We are hiring a total of ten Phd students and three PostDocs within the DFG and SNF funded research unit PhytOakmeter. The positions run for 4 years and will be tightly linked with each other – conducting research on the three experimental platforms of PhytOakmeter. PhytOakmeter will offer exciting research and publication opportunities within the subprojects as well as in synthesis publications across subprojects. We will have intense and regular scientific exchange between the working groups. In addition, we will offer workshops and summer schools.
Come, join us in an exciting international and interdisciplinary research project investigating acclimation and adaptation of a tree holobiont.
C1 – PostDoc position in PhytOakmeter coordination and synthesis
The Philipps University, founded in 1527, offers multiple award-winning teaching for around 22,000 students and tackles the important issues of our time with excellent research across a broad spectrum of science.
The Department of Biology, research group “Plant Ecology and Geobotany”, Prof. Dr. Lars Opgenoorth is currently accepting applications for a
Postdoc
The position will be offered for a period of 4 years, if no former times of qualification must be considered. Details for starting date will be posted shortly as will details for the application procedure. This is a full time position (100 % of regular working hours) with salary and benefits commensurate with a public service position in the state of Hesse, Germany (TV-H E 13, 100 %).
Project description
The position is embedded in the C1 coordination project of the DFG-SNF funded Research Unit “PhytOakmeter – Using clonal oak phytometers to unravel acclimation and adaptation mechanisms of long-lived forest tree holobionts to ecological variations and climate change”.
The successful candidate will be responsible for overseeing the synthesis process of the project with a focus on integrating the complementary omics approaches to develop a comprehensive understanding of acclimation and adaptation in oak. As first steps, the C1-PostDoc will be responsible for modeling the ecological niche of Quercus robur and defining drought conditions for Q. robur across its natural range and along the project’s European transect.
Additionally, the C1-PostDoc will investigate the resistance, resilience, and recovery of the out-planted Q. robur DF159 clonal plants as function of annual increment, volumetric wood moisture, and sap flow, making use of an extensive existing geo-referenced environmental database describing the sampling sites. As the various omics data from the subprojects become available, the C1-PostDoc coordinates the joint analyses of these data together with the subproject PostDocs.
The successful candidate will work closely with other postdoctoral researchers and the project leader to coordinate the interaction between working packages, including the overall data handling and data exchange. The C1-PostDoc will also oversee the technical implementation of the Experimental Platforms and will be responsible for promoting regular scientific exchange through the monthly PhytOakmeter Science Talk and the annual project meeting with a workshop character. This central position offers excellent opportunities to lead synthesis publications.
Your profile
You have a MSc and Ph.D. in biology, plant ecology, bioinformatics, or similar fields with excellent records. We are looking for a candidate with a proven foundation in plant ecological theory and a strong expertise, interest and creativity in data analysis and handling (in R and Unix environment), as well as a very good publication record. Research experience in forest ecology, spatial modelling, tree physiology with experiments, genetics or genomics and explicitly, with the bioinformatic analysis of omics data is advantageous. You have good communication and teamwork skills, and a meticulous way of working. You enjoy science and are driven by curiosity. If interested, please contact opgenoorth@uni-marburg.de
SP3 – Two Scientific researchers (Doctoral Researcher) in oak ecophysiology
The Chair of Ecosystem Physiology is seeking two junior scientists to study stress impacts on oak trees within the new Research Unit (DFG RU 5571). Start of work by September 15 (fixed-term for 4 years), 65% E13-TVL (PhD salary). We are particularly pleased to receive applications from women for the position advertised here.
Project description
The positions are embedded in the SP3 project Ecophysiology of the DFG-SNF funded Research Unit “PhytOakmeter – Using clonal oak phytometers to unravel acclimation and adaptation mechanisms of long-lived forest tree holobionts to ecological variations and climate change”.
Both PhD positions are integrated in the subproject 3 conducting experiments on drought memory and multiple abiotic and biotic stress under controlled conditions in the lab and in the field and applying ecophysiological measurements (chlorophyll fluorescence, water potential, gas exchange, stable isotopes) to quantify stress effects in oak. You will closely collaborate with doctoral researchers from our cooperation partners within the RU. Controlled climate change experiments at the university and joint field campaigns in Germany and along an European transect will be conducted.
