The National Programme on Conservation and Utilization of Microbial Genetic Resources and Invertebrates of Agricultural Importance

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COLLECTIONS OF FUNGI


VURV-F VURV-A VURV-M RIBM CCF CCPO RIFIS CCBAS SPCH UPOC-FUN CCM CCDM CCDBC


Collection of Agriculturally Important Fungi (VURV–F),
(VÚRV, v. v. i., Praha)

The collection was found in the 90-thies of the twenty century. Since this time Dr. Jiřina Krátká, Dr. Eliška Sychrová and Dr. Michaela Zemánková participated on the direction and focusing of it. Dr. David Novotný is the current head and curator of the collection.

• Characterization of collection
The collection holds strains of fungi from groups Ascomycota, Basidiomycota, Zygomycota and microorganisms from group Oomycota cultivable in in vitro conditions. The fungi are pathogens or potential pathogens of plant or edible or medicinally mushrooms. The collections keeps mycotoxinogenic or potential mycotoxinogenic fungi, fungi useful or potentially useful in plant protection or for detection of harmfully microorganisms of plant, fungi damaging stored agriculturally products or edible and medicinal mushrooms. At present time, the collection holds more than 750 strains of fungi or microorganisms similar to fungi (Oomycota).

• Activities, services
The main activities of the collection are collecting, maintaining, supplying cultures, providing information on strains in the collection and preserving genetic resources of fungi. Collection accepts strains of fungi or microorganisms similar to fungi free of charge from other subjects.
Collection provides service identification of fungi or fungus-like microorganisms (Oomycota), service freeze-drying of strains, safe deposit service of strains, patent deposit of cultures under Czech national rules, provides advisory and consultation services on taxonomy and ecology of fungi, isolation, identification and preservation of fungi

• Methods of culture maintenance
The strains are preserved in liquid nitrogen, in form freeze-dried conserves (only the strains creating spores and yeasts) and under paraffin oil on an agar slant in test tubes.

Contact:
Crop Research Institute (Výzkumný ústav rostlinné výroby, v. v. i.)
Culture collection of microorganisms of Crop Research Institute
Collection of agriculturally important fungi
Division of Crop Protection and Plant Health
Ecology and Diagnosis of Fungal Plant Pathogens
Drnovská 507/73
161 06 Praha 6 – Ruzyně
Czech Republic
https://www.vurv.cz/en/research/genetic-resources/culture-collection-of-microorganisms-crop-research-institute/
E-mail: sbirka@vurv.cz
Phone: +420 233 022 341, +420 233 022 358

Staff:
Head and curator: Dr. David Novotný,
e-mail: novotny@vurv.cz,
phone: +420 233 022 341, +420 233 022 358, mobil: +420 702 087 691

Other workers: Jitka Dunaiová, Kamila Mitrovská

Collection of Biotrophic Fungi (VURV–A), VÚRV, v. v. i., Praha)

Determination of physiologic races of wheat rusts started in the sixties of the last century. Results were periodically published in scientific journals (Genetika a šlechtění, at present Czech Journal of Genetics and Plant Breeding or in Ochrana rostlin, at present Plant Protection Science). Results of race surveys were discussed with wheat breeders and applied in the wheat breeding for rust resistance. Since that time determination of rust races (pathotypes) is being carried out till now and isolates are stored.

• Characterization of collection
The collection comprises 826 leaf rust isolates, 29 stem rust isolates, 2 proveniences of yellow rust and 15 isolates of powdery mildew.

• Activities, services
The rust isolates are used in the tests for resistance in the field as well as in the greenhouse. Rust inoculum is used by domestic and also foreign breeders and institutions.

• Methods of culture maintenance
Determined rust isolates are kept in collections as urediospores. Powdery mildew is kept on leaf segments. Isolates most frequently applied are kept in a refrigerator at 5°C, the core collection is kept at ultra low temperature at -85°C.

• Systems of quality
Determination of rust isolates is carried our on international sets of differentials. It is based on determination of single pustule isolates. Approved methods are used for storing the rust and powdery mildew isolates.

• Involvement to national and international organizations/platforms
Rust isolates have been used in international scientific collaboration (Australia, U.K., France, Hungary, and Slovakia). At the domestic level accessions of the collection are used by plant breeders and by the Central Institute for Supervising and Testing in Agriculture and a similar institution in Slovakia.

Application:
• utilization of strains
Isolates are used in the wheat breeding as well as resistance testing both in the Czech and Slovak Republics. They are used by the Central Institute for Supervising and Testing in Agriculture and the. They are also used in the research work on national and international level.

