Our International Max Planck Research School “Chemical Communication in Ecological Systems” offers 9 very cool PhD projects in Jena, Germany, is now online. Please apply from February 27 – April 16.

Who are we looking for? We are looking for internationally trained, enthusiastic applicants with a strong motivation to pursue a PhD, adequate competence in the English language and an excellent academic performance and MSc degree (including MSc thesis) in one of the following fields: bioinformatics, analytical chemistry, entomology, neurobiology, molecular biology, biochemistry, plant physiology, genetics, ecology or evolution.

What do we offer?

  • highly integrative projects which require willingness to embrace multiple disciplines and close collaborations with other researchers with different backgrounds
  • State-of-the-art equipment
  • An excellent research environment
  • A structured training program

Successful candidates will obtain a 3-year PhD position corresponding to TVöD (Collective Wage Agreement for the Civil Service). There are no tuition fees; consumables and equipment required for the project will be covered by the hosting lab. The working language is English.

Required documents: Please find a list of required documents below. All documents sent to our office must be in English or German. Certified copies of documents are not required at the time of submission. All applicants who have qualified for the group recruitment may be asked for certification of relevant documents before admission to the program is granted

The following documents are required for the application:

  • Complete and validated online application data – Please fill in forms 1-4 carefully and pay particular attention to the motivation statements and questions about your areas of interest for doctoral research.
  • Contact details of two referees – Please identify two academic or professional supervisors who are able to evaluate your personality, academic experience and intellectual merit. Upon successful pre-selection, your referees will be contacted for a reference.
  • Curriculum Vitae.
  • Last relevant academic certificate (usually M.Sc.) and transcript of study (study record).
  • Proof of proficiency in English for non-native speakers – TOEFL or equivalent scores; a signed letter from your university or one of your academic teachers stating that English was the medium of instruction and your English proficiency is excellent.  Click here for frequently asked questions on this topic.
  • Registration Number – You will receive a registration number by e-mail, if you have successfully submitted your application data on our website.

Any incomplete application or applications reaching the IMPRS coordination office after the deadline cannot be taken into consideration.

IMPRS Application FAQ:

1. Do I have to submit the results of a standardized English test (e.g. TOEFL, IELTS), if I have been taught primarily in English? Students whose medium of instruction was English do not need to submit the results of an English language proficiency test. However, they are urged to submit a signed letter from one of their academic teachers stating that English was the medium of instruction and that the student’s English proficiency is excellent (reading, writing, listening).

2. When is it not required to submit proof of English proficiency? In addition to the case mentioned above, no proof of English proficiency is required for applicants:

  • who are native English speakers
  • who are from an Anglophone country
  • whose medium of instruction was English

In some cases it may be possible to take an individual test with the Department of English at your university. English reading, listening, speaking and writing skills have to be evaluated. The results should be documented in an official letter of the Department and sent to the IMPRS coordination office in a sealed envelope. Please contact the IMPRS coordination office if you want to take this individual test.

All other students are required to submit the results of a standardized test. You should submit a copy of your test results together with your application. The Max Planck Institute for Chemical Ecology has no institutional code for receiving the results directly from the test center.

3. I have passed an English test but I will get the results after the application deadline. Will my application be accepted without the results? The application will be accepted and students will be considered for admission.  However, before a student is invited to the group recruitment, proof of English proficiency is required. Be aware that your application benefits from the submission of an excellent score in an English language proficiency test.

Timeline – 2023 application call:

  1. Application period: February 27 – April 16
  2. Phone Interviews: May 15 – 30
  3. Communication of selection results and invitation for Jena group recruitment: June 5
  4. Deadline for references: June 2
  5. Group recruitment (via videolink): June 29 – 30
  6. Communication of final admission decision: First week of July
  7. Start of the program: Admitted students can start their PhD anytime between September 2023 and January 1st, 2024, in agreement with their supervisors.