Your profile
We are looking for two highly motivated, enthusiastic candidates with excellent capacity for teamwork to join our motivated team in the green city Freiburg. Applicants must hold a MSc in Biology, Environmental Science or related disciplines ideally with experiences in plant ecophysiology, physiology or ecology. You should have knowledge of data analysis and basic ecological statistics, good writing and communication skills. You should enjoy fieldwork and conducting experiments with plants, work independently with high self-motivation and interest in interdisciplinary projects. Fluency in written and spoken English and a high motivation to learn the basics of the German language are required.
What we offer
We offer collaboration in a highly motivated team embedded in an exciting, newly approved large-scale project that brings together researchers from the different biological disciplines.
How to apply
Details on the documents required for your application and on the required form of the application are to be found on https://www.cep.uni-freiburg.de/forschungsprojekte/phytoakmeter. Please follow these rules strictly. Please send your application including supporting documents and two references (or letters of recommendation) citing the reference number by 30 June 2023 at the latest. Please send your
application to the following address in electronic form (pdf): sabine.pregger@ctp.uni-freiburg.de
SP4 – Two PhD positions to study the oak microbiome
PhD position at UFZ Halle (Germany)
The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.
Project description
The plant microbiome, i.e. the community of associated microorganisms, plays a crucial role for mutual acclimation to environmental changes and the subsequent evolutionary adaptation (A&A). Beneficial microbes can enhance plant tolerance traits against stress, which reinforces shoot and root protection by modifying phytohormonal levels, antioxidant and enzyme production, osmotic adjustment or biofilm formation to increase water and nutrient uptake, gas exchange and water use efficiency.
Since these findings were mainly retrieved from studies on crops or herbaceous plants, it remains little investigated how trees and their microbiomes react to environmental changes, including more frequent and intensified droughts and pathogenic pressures. Hence, this project aims to investigate, how oak-associated microorganisms respond to various environmental conditions and stresses.
Considering the endogenous rhythmic growth and the modularity of the oak, the project intends to determine an oak core microbiome and characterize key stone taxa, which enhance resilience against the applied stressors. The project uses molecular sequencing tools to monitor bacteria and fungi associated with above- and belowground compartments of clonal oak saplings in an Ecotron and Tree Canopy Exposition Experiments, and along the PhytOakmeter field monitoring sites.
Your tasks
- Contribution to joint samplings in the three platforms of the Research Unit
- Preparation and DNA extraction of soil, root and leaf samples
- Accessing microbial communities using molecular tools and high-throughput sequencing techniques
- Bioinformatical and statistical downstream processing of the sequencing data
- Presenting and publishing of results on international conferences and in international journals
We offer
- Excellent technical facilities which are without parallel
- The freedom you need to bridge the difficult gap between basic research and close to being ready for application
- Work in inter-disciplinary, multinational teams
- Excellent links with national and international research networks
- Excellent support and optimal subject-specific and general training with our HIGRADE graduate school
Your profile
- A scientific University degree (Diploma/ M.Sc.) in biology, microbiology, ecology, bioinformatics, or related fields of science
- Highly motivated and team-oriented
- Broad interest in plant-associated microbial communities
- Good statistical (preferable with R) and analysis skills
- Very good oral and written communication skills in English
- Travel availability
- Driving licence B
How to apply
PhD position at UMR Marburg (Germany)
The Philipps-Universität Marburg, Prof. Dr. Robert Junker and Prof. Dr. Anke Becker will be accepting applications for a PhD position. The position will be offered for a period of 4 years. More details e.g. with regards to the formal application procedure and the starting date will be announced shortly.
Project description
The position is embedded in the SP4 project ‘Cross talk between environmental conditions, oak tree performance, and the microbiomes of their soil, endo- and phyllosphere’ of the DFG-SNF funded Research Unit “PhytOakmeter – Using clonal oak phytometers to unravel acclimation and adaptation mechanisms of long-lived forest tree holobionts to ecological variations and climate change”.
More details about the PhD project will be announced shortly.
Your profile
Profile requirements will be announced shortly.
SP5 – Two PhD positions on oak ectomycorrhizal ecology and landscape genomics
PhD Researcher (m/f/d) at WSL Birmensdorf (Switzerland) – Landscape genomics of ectomycorrhizal fungi associated to oak
The Swiss Federal Institute for Forest, Snow and Landscape Research WSL is part of the ETH Domain. Approximately 600 people work on the sustainable use and protection of the environment and on the handling of natural hazards.
