.
PhD Project:

Identifizierung molekularer Targets potentieller Antibiotika

 
 
Mattern, Derek

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Molecular and Applied Microbiology
PhD Project:

Metabolic Engineering and Bioprospecting of Natural Products in Filamentous Fungi

 
 
Institute/Dep.
Max Planck Institute for Chemical Ecology
Dept. of Bioorganic Chemistry
PhD Project:

Using fluorescent Enterococcus mundtii to study the variation in its gene expression, spatially and temporally, in the gut of Spodoptera littoralis larva

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Abstract: Insects harbor a plethora of microorganisms within their gut, as their normal flora. They are not only non-pathogenic to them, but also have roles to play in the insect growth,...
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... development and immunity. There lies a complex interaction within the microflora and also, between the host and the microorganisms. This leads to variations in the microbial population with the development of the insect. Some get eliminated, some are added, whereas, some dominate throughout the insect life cycle. The gut microbiota of Spodoptera littoralis, a Lepidopteran insect of family Noctuidae, has been elucidated. The core community consists of Enterococci, Lactobacilli and Clostridia. The selection of one bacterial species over the other is quite evident throughout the life-cycle. The community varies with the stages of development of the larva, and spatially within the gut. By the time the larva reaches the 5th instar stage, Enterococcus mundtii and Clostridia sp persists and dominates. The class IIa antimicrobial peptide- mundticin KS, produced by Enterococcus mundtii, acts against the invading bacteria, and exercises its predominance. This way, they help preserve the host gut microbiota, reduce infection in the host and enhance its health. A method of fluorophore-labelling of Enterococcus mundtii has been developed to show that it is the persistent and metabolically active species in the gut microbiota, which in turn, intrigues us to find out the importance of this symbiotic species. Thus, the aim of my project will be to isolate the fluorescent Enterococcus mundtii from various regions of the larval gut, across its developmental stages, and study the variation in their gene expression. The Next generation method of RNAseq will be used to sequence the transcriptome. Thus, on analyzing the transcriptome of Enterococcus mundtii over the stages of Spodoptera littoralis larval development, we might conclude its specific role as a symbiont and its importance as a dominating gut microbiota. Once successful, the approach can be extended to other relevant gut bacteria and their role as symbionts, like, Clostridia sp, which dominate the gut till the later stages of development, even in depleting iron conditions.
 
 
Meichsner, Doreen

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of General Botany and Plant Physiology
Dept. of Plant Physiology
PhD Project:

Symbiosis-specific exudate components from the beneficial root-colonizing fungus Piriformospora indica and Arabidopsis thaliana

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Abstract: In this project, we will study the beneficial interaction between the root-colonizing fungus Piriformospora indica and the model plant Arabidopsis thaliana. The endophytic fungus P....
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... indica colonizes of the roots of many plant species. Similar to arbuscular mycorrhizal fungi, P. indica promotes plant growth, biomass and seed production and confers resistance to biotic and abiotic stress (Shahollari et al., 2007, Vadassery et al., 2009, Camehl et al., 2011, Nongbri et al., 2012, and references therein). P. indica is a member of Sebacinales, grows inter - and intracellularly and forms pear shaped spores, which accumulate within the roots and on the root surface. After the establishment of a beneficial interaction, barely any defense or stress genes are activated and no reactive oxygen species are produced by the host against P. indica (Camehl et al., 2011). The endophyte releases a small compound into the medium/rhizosphere which induces root-specific [Ca2+]cyt elevation in Arabidopsis and N. tabacum. [Ca2+]cyt elevation is followed by a nuclear Ca2+ response (Vadassery et al., 2009), similar to signalling events in arbuscular mycorrhizal fungi.
Using established cultivation and co-cultivation conditions, we will try to identify proteins, peptides and other biomolecules which are released from the two partners into the medium. Comparative analyses of the secretomes and metabolomes (released by the microbial and plant partners alone and in symbiotic interaction between the two partners) should identify those compounds which are symbiosis-specific. Since the genomes of both organisms are sequenced and available, the origin of the proteins and peptides can be identified. Furthermore, genome mining should help to identify the origin and biosynthesis of the symbiosis-specific biomolecules.
 