• users, clients
Plant breeding companies
Central Institute for Supervising and Testing in Agriculture
Central Controlling and Testing Institute in Agriculture in Slovakia
Foreign scientific institutes

Contact:
Crop Research Institute
Division of Plant Genetics, Breeding and Product Quality
Drnovská 507
161 06 Praha 6 – Ruzyně
Czech Republic

Staff:
Mgr. Alena Hanzalová, Ph.D. (curator)
e-mail: hanzalova@vurv.cz, tel: 233022243
Ing. P. Bartoš, DrSc

Collection of Edible and Medicinal Macromycetes (VURV–M),
(VÚRV, v. v. i., Olomouc)

Collection was established in 2006 as a collection of diaspores – spores, sclerotia, etc., but mostly sporeprints, with the goal to create the original set of accessions of edible and/or medicinal species of fungi autochthonous for the Central Europe. Since 2008, the collection has been a part of the National Programme on Protection of Genetic Resources of Economically Significant Microorganisms and Tiny Animals.

• Characterization of collection
Our goal is to create a specialised mycological collection focused on acquisition and conservation of genetically homogenous cultures of autochthonous species of macromycetes potentially important for both private and commercial cultivations, and on support of newly developing horticultural mycotechnologies. Recently, totally 130 strains are included in the collection. The species of family Morchellaceae are the most numerous, the other strains belong to edible and/or medicinal Basidiomycetes.

• Methods of culture maintenance
Isolates are maintained as mycelial cultures on rye grains or malt extract agar with glucose in refrigerator, and under cryopreservation in the Central Laboratory of the National Programme in Praha-Ruzyně.

Contact:
Workplace:
Centre of the Region Haná for Biotechnological and Agricultural Research
Department of Genetic Resources for Vegetables, Medicinal and Special Plants
Crop Research Institute
Šlechtitelů 29, 783 71 Olomouc

Contact persons:
Curator: Dr. Irena Petrželová, Ph.D.
CRH for Biotechnological and Agricultural Research
Dept. of Genetic Resources for Vegetables, Medicinal and Special Plants
Crop Research Institute
Šlechtitelů 29, 783 71 Olomouc
Phone: 585208966
Mob.: 702087798
E-mail: petrzelova@genobanka.cz

Collection of Brewery Microorganisms (RIBM), (VÚPS, a. s., Praha)

The collection of brewer's yeast was established in 1946 as part of a collection of yeasts and yeast-like microorganisms under the leadership of Dr. Kocková-Kratochvílová, and has operated independently since 1953. Since 1964 the collection has been a member of the Federation of Czech and Slovak Collections of Microorganisms and is internationally registered as RIBM under the number 655. By focusing on the production strains of brewing yeast it is unique in Central and Eastern Europe. In 1996 the brewer's yeast collection became (as one of very specifically targeted and industrially applicable collections) part of the "National Program of the Gene Pool of Microorganisms and Small Animals of Economic Importance and their Use in Reference Diagnostics." This project is also supported by the Czech government in the form of a grant by the Ministry of Agriculture. The program is led by the Council of Microbial Genetic Resources, which monitors the mandatory retention of a functional existence of collections of microorganisms of a corresponding character.

• Characterization of collection
RIBM collection includes two separate collections, collections of brewer's yeast and collection of bacteria and wild and wine yeast. The collection currently includes a total of 308 strains of yeasts and bacteria. The most important part of the collection consists of a collection of 118 strains of brewer´s yeast Saccharomyces cerevisiae and S. pastorianus, collected continuously since 1953 from Czech and foreign breweries. A collection of wild and wine yeasts contains 79 strains classified into genera Saccharomyces, Torulaspora, Zygosaccharomyces, Dekkera, Williopsis, Pichia, Schizosaccharomyces, Saccharomycodes, Candida, Kloeckera and Rhodotorula. Collection of bacteria houses 108 strains of Lactobacillus, Leuconostoc, Pediococcus, Tetragenococcus, Lactococcus and three strains of genus Pectinatus.

• Methods of culture maintenance
Collections of brewing and wild yeasts are kept on agar slants under paraffin-covered cotton wool plugs and simultaneously on wort agars overlayered with sterile paraffin oil separately in a refrigerator. These best ways of keeping the cultures allow the rapid delivery to a customer of a strain in an active state on an agar slant or fermenting in 1.5 liters of wort, which facilitates the transfer of the production strain into production. Since 2006 strains of brewer's yeast are stored in cryo-tubes with protective medium in liquid nitrogen at -196 ° C. Storing in liquid nitrogen (cryopreservation) is considered optimal for the long term preservation of yeast in a viable state. Lactic acid bacteria are stored in parallel freeze-dried in skimmed milk in liquid nitrogen.

Application:
Use of the collection:
Collection strains are primarily used for research projects of RIBM and other research organizations (MSM6019369701, 1M0570, 2B08022 2A-2TP1 / 031, FI-IM5 / 067, QF3299, QI91B226 etc.). The strains are also used for teaching and diploma and doctoral works at universities.

