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8 The Role of Herbaria and Culture Collections

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Systematics and Evolution

Part of the book series: The Mycota ((MYCOTA,volume 7B))

Abstract

The introduction to this chapter explains the role of fungal herbaria and culture collections as sources of reference material for scientists studying fungal biology and systematics. The second part presents an overview of herbarium best practices, including techniques for collecting, preparing, and properly preserving and annotating herbarium specimens. A special section is devoted to the use of herbarium specimens in molecular studies, discussing important aspects concerning the working area for doing DNA extractions, destructive sampling, main steps in the procedure of extracting DNA, and quality issues such as contamination and degradation of DNA. A third part deals with the maintenance of living cultures, in an actively growing state on agar media or preserved long-term in a metabolically inactive state, as cryopreserved or freeze-dried samples. The main principles of cryopreservation and freeze drying are explained, and more detailed procedures for these methods and the most important aspects in quality control are described.

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References

  • Baker B (2011) New push to bring U.S. biological collections to the world’s online community. Bioscience 61:657–662

    Article  Google Scholar 

  • Barnes CW, Szabo LJ, Bowersox VC (2008) Identifying and quantifying Phakopsora pachyrhizi spores in rain. Phytopathology 99:328–338

    Article  Google Scholar 

  • Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris EJ, Prance GT, Davidse G, Paige J, Penninton TD, Robson NKB, Scottland RW (2010) Herbaria are a major frontier for species discovery. Proc Natl Acad Sci U S A 107:22169–22171

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Berny J-F, Hennebert GL (1991) Viability and stability of yeast cells and filamentous fungus spores during freeze-drying: effects of protectants and cooling rates. Mycologia 83:805–815

    Article  CAS  Google Scholar 

  • Bidartondo MI, Read DJ, Trappe JM, Merckx V, Ligrone R, Duckett JG (2011) The dawn of symbiosis between plants and fungi. Biol Lett 7(4):574–577

    Article  PubMed Central  PubMed  Google Scholar 

  • Blackwell M (2011) The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438

    Article  PubMed  Google Scholar 

  • Brock PM, Döring H, Bidartondo MI (2009) How to know the unknown fungi: the role of the herbarium. New Phytol 181:719–724

    Article  PubMed  Google Scholar 

  • Calcott PH (1978) Freezing and thawing microbes. Meadowfield Press, Shildon

    Google Scholar 

  • Carpenter JF, Crowe JH (1988) The mechanism of cryoprotection of proteins by solutes. Cryobiology 25:244–255

    Article  CAS  PubMed  Google Scholar 

  • Carpenter JF, Arakawa T, Crowe JH (1991) Interactions of stabilizing additives with proteins during freeze-thawing and freeze-drying. Dev Biol Stand 74:225–239

    Google Scholar 

  • Coetzee MPA, Wingfield BD, Bloomer P, Ridley GS, Wingfield MJ (2003) Molecular identification and phylogeny of Armillaria isolates from South America and Indo-Malaysia. Mycologia 95:285–293

    Article  CAS  PubMed  Google Scholar 

  • Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science 289:1139

    Article  CAS  PubMed  Google Scholar 

  • Crouch JA, Szabo LJ (2011) Real-time PCR detection and discrimination of the southern and common corn rust pathogens Puccinia polysora and Puccinia sorghi. Plant Dis 95:624–632

    Article  Google Scholar 

  • Crouch J, Tomaso-Peterson M (2012) Anthracnose disease of centipedegrass turf caused by Colletotrichum eremochloae, a new fungal species closely related to Colletotrichum sublineola. Mycologia. doi:10.3852/11-317

    PubMed  Google Scholar 

  • Crous PW, Verkley GJM, Groenewald JZ, Samson RA (eds) (2009) Fungal biodiversity, vol 1, CBS Laboratory manual series. CBS, Utrecht

    Google Scholar 

  • Cubero OF, Crespo A, Fatehi J, Bridge PD (1997) DNA extraction and PCR amplification method suitable for fresh, herbarium-stored, lichenized, and other fungi. Plant Syst Evol 216:243–249

