Westerdijk Fungal Biodiversity Institute
The Westerdijk Fungal Biodiversity Institute is an independent research institute of the Royal Netherlands Academy of Arts and Sciences, situated on the campus of the largest university in the Netherlands (Utrecht).
It studies fungal biodiversity in the widest sense, focusing on three priority areas, agriculture, human health, and industry (indoor air and food).
Presently there are 6 research groups with a total of about 80 employees. The institute maintains a large culture collection of fungi and yeasts,
and research groups such as those of Pedro Crous (Evolutionary Phytopathology), Jos Houbraken (Applied and Industrial Mycology), Sybren de Hoog (Origins of Pathogenicity in Clinical Fungi),
Teun Boekhout (Yeast and Basidiomycete Research), Ronald de Vries (Fungal Physiology) and Vincent Robert (Bioinformatics).
Yeasts are among the best studied eukaryotes on earth due to some very well studied species, such as Saccharomyces cerevisae and Schizosaccharomyces pombe. This, however, covers only a fraction of the known diversity of yeasts.
Our research focuses on:
Understanding yeast biodiversity and evolution
Mechanism of pathogenicity
Fungal biodiversity and ecology
Producing food sufficient in quality and quantity remains paramount for sustaining quality of life. Inadvertent introductions of phytopathogenic fungi have had dire consequences to nature and to cultivated crops on various continents in the past. The economic impact of such introductions can be seen in yield loss and in increased input costs for cultivation and disease control, as well as in social impact. To combat these diseases on an international scale, it is important to clarify whether the same species and genotypes occur in various countries, since each different species and genotype can be expected to have different patterns of attack, as well as different responses to fungicides and to climatological conditions. With such pathogens, it is also important to know what their host ranges and mating strategies are, and how this relates to different disease control mechanisms. The global movement of agricultural and forestry produce is inextricably cross-linked, and will continue to be so in future. Knowing which pathogens occur where and on what crops facilitates trade in agricultural produce. In this programme, we address these economically vital matters by investigating the speciation and host adaptation of various important phytopathogenic fungi.
Understanding pathogenicity and virulence of fungi causing infections in humans is of prime importance in the hospital, predicting clinical course and applying adequate and cost-effective therapy. The clinical world is focused on the major causative agents of disease, particularly Candida, Cryptococcus and Aspergillus. Outside these groups, a large diversity of potentially harmful fungi exist which may be rare, but frequently have the pathogenic potential to be more important than the common clinical fungi. Several are able to cause fatal disease in otherwise perfectly healthy human hosts. Our objective is to reveal the natural ecology and routes of transmission of such fungi, in order to explain their pathology. We carry out a comparative approach, in order to place known virulence factors in perspective. Since most of the clinically significant fungi are opportunistic, a large share of our work is devoted to extremotolerant fungi that possess several factors in common to fungi of clinical significance.
Fungal physiology is the basis of biotope and global dispersion of fungal species. It determines the nutrients it can use, the environmental conditions it can endure and its competitive position in its ecosystem. The ability of fungi to survive in every known biotope, both natural and man-made, relies in part on their capacity to use a wide range of carbon sources. In nature, many fungi degrade polymeric carbon sources (e.g. polysaccharides, proteins, lignin) to use the monomeric components as carbon source. However, the available carbon sources vary strongly in nature, both between biotopes and in time. While some fungi have become specialists that focus on specific carbon sources or specific biotopes, others are more generalists that can grow in many biotopes and use a large variety of carbon sources. Differences in physiology may therefore also reflect species boundaries.
Degradation of polymeric carbon sources occurs extracellularly by a broad range of enzymes, of which the production is tightly controlled by a network of regulators. This enables fungi to produce an enzyme mixture that is tailored specifically for the available carbon sources at any given time. The released monomeric compounds are transported into the cell and metabolized through a variety of metabolic pathways. These pathways are often co-regulated with the extracellular enzymes that release the compounds entering the pathways, resulting in a highly complex regulatory and metabolic network. To study fungal physiology in relation to natural substrates it is therefore necessary to address all these aspects of fungal biology: production of extracellular enzymes, metabolic pathways and regulators controlling the fungal response to the substrates present in the environment.
Ronald de Vries is also Professor in Fungal Molecular Physiology at Utrecht University, The Netherlands, which forms a strong link between CBS and UU.