Contact:
Research Institute of Brewing and Malting
Lípová 15
120 44 Prague 2

• curator
RNDr. Dagmar Matoulková, Ph.D.
matoulkova@beerresearch.cz
phone.: 224 900 132

• others
Ing. Petra Kubizniaková
kubizniakova@beerresearch.cz
phone.: 224 900 152
WWW: https://www.beerresearch.cz



Culture Collection of Fungi (CCF), (PřF UK, Praha)

The CCF was established in 1964-65 under the leadership of Dr. Olga Fassatiová. In 2006, part of Culture Collection of Fungi was incorporated into the Czech National Programme of Protection of Genetic Resources of Economically Significant Microorganisms and Tiny Animals (NPPGR).

• Characteristic of collection (strains), number of cultures
Culture collection maintains saprotrophic filamentous microfungi, predominantly Ascomycota a Zygomycota.
Under the Czech National Programme, over 300 fungal strains are maintained (of total 4880 strains); i.e. food contaminants, toxigenic fungi, plant pathogenic fungi, entomopathogens and fungi of biotechnological potential.

• Research activities
Taxonomy of ascomycetes
Biodiversity and ecology of of microfungi in natural and anthropogennic environment
Clinically important fungi

• Services
Supplying of fungal strains under the Czech National Programme free of charge (for non-commercial use).
Customer pays postage and packaging.
A non-commercial use agreement (MTA, Annex MTA) must be concluded.

• Charged services
Supplying of strains for both inland and foreign researchers and institutions for teaching and research purposes. The cultures are distributed on agar slants or in lyophilized form.
Safe deposition of fungal strains.
Freeze-drying of fungal strains.
Identification of fungal cultures.

• Methods of culture maintenance
In tubes on slope agar media in a refrigerator at approx. 5°C
Freeze-drying (skim milk as a protective medium)
Alginate pellets
Under mineral oil

Utilization of collection:
Maintenance of fungi for teaching and research purposes
Supplying of strains for non-profit institutions as well as industrial laboratories Long term maintenance of microfungi important for science.

Contact:
Institution/place
Charles University in Prague
Faculty of Science
Department of Botany
Culture Collection of Fungi (CCF)
Benátská 2
CZ - 128 01 Prague 2
Czech Republic

Staff:
RNDr. Alena Kubátová, CSc. (curator)
doc. Ondřej Koukol, Ph.D.
MUDr. Vít Hubka, Ph.D.
Mgr. Miroslav Kolařík, Ph.D.

Lada Syrovátková
Kateřina Glässnerová
Ivana Borovičková


E-mail: kubatova@natur.cuni.cz
Phone: +420 221951656 (Dr. A. Kubátová)
Fax: +420 221951645
Web page: CCF
Lyophilisates


Living fungal collection on slopes


Ascosphaera apis – fruit-body,
bee parasite


Aspergillus clavatus – conidiophores,
feed contaminant


Monascus purpureus – colonies,
producer of monakolin


Penicillium verrucosum – colonies,
producer of ochratoxin A

Czech Collection of Phytopathogenic Oomycetes (CCPO),
(VÚKOZ, v. v. i., Průhonice)

The collection was established in 2005 under the leadership of Karel Cerny and was admitted in 2012 as a member of The National Programme on Conservation and Utilization of Genetic Resources of Microorganisms.

• Characterization of collection
There are approx. 312 strains of approx. 29 oomycetous taxa preserved which are belonging to Phytophthora and (23 taxa) Pythium (6 taxa) in the accessible part of the collection. The other 400 strains are deposited in the non-public section of the collection. The isolates were acquired from many various plant hosts including forest, ornamental, and fruit trees as well as other hosts from various other environments (riparian and forest stands, parks, urban greenery, orchards, public gardens, gardening centres, ornamental and forest nurseries etc.). The collection is operated by Marcela Mrázková (custodian), Markéta Hejná (molecular determination) and Liliya Fedusiv (technician).

• Methods of conservation
Individual isolates are maintained on agar slants (OA agar) in vials in a refrigerator at a temperature of about 12 ° C in four tubes. Their condition is regularly monitored and the strains are regularly re-inoculated at intervals of 1-2 years.

Overview of deposited taxa
Phytophthora
1. Phytophthora ×alni (Brasier & S.A. Kirk) Husson, Ioos & Marçais
2. Phytophthora uniformis (Brasier & S.A. Kirk) Husson, Ioos & Aguayo
3. Phytophthora bilorbang Aghighi & T.I.Burgess
4. Phytophthora cactorum (Lebert & Cohn) J. Schröt.
5. Phytophthora cambivora (Petri) Buisman
6. Phytophthora cinnamomi Rands
7. Phytophthora citrophthora (R.E. & E.H. Smith) Leonian
8. Phytophthora cryptogea Pethybridge & Lafferty
9. Phytophthora gallica T. Jung & J. Nechwatal
10. Phytophthora gonapodyides (H.E. Petersen) Buisman
11. Phytophthora gregata T. Jung, Stukely & T.I. Burgess
12. Phytophthora hedraiandra De Cock & Man in 't Veld
13. Phytophthora lacustris Brasier, Cacciola, Nechwatal, Jung & Bakonyi
14. Phytophthora megasperma Drechsler
15. Phytophthora multivora P.M. Scott & T. Jung
16. Phytophthora palmivora (E.J. Butler) E.J. Butler
17. Phytophthora plurivora T. Jung & T.I. Burgess
18. Phytophthora polonica Belbahri, E. Moralejo, Calmin & Oszako
19. Phytophthora ramorum Werres, De Cock & Man in 't Veld
20. Phytophthora rosacearum (H.E. Petersen) Buisman
21. Phytophthora syringae (Kleb.) Kleb.
22. Phytophthora taxon Raspberry
23. Phytophthora taxon Walnut