In the framework of the Project “PhytOakmeter” the Research Unit ‘Biodiversity and Conservation Biology’ and its ‘Ecological Genetics’ Group is searching for the duration of 4 years, with a start in summer/fall 2023 for a PhD student in “Landscape genomics of ectomycorrhizal fungi associated to oak” (f/m/d)
Project description
“PhytOakmeter” is a project funded by the German Research Foundation and the Swiss National Science Foundation revolving around acclimatization and adaptation of pedunculate oak. It explores a common oak clone from a holobiont perspective by 24 scientists from Germany and Switzerland. Symbiotic interactions with holobiont partners, including ectomycorrhizal fungi, can support host acclimation to changing conditions, with benefits for longlived trees facing climate change. However, there are serious gaps in our understanding of the ecological roles of ectomycorrhizal fungi at the level of inter- and intraspecific diversity: how do they mediate root functions and support tree adaptation and acclimation, and are ectomycorrhizal fungi adapted to their local environmental conditions?
Based on sampling sites distributed along a European transect, you will investigate signatures of local adaptation in the highly abundant ectomycorrhizal fungus Cenococcumgeophilum and how natural populations are adapted to dry conditions. You will study the effects of different C. geophilum genotypes on the symbiotic interactions with oak plants under changing biotic and abiotic environmental conditions using Ecotron, growth chamber and field experiments.
Furthermore, you will explore gene expression patterns of selected C. geophilum genotypes to stressful environments using the Ecotron experiment. By integrating the results obtained and cross-examining them with those of other working groups in the Research Unit, the project aims to provide valuable information on the role of the ectomycorrhizal symbiosis on oak holobiont acclimation as well as the adaptive capacity of ectomycorrhizal fungi.
Your profile
The successful candidate holds a master’s degree in biology or environmental sciences with a strong background in microbiology, population genetics, soil ecology and/or plant-fungi interactions. You should be keen on combining field observations with controlled experiments to perform integrative data analyses including next-generation sequencing data. The “PhytOakmeter“ project offers a unique opportunity to join forces with scientists from different backgrounds and to work on the same experimental oak system.
Consequently, it is essential that you have strong skills in interacting with scientists in an interdisciplinary team, spread over several institutions. In addition, we expect experience in bioinformatics, Unix and R programming, a good knowledge of English, and the ambition to communicate results in scientific papers and at conferences. Experience with geographic information system and spatial analyses would be an advantage. Conceptual and creative skills, an independent and structured way of working and a high level of motivation and team spirit complete your profile.
How to apply
Please send your complete application to Michèle Bucher, Human Resources WSL, by uploading the requested documents through our webpage. Applications via email will not be considered. The position remains open until filled. Benjamin Dauphin, benjamin.dauphin(at)wsl.ch and Martina Peter, martina.peter(at)wsl.ch will be happy to answer any questions or provide further information. The WSL strives to increase the proportion of women in its employment, which is why qualified women are particularly called upon to apply for this position.
PhD Researcher (m/f/d) at UFZ Halle (Germany) – Adaptation and acclimation of the clonal oak’s ectomycorrhizal fungi to biotic and abiotic environmental factors
The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.
The job
Symbiotic interactions with holobiont partners that enhance nutrient and water uptake by trees, the ectomycorrhizal fungi, can support host acclimation to changing conditions, with benefits for long-lived trees facing climate change. There are serious gaps in our understanding of the ecological roles of ectomycorrhizal fungi at the level of inter- and intraspecific diversity: how do they mediate root functions and support tree adaptation and acclimation? Furthermore, are ectomycorrhizal fungi adapted to their local environmental conditions?
The project aims to fill this knowledge gap by investigating the contribution of ectomycorrhizal symbiosis to the acclimation of oak holobiont under biotic and abiotic stressors, taking into account the endogenous rhythmic growth. The ectomycorrhizal root tip communities will be analysed in field-monitoring sites, Tree Canopy Exposition and Ecotron Experiments of the Research Unit 5571 “PhytOakmeter”.
These ecological gradients and experiments will represent a wide range of environments and controlled stress situations, and will allow analysis of the modulating influence of the endogenous rhythmic growth on ectomycorrhiza formation and function. A combination of morphotyping, enzyme activity, metabarcoding and gene expression analyses supports the project’s objectives. The Research Unit (https://www.uni-marburg.de/en/fb17/phytoakmeter) is funded by the German Research Foundation (DFG).
