PEER REVIEW CBS-KNAW 2008–2013 To Collect, Study and Preserve Self-evaluation report 2008–2013 of The CBS Fungal Biodiversity Centre (CBS-KNAW) Utrecht 2014 CBS directors Prof. Dr Pedro W. Crous, Director (2002-present) Dr Mariëtte A. Oosterwegel, Managing Director (2012-present) CBS Fungal Biodiversity Centre (CBS-KNAW) Uppsalalaan 8 3584 CT Utrecht The Netherlands T +31 (0)30 2122600 www.cbs.knaw.nl [email protected] Postal address: P. O. Box 85167 3508 AD Utrecht The Netherlands Preface It is with great pleasure that we herewith present the self-evaluation of the CBS Fungal Biodiversity Centre of the Royal Netherlands Academy of Arts and Sciences. The report evaluates our research accomplishments over the period of 2008–2013. As stipulated by the Dutch self-evaluation protocol, the report contains general documentation pertaining to the institute as whole, while the research programmes and future perspectives are also presented. The preparation of this report required input from numerous members of staff, and we would like to take this opportunity to thank all of them for their time and dedication. The present self-evaluation presents a good overview of the past performance of the CBS, and also clearly establishes our exciting future research goals in fungal biodiversity. April 2014 Prof. dr P.W. Crous (Director) Dr M.A. Oosterwegel (Managing Director) Contents 1. CBS Fungal Biodiversity Centre (CBS-KNAW) 1 2. Evolutionary Phytopathology Programme – P.W. Crous 15 3. Origins of Pathogenicity in Clinical Fungi Programme – G.S. de Hoog 24 4. Yeast Research Programme – T. Boekhout 33 5. Applied and Industrial Mycology Programme – R.A. Samson 44 6. Fungal Physiology Programme – R.P. de Vries 54 7. Bioinformatics Programme – V. Robert 62 8. Collection – G. Verkley 79 9. Appendix - Bibliometric analyses 91 Additional information online: www.cbs.knaw.nl/index.php/research e.g. access to PDFs of key publications. 1. CBS Fungal Biodiversity Centre (CBS-KNAW) 1.1 Objectives and research area Introduction and history The AIM of the CBS Fungal Biodiversity Institute (CBS) is to study all aspects of fungal biodiversity in three focused themes, namely Agricultural, Industrial, and Medical mycology. CBS is one of four life science institutes in the Royal Netherlands Academy of Arts and Sciences (KNAW). It employs around 70 scientific staff, plus 20–30 support staff, which it shares with the Hubrecht Institute, its neighbour institute on De Uithof in Utrecht. CBS has an annual Academy budget of approximately 3 million euros, and generates an additional 3–4 million euros from industry and research grants. The CBS was established in Baarn in 1904 to house a collection of fungal cultures following a decision taken at the 11th International Botanical Congress at Vienna. For some time between the two World Wars CBS was financially supported by the Royal Netherlands Academy of Arts and Sciences, of which it became an official institute in 1968. Professor F.A.F.C. Went, who was responsible for founding the culture collection, appointed the first female professor in the Netherlands, Prof. J. Westerdijk, as first director of the institute in 1907. In December 2000 the CBS moved to Utrecht where it was accommodated in a completely renovated building, previously occupied by the Hubrecht Institute. The complete staff and collection of the yeast department from T.U. Delft also joined the staff, followed by the Dutch bacterial culture collection NCCB, containing the wild- type collections of the T.U. Delft and the Phabagen collection of Utrecht University. The CBS culture collections of micro-organisms are embedded in a scientific environment, which guarantees state of the art quality checks, and simultaneously allows for the development of scientific programmes to improve the quality of the material entrusted to them. CBS was actively involved in setting the international standards for modern long-term preservation as well as for data storage, and recognising the necessity of data exchangeability. It was also one of the first public culture collections to make its complete open catalogue available on the internet. The CBS Collection has been ISO 9001:2008 certified since 2007. The Collection is partner of the Microbial Resource Research Infrastructure (MIRRI). MIRRI aims to build one pan-European infrastructure for microbial collections and to establish links across the distributed microbiological resource centre community, its users, policy makers and potential funders. As member of the Consortium for the Barcode of Life (CBOL), International Barcode of Life (IBOL), and coordinator of the European Consortium for the Barcode of Life (ECBOL), the CBS has undertaken an ambitious programme to generate DNA barcodes (ITS, LSU) of all its