Plant Germplasm Centers and Microbial Culture
Contents
1. 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 and Cypess R H 1998 Internal quality con trol audits for microbiology laboratories in cul ture collections SIM News 48 66 69 Kahn R P and Mathur S B 1999 Contain ment Facilities and Safeguards for Exotic Plant Pathogens and Pests American Phytopa thological Society St Paul MN Kirk P M Cannon P F David J C and Stalpers J A 2001 Dictionary of the Fungi 9th ed CABI Bioscience Wallingford Oxon UK Kristjansson G ed 2005 Containment guide lines for plant pests Draft for comment Bio hazard Containment and Safety Unit Science Branch Canadian Food Inspection Agency Ottawa Lapage S P Sneath P H A Lessel E F Skerman V B D Seeliger H P R and Clark W A 1992 International Code of No menclature for Bacteria American Society for Microbiology Washington DC Lichtenfels J R Kirkbride J H Jr and Chitwood D J eds 1998 Systematic Collec tions of the Agricultural Research Service U S Dep Agric Agric Res Serv Misc Publ 1343 Ma G Gu K T and Dugan F 1999 Fila mentous fungi and yeasts ATCC quality con trol and quality assurance Inoculum 50 1 2 Madden L V 2001 What are the nonindi genous plant pathogens that threaten U S crops and forests APSnet Feature American Phytopathological Society Onl2. Collections as Resources for the Scientific Community Plant germplasm centers and culture collections make substantial distributions of materials to the scientific community From 1990 to 2000 the NPGS distributed over 620 000 germplasm samples of which ca 25 were international 75 In 2004 the NPGS distributed over 168 000 packets of plant germplasm primarily seeds to researchers worldwide Of sam ples distributed internationally about one third of NPGS samples flowed to Europe slightly less than a third to other countries in the Americas and nearly a quarter to Asia with the remainder to Africa and elsewhere Nearly half 46 went to de veloping countries during 1990 to 1999 and another 17 went to the countries of eastern Europe 75 From a survey of germplasm recipients 78 of requested germplasm was intended for use in various breeding programs with pest and disease resistance or tolerance being of primary concern For the 5 years covered by the survey an average of 11 of accessions distributed had already been incorporated into breeding programs 75 The percent age of requested germplasm incorporated into breeding programs was highest 18 in developing countries Numerous spe cific examples of use of NPGS germplasm organized by crop or crop category have been provided often with reference to specified genes races of plant pathogens germplasm accession numbers and other particulars of interest
3. Federation of Culture Collections Simworth Press Richmond Surrey UK Hawtin G and Reeves T 1998 Intellectual property rights and access to genetic resources in the Consultative Group on International Ag ricultural Research Pages 41 58 in Intellec tual Property Rights III Global Genetic Re sources Access and Property Rights S A Eberhardt H L Shands W Collins and R L Lower eds Crop Science Society of America and American Society of Agronomy Madison WI Hoagland K E and Rossman A Y eds 1997 Global Genetic Resources Access Ownership and Intellectual Property Rights Beltsville Symposia in Agricultural Research The Association of Systematics Collections Washington DC Holmgren P K Holmgren N H and Bar nett L C 1990 Index Herbariorum Part I The Herbaria of the World 8th ed Regnum Vegetabile Vol 120 For International Asso ciation for Plant Taxonomy by New York Bo tanical Garden Bronx NY Hummer K E 1998 First clonal germplasm repository reaches adolescence Diversity 14 20 21 Hunter Cevera J C and Belt A 1996 Main taining Cultures for Biotechnology and Indus try Academic Press New York Johnson R C Johnston W J Golob C T Nelson M C and Soreng R J 2002 Charac terization of the USDA Poa pratensis collection using RAPD markers and agronomic descrip tors Genet Resour Crop Evol 49 349 361 Jong S C Dugan F M Birmingham J M
4. R Stamenova E K and Jong S C 2004 Comparative analysis of common indoor Cladosporium species based on molecular data and conidial charac ters Mycotaxon 89 441 451 Perdue R E Jr and Christenson G M 1989 Plant exploration Pages 67 94 in Plant Breeding Reviews 7 J Janick ed Timber Press Portland OR Petersen R H n d Glossary of type termi nology University of Tennessee Division of Biology BioComputing Online publication Peterson S W 2000 Phylogenetic relation ships in Aspergillus based on RDNA sequence analysis Pages 323 355 in Integration of 61 62 63 64 65 66 67 68 69 70 71 T2 73 74 75 76 T1 78 79 Modern Taxonomic Methods for Penicillium and Aspergillus Classification R A Samson and J I Pitt eds Harwood Academic Publish ers Amsterdam Raja K Selvaraju P and Palanisamy V 2003 Desiccation and cryopreservation of re calcitrant arecanut Areca catechu L em bryos Plant Genet Resour Newsl 133 16 18 Rhode C 2005 Postal quarantine and safety regulations Activities developments and con cerns World Federation of Culture Collections Committee on Postal Quarantine and Safety Regulations Report 2000 2004 WFCC Newsl Online publication Rhode C 2005 New Transport Regulations for Infectious Substances as of January 2005 WECC Newsl Online publication Richmond J Y and McKinney R
5. W eds 1999 Biosafety in Microbiological and Bio medical Laboratories 4th ed Centers for Dis ease Control and Prevention and National In stitutes of Health Washington DC Roos E E 1989 Long term seed storage Pages 129 182 in Plant Breeding Reviews 7 J Janick ed Timber Press Portland OR Ruff A M 1998 One hundred years of soli tude U S National Plant Germplasm System celebrates centennial and looks to challenges of 2000 Diversity 14 8 Ruff A M 1998 Remarkable success of GRIN has greatly increased value of NPGS collections Diversity 14 9 Ryan M J and Smith D 2004 Fungal ge netic resource centres and the genomic chal lenge Mycol Res 108 1351 1362 Schopmeyer C S 1974 Seeds of Woody Plants in the United States U S Dep Agric For Serv Agric Handb 450 Washington DC Secretariat of the International Plant Protection Convention 2006 Official contact points and directory of national and regional plant protec tion organizations International Plant Protec tion Convention www ippc int Shands H L and Wiesner L E eds 1991 Use of Plant Introductions in Cultivar Devel opment Part 1 Proceedings of a Symposium sponsored by Division C 1 of the Crop Science Society of America Las Vegas Nevada 19 Oct 1989 Crop Science Society of America Madison WI Shands H L and Wiesner L E eds 1992 Use of Plant Introductions in Cultivar Devel opment Part 2 Proceedings