Pythium
1. Pythium citrinum B. Paul
2. Pythium helicoides Drechsler
3. Pythium chamaehyphon Sideris
4. Pythium intermedium de Bary
5. Pythium ultimum Throw.
6. Pythium vexans de Bary

Application:
The collection aims for the preservation of genetic diversity of important phytopathogenic and other oomycetes in the Czech Republic for scientific and other purposes (tests of pathogenicity and host resistance, testing and development of control measurements, reference studies in science and phytosanitary services, systematics, education, etc.)

Contact:
Silva Tarouca research institute for landscape and ornamental gardening
Květnové nám. 391
252 43 Průhonice, Czech Republic
phone: +420 296 528 234
web CCPO

Staff:
Mgr. Markéta Hrabětová (Curator)
hrabetova@vukoz.cz

Ing. Marcela Mrázková
mrazkova@vukoz.cz

Molecular biolog:
Ing. et Ing. Šetinová Dita
setinova@vukoz.cz
Mgr. Markéta Hrabětová
hrabetova@vukoz.cz


Phytophthora alni (V8A, 20°C, 7 days)

Phytophthora citrophthora (V8A, 20°C, 7 days)

Phytophthora gonapodyides (PDA, 20°C, 7 days)

Phytophthora plurivora (V8A, 20°C, 7 days)


Collection of Industrially Utilizable Microorganisms (RIFIS), (VÚPP, v. v. i.)

• Activities, research activities, services
The Research Institute of Food Prague, v.v.i. manages and keeps the unique collection of industrially useful microorganisms RIFIS. The collection serves the needs of agriculture and food industries. The strains are used for processing food and agricultural commodities, for control analytical activities and research tasks solved in VUPP, v.v.i. and elsewhere.
We provide deposited bacterial strains with guaranteed characteristics in the required quality and quantity for scientific and research purposes.

• Collection characteristics (strains), culture counts
The collection contains bacteria, yeasts, and molds important in the food and agriculture industries. In 2023, the total number of strains was changed to 155, including 135 yeast strains, 13 bacterial strains, and 7 mold strains.

• Methods of strain preservation
The strains are preserved on slanted agar in an active state and stored in a refrigerator at 4 - 7 °C. Since 2020, strains have also been stored in cryovials with protective media in a deeply frozen state at a temperature of -80°C. Yeast and fungi strains are also long-term preserved by cryopreservation in liquid nitrogen, which is performed externally at the central laboratory of NPGZM at the VURV v.v.i. workplace.

Collection utilization
• Strains utilization
The most numerous group of microorganisms in the Collection are yeasts - 135 strains. The Collection contains strains of bakery, distillery, and wine yeasts used in the relevant fields, particularly in the area of research. There are also strains in the Collection used for special productions and strains used for the production of special dietician. These include strains such as Saccharomyces, Kluyveromyces, Cyberlindnera, Yarrowia, Candida, Pichia, Wickerhamomyces, Meyerozyma, Rhodotorula, and Toluraspora.
The Collection also preserves 7 mold strains. These include strains of Aspergillus, Penicillium, Trichoderma, and Phaerochaete.
Most of these strains are enzyme producers used in the food and agriculture industries, such as amyloglucosidase, glucose oxidase, and cellulase.

• Users and clients
 Collection users are primarily research institutes working in the field of microbiology, food production, and agriculture. Examples of clients include the Laboratory of Enzyme Technologies MBU AV CR Prague, Laboratory of Biology and Microbiology - Institute of Landscape Ecology AV CR, Ceske Budejovice, Brewing and Malting Research Institute, Research Institute of Antibiotics and Biotransformations Prague, and others.

Contact:
Workplace: Food Research Institute Prague, v.v.i.

Responsible researcher/curator: Ing. Markéta Begany
phone: 737 287 018
marketa.begany@vupp.cz

Representative of the responsible researcher: Ing. Zdeněk Moučka
phone: 737 287 009
zdenek.moucka@vupp.cz

Other researcher: Ing. Marian Urban, Ph.D.
phone: 737 287 003
marian.urban@vupp.cz
fermentor


strains on sloping agars


Sacharomyces cerevisiae


Y lipolytica Candida sp. lipase detection

Culture Collection of Basidiomycetes (CCBAS), (MBÚ AV ČR, v. v. i., Praha)

Culture Collection of Basidiomycetes Important for Agriculture (CCBAS-A) is an integral part of the mother Culture Collection of Basidiomycetes (CCBAS), which was established in 1959 at the Institute of Microbiology AS CR in Prague. Since 2003 the CCBAS-A is incorporated in the National Programme of Protection and Utilization of Genetic Resources of Microorganisms and Tiny Organisms Economically Significant for Agriculture. At present it includes 346 strains of basidiomycetes belonging to 168 species, mostly wood-rotting, and is continually extended by adding new verified strains.

