September 2018

New yeast species from Dutch garden soil
Pedro Crous, member of the Royal Dutch Academy of Sciences
Karoline Dukik successfully defended her thesis
Sara Casado Lopez successfully defended her thesis
A Day in a Cell
Heineken Prize!
Course Fungal Biodiversity 2019

New yeast species from Dutch garden soil

The idea was: involve primary schools in isolating fungi and hopefully describe new species which would get the name of their discoverer.
A Citizen Science project of Westerdijk Institute together with the University Museum Utrecht led to about 290 soil samples which contained over 2000 different species of fungi and the isolation and description of about 150 new species.
A great success. 
At first no one was especially focused on yeasts, but they showed up anyway and Marizeth Groenewald, Yeast Curator of the Westerdijk Institute, was asked to look into them. ‘It is hard to find yeasts between fungi, as the fungi overgrow the yeasts quickly so it is not easy to isolate pure colonies of yeasts.’
Yet Marizeth et al. succeeded to isolate 335 yeast isolates representing 67 different species. 15 isolates represent potentially new species, of which six novel ascomycetous species. The six new yeasts go by Dutch sounding names as: Ogataea  degrootiae, or Pichia gijzeniarum (try to pronounce that correctly if you’re not Dutch), Sacharomycopsis oosterbeekiorum, Trichomonascus vanleenenius, Hanseniaspora mollemarum and Zygoascus flipseniorum.
The proud name givers will receive a certificate with ‘their’ yeast at the ‘Day in a Cell’ during the Weekend of Science on the 7th of October.
Marizeth Groenewald is amazed by the amount of new yeasts discovered in this small flat country during this one project. She gets a bit excited talking about the one species caught in the act of having sex: Sacharomycopsis oosterbeekiorum. ‘Two filaments meet each other and in the middle they form spores. Very clearly, you don’t often see that.’ 
Two yeasts we can expect to hear more from: they are both capable to ferment glucose at high temperatures:  Z. flipseniorum and T. vanleenius. We will keep you posted!

The article: Diversity of yeast species from Dutch garden soil and the description of six novel Ascomytes was published in: FEMS Yeast Research, Volume 18, Issue 7, 1 November 2018, foy076,

Pedro Crous, member of the Royal Dutch Academy of Sciences

‘It’s not something I ever expected because I am not from the Netherlands, I am from South-Africa and I don’t have a large old boys' network here. So, no, I didn’t expect to be appointed at such a prestigious institution.’
Despite this it happened: Pedro Crous, director of the Westerdijk Fungal Biodiversity institute is appointed member of the Royal Dutch Academy of Sciences : the Koninklijke Nederlandse Akademie van Wetenschappen, (KNAW) as of today.
Pedro Crous looks upon his appointment as a chance for mycology, he will meet other scientists at the Academy that play an important role in biodiversity research and conservation.
Talking about the appointment Pedro Crous is mentioning especially the opportunities it offers for mycology, he is not speaking about the honor for himself, although he sure is honored by the offered lifelong membership. ‘Life is to short for that’, he answers, asked about his own pride.
The main thing he hopes to achieve with this appointment is drawing extra attention to a large international citizen science project the Westerdijk Institute is going to launch, to emphasize the huge importance of fungal biodiversity. The citizen science project is an international follow up of a very successful Citizen Science project in the Netherlands last year, set up by the Westerdijk Institute in cooperation with University Museum in Utrecht.
‘World fame, fungi with your name’ is the literal translation of the project.
And then there is this other huge issue. The humanitarian disaster Crous expects to happen in Africa, the continent he was born. The coming years Africa has to deal with an explosion of the population while at the same time, due to drought, there will be less food. That fact, combined with the lack of knowledge about fungal diseases that threaten crops on the African continent, can lead to a disaster. ‘Of all new fungi described in 2017, only 4 percent came from the African continent. It is not an issue of interest there’, Crous asserts. If only he could bring about a tiny little bit of change here…
As far as president of the Academy Wim van Saarloos is concerned, the opportunity will certainly be there; at least, in his speech to welcome the new members he says: ‘The strength of the Dutch scientific community is its traditional opennes and the intertwinement with the international community. We see that reflected in many international scientific cooperations and increasingly in the international background of our staff’
From now on Pedro Crous is one of them.

(Photo: KNAW/Inge Hoogland)

Karoline Dukik successfully defended her thesis

On 11 September 2018, Karoline Dukik, PhD in the Medical Mycology Research Group, successfully defended her thesis "A journey through onygenalean families Arthrodermataceae and Ajellomycetaceae" at the University of Amsterdam.