Your tasks
- Contribution to joint samplings in the three platforms of the Research Unit
- DNA, RNA and enzyme extractions of oak ectomycorrhizas and roots
- Accessing fungal and bacterial communities by amplicon, and fungal and plant gene expression by RNA sequencing
- Bioinformatical and statistical downstream processing of the sequencing data
- Presenting and publishing of results on international conferences and in peer-reviewed journals
- PhD thesis
We offer
- Excellent technical facilities which are without parallel
- The freedom you need to bridge the difficult gap between basic research and close to being ready for application
- Work in inter-disciplinary, multinational teams
- Excellent links with national and international research networks
- Excellent support and optimal subject-specific and general training with our HIGRADE graduate school
- Place of work Halle (Saale)
- Contract limitations 4 years
- Salary Remuneration according to the TVöD public-sector up to pay grade 13 including attractive public-sector social security benefits.
Your profile
- A scientific University degree (Diploma/ M.Sc.) in biology, microbiology, ecology, bioinformatics, or related fields of science
- Highly motivated and team-oriented
- Broad interest in plant-associated microbial communities
- Good statistical (preferable with R) and analysis skills
- Very good oral and written communication skills in English
- Travel availability
- Driving licence B
How to apply
Contact
Mika Tarkka (Tel. 0345 558 5221)
SP6 – PostDoc and PhD position in oak-herbivore interaction
PostDoc Position at WSL
The Swiss Federal Institute for Forest, Snow and Landscape Research WSL is part of the ETH Domain. Approximately 600 people work on the sustainable use and protection of the environment and on the handling of natural hazards. In the framework of the Project “PhytOakmeter” the Research Unit ‘Forest Health and Biotic Interactions’ and its ’Forest Entomology’ Group is searching for the duration of 2 years (with option for a 2-year extension), with a start in fall/winter 2023 for a Postdoc in Chemical Ecology, Oak-Herbivore Interactions (80-100%, f/m/d).
Project description
“PhytOakmeter” is a research unit project funded by the German Research Foundation and the Swiss National Science Foundation revolving around acclimatization and adaptation of pedunculate oak. It explores a common oak clone from a holobiont perspective.
Pedunculate oak displays a distinct endogenous rhythmic growth which is characterized by multiple alternating root and shoot flushes. Changes in a plant growth stage can have profound effects on phyto-chemistry and plant-herbivore interactions. However, only little is known about how the interaction between growth stages, defense chemistry and the trade-offs between growth and chemical defenses are modulated by environmental variation and stress.
Based on Ecotron and field experiments you will explore the interaction between oak growth and defense and its consequences for insect herbivores in response to drought and herbivory. Furthermore, you will study how changes in vertical microclimatic conditions within a forest affect the relationship between shoot flushes, leaf chemistry, and herbivory. Finally, you will support the development of a tool aiming to automatically detect and quantify herbivory based on digital images captured by Phenocams.
Your profile
The successful candidate holds a PhD degree in Biology or Environmental Sciences with a strong background in chemical ecology, plant-herbivore interactions, statistical analyses, and experimental design. Moreover, you should be keen on combining field observations with controlled experiments and analyses in the lab. ”PhytOakmeter” allows scientist with different scientific backgrounds to work on the same experimental oak system, thereby
strongly fostering interdisciplinary work.
Consequently, most research projects will be conducted in close collaboration with other “PhytOakmeter” research groups. As such it is essential that you possess excellent skills in interacting with scientists of an interdisciplinary team, spread over several institutions. Furthermore, we expect good knowledge in R programming, a good command of English, as well as the capability for scientific paper writing. Conceptual skills, an independent and structured way of working and a demonstrated high level of motivation and team spirit complete this profile.
How to apply
Please send your complete application to Michèle Bucher, Human Resources WSL, by uploading the requested documents through our webpage. Applications via email will not be considered. Martin Gossner, martin.gossner(at)wsl.ch and Michael Eisenring, michael.eisenring(at)wsl.ch will be happy to answer any questions or offer further information. The WSL strives to increase the proportion of women in its employment, which is why qualified women are particularly called upon to apply for this position.
PhD position at UMR
The Faculty of Geography, Department of Environmental Informatics, is currently accepting applications for a Research Assistant (Doctoral Researcher). The position is offered for a period of 4 years. The starting date is as soon as possible. The position is part-time (65 % of regular working hours) with salary and benefits commensurate with a public service position in the state Hesse, Germany (TV-H E 13).