 
Meinel, Christian

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Research Group:
Infection Biology
PhD Project:

Immunevasion of the Gram positive bacterium Streptococcus pneumoniae

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Abstract: S. pneumoniae is a Gram positive bacterium, which can asymptomatically exist in the upper respiratory tract of healthy individuals. However, S. pneumoniae can also cause severe and life...
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... threatening diseases, including pneumonia, meningitis, sepsis and also hemolytic uremic syndrome (HUS). Especially children, immunocompromised persons and older individuals are at risk for an invasive S. pneumoniae disease 1. Upon infection S. pneumoniae is challenged by the complement system, a part of the human innate immune response. In order to persist and to establish pathogenesis this bacterium has to evade the complement attack of the human host. To this end, S. pneumoniae has evolved several efficient strategies to evade the human innate immune response. One complement evasion strategy that is used by S. pneumonia and other pathogenic microbes is the recruitment and exploitation of human complement regulators to disturb complement activity 2. The pneumococcal surface protein C (PspC) and the translation elongation factor Tu (Tuf) are two surface expressed virulence proteins of S. pneumoniae, which support the immune evasion of this bacterium e.g. by recruiting human complement regulators to the pneumococcal surface 3,4. Until now, the various features by which these bacterial immune evasion proteins contribute to the pathogenesis of S. pneumoniae are only rudimentarily understood. Therefore, the aim of this project is to elucidate the exact mechanisms how PspC and Tuf contribute to the immune evasion of S. pneumoniae and how they support pathogenicity in life threatening diseases.
 
 
Merker, Holger

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JSMC Fellow

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Institute/Dep.
Max Planck Institute for Chemical Ecology
Dept. of Bioorganic Chemistry
PhD Project:

Chemical ecology and coevolution of bacterial consortia

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Abstract: Interactions between microbial species, such as competition and cooperation, influence the abundance and distribution of the respective species. Metabolic cooperation among multiple...
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... bacterial species for example plays a key role in shaping and maintaining microbial consortia. This study aims at identifying the ecological selection pressures that govern the coevolution of two coexisting bacterial species as well as unravelling the mechanisms responsible for stabilising these communities. To this end, different pairwise combinations of soil-borne bacterial species will be co-cultured and the structural basis of the resulting ecological interaction characterized by using methods of analytical chemistry. In long-term experiments, in which two interacting partners are exposed to different ecological environments, both species are not only expected to adapt to each other but also the quality of the ecological interaction is likely to change (e.g. from neutral to cooperative, or from cooperative to exploitative), depending on the ecological environment the interaction has experienced. Detailed genetic, chemical and microbiological analyses of the ancestral and the derived consortia will be performed to identify qualitative and quantitative changes of the interspecific interactions as well as the causal evolutionary forces.
 
 
Meyer, Nils

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ChemBioSys Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute for Inorganic and Analytical Chemistry
PhD Project:

Algicidal Bacteria in Plankton Communities: Resistance, Lysis and Heterotrophy

 
 
Mhatre, Eisha

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Junior Research Group Terrestrial Biofilms
PhD Project:

Phenotypic heterogeneity in bacterial biofilms

 
 
Möckel, Lars

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FungiNet Student

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute and Friedrich Schiller University Jena
Jena Microbial Resource Collection (JMRC)
Friedrich Schiller University Jena
Institute of Systematic Zoology and Evolutionary Biology with Phyletic Museum
Dep. Entomology
PhD Project:

The interaction between the entomo- and human pathogenic zygomycete Conidiobolus coronatus and insect hosts on the basis of genomes and transcriptomics

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Abstract: The zygomycete Conidiobolus coronatus with its generalist lifestyle is mainly located in soil, but also occurs as an insect pathogen or a human pathogen. The property by removing its...
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... cell wall while entering the host body Conidiobolus coronatus represents an interesting research organism. The core of the project is listed in the following points: 1. Establishing of an infection model with the house fly Musca domestica (Cooperation partner in Denmark) 2. Analysis of the fungal morphology during the infection process by imaging techniques (LM, SEM, DESY- cooperation with Prof. Dr. Beutel and DESY, Hamburg) 3. Transcriptome analysis fungi vs. fungi- insect- interaction at four different time points of the interaction (cooperation with Denmark and HKI-bioinformatician: Jörg Linde, Dr. Ekatarina Shelest) with the aim of establishing a gene- regulatory- network. We compare the transcriptome-data of the not infected control- fly with three different stages of infected flies (every 24/36 hours) The project aims at the microscopic visualization of the infection process of insect-killing, entomophthoralean fungi (Zygomycetes) with insect hosts. Conidiobolus coronatus will subjected to extensive infection assays in both, insect hosts and human epithel cell lines followed by RNAseq transcriptomics during the time course of infection including colonization, manifestation and occurence of the first infectious symptoms. The project will provide insights into the differences and similarities of the fungal infection at the direct level of gene expression accompanied with micromorphological observations. Also it will help to identify genes encoding putative factors, which play a role in recognition and could be used as potential targets for antifungal therapy or enhanced immune therapy.
 