6. im mersion in liquid nitrogen or liquid nitro gen vapor or maintenance in ultra low temperature freezers ca 80 C Fig 1 Some collections may also preserve strains Table 4 Major gateways to genetic resources on agar media filter paper silica gel ster ile soil sterile water or sterilized plant materials by methods that may also be suitable for recipients of collections mate rials 22 39 54 74 76 77 Seeds and clonal stocks of higher plants are usually pre served under moderate humidity at tem peratures slightly above freezing 12 21 25 69 or are frozen for long term storage 28 65 82 Fig 2 Special protocols exist for preservation of recalcitrant seeds 61 Persons obtaining microorganisms from Name Acronym Resource Botanic Gardens Conservation BGCI Contact information for botanic International gardens Common Access to Biological Resources CABRI Links to biological resources in and Information Europe Consultative Group on International CGIAR Home pages of international plant Agricultural Research germplasm centers International Genetic Plant Resources IPGRI Directory of plant germplasm Institute collections As of Dec 2006 Biodiversity International North American Plants Collections NAPCC American Association of Botanical Consortium Gardens and Arboreta catalogs World Federation of Culture Collections WFCC Home pages of culture collections of the world T a N collections should ampli
7. use analogous to the purchase and use of computer software Nonetheless many collections still distribute the majority of holdings without burdening the user with IPR requirements 4 35 Correct Identification of Materials Although living collections offer an ex cellent range of materials to the scientific community the documentation associated with these materials is not free from error and misidentification occurs For example with regard to DNA sequences deposited in public gene banks it has been claimed that up to 20 of sequences associated with some groups of fungi are from misidenti fied specimens many of which were ob tained from culture collections 6 20 Users of herbaria are urged to similar cau tion 78 and we have personally encoun tered analogous situations in seed banks Fortunately collections themselves often sponsor research that corrects such mis identifications 20 40 57 Peterson 60 provides an excellent example of how collection scientists navigate taxonomic and nomenclatural issues when assigning appropriate names to large numbers of isolates Type Cultures Users for whom the taxonomic assign ment of an accession is critical should be aware of the importance and utility of types Several microbial collections de scribe accessions of material as type al though technically many fungi are actually ex type derived from the type because the type itself is usually a dried
8. virtually all fungi documented in any clinical context are also addressed in a single reference 19 As of yet there is no single analogous reference for plant pathogens Viruses are parasites and usually considered pathogens and never saprobes But which fungi and bacte ria are designated plant pathogens for regulatory purposes Obviously any pathogens mentioned in the CFR and or APHIS lists above are plant pathogens Other pertinent lists include that of the APS Committee on Standardization of Common Names for Plant Diseases 3 threatening pathogens not reported in the United States and threatening pathogens of limited distribution in the United States 48 phytopathogenic fungi from South Africa 15 and phytopathogens of re gional and or worldwide importance in the context of regulation and quarantine 81 The ATCC website specifically designates certain strains as requiring a USDA APHIS PPQ permit prior to distribution Table 1 Persons contemplating import ing isolates of phytopathogens should also check any regulations promulgated by their state departments of agriculture Some fungi commonly inhabiting or causing disease in plants are classified as Biosafety Level BSL 2 e as having potential to cause disease in humans or animals and of moderate hazard in one or more systems of classification Examples are Aspergillus fumigatus Sporothrix schenckii and several Fusarium species BSL assignment for a given or
9. 0 fungal accessions associated with seeds DSZM and ATCC have materials for teaching microbiology and mycology Interactive searches by application environment or other parame ters are possible in most online collection catalogs Tables 1 to 4 Databases of Germplasm and Culture Collections In addition to germplasm databases as sociated with collections are exceedingly ki a as useful to researchers regulatory officials and others Prime examples are the taxo nomic and nomenclatural databases avail able through NPGS www ars grin gov npgs searchgrin html and CABI www indexfungorum org and anamorph teleomorph connections genus specific e g Fusarium Penicillium databases and interactive keys at CBS www cbs knaw nl Although the USDA ARS Systematic Botany and Mycology Labora tory SBML does not routinely distribute its cultures its databases for fungus host distributions and literature citations are publicly available nt ars grin gov fungaldatabases index cfm The SBML site also has online keys links to other databases keys and descriptions and has published protocols for handling living fungal cultures 29 Most collection online catalogs also serve as databases for species or strain specific literature media growth conditions and preferred preserva tion method The ATCC catalog gives regulatory information see below perti ac Wi E S Fig 2 Cold storag
10. 11 06aa pdf a at ees haa ey ee 1 a Peter Green State University His B S M S and Ph D degrees were earned at University of Washington University of Montana and Washington State University respectively Prior to his service with Plant Introduction and the USDA ARS National Plant Germplasm System he was collection scientist for mycology and botany at American Type Culture Collection Mr Goates is a plant pathologist with the USDA ARS Na tional Small Grains Germplasm Research Facility in Aber deen ID He received a B S degree from Utah State Univer sity where he continued graduate studies in botany and plant pathology Mr Goates has researched various aspects of bunt and smut fungi for over 30 years including studies of cytology ultrastructure histology host resistance pathogen virulence epidemiology and chemical control He also main tains a unique collection of the named pathogenic races and numerous other isolates of common bunt and dwarf bunt fungi Dr Green is curator of the National Collection of Industrial Food and Marine Bacteria NCIMB the major UK repository for nonpathogenic environmental bacteria He obtained his Ph D in 1981 from Heriot Watt University in Edinburgh His areas of interest include taxonomy of methylotrophic bacteria and culture collection management He is currently a Fellow of the Institute of Biology a member of the executive board of World Federation of Culture Collect