• Characterization of Collection
potential to decompose polutants (organic compound) with their enzymes
metabolize pesticides thanks to extracellular enzyme lacasa
thus help with bioremediation of contaminated soil
332 isolates

• Activities/research activities
The main goal of the work of the collection staff is to develop alternative and to optimize current procedures of cryopreservation and other methods of maintenance of fungal cultures. These methods are then verified and introduced into practice. A new original method of cryopreservation of fungal cultures on perlite was developed and verified in our laboratory. This method is now used for the preservation of fungi not only in our, but also in many other collections in the world. Our cultures can serve as a reference material for further taxonomic, phylogenetic and other studies including studies of their biotechnologically exploitable properties. They are plentifully utilized by home and foreign research scientists. Another activities lie in consultations regarding cultivation, physiology and genetics of basidiomycetes and publishing of the achieved results in impacted international journals. Dr. Homolka takes part in home and international conferences and congresses and gives lectures at the Faculty of natural sciences (Essentials of physiology and genetics of filamentous fungi). He is also engaged in the training the staff of the collections in database operation.

• Methods of culture maintenance
The cultures are maintained by two independent principal methods (subculturing on solid agar media and cryopreservation on perlite) to preserve their quality and quantity. The crucial characteristics of the cultures are recorded in the database of the National Programme. The cultures on perlite can be distributed directly without reinoculation and reused for successive inoculations. They also turned out to be a good substitute for agar cultures in long-term maintenance of fungi. The viability of the cultures and their crucial characteristics (macro- and micromorphology, growth rate, purity) is tested every year in case of agar cultures and every second to fifth year in case of perlite cultures. If needed, the specific characteristics are tested, e.g. enzymatic or genetic ones. The data on cultures and collection operation are stored in a local operation database (developed especially for this purpose) and also in a central database of the National Programme.

• Database
involvement to national and international organizations/platforms
CCBAS is a member of Federation of Czechoslovak Collections of Microorganisms (FCCM) and World Federation of Culture Collections (WFCC), where it is listed under the number 558. In the frame of the international cooperation and information exchange, our collection provides the interested persons with the data on the maintained basidiomycete cultures (see the databases of NP, FCCM or WFCC) and on the basis of order also cultures to abroad. CCBAS cooperates with home and renowned foreign culture collections (e.g. CBS at Utrecht or MUCL at Louvain-la-Neuve) and universities (e.g. at Wageningen or at Oslo).
As mentioned above, the strains are used predominantly for noncommercial research and teaching purposes.

Contact:
Institute of Microbiology of the Academy of Sciences of the Czech Republic
Laboratory of Environmental of Microbiology
Vídeňská 1083
142 20 Prague 4
Czech Republic

Staff:
• head and curator
RNDr. Ivana Eichlerová, PhD,

• others
Ing. Petra Dobiášová
e-mail: eichler@biomed.cas.cz
tel.: 241 062 397
fax: 241 062 384
web CCBAS: http://www.biomed.cas.cz/ccbas/fungi.htm

Collection of Hop Pathogens, (ChI, s. r. o., Žatec)

The collection was established in 2003. The main attention is paid to hop pathogens - viruses and viroids.

• Characterization of collection
8 virus isolates
1 fungus isolate

• Methods of culture maintenance
infected hop plant, CaCl2, lyophilization

• Control
Each year monitoring is performed pathogens control by ELISA and RT-PCR, the same time there is a continuous obtaining of new isolates
Isolates: ApMV, ArMV, HLV, HMV, HLVd

Application:
Diagnosis of pathogens - ELISA, PCR, phytopathological – virology

Utilization of strains
positive controls for testing of nursery material
providing of strains for research

Users
The Central Institute for Supervising and Testing in Agriculture (CISTA)
The Czech University of Life Sciences Prague (CULS), Institute of Plant Molecular Biology - The Biology Centre of the Czech Academy of Sciences, České Budějovice

Contakt:
Hop Research Institute Zatec

Staff:
Ing. Petr Svoboda, CSc., curator
svoboda@chizatec.cz
+420 415 732 121
fax +420 415 732 150
www.chizatec.cz





Collection of Phytopathogenic Microorganisms UPOC

The collection of fungal microorganisms pathogenic to plants has been formed by Prof. Lebeda from 1977, during his work in Plant Breeding Station of Sempra company in Smržice. Following his employment (from 1994) at the Dept. Botany, Faculty of Science, Palacký University in Olomouc the collection was enlarged by isolates of cyanobacteria and algae (administered by Dr. Hašler and managed by prof. Poulíčková) and collection of viruses and phytoplasmas (managed by Prof. Navrátil at Department of Cell Biology and Genetics). The UPOC collection has expanded by expeditions organized yearly to collect new samples.