Culture collections such as the Centraalbureau voor Schimmelcultures (CBS, The Netherlands) need to manage large numbers of strains (the records) and characters (the fields). Until a few years ago, collected data were essentially used for taxonomic purposes. Most of the time, these were not disclosed to users outside the institute. Only the strain’s species name was available together with a few additional data such as depositor, substrate, and strain origin, in printed catalogues. Several years ago, CBS decided to tackle this problem and to create databases that would contain all possible sources of information at the strain and species levels. This task was far from trivial since it involved integration of many different sources of information (e.g., administrative data, bibliography, geography, pictures, nomenclature, morphology, physiology, biochemistry, molecular data [electrophoresis results, sequences, …]), as well as hyperlinks to other web based repositories. From the beginning, it was apparent that conventional searching tools in commercially available databases did not fit CBS needs. Therefore, new software called BioloMICS was developed capable of searching, identifying, classifying, and analyzing all available data in a polyphasic way. Many new tools and algorithms were programmed and the current version of this software is fully adaptable to the end-users’ needs (e.g., lists of and weighting of characters can be changed dynamically).
The group is now focusing on the incorporation of genomic data into our system and use them as product and functional discovery tools.
Filamentous fungi are playing an important role in our daily life, for instance as parts of food products or as food spoilers. In addition, they also occur inside human dwellings in air and on walls as so-called indoor fungi. These genera are overrepresented as spoilage agents of food and beverages, as producers of toxic compounds and as fungi in human dwellings. They even occasionally occur as human and animal pathogens. On the other hand, many species of these genera are very important industrial microorganisms in food fermentation and biotechnology. Finally, the organisms are avid producers of a wide variety of (putative) bioactive compounds. The area of the research group is to study the biodiversity, phylogeny and cell biology of fungi with special relation to food and indoor mycology, with an emphasis on the genera Penicillium, Aspergillus, Paecilomyces and Talaromyces.
The mission of the program is to reach a deeper understanding of applied and fundamental aspects of fungi in their relation to food-association and indoor situations. These include a novel polyphasic classification of the subgroups of the order Eurotiales, and the development of tools for a practical barcoding system of these groups. To understand the biology of the important fungi in these applied fields, the biology of the fungal cell is studied, in particular on the topic of cell stress. These studies include extreme stress resistant ascospores, the sensitivity of fungal conidia for antifungal compounds and the reaction of growing fungi on drops in relative humidity. The research of the group has always been intertwined with numerous (smaller) projects with external parties (industrial companies and governmental institutions) that request expertise with problems related to food spoilage, indoor environments and industrial applications. This is illustrated by the fact that several large fundamental or applied research projects have been directly initiated as a result of these smaller projects.
The CBS Collection of Fungi has more than 60.000 strains in its public collection, making it the largest mycological culture collection in the world. CBS is unchallenged as a reference collection for mycological research, as practically all culturable groups of the Fungal Kingdom are represented. Annually, thousands of CBS strains are delivered to some 50 countries. To underpin its dedication to quality in materials and services, CBS set up a quality management system, for which it obtained an ISO 9001:2000 certificate in November 2007. CBS strains are also selected for DNA sequencing projects in the framework of global initiatives, such as the Fungal Tree of Life and DNA Barcoding. The CBS Bacterial Collection (NCCB) consists of another 10.000 strains, including a unique Plasmid and Phage Collection. The high quality of CBS strains is ensured by the practice of having identities and typical features authenticated by specialists of CBS and elsewhere. Scientific and other data related to the strains are constantly added. Much attention is given to expanding and improving CBS web-services, not only by digitising publications, but also by allowing clients to use various types of collection data. CBS has developed web-based polyphasic identification for specific groups such as yeasts, and plans to also include additional economically important groups. Moreover, CBS developed MycoBank, an on-line registration system for new fungal taxonomic names now under the auspices of the International Mycological Association (IMA).
Daily Website Users
Researchers & Employees
3584 CT, Utrecht
P.O. Box 85167
3508 AD, Utrecht
Phone: +31 (0)30 21 22 600
Fax: +31 (0)30 21 22 601
Fungal collection curator:
Dr. Gerard Verkleij
Yeast collection curator:
Dr. Marizeth Groenewald
Collection of Bacteria:
Mrs. Marian Figge
Restricted collections (Budapest Treaty & safe deposits):
Mrs. Francis Claus (sales)
Ordering Books, Journals & information on Courses:
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