11. 71 72 In some instances collection personnel are active participants in evaluation of collection germplasm and or cultivars that incorpo rate such germplasm e g resistance to dwarf bunt and common bunt in wheat and barley e g 5 31 The ARS Culture Collection in Peoria and CBS in the Netherlands annually dis tribute approximately 4 000 and 5 000 microbial strains respectively of which the latter includes about 1 000 plant patho gens Distribution figures for ATCC are also significant with reference to plant associated strains Each of the other major culture collections also distributes thou sands of strains annually to bona fide re searchers Because these collections differ in areas of emphasis neither holdings nor distribution statistics are directly compara ble but the above numbers indicate the substantial service provided by all these collections to agricultural science Collections are often sources of germ plasm associated with specific applications or environments For example ATCC has more than 260 fungal or bacterial acces sions documented as pertinent to biologi cal control CBS has more than 80 fila mentous fungal accessions parasitic on nematodes BCCM has more than 160 accessions of yeast associated with apple trees or fruits The UKNCC has more than 100 accessions associated with barley 100 associated with maize 190 associated with rice and 230 associated with wheat CCFC possesses more than 30
12. Carolyn Babcock Canadian Collection of Fungal Cultures Agriculture and Agri Food Canada Ottawa Ontario K1A OC6 Xianming Chen USDA ARS Wheat Genetics Quality Physiology and Disease Research Unit Pullman WA 99164 Pedro W Crous Centraalbureau voor Schimmelcultures P O Box 85167 3508 AD Utrecht the Netherlands Frank M Dugan USDA ARS Western Regional Plant Introduction Station Pullman WA 99164 Blair Goates USDA ARS National Small Grains Germplasm Research Facility Aberdeen ID 83210 Peter N Green NCIMB Ltd Ferguson Building Craibstone Estate Bucksburn Aberdeen AB21 9YA Scotland Plant Germplasm Centers and Microbial Culture Collections A User s Guide to Key Genetic Resources for Plant Pathology Collections containing microbes often referred to as culture collections and collections of seeds or clonal materials for higher plants often referred to as germ plasm collections can provide abundant resources for plant pathologists breeders geneticists and other plant science profes sionals However many such professionals including graduate students postdoctoral fellows and technical staff lack adequate guidance on locating obtaining and proc essing such materials Regulatory proce dures and considerations of biological security ambiguities regarding intellectual property rights lack of knowledge about collection databases and other hurdles dissuade many professional
13. al materials prefer a basic triple packaging system wherein the primary container is watertight leak proof and wrapped in absorbent material and a secondary con tainer is crush resistant and contains one or more primary containers The secondary container fits within an outer shipping package bearing addresses of sender and recipient description of contents and a customs form Packing to the same stan dard as clinical infectious agents minus the biohazard label will facilitate shipping and handling Packaging for infectious etiologic agents is described in Federal Register 42 CFR part 72 and by the World Health Organization and the U S Depart ment of Transportation 79 85 The World Federation for Culture Collections WFCC provided comprehensive analysis of the rationale and status of shipping regulations applicable to culture collec tions and their clients 62 63 Details of air transport of dangerous goods are avail able from the International Air Transport Association http www iata org whatwe do cargo dangerous_goods index htm Guidelines are available from FAO IPGRI for the safe movement of higher plant germplasm Specifically ad dressed are small grains 24 legumes 30 Allium spp 23 and more than 20 other crops For each crop the movement guidelines cover diseases and causative agents disease detection treatment and other aspects pertinent to safe transport of seeds and or clonal materials A co
14. d databases are available 50 Public seed banks have been subjected to similar review The USDA Agricultural Research Service National Plant Germ plasm System NPGS was the subject of detailed reporting covering history 66 83 management 16 quality control and preservation 10 65 82 structure 1 16 86 personnel 86 information technology 53 67 conserved species 38 66 collecting of germplasm 58 84 and examples of associated research 86 For Canada the locations and holdings of seed banks and clonal repositories were reviewed and instructions were provided for online viewing and ordering of hold ings 8 Earlier multifaceted reviews 7 9 gave a worldwide perspective on plant germplasm The fiscal health of collections has been the subject of repeated reviews or perhaps more accurately laments and news items 2 11 73 Although we firmly acknowledge the importance of nonliving collections mu seums and herbaria we have chosen to restrict our discussion to collections of living materials Readers wishing to learn more about herbaria and other nonliving collections are referred to other sources 37 46 87 Here we concentrate on col lections containing organisms that can be maintained in refrigerated conditions as with many seeds or clonal stocks of higher plants or grown in culture and then ly ophilized or kept in cryogenic storage at ultra low temperatures as with many mi croorganisms Some obli
15. e at 5 C and 25 relative humidity preserves seed of many higher plants at the Western Regional Plant Introduction Station Pullman WA These seeds are for regeneration and for distribution to customers Seeds from most original col lections are stored at colder temperatures for longer survival Photo by Frank Dugan Plant Disease May 2007 479 nent to individual strains and by inference species CBS CABI and Landcare New Zealand are coordinating MycoBank www MycoBank org a collaborative effort documenting all new names of fungi and associated data descriptions links to cultures specimens DNA sequences etc MycoBank also includes geographic coor dinates for all strains of fungi deposited at CBS 14 Information on geographic dis tribution found in databases like SBML and MycoBank is useful not only for re searchers but also for regulatory officials including potential resolution of trade disputes Focused use of collection data bases greatly facilitates access to original and subsequent species descriptions cor rect citation of authors of species names synonyms geographic and host ranges cultivation requirements agricultural ap plications biosafety level and other vital information Most collection websites also provide many useful links of interest to phytopathologists Regulatory and Safety Aspects of Management and Utilization Persons ordering cultures in the United States need to be aware of the requ
