NATARC

Database of Estonian fungi collections

The database comprises data of specimens of fungi preserved in the collections of the University of Tartu (TU) and in the Estonian University of Life Sciences (TAAM, EAA), as well as in the herbarium of the Tallinn Botanic Garden (TALL). In the creation and improving of the database people from all these three institutions participate.

Presently 307 702 specimens are recorded in the database, of which:

TAAM: 127 576 specimens
TAMM: 3 973 specimens
TALL: 22 963 specimens
EAA: 24 379 specimens
TU: 128 811 specimens

Locality points are clickable and linked to specimen. Intensive circles mark groups of country centroids where exact location is not available.

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About the database

In the Estonian fungi collections ca 320 000 specimens of fungi and lichens are preserved, of these about 100 000 are recorded in the database now, this is a work in progress. The accessibility of data is improving, this is a work in progress as well. These days data may already be searched in multiple ways, one can submit inquiries quite according to ones’s interests already, but possibilities to do so are being improved in the near future. All the data on the labels of specimens has not been represented, as it has been considered to be more important to give a good overview of the relevant data. The scientific web-based relational database has been in development since the 1990s. Work on it was begun in the Department of Mycology of the Institute of Zoology and Botany (now belonging to the Institute of Agricultural and Environmental Sciences of the Estonian University of Life Sciences). As creation of a relational database is a long process, the system of the database Biota (The Biodiversity Database Manager, vers. 1 and 2.02) was used in the beginning, this system has been used in inserting the data of mycological collections in several instututions before. Meanwhile a relational database was being developed, with web-based outputs and modules for inserting data. The data from Biota have now been transferred into the new database PlutoF. PlutoF has been built on the software platform MySQL which „runs“ in the server Red Hat Linux/Apache. The web pages are created using programming languages PHP, Perl, AJAX, et al.

The lichenized fungi have been inserted in databases since 1990s, back then it took place in the Institute of Botany and Ecology of the Tartu University (now the Institute of Ecology and Earth Sciences, Department of Botany). Data was inserted using the BRAHMS program (Botanical Research And Herbarium Management System, University of Oxford). In 2008, data of 39 500 specimens recorded in BRAHMS at that time was transferred into the new database, PlutoF. The staff of the institute is developing another database as well, namely eSamba.

Fungariums

The dried specimens of fungi (including lichenized fungi) are mainly preserved in four collections in Estonia, the total number of the preserved specimens is ca 320 000.

TU - the fungi and lichen collections of the Botanical and mycological museum in the University of Tartu Natural History Museum. The acronym TU is shared by all the collections in the Botanical and mycological museum in the University of Tartu Natural History Museum.

The lichen collection resides in the University of Tartu Botanical Gardens, in Lai 28. The collection holds an estimated 75 000 specimens of lichens, oldest of which come from the late 19th century. In the lichen collection the materials collected from Estonia (Herbarium Estoniae) and materials collected from abroad (Herbarium Generale) are kept separately. Most of the lichens preserved in the Estonian collection have been gathered in the second half of the 20th century in many different scientific projects. The largest and most valuable part of the general collection of lichens – ca 20 000 specimens – was brought from the Estonian scientists’ expeditions to the Russian Far East and the area of Baikal. The collection of over 3500 specimens from Australia, New Zealand and Papua New Guinea is remarkable also. In the lichen collection 65 type specimens of species and intraspecific taxa are preserved.

The older part of the University of Tartu fungi collection (mostly Agaricales) were deposited in 1969 in the fungi collection of the Estonian University of Life Sciences (TAAM). Most of the 11 000 specimens were gathered by Kuulo Kalamees and his students in 1958–1969. Materials gathered in the 21st century are preserved in the Tartu University building in Ravila 14A. In recent years the fungi collection of the University of Tartu Natural History Museum has grown fast via the scientific expeditions all over the world. In few recent years type specimens of 12 new species have been deposited here.