During her PhD, Karolina Dukik, a researcher in the Medical Mycology Research Group at the Westerdijk Institute, was working on the two medically important groups of fungi, the dermatophytes and dimorphic systemic fungi. The main focus of the research was the phylogeny of these fungi based on multilocus analysis. Additional work was done on developing new identification methods based on mass spectrometry LC-MS/MS method and the polyphasic approach and the antifungal susceptibility testing for the newly described dimorphic fungi. This research was done under the supervision of Sybren de Hoog.

White-rot thesis defended by Sara Casado Lopez

At first she didn’t know them that well, but now she knows, she is impressed; no she is “superimpressed, with all the things we can get from fungi!”
Sara Casado Lopez succesfully defended her thesis today about ‘The role of a white-rot fungus and its offspring in wood colonization and degradation.’
Why white-rot? Because those fungi could be of interest in the bio-fuel and biochemical industry and because they are not well-studied. At the moment most research is performed on ascomycetes instead of basidiomycetes. This is because the first are efficient producers of enzymes, they are relatively easy to genetically manipulate and they behave well in fermenters. Basidiomycetes are less easy to manipulate. Sara Casado Lopez focused on white rot in her research because of one very interesting property: the capability of white-rot fungi to decompose all wood polymers including lignin, the stuff that gives wood cells and plant cells their rigidity. And it is especially that stuff that is a problem in the paper and textile industry and in the world of bio-fuels. Not that Sara Casado Lopez solved the problems, but she made some important steps towards dissecting the regulatory network driving the expression of the genes encoding biomass degrading enzymes in the white-rot fungus, D. squalens. 
The next steps have to be taken by others. “I spent some time with white-rot and I stay impressed: this is the only group able to decompose lignine. I saw it: massive blocks of wood turned to gelatine in months. I saw it with my own eyes. We have to use this property.”.

A Day in a Cell
meet your tiniest parts at the weekend of science

Meet, feel, see, measure and construct cells at three worldfamous institutes:
The Westerdijk Fungal Biodiversity Institute, the Hubrecht Institute and the Regenerative Medical Center Utrecht closely work together, that’s why they present this day together too.
Ever looked inside a cell? No? Now you can, at the Weekend of Science. Stick your head into a cell enlarged 100.000 times and see what’s inside.
You can also have a look at the real thing. Watching through a microscope, you see cells  dividing right under your nose. See them grow, colour them, look at the differences between cells with the same DNA. For a small group of people there will even be a rare opportunity to look through a confocal microscope, the state-of-the-art microscope that enables you to see chromosomes of a living dividing cell: mitosis caught red-handed.
There is lots to discover for children and grown-ups at the Weekend of Science.
The Westerdijk Fungal Biodiversity Institute lets you taste fungi and smell fungal farts.
You can make your own drawing with yeast.
Learn how our scientists discover new microfungi. Meet the people that gave their name to 16 new fungi: theywere the persons that found them participating in a citizen science project.
Admire the amazing beauty of fungi, see them grow in breathtaking movies and make pictures with your own smart phone through a microscope.
Play a ball game to learn about fungal resistance.
And last but not least: speed-date with scientists and other employees and ask them everything you always wanted to know about their work.

What else is there to do? Among other things this:

The Hubrecht Institute presents several activities. Get an impression of the length of DNA folded in each cell, make a necklace of nucleosomes (and learn what they are). Isolate your own DNA, colour your own cells and see how they turn out.
There is a striking similarity between organoids and popcorn. Taste some popcorn while looking at these organoids; living 3D mini-organs that grow outside the body.
Looking through a microscope boring? Not if you see a worm and a fish embryo growing under your eyes.
It is very difficult to imagine how small a human cell is and how many we have. Yet we can now look on a molecular level what each single cell produces. See in the lab how they do it.
Our body is object of study by Regenerative Medicine Centre Utrecht.
When do you realise how difficult a task is? When you try to do it. Trying to build an artificial kidney makes you realise how incredible complex this organ is. The first artificial kidney, invented by Willem Johan “Pim” Kolff will be on display, next to the latest one.

A Day in a Cell, 7 October,
Westerdijk Fungal Biodiversity Institute 
Uppsalalaan 8, 3584 CT Utrecht,
From 11.00 to 16.00

Preparations are in full swing

Heineken Prize!