16. e publications Persons with a special interest in containment should be aware of a draft document whose recommendations may become official regulations at a future date in Can ada 44 USDA APHIS regularly inspects facilities prior to issuance of PPQ permits Recipients of plant pathogens should an ticipate inspections of their facilities by their state municipal and or organiza tional biosafety personnel Inspectors want to see that microorganisms can be con tained in biological safety cabinets as opposed to laminar flow hoods that do not contain the microorganism restricted access to work and storage areas close access to autoclaves locked incubators and freezers and laboratories that either lack windows or have sealed windows Nonindigenous pathogens should not be manipulated or stored in areas in proximity to potential arthropod vectors Safe Transport of Cultures and Germplasm It is essential to practice the safe receipt opening and disposal of containers Also many collections offer germplasm to cli ents on an exchange basis so knowledge of safe sending of organisms is also man datory Culture collections will often have blanket permits bestowing approval from regulatory agencies to receive ship ments of regulated organisms Potential depositors should inquire prior to ship ment Sending of microbial and higher plant germplasm is subject to regulations and guidelines In general carriers of microbi
17. errors Users also should re member that germplasm is only as valu able as its accompanying documentation Some collections cite in their catalogs extensive amounts of accompanying documentation such as depositor identi fier literature used for identification and or literature citing a particular isolate Funding and the Problem of Endangered Collections Some collections are provided with rou tine government support Others obtain Plant Disease May 2007 481 support by competing for government grants and contracts Occasionally collec tions may receive funding from private sources Collections that have enjoyed seemingly stable funding can be subjected to fiscal crisis if funds are diminished or terminated Some collections recover costs through fees charged to clients but fees that actually cover all costs to the collec tion may not be affordable to many poten tial collection users Support for collec tions varies widely and so user costs vary from negligible to costs that are prohibitive for potential clients with small budgets Passing all costs onto users can be ex tremely onerous when multiple isolates are required as in many instances of taxo nomic research or when assessing genetic variability within a pathogen One solution benefiting both collections and users is for granting agencies to recognize the true costs of germplasm and accept those costs as legitimate when assessing proposals Even when support
18. es APSnet Ameri can Phytopathological Society Online publication 4 Bass S P and Muller M R 2000 Protecting Biodiversity National Laws Regulating Ac cess to Genetic Resources in the Americas In ternational Development Research Centre Ot tawa 5 Bonman J M Bockelman H E Goates B J Obert D E McGuire P E Qualset C O 10 11 12 13 14 15 16 17 18 19 20 Zale 22 23 24 and Hijmans R J 2006 Geographic distribu tion of common and dwarf bunt resistance in landraces of Triticum aestivum subsp aesti vum Crop Sci 46 1622 1629 Bridge P D Roberts P J Spooner B M and Panchal G 2003 On the unreliability of published DNA sequences New Phytol 160 43 48 Brown A H D Frankel O H Marshall D R and Williams J T eds 1980 The Use of Plant Genetic Resources Cambridge Univer sity Press Cambridge UK Buchwaldt L and Richards K W 2004 Plant gene resources of Canada and the Cana dian plant germplasm system Can J Plant Pathol 26 48 51 Chang T T Goodman M M and Krugman S L 1989 Plant genetic resources key to fu ture plant production Plant science lecture se ries 1984 Iowa State J Res 59 323 539 Clark R L 1989 Seed maintenance and storage Pages 95 110 in Plant Breeding Re views 7 J Janick ed Timber Press Portland OR Colwell R R 1992 Endangered Cu
19. esearch However in the absence of fiscal and tech nical support for collections or users costs of materials may escalate to the point where they are available only to the most well financed laboratories Persons or institutions lacking the financial resources to pay escalating fees including legal costs associated with IPR and regulatory hur dles may simply be out of the running This would diminish the numbers of capa ble researchers having access to germ plasm a result discordant with the better interests of scientific advancement but certainly favorable to entities with the capacity and desire to monopolize access to germplasm The challenge is to find ways to simultaneously support collec tions respect IPR and regulatory require ments and keep materials affordable to the entire spectrum of bona fide researchers Acknowledgments We thank Michael Kenney David Ellis and Stephen Peterson for constructive review of the manuscript and Rich Hannan Cletus Kurtzman and David Stout for provision of pertinent statistics and information on collection holdings Literature Cited 1 Anonymous 1998 The National Plant Germ plasm System A sum greater than its parts Diversity 14 6 7 2 APS Collections and Germplasm Committee 2005 Is your favorite pathogen collection en dangered Abstr Phytopathology 95 S4 3 APS Committee on Standardization of Com mon Names for Plant Diseases 2005 Com mon Names of Plant Diseas
20. for routine operations is sufficient fiscal support may be lacking for backing up critical parts of the collec tion preferably on an alternative site It is essential that financial support for collections be adequate for routine mainte nance of living materials and associated data replenishment of living material and distribution to users Equally essential is support on regulatory requirements and IPR issues so that both collections and users are able to maintain and utilize mate rials within established legal constraints We realize that collection budgets inevita bly fluctuate with shifts in policies and programmatic priorities of public agencies and with fiscal resources of users We therefore recommend that professional societies take an active interest in monitor ing the health of collections and have mechanisms to assist collections that be come imperiled Collections whose existence is severely imperiled have the option of appealing to the World Federation of Culture Collec tions Endangered Collection Task Group ECTG Assistance from the ECTG can be in the form of lobbying activities ad vice on collection management or small grants for supplies and basic equipment As a last resort a rescue mission may be undertaken including transfer of critically important accessions to other collections 32 Decisions on the future importance of accessions are exceedingly difficult when only a portion of a collectio