Advertised PhD Projects in Current Call:

Project 1 Fungal life in soil: attachment and microbial communication:


Prof. Dr. Erika Kothe (main supervisor) Institute of Microbiology, Friedrich Schiller University

Dr. Katrin Krause (co supervisor) Institute of Microbiology, Friedrich Schiller University

Prof. Dr. Jonathan Gershenzon (co supervisor) Department of Biochemistry, Max Planck Institute for Chemical Ecology


Fungi are drivers for soil bacterial community structure. At the same time, fungal hyphae are “highways” for bacterial movement in soil. We could show that a white rot fungus can survive and grow in soil and participate in rock bioweathering. With this model fungus, ecological interactions are to be explored taking full advantage of -omics strategies and collaborations.

Project description:

Using the model basidiomycete Schizophyllum commune, for which the genome sequence is available, it can grow in a haploid as well as a mated state on artificial media, and genetic amenability has been proven. With this project, hyphal decoration (for attraction of bacteria), surface interactions via cell wall attached proteins (hydrophobins), and exchange of signals with co-occurring bacteria (based on morphological responses of the fungus to isolates obtained from the same environment) are investigated.

Candidate profile:

MSc in microbiology and knowledge in molecular biology, knowledge with basidiomycete genetics is advantagous.

Project 2: Adapting SIRIUS and beyond for Electron Ionization fragmentation:


Prof. Dr. Sebastian Böcker (main supervisor) Bioinformatics, Faculty of Mathematics and Computer Science, FSU Jena

Prof. Dr. Georg Pohnert (co-supervisor) Instrumental Analytics, Institute for Inorganic and Analytical Chemistry, Faculty of Chemistry and Earth Sciences, FSU Jena


Mass spectrometry (MS) is the analytical platforms of choice for high-throughput screening of small molecules. MS is typically used in combination with a chromatographic separation technology; gas chromatography (GC-MS) is arguably still the best separation tool for compounds amenable to the technique.

Electron (impact) Ionization (EI) simultaneously ionizes and fragments the molecules; resulting spectra are fragment-rich but often show a low-intensity or missing molecular ion peak, meaning that the mass of the compound is often unknown. Lately, technically mature GC-MS instruments with high mass accuracy are available, making de novo interpretation of EI fragmentation data possible.

The Böcker group is one of the leading research groups developing computational methods for untargeted metabolomics.

Numerous scientific approaches for this task were developed in our lab during the last decade, including CSI:FingerID for searching in molecular structure databases (PNAS, 2015), SIRIUS for molecular formula annotation and processing of full datasets (Nat Methods, 2019), CANOPUS for comprehensive compound class assignment (Nat Biotechnol, 2021), and COSMIC for assigning confidence in annotations (Nat Biotechnol, 2022). We have won numerous CASMI challenges on the topic, and our web services for small molecule annotation have processed about half a billion queries.

Project description:

With the advent of high mass accuracy GC-MS instrumentation, it becomes possible to adapt our computational tools for GC-MS data. GC-MS and EI fragmentation is different in many details from LC-MS and tandem MS, and several subproblems must be addressed; for example:

  • EI mass spectra are often missing the molecular ion peak, and the mass and/or molecular formula of the compound has to be reconstructed from the fragments using Machine Learning and combinatorics.
  • EI mass spectra contain isotope patterns, which can be used to improve fragmentation tree quality. Unfortunately, radical losses H and H3 often interfere with the interpretation of the isotope patterns.
  • Available reference data for high mass accuracy GC-MS is insufficient to train Machine Learning methods. To bypass this, we want to “lift” low mass accuracy spectra and add them to the training data.

We will also promptly apply developed methods to biological data. The project will be conducted in close collaboration with experimental research groups around the globe, in particular that of Prof. Georg Pohnert.

