PhD position in Fungal Networks and Nutrient Transport related to Mushroom Production (1.0 FTE)

PhD position in Fungal Networks and Nutrient Transport related to Mushroom Production (1.0 FTE)

Job description

The Microbiology research group of Utrecht University (UU) is looking for a PhD candidate in fungal biology for a full-time 4-year research position.
Mushrooms provide a high quality, sustainable alternative for meat consumption. White button mushrooms are formed after colonisation of a manure and straw based compost by the hyphae of the fungus. Half of the nutrients are still present in the compost after harvesting the mushrooms. Enhancing substrate degradation or adding nutrients does not proportionally increase yield. These findings led us to propose that the architecture of the network of hyphae, that is called mycelium and that acts as the rooting system for the mushrooms, limits the feeding process and thereby the yield. The network architecture consists of single hyphae and bundles of hyphae, called cords. Single hyphae effectively take up nutrients, while cords predominantly transport water and nutrients. Little is known about how colonisation and cord formation is regulated and which signals are involved.
The aim of this project is to understand colonisation and the resulting network architecture, and the interplay of factors that impact transport therein. This knowledge will be used to drive the optimal feeding of the mushrooms. Until recently, it was very hard to address these topics but technology is now available. For instance, we have developed an imaging system that can resolve the network architecture of natural isolates grown on compost. We will link this architecture to transport within this network, allowing us to model the optimal rooting system for mushroom formation. Such an optimal rooting system can be obtained by crossing in specific genes. We will identify these genes by genome sequencing, RNA transcriptomics, and genetic modification combined with varying culturing conditions. These studies will reveal a fundamental understanding of network formation and transport, and in optimal feeding of mushrooms, ultimately resulting in higher yields of commercial mushrooms.
You will work as the PhD candidate on the Vidi project of Robert-Jan Bleichrodt (PI). You will perform multidisciplinary research in collaboration with Geosciences UU, Technical University Delft and Oxford University and several players in the mushroom and fungal material industry.
Specifically you will:

• establish CRISPR-Cas9 mediated gene deletion in Agaricus bisporus or use Agrobacterium mediated transformation as an alternative;
• perform DNA and RNA isolation for sequencing and ideally also perform genomic/transcriptomic analysis;
• analyse the fungal network architecture by imaging using visible light and X-ray tomography and subsequent image segmentation;
• image and quantify water and nutrient transport in the mycelium using light microscopy and neutron tomography, and heavy isotopes that will be detected by mass spectrometry;
• supervise Bachelor's and Master's student projects.

Qualifications

We are looking for a candidate with the following qualifications and characteristics:

• You have completed a Master's in biology or a related Life Sciences programme or you will complete one within the next six months.
• You have experience in molecular biology preferably with fungi and have successfully applied microscopy/image analysis and/or CRISPR-Cas9 technology.
• You are an enthusiastic, upright, and perseverant team player.
• You work accurately and systematically, but you also like to perform large scale experiments.
• You have basic programming skills such as R or Python (bioinformatics skills are a bonus).
• You are fluent in English, both in speech and writing.

Offer

• a full-time position for four years;
• a full-time gross salary starting at €2,434 in year one and increasing to €3,111 in the last year (scale P Collective Labour Agreement Dutch Universities);
• 8% holiday bonus and an 8.3% end-of-year bonus;
• a pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities (cao).

In addition to the employment conditions laid down in the cao for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow.
More information about working at the Faculty of Science can be found here .

About the organization

The Microbiology group led by Professor H.A.B. Wösten conducts research on Fungal Biotechnology, Genomics, and Infections. You will be working in the Fungal Biotechnology group on Agaricus bisporus as model system and you will be supervised by Dr R. Bleichrodt (PI) and work closely together with him in the lab.
Microbiology is part of the Institute of Environmental Biology which is focused on researching the biological mechanisms that determine how plants, microbes and animals interact with each other and how they are able to adapt to their constantly changing and often harmful environment. Inspired by nature, the Institute of Environmental Biology aims to contribute to the development of sustainable solutions for urgent societal problems such as future food security, ecological consequences of climate change, and the protection of our natural resources. You will attend and present at the annual institute meetings.
At the Faculty of Science there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing problems. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects.

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities. We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education. We are equally well-known for our familiar atmosphere and the can-do attitude of our people. This fundamental connection attracts researchers, professors and PhD candidates from all over the globe, making both the university and the Faculty of Science a vibrant international and wonderfully diverse community.

Additional information

If you have any questions regarding the position, please contact Dr Robert-Jan Bleichrodt ([email protected] ).
Questions about the application procedure? Please send an email to [email protected] .

Apply

Everyone deserves to feel at home at our university. We welcome employees with a wide variety of backgrounds and perspectives. If you have the expertise and the experience to excel in this role, then simply respond via the “Apply now” button! Please enclose:

• your letter of motivation;
• your curriculum vitae;
• the names, telephone numbers, and email addresses of at least two references;
• a copy of your MSc certificate, or a letter from your university stating when your degree will be issued (in case you have not completed your Master's yet, please indicate your planned finishing date on your curriculum vitae. This should be within six months from the application deadline).

If this specific opportunity isn’t for you, but you know someone who may be interested, please forward this link to them.
Some connections are fundamental – Be one of them

The application deadline is 06/12/2021