Trees are a central element of the urban green infrastructure. They increase the quality of the urban living environment by providing diverse ecosystem services to city dwellers. However, growing conditions for trees in urban environments are often suboptimal at best. Limited underground space for the root system to develop and different degrees of aboveground hardening and soil compaction pose challenges to the tree itself and its associated soil/root microbiome. Yet only few studies have addressed the prokaryotic and fungal diversity associated with trees in urban environments worldwide. In the Netherlands, with its high population density and degree of urbanisation, urban soil biodiversity is still a ‘black box’.

This PhD project will use environmental DNA metabarcoding by high-throughput sequencing to unravel the diversity of soil prokaryotes and fungi associated with trees in Dutch cities. Soil samples from different growth experiments and locations in Amsterdam, Leiden and Rotterdam will be analysed to gain insights into soil biodiversity development from young to old trees and possible correlations of soil biodiversity with tree species, tree vitality and levels of aboveground isolation, hardening and soil compaction.

The PhD project is part of the HiddenBiodiversity project financed by the Dutch Research Council (NWO) under the Dutch Research Agenda (NWA). HiddenBiodiversity comprises a diverse consortium of partners from universities, universities of applied sciences, municipalities, companies, nature organisations and other societal stakeholders. The candidate will work closely together with different consortium partners and in particular with three other PhD candidates, who will address soil animal diversity (VU Amsterdam), aboveground biodiversity (Leiden University/Hortus botanicus Leiden), and ecosystem services of mosses (TU Delft), respectively.  

The PhD project will be carried out in Naturalis in the Understanding Evolution research group. The candidate will be supervised by Dr. Jorinde Nuytinck, with co-supervision by Dr. Lucie Zinger and Dr. Michael Stech. The candidate will receive his/her PhD degree at the University of Amsterdam (UvA) and Dr. Vincent Merckx will be the promotor.

• The candidate must have a MSc degree in a relevant field (for example, biodiversity, ecology, soil biology) with a strong interest in prokaryotic/fungal diversity and DNA metabarcoding.
• Preferably the candidate has experience with field work, molecular lab work and/or common statistical methods.
• Excellent knowledge of the English language (written and verbal) and at least basic knowledge of the Dutch language is essential, as well as a scientific and critical attitude, outstanding time management and organisational skills, and the ability to work independently as well as collaboratively within the project consortium and the Naturalis research group.
• The candidate should have good communication skills and be enthusiastic to contribute to knowledge dissemination and outreach activities within the HiddenBiodiversity project.
• Teaching experience is an advantage.

Fixed-term contract: one year, to be extended with three more years after a successful first year evaluation.

We offer 

A contract (36 hours per week) for a period of one year, to be extended with three more years after a successful first year evaluation, and a monthly starting salary of € 2,940.- (circa € 38,500.- gross per year). The starting date is between September 1 and 28, 2022. The successful candidate will be employed by Naturalis in Leiden. Naturalis Biodiversity Center offers an inspiring working atmosphere with effective and efficient supervision of our PhD candidates. Our Research Coordination Office also provides ample support to our scientific staff. Our institute promotes gender equality and wants to enhance the diversity of staff members.

Naturalis Biodiversity Center

Naturalis Biodiversity Center in Leiden is the Dutch national research institute for biodiversity and systematics. With our collection of 42 million specimens, one of the world's largest natural history collections, and our state-of-the-art research facilities we offer the (inter)national research infrastructure for species, identification and monitoring (for example in the ARISE and DiSSCo projects). We closely collaborate with many Dutch universities, research institutes, industry, and government. We host over 120 researchers including 14 academia embedded professors and 40 PhD students. We present the history of our planet, and the diversity of life on Earth, through permanent and temporary museum exhibitions, educational programmes, and online presence, with more than 400,000 visitors per year. All in all, a unique combination of science and culture in the Netherlands and elsewhere in the world!

The research department is organised in 8 research groups comprising researchers and their postdocs and PhD-students. The current position will be in the research group Understanding Evolution, led by Dr. Vincent Merckx. Naturalis has a completely new lab building, including state-of-the-art molecular facilities, microCT scanners and electron microscopy (SEM and TEM).