• Characteristic of collection (strains), number of cultures

The national database include
177 isolates of 15 species of phytopathogenic fungi and fungi-like organisms
31 strains of 31 species of cyanobacteria (12) and algae (7)
5 isolates of 4 species of phytoplasmas and 28 isolates of 7 virus species
others are part of working collection.

• Activities/research activities of Department of Botany
Genetic variability of plant pathogenic fungi;
Biodiversity and genetic variability of host-pathogen interactions in crop and wild plant pathosystems;
Mechanisms of resistance in host-pathogen interactions;
Plant breeding (classical and biotechnological approaches) in disease resistance;
Tests of plant pathogen for fungicide resistance;
Biology, ecology and genetics of cyanobacteria and algae
Epidemiology, biology and genetics of phytoplasmas and viruses

• Services
providing samples for non-commercial purposes
consultancy and determination
methods of culture maintenance see methodology (in Czech language)
quality systems, internal norms, correct laboratory practice
according to requirements of the National programme

• Involvement to national and international organizations/platforms
IBEB (International Bremia Evaluation Board)

• international cooperation

interchange of isolates, developing methods for storage, cultivation and testing of host plants resistance

• catalogue - on www VURV Praha

Utilization of collection:

• Utilization of strains
teaching, research, screening of plant resistance, reference strains for phytosanitary diagnostics, State phytosanitary administration and Central Checking and Testing Agricultural Institute, consultancy activities and postgraduate teaching of professional staff of water management institutions/authorities

• Users, clients
students, teachers, scientists, specialists of State Phytosanitary Administration, breeding companies and water authorities, …

Microorganisms in UPOC collection

Contact:

Institution/place
Palacký University in Olomouc
Faculty of Science
Department of Botany
Šlechtitelů 11
783 71 Olomouc-Holice

Staff, contacts:

• head/responsible person
Prof. Ing. Aleš Lebeda, DrSc. (curator)

• others
Doc. RNDr. Michaela Sedlářová, Ph.D.
Mgr. Pavla Šiková
RNDr. Barbora Mieslerová, Ph.D.
RNDr. Božena Sedláková, Ph.D.
RNDr. Petr Hašler, Ph.D.
Prof. RNDr. Milan Navrátil, CSc.

• contact: e-mail, telephon, fax: 585634824,
ales.lebeda@upol.cz
585634800
michaela.sedlarova@upol.cz
585634809
fax 585634824

Czech Collection of Microorganisms (CCM), (MU, Brno)

The Czech Collection of Microorganisms (CCM) is a nonprofit organization established at the Faculty of Science, Masaryk University in 1963 and in the present serves as a specialized research and service division within the Department of Experimental Biology. The CCM was included into the National Programme (NPGZM) in 2019 with selected collection of approx. 200 bacterial strains in the frame of the project: „Microorganisms related to dairy technologies and products“.

• Characterisation of the CCM
The CCM serves as a depository for cultures of bacteria and filamentous fungi. The main goal of the CCM is to collect, maintain and preserve authentic cultures of living bacteria and filamentous fungi relevant to applied microbiology, biotechnology, education and those of general scientific interest A special set of strains is used as reference cultures for clinical, veterinary, food and water testing laboratories. The CCM public collection contains about 3400 bacterial strains covering more than 1700 species and about 800 fungal strains with more than 550 species. All cultures are available via a public catalogue of strains (www.sci.muni.cz/ccm). The CCM also maintains a unique collection of aquatic hyphomycetes containing approx. 500 strains (60 genera and 130 species) and a collection of staphylococcal bacteriophages and their propagation strains which was established in 2011. Since 1992, the CCM is an International Depositary Authority (IDA) for deposits of bacteria, yeasts and filamentous fungi for patent purposes under the Budapest Treaty. There are more than 200 patent strains of bacteria and fungi maintained in the CCM at present.

• Research activities
The major activities of the CCM focus on the preservation and distribution of microorganisms. The CCM continuously extents and diversifies its holdings (approx. 100 cultures per year) and contributes to the biodiversity conservation ex situ. Research activities funded in the frame of national research programmes are focused on the taxonomy of Gram-positive cocci and rods (mainly the phylum Firmicutes), Gram-negative rods (mainly the phyla Proteobacteria and Bacteroidetes) and aquatic hyphomycetes. Since 2008, the CCM has been actively involved in the microbiological exploration of Antarctic environment.