holdings [80 000 strains of filamentous fungi (open and non-public collection), and 9 500 yeast strains], transforming it into a Genetic Resource Centre that can actively serve the research community of the future. The present self-evaluation covers the period 2008–2013 of the research activities of the CBS. Vision, mission and objectives of the institute Vision: CBS is one of the major microbial Genetic Resource Centres in the world. As such, our unique fungal collection and databases, linked to a strong research staff component, enable us to participate in diverse EU, national and international research programmes, focusing on innovative research in industrial, medical and agricultural mycology. Our vision is to collect, study and preserve as much of the world’s fungal biodiversity as possible, and to unlock this resource for the international research community, using current state of the art techniques. Initiatives such as MycoBank, EU-BOLD, and Open Access Journals (Studies in Mycology, Persoonia, IMA Fungus) are true to the CBS mission and focus, and will further strengthen the institute, and promote mycology as discipline. Part 1 - CBS Fungal Biodiversity Centre (CBS-KNAW) 1 Mission: The CBS Fungal Biodiversity Centre was established more than 110 years ago with the specific mission to preserve the world’s fungal biodiversity. Presently the CBS includes the largest known public service collection of living fungi. The CBS is the world leader for the elucidation of fungal biodiversity, of which presently is estimated that less than 10% is known. From its fast growing culture collection, the CBS aims to initiate fundamental and applied research with other (inter)national research groups on the exploration of the vast potential that fungi represent with respect to agricultural, industrial and medical themes. As such, the CBS as genetic resource centre is an (inter)national hub for mycological research. Objectives: CBS has chosen to transform itself from simply being an international culture collection to being the trendsetter and gold standard of mycology. Our core business is the collection, and our research programmes add value to that collection. Each research programme consists of several projects. While some projects represent “discovery science”, focusing on discovering biodiversity, others are focused on “understanding processes”, and thus on striving to unravel metabolomic, proteomic or genomic complexities of specific fungal groups or species. A third approach is “recognition science”, developing diagnostic tools for practical use in industry, plant pathology, and in the hospital. Our main objective, however, is to collect, study, preserve and unlock the world’s fungal biodiversity, enabling us to do innovative research in agriculture, human health and industry. Research area The CBS Fungal Biodiversity Centre is an institute of biosystematics, with the culture collection at its core. The primary aim of its research programmes is to enhance its unique living collection of fungi by adding valuable new data and cultures. Research activities and programmes are coordinated in three focus areas (based on national and international relevance, impact, service to society, and available expertise). Table 1.1. Research themes and programmes. Theme Programme Leader Period Agriculture Evolutionary Phytopathology Prof. dr P.W. Crous 2002– Medical Origins of Pathogenicity in Clinical Fungi Prof. dr G.S. de Hoog 2002– Medical Yeast Research Dr T. Boekhout 2002– Industry Applied and Industrial Mycology Prof. dr R.A. Samson 2002– Industry Fungal Physiology Programme Prof. dr R.P. de Vries 2009– All themes Bioinformatics Programme Dr V. Robert 2009– 1.2 Composition Structure The institute has three research themes containing six programmes (Table 1.1, Fig. 1.1). Each programme has at least a group leader, and senior technician. Each group leader is expected to build his/her own group through acquisition of external funds. Biosystematics requires combined expertise, and thus various members from different groups, including the collection and the bioinformatics programme, frequently work together on specific projects between the various groups. The present evaluation presents condensed information pertaining to the various research programmes. Additional information, such as publications, can be found online. Research is supported by technical staff with different expertise (e.g. molecular, culture collection, bioinformatics). Although technicians are assigned to specific programmes, most provide support CBS-wide, as well as to visiting scientists and students, pending on their fields of expertise. Non-scientific support is provided by the Collection, and 2 the Central Management & Services staff (Financial Administration,