The Royal Netherlands Academy of Arts and Sciences has awarded the 2018 Dr A.H. Heineken Prize for Environmental Sciences to Paul Hebert, Research Chair in Molecular Biodiversity at the University of Guelph (Canada).
‘A good decision. He deserves it, without any doubt’ is the reaction of Pedro Crous, director of Westerdijk Fungal Biodiversity Institute.
Paul Hebert is known as the ‘father of DNA barcoding’. Key is the idea of using a short distinctive section of DNA to identify different species and in that way assign barcodes to practical all species on Earth. A great idea and useful too, according to Pedro Crous, you need it to know which fungus you are dealing with: ‘If you don’t know it, you can’t protect it.‘
Paul Hebert started out with butterflies, Crous and the Westerdijk Institute started with fungi. That is, only after a lot of discussion about the best DNA region to use as a universal barcode marker for Fungi. It became the ITS region, proposed by C.L. Schoch et al. and the Fungal Barcode Consortium in a 2012 PNAS paper called: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. In that article the authors already mentioned that it was ‘unlikely that a single-marker barcode system will be capable of identifying every specimen or culture to species level.’ Indeed a few years on, a second barcode marker was proposed in the 2015 Persoonia  article  One fungus, which genes by J.B. Stielow et al.
From that day on it went fast. No less than 100.000 fungi have been marked with their own barcode, some of which date from as early as 1887.
Back to the ‘father’ of all this: Paul Hebert, this years Heineken Prize for Environmental Sciences laureate, (worth USD 200.000). He is now the scientific director of the International Barcode of Life Project, iBOL, in which researchers of 25 countries try to assign barcodes to millions of species on Earth.  So far genetic codes of approximately 600.000 species are available for the science community. According to the announcement of the KNAW (Royal Dutch Academy of Arts and Sciences): ‘If the projects succeeds, its legacy will yield lasting benefits to humankind’

From left to right: Erik van Lieshout, Xiaowei Zhuang, Peter Carmeliet, Paul Hebert, John McNeill, Nancy Kanwisher, Charlene de Carvalho-Heineken, Wim van Saarloos (Photo: Frank van Beek) 

Course Fungal Biodiversity 2019

4-15 February 2019

Location: Westerdijk Fungal Biodiversity Institute, Utrecht, Uppsalalaan 8, The Netherlands.
Registration € 2000,-

This two-week course provides a concise overview of the biodiversity of organisms making up the Kingdoms Fungi and Chromista. The course focuses on systematics and general ecology of fungi, as well as related topics such as soil mycology and diagnostics of plant pathogens. Both visual and molecular recognition methods will be discussed and practical hands-on experience will be gained in the morphological recognition, isolation and cultivation of fungi. The course is intended for (micro)biology students, PhD students, technicians and scientists/students who would like to obtain a fundamental understanding of fungi

Outline of the topics treated in this course:

  • General Introduction  
  • General methods: Aseptic working, media and incubation, microscopic examination of Fungi 
  • Introduction to the Fungal Kingdom with examples: Oomycota, Zygomycota, Ascomycota, Basidiomycota, deuteromycetes, yeasts 
  • Oomycota and Chytridiomycota with examples 
  • Zygomycota (Mucoromycotina) 
  • Nomenclature of Fungi
  • Conidiogenesis with examples 
  • Aspergillus, Penicillium, Paecilomyces and sexual morphs with examples 
  • Ascomycota 
  • Basidiomycota (Pucciniomycotina, Ustilaginomycotina, Tremellomycetes )
  • Isolation techniques (soil, plants and dung) 
  • Trichoderma, Fusarium, Cylindrocladium and Cylindrocarpon 
  • Fungal ecology 
  • Coelomycetous asexual morphs 
  • Genera with septate and pigmented poroconidia (Alternaria, Bipolaris, Cladosporium, Curvularia)
  • Basidiomycota (Agaricomycetes, incl. wood decay fungi)
  • Molecular methods for identification such as DNA-barcoding and phylogenetic inference
  • Yeasts: biology, phylogenies and polyphasic identification 
  • Polyphasic identification and other aspects of bioinformatics 
  • Nagoya protocol (Access and benefit Sharing)
  • Diagnostics of plant pathogens 
  • Preventing the spread of plant pathogens 
  • Life-cycles of obligate biothrophic plant pathogens (Uredinales, Ustilaginales, Erysiphales) 
  • Introductory lecture on material available living plants with disease symptoms 
  • Ecology of extremophilic  and clinical fungi  
  • Fungi in our daily life  
  • Demonstrations: CBS collection (lyophilization, liquid nitrogen)

Course leaders:
Prof Dr Pedro Crous and Dr Gerard Verkley
Topical lectures will be presented by specialists from the Westerdijk Institute and invited speakers

Language of instruction:
The course is given in the English language, but several other languages are spoken (Dutch, German).

The course will take place at Westerdijk Institute, Utrecht, Uppsalalaan 8, the Netherlands

Course fee:
€ 2000 (accommodation and food not included).

Lunches and the Course book Laboratory Manual Series I: Fungal Biodiversity by Crous et al. are included in course fee. Accommodation excluded.


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