Candidate profile:

  • M.Sc. in bioinformatics, cheminformatics, computer science, mathematics
  • Expertise and interest in algorithmics and bioinformatics methods development
  • Experience in biochemistry desirable
  • Expertise in Machine Learning highly desirable
  • Experience in software development (Git, artifactory) is a must
  • Experience in Java, Python and ML frameworks is desirable
  • Ability to interact with coworkers, collaboration partners and software users

Project 3Processing of olfactory and auditory cues in the insect brain;


Prof. Dr. Manuela Nowotny (main supervisor) Institute of Zoological Research and Evolution, Friedrich Schiller University

Dr. Silke Sachse (co supervisor) Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology


As peripheral sensory organs, insect antenna detect multimodal environmental information. The receptor neurons that path information to the brain code for instance auditory, olfactory and hygro-thermosensitive information. Especially for mate recognition and selection during courtship, female Drosophila uses near field sound information and olfactory cues of the male. How processing of these different modalities interferes in the brain is unknown and subject of the planned project.

Project description:

The goal of our PhD project is to examine bimodal processing of acoustic and olfactory information in the insect brain (bushcrickets/katydids and Drosophila). This study combines a broad spectrum of methodological approaches, starting from mechanical measurements of the antennal motion in Drosophila by optical coherence measurements [1] up to neurophysiological and functional imaging techniques [2]. We aim to identify interaction and modulatory processes of these sensory modalities in the insect brain, which also offers the use of neurogenetic tools.

Candidate profile:

We are looking for a highly motivated and creative candidate with training in ear mechanics, neurophysiology or neurogenetics. Experiences with insect research is useful. A master’s degree in Neuroscience, Biology or related discipline is required for this PhD position.

Project 4 A miRNA taming floral homeotic genes:


Prof. Dr. Günter Theißen (main supervisor) Matthias Schleiden Institute – Genetics, Friedrich Schiller University

Dr. Lydia Gramzow (co supervisor) Matthias Schleiden Institute – Genetics, Friedrich Schiller University

Dr. Axel Mithoefer (co supervisor) Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology

Prof. Dr. Jonathan Gershenzon (co supervisor) Department of Biochemistry, Max Planck Institute for Chemical Ecology


The floral structure significantly influences the interaction of angiosperms with their environment, not least because it defines the set of species by which plants are pollinated. The genetic basis of how floral organ identities develop has, to a great extent, been elucidated: Mainly three clases of floral homeotic genes, termed A-, B- and C-class genes, determine in a combinatorial fashion which organs are formed where in a flower [1, 2]. According to the so called ABC-model of flower development, expression of only A-class genes leads to the development of sepals, expression of A- and B-class genes together leads to the formation of petals, B- and C-class genes expressed together determine stamens and the expression of C-class genes alone gives rise to carpels. All of the ABC genes encode transcription factors.

However, also genes encoding for microRNAs (miRNAs) have been shown to be of major importance for development [for a review, see ref. 3]. ABC genes and miRNAs may even act together. One miRNA, miR5179, has been found to regulate members of one clade of B-class genes, the DEF-like genes in orchids [4]. This miRNA is quite remarkable.

While genes encoding miRNAs (miR genes) have usually high birth and death rates and hence exist only for a short while on evolutionary time scales, very few acquired important developmental functions and hence were conserved in a broad range of taxa for hundreds of millions of years. However, miR5179 does not fit either pattern.

Analyses of genome, transcriptome and miRNome data in our lab revealed that miR5179 likely originated in the stem group of flowering plants about 200 million years ago and was conserved in several plant lineages. It hence turns up in a number of extant species, like Actinidia eriantha (kiwifruit), Citrus sinensis (orange), Musa accuminata (banana) and Oryza sativa (rice), indicating an important function of miR5179.

In contrast, however, miR5179 has been lost independently in many other lineages of flowering plants, like in the orders Vitales, Malvales and Pandanales showing that miR5179 was dispensable in these cases. So miR5179 provides a fascinating conundrum: it is ancient, but not universally conserved. Why is it functionally important in some plants, but dispensable in others?

By specifying stamen identity DEF-like genes have an indispensable function in all flowering plants. Since miR5179 seems to control DEF-like genes, this raises the intriguing question: why is the evolutionary dynamic of the miR5179 gene so different from that of the ultraconserved DEF-like target gene? In other words: what is the ultimate function of miR5179 in those species in which it still exists? Answering this question may require the study of a miR5179 knockout mutants. Such mutants have not been reported yet, however.

