PhD Candidate Urban Ecology

PhD Candidate Urban Ecology

Published Deadline Location
17 Oct 25 Nov Leiden

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The Faculty of Science / the Institute for Biology is looking for a :

PhD Candidate, Urban Tree-Microbe Interactions
Vacancy number: 14166

Job description

In urban landscapes, the challenges posed by multiple environmental stressors, such as nutrient enrichment, heat, and drought, are more pronounced compared to rural natural environments. While we recognize the significant impacts of these stressors on biodiversity, there remains a substantial knowledge gap regarding their effects on species interactions. Trees, in particular, engage in complex interactions with a diverse array of soil organisms that aid in nutrient uptake, water absorption, and resilience against climate change. In addition, urban trees also affect micro-habitat conditions for plants, animals, and humans, extending the importance and interest of tree-microbe interactions to a 'One Health' perspective.

Current theories suggest that urban nutrient enrichment should alleviate nutrient limitations typically observed in rural natural areas, potentially leading to a weakening of mutualistic interactions. Simultaneously, heightened stressor exposure (e.g. to heat and drought) is expected to select for beneficial microbes that help mitigate these challenges. For trees, this could imply a shift in mutualistic relationships with soil microbes, such as mycorrhizal fungi, from rural to urban ecosystems, potentially decreasing diversity and favoring more antagonistic interactions. However, these shifts may also equip trees with the tools needed to withstand climate change stressors, with ripple effects on other types of interactions both below and aboveground.

Want to be a part in uncovering the secrets of urban tree-microbe interactions and their far-reaching consequences?

We are looking for a creative and passionate PhD candidate that will explore the effects of urbanization on species interactions, in particular but not exclusively, involving tree-microbe mutualisms. In this PhD project, we seek to unravel how tree-microbe interactions undergo functional shifts as urbanization levels increase and explore the cascading effects on other interaction types, under current and future climate scenarios.

Key responsibilities
  • Design and execute field sampling to study the ecology and evolution of mutualisms in urban vs non-urban settings or along urban gradients
  • Conduct controlled experiments focused on interaction outcomes primarily between plants and microbes in urban settings under current and projected future climate scenarios
  • Microbiology and/or molecular laboratory work and data analysis, including DNA-related bioinformatics and statistics.


Leiden University


Selection Criteria
  • A MSc degree in (urban) ecology, plant sciences, microbial ecology, environmental sciences, or a related discipline (preferred experience with plant-microbe interactions, microbiome analysis)
  • Passion for fieldwork in rural and urban areas and affinity to perform plant growth experiments, involving microbiology techniques and DNA-related lab analysis (DNA extraction, PCR, library preparation for metabarcoding, and bioinformatics)
  • Strong quantitative skills (including multivariate statistical analyses)
  • Team player and collaborative attitude
  • Proficiency in spoken and written English
  • Ability to effectively disseminating the findings through scientific publications and outreach to public audiences or relevant stakeholders

Conditions of employment

Research at our faculty
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2300 {see} staff and almost 5000 {see} students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together.

For more information, see and

The Institute for Biology
The research within the Institute of Biology Leiden (IBL) aims to work on the science base of biodiversity and health, which is reflected in our leading principle Harnessing Biodiversity for Health. We perform innovative curiosity-driven research to answer fundamental questions, and solutions-driven research to help solving major societal challenges. The latter include protecting nature’s biodiversity, creating sustainable biotechnology and agriculture and increasing good health. Our research focuses on four Research Themes: Bioactive Molecules, Host-Microbe Interactions, Development & Disease and Evolution & Biodiversity. Located in a thriving scientific environment with our Faculty of Sciences, Naturalis Biodiversity Centre, the Leiden University Medical Centre and the Leiden Bioscience Park, IBL offers an exciting, internationally oriented and inclusive place to work and study.

Terms and conditions
We offer a full-time 1 year term position for initially one year. After a positive evaluation of the progress of the thesis, personal capabilities and compatibility the appointment will be extended by a further three years. Salary range from € 2.770,- to € 3.539,- {see} gross per month (pay scale P in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses(8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break.
All our PhD students are embedded in the Leiden University Graduate School of Science Our graduate school offers several PhD


  • PhD
  • Natural sciences
  • 38—40 hours per week
  • €2770—€3539 per month
  • University graduate
  • 14166



Rapenburg 70, 2311EZ, Leiden

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