• Services
Cultures supply - CCM cultures are used for basic and applied research, industrial applications, education and general scientific interest. The cultures are distributed under the conditions of the CCM Material Transfer Agreement (MTA) following the OECD Best Practice Guidelines for BRCs and WFCC Culture Collections Guidelines. Holdings - the CCM holds strains of bacteria, fungi and bacteriophages in pure cultures, covering a wide range of applications (type or ex- type cultures derived from type, quality control strains for testing of media, assay of antibiotics, vitamins and amino acids, testing of disinfectants, commercial diagnostic kits, enzymes and secondary metabolites producing strains, biodegrading strains for biotechnology, etc.). Safe keeping - the CCM offers a long-term preservation of viable and genetically unaltered customers' bacterial and fungal cultures under optimal conditions. Deposited cultures remain the property of the depositor. The CCM does not provide these cultures nor any information about them to third parties without the owner's written permission. Freeze-drying - the CCM is able to prepare freeze-dried ampoules to customers who require keeping their cultures for a long time in their own laboratory. Identification of microorganisms - the CCM offers isolation and purification of cultures from provided samples and identification of bacteria and fungi by using phenotypic and molecular techniques. Consultancy – the CCM provides advisory and consultation services on enrichment, isolation, identification and preservation of microorganisms.

• Maintenance of CCM cultures
CCM cultures are preserved mainly as freeze-dried conserves (lyophilisation), also frozen in liquid nitrogen at -196 °C and deep-frozen at -70 °C.

• International cooperation
The CCM cooperates with other culture collections within the Czech Republic as well as abroad. It is recognized by the World Federation for Culture Collections (member No. 65) and is also a member of the European Culture Collections’ Organisation and the Federation of Czech and Slovak Culture Collections.

• Quality system and in-house rules
The CCM introduced the System of Quality Management and was certified according to the ČSN EN ISO 9001:2001 standards on June 22, 2006. Recertification according to the ČSN EN ISO 9001:2015 has been validated since June 4, 2017. All laboratory procedures follow the standard operation procedures complying with the Good Laboratory Practice rules. All information concerning CCM strains and their preservation and distribution is unified in a database based on the MINE (Microbial Information Network Europe) format.

Application of CCM cultures, users
CCM strains are used primarily for the diagnostic purposes as well as for research and education in the Czech Republic or abroad. The most frequent users are public health institutions and laboratories of veterinary medicine but also other research institutions, universities, agricultural laboratories or food and water testing laboratories.

Contact:
Czech Collection of Microorganisms
Department of Experimental Biology
Faculty of Science,
Masaryk University Kamenice 5, buiding A25,
625 00 Brno,
Czech Republic
Tel.: +420-549496922
Web pages www.sci.muni.cz/ccm

Responsible person:
Assoc. Prof. RNDr. Ivo Sedláček, CSc.,
Head of the CCM ivo@sci.muni.cz, +420-549496922

Other workers Ing. Sylva Koudelková, Ph.D.,
Curator of bacterial collection sylvak@sci.muni.cz

Ing. Monika Laichmanová, Ph.D.,
Curator of fungal collection monikadr@sci.muni.cz



Culture Collection of Dairy Microorganisms Laktoflora® (CCDM), (Milcom, a. s., Tábor)

The Culture Collection of Dairy Microorganisms, Laktoflora® (CCDM) is a unique collection of bacterial cultures (monocultures and mixed cultures) and fungal organisms. The collection was established in 1956 in Prague and is currently located at the workplace of the Dairy Research Institute in Tábor (MILCOM a.s.). In 2021, a total of 974 strains were registered in the Laktoflora® collection. Most bacterial cultures are stored in a lyophilized state and at the same time deep-freezed by cryopreservation. Yeasts, molds, and some bacterial strains are kept on nutrient agar medium and are stored by cryopreservation. The collection is significantly funded by National Program for the Conservation and Utilization of Genetic Resources of Microorganisms and Small Animals of Economic Importance (NPGZM). Since 2019, the CCDM collection includes the so-called bakery collection consisted of bacteria and yeasts with specific technological properties predominantly isolated from different kinds of sourdough and used in the bakery industry.

• Collection characteristics, numbers of cultures
In 2021, a total of 164 strains were deposited in the CCDM collection including yeasts (86) particularly the genera Debaryomyces, Kazachstania, Kluyveromyces, Naumovozyma, Pichia, Saccharomyces, Trichosporon and Zygosaccharomyces. Filamentous fungi (78 strains) are represented by strains of Penicillium camemberti, Penicillium nalgiovense and Penicillium roquefortii. These strains are used in the production of Camembert and Blue type mold cheeses. The existing CCDM collection will be extended in the future with new isolates with functional properties corresponding to current trends and requirements of the dairy and bakery industry.

• Methods of storage
Two methods are used: cryopreservation - recovery interval 5 years slant nutrient agar - short-term storage of strains, annual reinoculation

• Quality systems, internal standards, good laboratory practice
The activity of the CCDM collection is defined by the Directive for the management of the activity of the collection according to ISO 9001. Based on the control audits, the Laktoflora® collection was certificated in 2002. The operations of the collection are further ensured in accordance with the internal guidelines. All methods of deposition are described in managed documents.