Project description:

We hypothesize that miR5179 functions in the restriction of the expression of members of one clade of B-class genes. This restriction may be necessary to prevent the development of aberrant floral structures, which would compromise the interaction of the respective flowering plants with their environment, especially pollinators. The species in which miR5179 was lost may have evolved other mechanisms to control the expression of B-class genes.

To determine the function of miR5179 we will generate mutants of this miRNA. As many of the species in which miR5179 is conserved are not genetically tractable, we will focus our quest on the grass species Brachypodium distachyon and Oryza sativa (rice). We will use the CRISPR-Cas9 system according to the latest recommendations for the generation of miRNA mutants [5].

 Towards this goal, we will cooperate with the group of Jochen Kumlehn at the IPK in Gatersleben, in which gene editing using CRISPR-Cas9 as well as transformation of grasses is well established [6]. The phenotypes of the produced mutants will be carefully characterized with special focus on floral structure and compared to the phenotypes of the wild-type plants.

Moreover, we will closely monitor the expression of miR5179 and its target genes in floral buds and flowers of wild-type and mutant plants using qRT-PCR and in-situ hybridization, methods that have been well established in our lab [7]. The results of these experiments will help to elucidate as to whether miR5179 functions to tame B-class floral homeotic genes or may have another unexpected function.

Candidate profile:

We are looking for a candidate with proven skills in molecular biology and a strong interest in plant ecology, development, and evolution. The project involves cooperation with the IPK in Gatersleben, hence the ideal candidate has strong communication skills and the ability to cooperate with researchers with different backgrounds (bioinformatics, developmental biology, chemical ecology, evolution). Good time management and organizational skills as well as proficiency in written and spoken English are essential. The candidate should be keen on learning and applying several and diverse state-of-the-art techniques.

Project 5 Genetic determination and phenotypic plasticity of color polymorphisms in grasshoppers:


Prof. Dr. Holger Schielzeth (main supervisor) Institute of Ecology and Evolution, Friedrich Schiller University Jena


All species are variable in coloration, but in some species, multiple discrete color variants coexist within local population. The maintenance of such color polymorphisms requires special ecological and evolutionary conditions. Otherwise: Why does not one variant succeed as the best adapted? Orthoptera (grasshoppers and bush-crickets) are exceptional in that about 1/3 of the species are color polymorphic – more than in any other large group of organisms. This calls for a general explanation.

It has long been believed that grasshoppers are able to change their body color during ontogeny. But mounting evidence shows that at least in some groups, color morphs are determined by simple Mendelian genetics. It is currently unknown which species (groups) are color changes and which show genetic determination without plasticity. Precisely this knowledge is knowledge is critical to understanding how Orthoptera maintain their extraordinary color diversity.

Project description:

The project will screen multiple species of Orthoptera for how their color morphs are determined during ontogeny. This involves breeding of species in the laboratory. Breeding facilities and protocols are well established at the Institute of Ecology and Evolution. For species with genetic determination, we will determine the exact mode of inheritance and how it has compares to other Orthoptera.

This knowledge will give insights into how the color loci have evolved. For species with phenotypic plasticity in color, we will determine if there is a genetic basis do plasticity. This will shed light onto the interaction between genetics and the environment.

Candidate profile:

– Proactive, dynamic and curious

– Excellent communication and organizational skills

– Fluent in written and spoken English

– Willing and able to handle grasshoppers

– Experience in data analyses and R is desirable

Project 6 Structural basis of two-component system signaling:


Prof. Dr. Ute Hellmich (main supervisor) Biostructural Interactions Group, Friedrich-Schiller University Jena

Prof. Dr. Sarah O’Connor/ (co-supervisor) Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology


As bacteria explore new habitats, go to war with competitors or collaborate against common enemies, they rely heavily on intra- and interspecies communication and precise molecular scouting of their environment. So-called two-component systems (TCS) are essential molecular communication modules in quorum sensing and enable bacteria to probe and react to environmental cues (e.g. redox state, nutrients, pH).