You will be based in the lab of Environmental Informatics, where we explore spatial sensing of social-ecological systems through networked sensing, remote sensing, and AI (https://uni-marburg.de/kJLc3)
Project description
The position is embedded in the subproject SP6 ‘Elucidating the links between environmental variation, plant phenology, and plant-herbivore interactions’ of the DFG-SNF funded Research Unit “PhytOakmeter”. To enable real-time monitoring of trees, a camera network is to be established that transmits time-lapse images of tree shoots from the field. The generated images shall be examined for patterns in feeding damage (herbivory) and growth using artificial intelligence.
Your tasks
- Setting up a camera network (“Phenocams”)
- Applying neural networks to recognize individual leaves and detect leaf growth and herbivory
- Participation in the international DFG research group “PhytOakmeter”
Your qualifications
- MSc-degree or equivalent in Geography, Informatics, Data Science, Biology or equivalent
- Experience with machine learning and programming languages (e.g. R, Python, Java)
- Strong English skills, both written and spoken
- Team orientation with strong organizational skills
- Technical affinity
- Personal motivation in regard to the announced position
Disposition to own scientific qualification (e.g. a doctorate project in the area) is expected.
We actively support the professional development of junior researchers, e.g. by the offers of Marburg Research Academy (MARA), the International Office, the Higher Education Didactics Office and the Human Resources Development Office.
How to apply
Application details will be posted shortly. For more information, contact Vertr. Prof. Dr. Dirk zeuss: dirk.zeuss@uni-marburg.de
SP7 – Two PhD positions in oak-nematode interactions
The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.
The job
Within the PhytOakmeter project, the project SP7 investigates “The role of tree-nematode interactions in the acclimation and adaptation of trees”. The health of trees, as well as their ability to adapt and acclimate (A&A) to a changing environment, is intimately linked to soil biota.
While the role of soil microbes in tree health has been demonstrated across a range of species, the role of soil nematodes, which interact with both the tree and the associated microbes, has received little attention. Soil nematodes occupy all trophic levels in soil and can modulate above-belowground relationships, affecting the tree directly through feeding (i.e., plant-parasitic nematodes) and indirectly by selectively feeding on soil microbial communities (i.e., fungivorous and bacterivorous nematodes).
At the same time, these interactions can affect the gene expression of plants and induce defense mechanisms (i.e., the release of root exudates and volatiles) which may alter nutrient cycles and further modulate tree health, A&A, and susceptibility to environmental stress like drought. In particular, as they inhabit soil water films, nematodes are sensitive to changes in moisture availability triggered by drought. Thus, drought can alter nematode communities and their direct and indirect influence on plant health and A&A mechanisms.
This project will determine the role of soil nematode communities in modulating the A&A of drought- stressed DF159 oak clone trees and their associated microbiota. The doctoral researcher will combine taxonomic and molecular nematode monitoring approaches with soil function (substrate-induced respiration (SIR) method, phospholipid fatty acid (PLFA) analysis, and enzyme analysis) data to fine-tune techniques for nematode detection; and assess the direct and indirect effects of drought-induced alterations in soil nematode communities on tree health and A&A across a European aridity gradient and in a canopy crane experiment
Your tasks
- Analysis of experimental treatment effects on the soil nematode community (taxonomic and metabarcoding approaches) and soil ecosystem functions (microbial respiration, microbial biomass, enzyme activity)
- Planning and execution of joint field samplings with the rest of the Research Unit, including a Canopy Crane experiment and the sampling of a European tree transect.
- Synthesis and analysis of datasets from different disciplines (molecular, taxonomic, functions, etc.)
Participation in the working group seminars, lab meetings, and the HIGRADE graduate school
We offer
- Excellent technical facilities which are without parallel
- The freedom you need to bridge the difficult gap between basic research and close to being ready for application
- Work in inter-disciplinary, multinational teams
- Excellent links with national and international research networks
- Excellent support and optimal subject-specific and general training with our HIGRADE graduate school
Your profile
- Master’s or equivalent degree in a project-related field (e.g., ecology, environmental sciences)
- Very good ecological and molecular knowledge and strong interest in biotic interactions
- Very good quantitative and statistical skills in R are essential
- A clear drive to do science, and follow a hypothesis-driven approach
- Lab-work experience, especially with molecular techniques (i.e., PCR and/or sequencing)
- Experience in fieldwork, especially with soil sampling, and belowground plant-trait assessments, is advantageous
- Excellent English communication skills (spoken and written)
- Flexible and willing to adapt to different working environments and well-organized, hands-on mentality
- Motivation to be a proactive team player in an international and interdisciplinary research consortium
- Drivers licence is advantageous