EAA - the collection of the phytopathogenic fungi in the Estonian University of Life sciences, also known as the collection of E. Lepik (Leppik), or, as the fungi collection of the University of Tartu Cabinet of Plant Diseases, later of the University of Tartu Chair of Botany (1922–1952), of the Estonian Academy of Agriculture, later of the Department of Plant Protection in the Estonian Agricultural University (1952–2005). Founded in 1922. Postal address: 51014 Tartu, Kreutzwaldi 5D, Estonian University of Life Sciences, Institute of Agricultural and Environmental Sciences, Department of Mycology. Phone: 7 311 895. Contact: curator Kadri Pärtel, kadri.partel@emu.ee.

23 000 specimens of over 9000 species of fungi, most of these published in Europe as exsiccata or doublets from famous mycologists (F. Petrak, K. Linkola, K. Starcs, A. Kirulis, E. Kari et al, E. Lepik). The collection also includes the herbarium of F. Bucholtz, the Hungarian (Slovakian) materials bought from J. A. Bäumler, and fungi gathered by E. Lep(p)ik in 1920–1940 mainly from Estonia. Fungi from Estonia that have been taken in in the last fifty years have been gathered mainly by K. Kivi and A.-L. Sõmermaa.

TAAM - herbarium of the Department of Mycology in the Institute of Agricultural and Environmental Sciences of the Estonian University of Life Sciences (in 1950–2000, of the Institute of Zoology and Botany of the Estonian Academy of Sciences; in 2002–2005 of the Institute of Zoology and Botany of the Estonian Agricultural University). Founded in 1950. Address: Department of Mycology, Institute of Agricultural and Environmental Sciences of the Estonian University of Life Sciences, Kreutzwaldi 5D, 51014 Tartu. Phone: 7 311 895. Contact: curator Kadri Pärtel, kadri.partel@emu.ee.

Over 185 000 specimens, ca 7000 of these belonging in the collections of exsiccata. Ca 400 type specimens, most of which are materials of species described by the staff of the former Institute of Zoology and Botany (Erast Parmasto, Ain Raitviir, Kuulo Kalamees, et al). Most of the collection has been gathered by the mycologists of the former Institute of Zoology and Botany from Estonia, Caucasus, Siberia, Central Asia, Russian Far East, somewhat less from Australia, Austria, Belgium, Greenland, Spain, India, Italy, Canada, Lithuania, Latvia, Netherlands, Norway, Poland, France, Sweden, Germany, Finland, Switzerland, Thai, Tanzania, Czech, USA, European part of Russia, United Kingdom. Each year specimens are being lent out by scientists from abroad.

TAMM - collections of the Estonian Museum of Natural History are founded on the collections transferred from the Provincial Museum of Estonia established in 1864. The mycological collection contains approximately 3 000 specimens, the oldest of which date from the second half of the 19th century. The bulk of the collection is composed of the collection of lichens, or lichenized fungi. About 2 000 of the more than 2 700 herbarium specimens have been collected from Estonia by a number of Estonian scientists, amateurs and employees of the Museum of Natural History (Herbarium Estonicum). Over 500 specimens have been collected from abroad, mainly from Scandinavia and elsewhere in Europe (Herbarium Generale). The exsiccate collection of lichens (Herbarium Exsiccatae) contains about 230 specimens. The collection of non-lichenized fungi comprises roughly 250 specimens.

TALL - Herbarium of the Tallinn Botanic Garden. Founded in 1962. Address: Kloostrimetsa tee 52, 11913 Tallinn. Phone: 6062673; e-mail: merlyn.pajur@botaanikaaed.ee. Curator: Merlyn Pajur.

The collection of fungi comprises ca 8000 specimens. Most of the collection (the representatives of the family of Erysiphaceae) has been collected by the former staff of the Tallinn Botanic Garden, Harry Karis and Thea Normet, from Estonia, but also from the European part of Russia, from Siberia and the Far East.

The collection of lichens includes an estimated 40 000 specimens, of which ca 4900 have been ordered and inserted in the database. Many of the Estonian lichens have been gathered while on field studies on lichenoindication. Many samples have been gathered by the former curator of the Tallinn Botanic Garden, Taimi Piin-Aaspõllu (03.09.1940–02.09.2012) from the Taimõr Peninsula in Russian region of the Arctic.