21. fy the material to form their own seed stocks always main tained in an inactive state and a greater number of working stocks for experimental manipulation To best maintain original characteristics especially pathogenicity additional working stocks should be re plenished from seed stocks rather than by serial transfer 27 Persons contemplating long term use of plant seed should also set aside a portion of the original stock for extended storage Maintaining genetic in Country URL UK www bgci org n a srs71 cabri org USA home www cgiar org office Italy home www ipgri cgiar org germplasm office dbintro htm www bioversityinternational org USA www ars grin gov npgs napcc html Japan home wdcm nig ac jp hpcc html office 1 Fig 1 Liquid nitrogen tanks each containing thousands of vials of germplasm at the USDA ARS National Center for Genetic Re sources Preservation Ft Collins CO Liquid nitrogen can be used to store small seeds cultured tissues and microbial germplasm Photo by David Ellis 478 Plant Disease Vol 91 No 5 tegrity of plant seed can entail special challenges such as avoidance of out cross ing Fig 3 For long term storage mois ture content around 6 and temperature of 20 C is appropriate for many seeds 28 In addition to preserving the cultures them selves some collections are setting up DNA banks to facilitate future orders of DNA from specified isolates
22. ganism may vary with country 18 64 88 Guidelines for handling fungi of potential infectivity allergenicity or toxicity in humans are available 56 Facilities requirements for handling of BSL2 microorganisms are generally congruent with those required by USDA APHIS for manipulation of im ported plant pathogens 1 e restricted ac cess use of biological safety cabinets and autoclaving of cultures Handling of phy topathogens in a manner analogous to BSL2 is good biosecurity practice Although there is no legislation in the United States setting specific criteria for construction of collection facilities there are published guidelines with concrete examples of containment facilities 42 and or instructive descriptions and dia grams 17 Draft guidelines for contain ment facilities for fungal plant pathogens plant pathogenic nematodes bacterial plant pathogens and viruses and their vectors are available from the Containment Facilities Program at USDA APHIS PPQ Unit 133 4700 River Road Riverdale MD 20737 The European Plant Protection Organization EPPO anticipates publica tion of similar information for laboratories and greenhouses in the EPPO Bulletin A S Roy Information Officer EPPO Analogous guidelines have been proposed for culture collections 34 Scientists con templating research on nonindigenous plant pathogens can study the principles practices and facility designs in one or more of the abov
23. gate parasites or symbionts are also kept in collections e g plant viruses vesicular arbuscular my corrhizal fungi and rusts either in cryo genic storage or by maintaining them on their plant hosts Major and Specialty Culture Collections of Plant Pathogens In general holdings of major culture collections are dominated by ascomycetes and or anamorphic ascomycetes basidiomycetes zygomycetes oomycetes and prokaryotes that are amenable to growth on agar media Table 1 Some collection holdings of these organisms are extensive e g 27 000 accessions often referred to herein as strains of fungi at American Type Culture Collection ATCC 25 000 analogous strains in Bel gian Coordinated Collections of Microor ganisms BCCM 60 000 at Centraalbu reau voor Schimmelcultures CBS 10 500 at Canadian Collection of Fungal Cultures CCFC and 19 000 at the United King dom National Culture Collection UKNCC CABI Bioscience Genetic Re sources Collection ATCC BCCM CBS Deutsche Sammlung von Mikroorganis men und Zellkulturen DSMZ and UKNCC have smaller but significant hold ings of plant pathogenic bacteria The USDA Agricultural Research Service Cul ture Collection often called NRRL after the old name of the laboratory Northern Regional Research Laboratory maintains approximately 80 000 strains 45 000 fila mentous fungi 15 000 yeasts 10 000 ac tinomycetes and 10 000 bacteria All
24. in cereal rust laboratories in Austra lia Canada Denmark France Germany Netherlands United Kingdom and other countries Such laboratories do not nor mally publish catalogs but inoculum can be made available to collaborators Simi larly individual laboratories have pre served downy or powdery mildews for varying lengths of time at low tempera tures but these laboratories do not rou tinely function as centers for distribution of these pathogens Seed Banks and Germplasm Collections Larger seed banks and clonal reposito ries have extensive materials The NPGS collections comprise over 460 000 acces sions representing over 11 000 genera The NPGS website allows review of summary accession Statistics by crop or genus Table 3 The Millennium Seed Bank Project at Kew has the stated aim of accessioning 24 000 plant species and registered users Table 1 Major culture collections with extensive holdings pertinent to plant pathology Name American Type Culture Collection Belgian Coordinated Collections of Microorganisms Canadian Collection of Fungal Cultures Centraalbureau voor Schimmelcultures Deutsche Sammlung von Mikroorganismen und Zellkulturen National Center for Agricultural Utilization Research United Kingdom National Culture Collection CABI Bioscience Table 2 Specialty culture collections Name Center for Forest Mycology and Research Fungal Genetics Stock Center Fusarium Research Center Inter
25. ine publication Mayo M A Maniloff J van Regenmortel M H V and Fauquet C M 2002 The type species in virus taxonomy Arch Virol 147 1271 1274 McCluskey K 2003 Fungal germplasm and databases Pages 295 310 in Applied Mycol ogy amp Biotechnology Fungal Genomics G G Khachatourians and D K Arora eds San Diego Technical Books San Diego McCluskey K 2003 Plant pathology related culture collection resources APSnet Feature December American Phytopathological Soci ety Online publication McDaniel L L Jong S C and Gherna R L 1992 The American Type Culture Collec tion Germplasm resources for plant patholo gists Plant Dis 76 762 767 Mowder J D and Stoner A K 1989 Infor mation systems Pages 57 65 in Plant Breed ing Reviews 7 J Janick ed Timber Press Portland OR Nakasone K K Peterson S W and Jong S C 2004 Preservation and distribution of fun gal cultures Pages 37 47 in Biodiversity of Fungi Inventory and Monitoring Methods G M Mueller G F Bills and M S Foster eds Elsevier Amsterdam Office of Technology Assessment Congress of the United States 1990 New Developments in Biotechnology Patenting Life Marcel Dekker New York Padhye A A Bennett J E McGinnis M R Sigler L Flis A and Salkin I F 1998 Bio safety considerations in handling medically important fungi Med Mycol 36 Suppl 258 265 Park H G Managbanag J