Prototypical TCS consist of a membrane-bound histidine kinase (HK) with an extracellular sensor domain, a transmembrane region, and an intracellular kinase domain as well as a soluble response regulator that acts as a dedicated transcription factor. Despite their importance in all areas of intra- and interspecies signalling, the molecular basis of TCS-activation and regulation, as well as the structural interplay of the three elements (signal molecule-histidine kinase- response regulator) are not well understood.

Project description: 

In this project, you will use state of the art structural, biophysical and biochemical approaches to determine how a two component sensing system works. Specifically, you will   use these methods to elucidate the allosteric pathways between the histidine kinase’s sensor and kinase domain. Embedded in a highly interdisciplinary team, you will explore how bacterial and plant-derived signalling molecules activate and shape two component system signalling.

 Methods include protein biochemistry, microbiology, functional assay development, NMR spectroscopy, cryo-electron microscopy and/or X-ray crystallography, natural product extraction and analysis and molecular dynamics simulations.

Candidate profile: 

We seek a dedicated team player enthusiastic about the structure, function and dynamics of membrane proteins. Successful candidates will have an MSc in Biochemistry, Chemistry, Molecular Biology, Biophysics or a related discipline. Prior experience with protein purification, molecular biology and/or structural biology methods is an advantage. Proficiency in English (writing and oral) is necessary.

Project 7 Give and take – substrate shuttling in microbial communities on macroalgae:


Prof. Dr. Georg Pohnert (main supervisor) Institute for Anorganic und Analytic Chemistry, Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology

Prof. Dr. Martin Kaltenpoth (co-supervisor) Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology


Diatoms are photosynthetic microalgae that contribute to approximately 20% of global CO2 fixation. These algae were for a long time considered as phototrophs using exclusively photosynthesis to serve their metabolic requirements. We have recently shown that this is not true and that diatoms are surprisingly efficient in taking up dissolved organic matter from the seawater. In their natural environment of the plankton, diatoms are exposed to a plethora of metabolites, especially when competitors and bacteria are present. These metabolites can be assimilated and are incorporated into the metabolome.

One of the most dominant phytoplankton groups is thus competing with other heterotrophs for organic material, suggesting that a form of absorbotrophy may have a substantial impact on organic material fluxes in the oceans. This calls for the refinement of our understanding of competition in the marine environment, which is the objective of this project.

Project description:

Within this project, we will address the hypothesis that marine diatoms are interacting with their environment via metabolite exchange. The algae serve both as sources and sinks for organic material dissolved in the ocean waters. We will use a combination of (co-)culturing and metabolomic investigations to follow the metabolic flux during alga-alga interactions. Therefore, we will use macroalgae that serve as a substrate for the settlement of microalgae.

To investigate the metabolic flux between these partners one will be labeled with stable non-radioactive isotopes. Using mass spectrometry techniques, we will reconstruct the release and uptake of metabolites during the interaction situation. The developed methodology will also be used to address metabolic fluxes in other systems, like insect symbiosis or microbial communities.

Taken together this project can re-define the role of one of the most proliferative organismic classes in the oceans, the diatoms, within their community.

Candidate profile:

The ideal candidate has a strong interest in analytical investigations, involving mainly top-level mass spectrometry, and is curious to answer questions of ecological impact.

Project 8 Evolutionary significance of mixtures of defense chemicals in trophic interactions:


Prof. Dr. Stefan Schuster (main supervisor) Dept. of Bioinformatics, Matthias Schleiden Institute, University of Jena

Prof. Dr. Jonathan Gershenzon (co supervisor) Department of Biochemistry, Max Planck Institute for Chemical Ecology


In many trophic (and parasitic) interactions, the prey organisms defend themselves by toxic compounds (defense chemicals). Many of the attacking organisms (e.g. herbivores), in turn, produce enzymes degrading the toxins. This can be considered as a counter-defense [3]. Many defense chemicals occur as mixtures of several similar compounds.