 
Mohr, Jan Frieder

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ChemBioSys Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute for Inorganic and Analytical Chemistry
PhD Project:

Metallophores as mediators for metal cycling: Development of libraries for metal ion buffering and as redox carriers as well as profiling of metallophores

 
 
Mori, Jiro

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GRK1257 Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Systematic Zoology and Evolutionary Biology with Phyletic Museum
Dep. Entomology
PhD Project:

Unique algae bacteria mineral assemblages in highly metal-contaminated stream

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Abstract: Highly metal-contaminated, slightly acidic (~pH 6.0) underground water emerges in a former uranium mining district (Ronneburg, Germany). Recently, massive upweJling formed sm all...
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... streams and iron-rich terraces along grassland down to the drainage creek. These streams are characterized by conspicuous greenish and brownish algae (streamers) during the summer months that show iran incrustations. Since these streamers have not been characterized, the aim of the study is to elucidate (a) if the algal streamers are colonized by microorganisms that might be involved in iran oxidation, (b) the spatial arrangement of microbial constituents, and (c) the type of iran minerals and their location in the streamers, Observation of streamers with ClSM and SEM revealed that streamer-forming filamentous microalgae are encrusted with iron mineral precipitates that are coJonized by bacteria, Mineral precipitates are distributed in a regular but discontinuous pattern on the algal filaments, Moreover, EP5-like polysaccharides were observed on the minerals, Chemical analyzes (FTIR, ICP-MS, and Raman spectroscopy) of the mineral precipitates revealed that ferrihydrite was the major constituent of the mineral fraction, Microbial community structures of the streamers were analyzed by amplicon pyrosequencing targeting 165 rRNA genes with bacterial primers. Abundances were quantified by qPCR assays employing primers specific for different groups of iron oxidizing bacteria. Results indicated that Gallionella-related iron-oxidizing bacteria were the most abundant Bacteria. They were not only attached to the surface of algal filaments but were also metabolically active in streamer communities. Gallionella seem to preferably colonize algal filaments and cause formation of ferrihydrite. The site-specific colonization of Gallionella and accumulation of ferrihydrite likely were induced by the algal physiological activity and its morphoJogy.
 
 
Mrozinska, Anna

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IMPRS Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute of General Botany and Plant Physiology
Dept. of Plant Physiology
PhD Project:

Molecular analysis of the interaction between Arabidopsis thaliana and Piriformosphora indica

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Abstract: The goal of my PhD project is the analysis of a newly discovered signaling cascade for the beneficial interaction between root-colonizing endophytes and plants. For this, a...
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... well-established model system Piriformospora indica/Arabdiopsis thaliana is used. The endophyte colonizes the roots of many plant species and promotes their growth and performance. For establishing the interaction, the second messanger phosphatidic acid, phospholipases, the protein kinase PDK1 and the AGC kinases OXI1 and AGC2-2 are nesessary. I will focus on the role of phospholipases and the AGC kinases in this symbiosis. I am also interested in the role of chitin and other small signaling compounds that are secreted by the fungus and recognized by the plant. For all this I am using a physiological and molecular approach.
 
 
Müller, Tina

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JSMC Fellow

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Institute/Dep.
University Hospital Jena
Clinic of Anaesthesiology and Intensive Care Medicine
Research Unit Experimental Anesthesiology
PhD Project:

Host defense mechanisms against pathogens mediated by sphingolipids

 
 
Munser, Anne-Sophie

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Institute/Dep.
Fraunhofer Institute for Applied Optics and Precision Engineering, Jena