26. inson C A Batt and P D Patel eds Academic Press London Ellis R H et al eds 1985 Handbook of Seed Technology for Genebanks Vol 2 Inter national Board for Plant Genetic Resources 1985 IBPGR Rome Farr D and Paul B 2001 Protocols for handling living fungal cultures at the SBML Inoculum 52 13 Frison E A Bos L Hamilton R I Mathur S B and Taylor J D eds FAO IPGRI tech nical guidelines for the safe movement of leg ume germplasm Food and Agriculture Organi zation of the United Nations Rome International Board for Plant Genetic Re sources Rome Goates B J 1997 Host resistance to dwarf bunt Pages 317 326 in Proceedings Bunts and Smuts of Wheat An International Sympo sium V E Malik and D E Mathre eds Ra leigh NC August 17 20 1997 Green P N Endangered culture collections The baby or the bath water WFCC Newsl In press Greuter W McNeill J Barrie F R Burdet H M Demoulin V Filgueiras T S Nicolson D H Silva P C Skog J E Tre hane P Turland N J and Hawksworth D L eds 1999 International Code of Botanical Nomenclature Saint Louis Code adopted by the XVI International Botanical Congress St Louis MO July August 1999 Regnum Veg 138 1 474 Hawksworth D L Sastramihardja I Kokke R and Stevenson R 1990 WFCC Guidelines for the Establishment and Operation of collec tions of Cultures of Microorganisms World
27. ions and chair of that organization s Endangered Culture Collection Task Group 86 Worthington L F 1998 National Genetic Resources Advisory Council seeks to improve NGRP through far reaching activities in germ plasm and genomic research Diversity 14 12 Sicherheit n d Liste risikobewerteter Spender und Embfangerorganismen fiir gentechnischen Arbeiten www verwaltung uni hamburg de k
28. irement for a USDA APHIS PPQ permit if they are importing a plant pathogen from another state or a foreign country APHIS has es tablished a very useful website www aphis usda gov plant_health permits with instructions on applying for a permit in cluding e permits designed to facilitate the permitting process Plant pathologists should be aware of lists of regulated mi croorganisms 1 biological agents and toxins select agents see Federal Reg ister 7 CFR 331 2 www aphis usda gov programs ag_selectagent index html 11 regulated pest list from 7 CFR 300 399 www aphis usda gov ppq regpestlist and ii widely prevalent plant pathogen lists available from the USDA APHIS permits site above The first two lists designate organisms that are the subject of height ened and stringent regulation the latter list is for plant pathogens that are widely dis tributed and for which permits may be expedited Currently agents of plum pox and soybean rust have been taken off the select agent list Outside the United States persons seeking regulatory information can consult the web pages of the European Plant Protection Organization www eppo org Biosecurity Australia www daff gov au Australia Quarantine and Inspection Service www aqis gov au Biosecurity New Zealand www biosecurity govt nz and MAF Quarantine Service www maf govt nz mafnet or the Plant Health Divi sion of the Canadian Food Inspecti
29. lture Collections Proceedings of the First and Sec ond International Symposia World Federation for Culture Collections and Maryland Biotech nology Institute MD Copeland L O and McDonald M B 2001 Principles of Seed Science and Technology 4th ed Kluwer Boston Crous P W 2003 Fungi and research collabo rations with the Centraalbureau voor Schimmelcultures CBS in the Netherlands Inoculum 54 11 13 Crous P W Gams W Stalpers J A Robert V and Stegehuis G 2004 MycoBank An online initiative to launch mycology into the 21st century Stud Mycol 50 19 22 Crous P W Phillips A J L and Baxter A P 2000 Phytopathogenic fungi from South Af rica University of Stellenbosch Dept of Plant Pathology Press Stellenbosch South Africa Day P R chair 1991 Managing Global Genetic Resources The U S National Plant Germplasm System Board on Agriculture Na tional Research Council National Academy Press Washington DC De Clerke Floate R Plue P and Lee T eds 2005 A tour of the Lethbridge Research Cen tre Insect Microbial Containment Facility Ag riculture and Agri Food Canada Lethbridge Catalogue No A42 102 2005E de Hoog G S 1996 Risk assessment of fungi reported from humans and animals Mycoses 39 407 417 de Hoog G S Guarro J Gen J and Figueras M J 2000 Atlas of Clinical Fungi 2nd ed Centraalbureau voor Schimmelcul tures Utrecht Netherlands and U
30. major culture collections have searchable catalogs online as do several smaller spe cialty collections Tables 1 and 2 Both ATCC and DSMZ also maintain collec tions of plant viruses In addition USDA ARS is currently in the process of estab lishing an online catalog for the Interna tional Collection of Phytopathogenic Bac teria Norman Schaad personal commu nication Obligate microbes requiring plants for propagation are more expensive to main tain as are races of pathogens that must be tested against specific host genotypes In the latter instance especially the most reliable collections tend to reside with individual researchers active in host pathogen genetics and or plant breeding programs These researchers are also gen erally the best source of differentially re sistant cultivars For example in the United States collections of Puccinia graminis pathogens of wheat barley and other cereal crops and grasses P triticina causal agent of wheat leaf rust P coro nata causal agent of crown rust of oats and some other Puccinia spp are main tained by the USDA ARS Cereal Disease Laboratory www cdl umn edu at St Paul MN Major collections of Puccinia stri iformis causal agent of stripe rust of wheat barley and grasses were main tained by the USDA ARS Wheat Genetics Quality Physiology and Disease Research Unit at Pullman WA Similar collections of agents of cereal rusts also were main tained
31. mplete list of titles is available from the United Nations Environmental Program at www earthprint com Impact of Intellectual Property Rights on Germplasm Users Subsequent to the Convention on Bio logical Diversity CBD a series of agree ments on preservation and utilization of biological diversity signed by 150 coun tries in Rio de Janeiro 1992 procurement and utilization of both microbial and plant germplasm are often subject to increased restrictions Parties to the CBD are dis cussing the terms Access and Benefit Sharing and Prior Informed Consent Canada for example is in the process of holding across country forums to examine the issues of native rights and traditional knowledge Persons obtaining germplasm may be under obligation to honor condi tions of use as stated in laws treaties pat ents or material transfer agreements MTAs 4 36 Moreover many cultures in leading culture collections were depos ited with reference to one or more patents because the collection was designated as a repository for such cultures under the Bu dapest Treaty The Office of Technology Assessment 55 provided a capsule his tory of the Budapest Treaty and establish ment of patent repositories Persons order ing such cultures are advised to avoid uses infringing on the specified patent Some collections make use of shrink wrap MTAs whereby acceptance of the agree ment is implicit in product purchase and