For example, glucosinolates in Brassicaceae plants occur in various versions and chain lengths [4] and the cocoa plant produces several methylxanthines such as theobromine, theophylline and caffeine.

Project description:

One might argue that mixtures of several similar defense chemicals increase the effect on the attacker. On the other hand, the attacking organism could respond by producing detoxification enzymes with broader substrate specificity. Rather, the advantage of mixtures may be that some chemicals may act as competitive inhibitors of those enzymes.

This can then be viewed as a counter-counter defense in combination with direct defense. Defense compounds might then act both as substrates and inhibitors of the enzyme, but this possibility has not been tested theoretically or experimentally.

In this project, we will attempt to derive kinetic equations for detoxification enzymes to determine whether mixtures of defensive chemicals might have an evolutionary advantage. The approach will be based on earlier work in enzyme kinetics [2,5], and will involve methods of mathematical optimization. Previous research on fatty-acid oxidation [1,5] is also relevant, since the enzymes for chain shortening of a given fatty acid may be subject to competitive inhibition by fatty acids of other chain lengths.

In particular, we seek to identify conditions in terms of Michaelis constants and inhibition constants under which adding a further defense chemical to the mixture is favorable in comparison to increasing the concentration of the existing toxins.  The results may have practical relevance for future applications in plant protection and pharmacology (e.g. overcoming drug-resistant pathogens with mixtures of antibiotics). 

The candidate can work in a productive bioinformatics/mathematical biology environment at Jena University and can benefit from a close cooperation with an experimental group at the MPI-CE Jena. If desired by the candidate, s/he can perform experiments in addition to the theoretical work.

Candidate profile:

The ideal candidate should have a master degree, preferably in bioinformatics, biomathematics, biochemistry or similar disciplines. S/he should have a strong background in mathematical modelling, computer science and the biological aspects of this topic.

Project 9 The molecular basis of symbiosis establishment in beetles:


Prof. Dr. Martin Kaltenpoth (co-supervisor) Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology

Dr. Tobias Engl (co-supervisor) Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena


Beneficial symbioses with bacteria are widespread and important in insects, allowing them to exploit otherwise inaccessible ecological niches. While symbiont contributions to host fitness are often well characterized, the molecular interactions between hosts and symbionts that enable establishment and maintenance of the symbiosis remain poorly understood, due to the scarcity of experimentally and genetically tractable systems.

Across multiple beetle symbioses, we have cultured symbiotic microbes and established tools for genetic manipulation, which now allow for unraveling the molecular host-symbiont interplay at unprecedented levels of detail.

Project description:

The aim of the project is to unravel the molecular factors that are important for symbiont establishment and the beneficial function for the beetle host. To this end, molecular tools will be employed for targeted and random mutagenesis of the symbionts. The manipulated symbionts will then be introduced into the host, and the impact of the mutations on symbiont establishment and on host phenotypic traits will be characterized using bioassays, microscopy, and chemical analytics.

The results are expected to shed light on the molecular underpinnings of an insect-associated lifestyle in bacteria and reveal why some clades of bacteria have been particularly successful in establishing symbiotic associations with insects. In addition, lifestyle switches between insect mutualism and plant pathogenicity can be characterized on the molecular level to understand whether shared pathways are responsible for colonizing disparate hosts.

Candidate profile:

  • a deep interest in the molecular biology and evolutionary ecology of insect-microbe interactions
  • a strong background in molecular (micro)biology, alternatively in insect or bacterial physiology
  • excellent skills in targeted and untargeted mutagenesis of bacteria will be required for the project, so expertise on relevant techniques is highly desirable
  • critical scientific thinking skills
  • curiosity, creativity, and ambition
  • excellent time management and organizational skills
  • the ability and willingness to interact with other scientists in the group
  • very good communication skills
  • proficiency in written and spoken English

How to apply:

Please follow the link to the application portal to apply and refer to the time line to follow the selection process. APPLY NOW via Application portal

Application period: February 27 – April 16 – 2023

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