• Services
all the strains of the CCDM collection are provided free of charge for the teaching and research institution in accordance with the national program (NPGZM) the service of isolation, cultivation and identification of strains is provided long-term deposition of your strains into the collection professional advisory and consulting activities • National and international organizations
The CCDM collection is a part of the National Program for the Conservation and Utilization of Genetic Resources of Plants, Animals and Microorganisms Important for Food and Agriculture (NPGZM). Worldwide, the CCDM collection cooperates with the collections of CBS, Westerdijk Institute (Netherlands), MIRRI (France) and CCY (Slovakia). The CCDM collection is registered in the National Library of Medicine Database Maintenance Project and in the World Data Center for Microorganisms (WFCC 874).

Contacts:

Culture Collection of Dairy Microorganisms Laktoflora®
MILCOM a.s., Soběslavská 841, 390 02 Tábor, Czech Republic
phone: +420 733 591 080
e-mail: sbirka@vum-tabor.cz
www.ccdm.cz

Staff:
Ing. Miloslava Kavková, Ph.D., the head of the collection CCDM
m.kavkova@vum-tabor.cz
+420 723 679 012

Mgr. Ladislav Bár, the curator of the collection CCDM
l.bar@vum-tabor.cz
+420 733 591 080

 Biohazard flow box


Yeast deposition on agar media

Penicillium strains

Cryopreservation in the freezer

Cultures in broths and in lyophilized form

Microscope Olympus BX-43

Morfology of filamentous fungi (P. roqueforti, YES, 25 °C, 7 days)

Thermal cycler Biometra

Culture Collection of Dairy and Bakery Contaminants (CCDBC), (Milcom, a. s., Tábor)

The Collection of Dairy and Bakery Contaminants (CCDBC) was established in 2019 with the support of the Ministry of Agriculture of the Czech Republic as part of the National Program for the Conservation and Utilization of Genetic Resources of Plants, Animals and Microorganisms Important for Nutrition and Agriculture (NPGZM). The collection is located at the Research Institute of Dairy in Tábor (MILCOM a.s. company premises) and deals with the preservation of strains of bacteria, yeasts and filamentous fungi contaminating dairy and bakery products, which due to their properties have the potential for use in further research.
In the first year (2019), about 50 contaminating strains isolated from dairy products and dairies were included in the collection. Over the next two years, the collection expanded by another 29 contaminating strains. In the future, the collection will be expanded by isolates from bakery operations, especially from various yeasts, in accordance with the solution of NAZV projects, which are focused on antifungal activity and functional and technological properties of microorganisms in dairy products and yeasts.

• Collection characteristics, numbers of cultures
In 2021, 37 strains of filamenous fungi and 19 strains of yeast isolated mainly from cheese, salt baths and fallout in dairies were deposited in the collection.
Filamentous fungi play an important role in the production of mold cheeses in the dairy. These are practically represented by only a few species - Penicillium camemberti, P. roqueforti and P. nalgiovense. However, most filamentous fungi in dairy and bakery are serious and undesirable contaminants (eg the whole spectrum of the genera Penicillium, Cladosporium, Alternaria, Fusarium and many others). They are also responsible for their visible and invisible defects - odor, discoloration, toxin production.
Representatives of deposited yeasts are Debaryomyces hansenii, Geotrichum candidum, Trichosporon sp., species of the genus Candida and others.

• Strain storage methods
The CCDBC collection preserves strains of fungal microorganisms in two ways:
cryopreservation - recovery interval is 5 years
slant nutrient agar - reinoculated once a year

• Quality systems, internal standards, good laboratory practice
The CCDBC has fully taken over the ISO 9001 quality management system, which was introduced at the workplace where the collection is located, in 2002 as part of the Collection of dairy microorganisms - Laktoflora®. The activities of the collection are further ensured in accordance with the internal guidelines. All storage methods are described in managed documents.

• Services
all the strains of the CCDBC collection are provided free of charge for the teaching and research institution in accordance with the national program (NPGZM)
the service of isolation, cultivation and identification of strains is provided
professional advisory and consulting activities

• Inclusion in national and international organizations
The recently established CCDBC collection is part of the National Program for the Conservation and Utilization of Genetic Resources of Plants, Animals and Microorganisms Important for Food and Agriculture (NPGZM). It is not yet integrated into any international system.

Contact:
Culture Collection of Dairy and Bakery Contaminants
MILCOM a.s., Soběslavská 841, 390 02 Tábor, Czech Republic
Tel.: +420 733 591 080, www.ccdm.cz

Staff: Ing. Miloslava Kavková, Ph.D., the head of the collection CCDBC
m.kavkova@vum-tabor.cz
+420 723 679 012

Ing. Zuzana Dlouhá, the curator of the collection CCDBC
z.dlouha@vum-tabor.cz
+420 733 591 080
Biohazard flow box


Cryopreservation in the freezer


Yeast deposition on agar media


Microscope Olympus BX-43


Morphology of filamentous fungi (P. crustosum, CYA, 25 °C, 7 days)


Morphology of filamentous fungi (P. paneum, CYA, 25 °C, 7 days)


Thermal cycler Biometra