32. n can be res cued 32 Cultures of vital importance to plant pa thology and currently subsisting on soft monies include the World Phytophthora Collection at The University of California Riverside UCR and the National Soy bean Pathogen Collection Center in Ur bana IL Table 2 The nearly 6 500 acces sions ca 90 species in the World Phytophthora Collection at UCR are still threatened with extinction Michael D 482 Plant Disease Vol 91 No 5 Coffey personal communication This collection assembled over the past 40 years may be lost forever in the absence of more secure financial support Similarly the National Soybean Pathogen Collection Center NSPCC established in August 2002 with representative cultures of Fusa rium solani f sp glycines cause of sudden death syndrome Heterodera glycines soybean cyst nematode Meloidogyne spp root knot nematode Phytophthora sojae cause of Phytophthora stem and root rot and other common soybean pathogens also is in urgent need of funding NSPCC has more than 1 000 isolates of 24 species plus minor collections of soybean viruses and bacterial pathogens and is the only major collection established to preserve soybean pathogens but operations have been drastically curtailed due to lack of funding S Li personal communication The Future of Living Collections and Prospects for the User Collections will undoubtedly continue to play a role in plant pathology r
33. national Collection of Vesicular Arbuscular Mycorrhizal Fungi National Soybean Pathogen Collection Center USDA ARS Collection of Entomopathogenic Fungi USDA ARS National Rhizobium Germplasm Collection Soybean Genomics and Improvement Laboratory USDA ARS Systematic Botany and Mycology Laboratory World Phytophthora Collection may inspect holdings Table 3 Canadian plant germplasm may be reviewed via the website of Plant Gene Resources of Can ada Table 3 Websites for approximately 20 U S based plant germplasm organiza tions and approximately 40 international plant germplasm organizations are linked to the NPGS website The National Collec tions of Industrial Marine and Food Bac teria NCIMB ATCC NRRL and other collections also maintain plant seeds usu ally as part of their patent deposit facilities within their remit as an IDA International Depository Authority under the Budapest Treaty This treaty governs the deposit of biological materials involved in patent processes in a recognized national culture collection which is approved as an IDA see section on intellectual property rights below Nearly 500 smaller culture collections have home pages that can be accessed via the website of WFCC Table 4 Contact information for hundreds of seed banks Acronym Country Current URL with catalog ATCC USA www atcc org BCCM Belgium bccm belspo be index htm CCFC DAOM Canada sis agr gc ca brd ccc CBS Netherlands w
34. ngen Netherlands He received his B S and M S degrees from University of Stellenbosch and his Ph D from University of the Orange Free State Principal research interests include Mycosphaerella and its anamorphs diseases of Eucalyp tus and fungal biodiversity Dr Dugan is research plant pathologist USDA ARS Western Regional Plant Introduction Station Washington 484 Plant Disease Vol 91 No 5 Plant Breeding Reviews 7 J Janick ed Tim ber Press Portland OR White G A Shands H L and Lovell G R 1989 History and operation of the National Plant Germplasm System Pages 5 56 in Plant 15 Breeding Reviews 7 J Janick ed Timber 87 Wu F W Thiers B M and Pfister D H 2004 Preparation preservation and use of fungal specimens in herbaria Pages 23 36 in Biodiversity of Fungi Inventory and Monitor ing Methods G M Mueller G F Bills and Press Portland OR R B 2000 Virus Taxonomy Classification 84 Williams K A 1998 Plant exchange office leads way in establishing non monetary bene fit sharing regimes Diversity 14 23 24 World Health Organization 1997 Guidelines for the safe transport of infectious substances 88 Zentral Kommission f r die Biologische and diagnostic specimens WHO EMC 97 3 World Health Organization Emerging and Other Communicable Diseases Surveillance and Control Geneva Blair Goates M S Foster eds Elsevier Amsterdam Division of 9 handbuch 3
35. niversitat Rovira 1 Virgili Rues Spain CD ROM ver sion September 2005 de Hoog G S and Horr R 2002 Molecular taxonomy of the Alternaria and Ulocladium species from humans and their identification in the routine laboratory Mycoses 45 259 276 Desai B B 2004 Seeds Handbook Biology Production Processing and Storage 2nd ed Marcel Dekker New York Dhingra O K and Sinclair J B 1994 Basic Plant Pathology Methods CRC Boca Raton FL Diekmann M 1997 FAO IPGRI technical guidelines for the safe movement of germ plasm No 18 Allium spp Food and Agricul ture Organization of the United Nations Rome International Plant Genetic Resources Institute Rome Diekmann M and Putter C A J 1995 FAO IPGRI technical guidelines for the safe movement of germplasm No 14 Small grain temperate cereals Food and Agriculture Or ganization of the United Nations Rome 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 International Plant Genetic Resources Institute Rome Doijode S D 2001 Seed Storage of Horticul tural Crops Haworth Press New York Dugan F M and Nakasone K K 1998 Mapping the microbial universe The impor tance of living collections for fungal systemat ics Diversity 14 3 amp 4 35 39 Dugan F M and Tang J S 2000 Culture collections Pages 498 502 in Encyclopedia of Food Microbiology Vol I R K Rob
36. nonviable herbarium specimen Essentially a type is the specimen that was used to describe a given species in the original species de scription The type therefore defines the species and users of type material can have high confidence that the name at tached to the isolate is appropriate Para doxically some types turn out to be atypi cal of a species but this is not the norm References can be consulted for the no menclature of types and the application of names 33 43 45 80 including a concise review of type species in virus taxonomy 49 Some specimens may carry the label authentic if they are not type but were identified as a given species by the same person who authored the species Repre sentative specimens are isolates that are said by an expert but not the author of a given species to exemplify that species The utility and pitfalls of representative authentic and miscellaneous types have been summarized with regard to fungi 59 In general collections will guarantee that material distributed is viable free of contamination and the same as that depos ited but they cannot guarantee that a given accession will demonstrate properties specified in publications or patents pro duction of metabolites formation of sexual structures etc Users should also be aware that some changes in the scientific names of accessions are reflective of taxo nomic or nomenclatural advances rather than initial
37. of a Symposium sponsored by Division C 1 of the Crop Science Society of America Las Vegas Nevada 19 Oct 1989 Crop Science Society of America Madison WI Sigler L 2004 Culture collections in Canada Perspectives and problems Can J Plant Pathol 26 39 47 Simione F and Brown E M 1991 ATCC Preservation Methods Freezing and Freeze Drying 2nd ed ATCC Rockville MD Smale M Day Rubenstein K Zohrabian A and Hodgkin T 2001 The demand for crop genetic resources International use of the U S National Plant Germplasm System Interna tional Food Policy Research Institute Wash ington DC and International Plant Genetic Resources Institute Maccarese Italy Smith D and Onions A H S 1994 The Preservation and Maintenance of Living Fungi 2nd ed CAB International Wallingford Oxon UK Smith D Ryan M J and Day J G eds 2001 The UK National Culture Collection UKNCC Biological Resource Properties Maintenance and Management UKNCC Sur rey UK Trappe J 2004 The ways of herbaria A cau tionary note for users of herbarium collections Inoculum 55 3 4 U S Department of Transportation n d Infectious substances What you need to know Plant Disease May 2007 483 80 81 82 U S Department of Transportation Research and Special Programs Administration Hazard ous Materials Safety Washington DC 83 van Regenmortel M H V Fauquet C M Bishop D H L Cars
38. on Agency www inspection gc ca The latter website includes useful links to sites of plant protection organizations of miscella neous countries Persons receiving germplasm of higher plants from outside their country must often obtain a phytosanitary certificate that testifies to the pest and disease free status of a given shipment The directory of plant protection organizations 70 provides contact information for nearly all national international and regional organizations Persons importing plant germplasm into the United States should note that some plants or plant parts are subject to restric tions and require an appropriate permit application with APHIS these types of permits are sometimes referred to as de partmental permits or experimental per mits for import of seed of maize rice etc Fig 3 Some germplasm such as these accessions of safflower at Central Ferry WA must be grown inside insect proof cages and supplied with pollinators in order to avoid crossing with other accessions The objective is to retain the original genetic composition of the accession Photo by Vicki Bradley 480 Plant Disease Vol 91 No 5 Plant seeds for import into the U K are subject to similar import requirements defined in The Plant Health Guide for Importers www defra gov uk Which microorganisms are designated phytopathogens Most clinical microor ganisms are directly addressed in a single reference 64 and
39. s from effec tively exploiting collection resources The Collections and Germplasm Committee of the American Phytopathological Society together with colleagues from international collections and the World Federation of Culture Collections has assembled this guide summarizing the benefits and utili zation of living collections for plant pa thology We show how to locate major and minor collections obtain biological mate rials and comply with regulatory and shipping requirements We briefly discuss the relevance of intellectual property rights the problem of endangered collec tions especially those with invaluable and irreplaceable materials and make specific recommendations for the support of living collections Prior reviews of culture collections originated from diverse perspectives Ex amples from an extensive literature are Corresponding author Frank Dugan E mail fdugan wsu edu doi 10 1094 PDIS 91 5 0476 This article is in the public domain and not copy rightable It may be freely reprinted with custom ary crediting of the source The American Phyto pathological Society 2007 476 Plant Disease Vol 91 No 5 quality control and preservation 27 41 47 54 68 taxonomy and research 13 26 organizations legislation and regulation 77 relevance to plant pathology and other disciplines 51 52 73 and genomics 50 68 Capsule histories of several cul ture collections plus extensive lists of associate
40. tens E B Estes M K Lemon S M Maniloff J Mayo M A McGeoch D J Pringle C R and Wickner and Nomenclature of Viruses Seventh Report of the International Committee on Taxonomy of Viruses Academic Press San Diego 85 Waller J M Lenn J M and Waller S J 2001 Plant Pathologist s Pocketbook 3rd ed CABI New York Westwood M N 1989 Maintenance and storage Clonal germplasm Pages 111 128 in Carolyn Babcock i ie Frank Dugan Ms Babcock has for the past 15 years been curator of the Canadian Collection of Fungal Cultures Agriculture and Agri Food Canada Ottawa Ontario Canada She received her B S degree at Carleton University Ottawa Ontario Canada In addition to her many activities as curator she spent 9 years publishing on Pyrenomycetes with Dr R A Shoemaker Dr Chen is research plant pathologist USDA ARS Wheat Genetics Physiology Quality and Disease Re search Unit Washington State University He received his B S degree from Northwest University of Agriculture China and M S and Ph D degrees from Washington State University Dr Chen has spent most of his career research ing stripe rust with emphasis on genetics of host pathogen interactions Dr Crous is director of the Centraalbureau voor Schimmelcultures at Utrecht Netherlands and professor in the Departments of Plant Pathology at the universities of Stellenbosch and Pretoria South Africa and Wageni
41. ww cbs knaw nl DSMZ Germany www dsmz de NRRL USA nrrl ncaur usda gov UKNCC UK www ukncc co uk CABI IMI www cabi bioscience org docs pdf GRCCatalogue pdf Acronym Resource Country URL CFMR Wood decay fungi USA www fpl fs fed us FGSC Plant pathogens used as genetic USA www fgsc net models e g Magnaporthe Aspergillus FRC Fusarium USA frc cas psu edu INVAM Vesicular arbuscular mycorrhizal USA invam caf wvu edu fungi NSPCC Pathogens of soybean USA nspcc cropsci uiuc edu ARSEF Fungi pathogenic to insects USA www ars usda gov is np systematics fungibact htm SGIL Rhizobium USA www ars usda gov is np systematics rhizobium htm SBML Diaporthales Hypocreales amp other USA www ars usda gov main site_main taxa available to collaborators htm modecode 12 75 39 00 WPC Phytophthora USA phytophthora ucr edu Table 3 Major national public collections of seeds and clonal materials Name Millennium Seed Bank Project Kew Plant Gene Resources of Canada USDA National Plant Germplasm System Acronym Country URL MSBP UK PGRC Canada NPGS USA www rbekew org uk msbp pgrc3 agr gc ca search_grinca recherche_rirgc_e html www ars grin gov npgs Plant Disease May 2007 477 botanical gardens and arboreta many with online catalogs is available from websites of national and international plant conser vation organizations Table 4 Preservation Methods Most microorganisms in culture collec tions are preserved by lyophilization
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