    Article  Google Scholar 

  • Eberhardt U (2012) Methods for DNA barcoding fungi. In: Kress JW, Erickson DL (eds) DNA barcodes: methods and protocols. Humana Press, New York

    Google Scholar 

  • Elliot TJ (1976) Alternative ampoule for storing fungal cultures in liquid nitrogen. Trans Br Mycol Soc 67:545–546

    Article  Google Scholar 

  • Elliott TJ, Challen MP (1979) The storage of mushroom strains in liquid nitrogen. Glasshouse Crops Res Inst Annu Rep 1979:194–204

    Google Scholar 

  • Farr DF, Farr ER (2004) Electronic information resources. In: Mueller GM, Bills GF, Foster MS (eds) Biodiversity of fungi: inventory and monitoring methods. Elsevier, Amsterdam, pp 49–57

    Chapter  Google Scholar 

  • Forman L, Bridson D (eds) (1989) The herbarium handbook. Royal Botanic Gardens, Kew, Surrey

    Google Scholar 

  • Franks F (1990) Freeze-drying: from empiricism to predictability. The significance of glass transition. Dev Biol Stand 74:9–19

    Google Scholar 

  • Fredericks DN, Smith CA, Meier A (2005) Comparison of six DNA extraction methods for the recovery of fungal DNA as assessed by quantitative PCR. J Clin Microbiol 43:5122–5128

    Article  Google Scholar 

  • Friedberg EC, Walker GC, Siede W (1995) DNA repair and mutagenesis. ASM Press, Washington, DC

    Google Scholar 

  • Gilbert MTP, Cuccui J, White W, Lynnerup N, Titball RW, Cooper A, Prentice MB (2004) Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150:341–354

    Article  CAS  PubMed  Google Scholar 

  • Hall DV (1981) Microwave: a method to control herbarium insects. Taxon 30:818–819

    Article  Google Scholar 

  • Hatley RHM (1990) The effective use of differential scanning calorimetry in the optimization of freeze-drying processes and formulations. Dev Biol Stand 74:105–122

    Google Scholar 

  • Hawksworth DL (1974) Mycologist’s handbook. An introduction to the principles of taxonomy and nomenclature in the fungi and lichens. Commonwealth Mycological Institute, Kew, Surrey

    Google Scholar 

  • Hawksworth DL (2004) Fungal diversity and its implications for genetic resource collections. Stud Mycol 50:9–18

    Google Scholar 

  • Heckly RJ (1978) Preservation of microorganisms. Adv Appl Microbiol 24:1–53

    Article  CAS  PubMed  Google Scholar 

  • Hesseltine CW, Bradle BJ, Benjamin CR (1960) Further investigations on the preservation of molds. Mycologia 52:762–774

    Article  Google Scholar 

  • Hill SR (1983) Microwave and herbarium specimens: potential dangers. Taxon 32:614–615

    Article  Google Scholar 

  • Hoffmann P (1991) Cryopreservation of fungi. DSM Technical information sheet no. 5. World J Microbiol Biotechnol 7:92–94

    Article  Google Scholar 

  • Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S (2001) Ancient DNA. Nat Rev Genet 2:353–359

    Article  CAS  PubMed  Google Scholar 

  • Johnson GC, Martin AK (1992) Survival of wood-inhabiting fungi stored for 10 years in water and under oil. Can J Microbiol 38:861–864

    Article  Google Scholar 

  • Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200–203

    Article  CAS  PubMed  Google Scholar 

  • Jong SC (1989) Prevention and control of mite infestations in fungal cultures. ATCC Q Newslett 7:1127

    Google Scholar 

  • Jong SC, Birmingham JM (2001) Cultivation and preservation of fungi. In: McLaughlin DJ, McLaughlin EG, Lemke P (eds) The mycota, vol 7B. Springer, Berlin, pp 193–202

    Google Scholar 

  • Kirk PM, Cannon PF, Minter DW, Stalpers JA (eds) (2008) Ainsworth and Bisby’s dictionary of the fungi, 10th edn. CAB International, Wallingford

    Google Scholar 

  • Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, Baroni C (2002) Rates of evolution in ancient DNA from Adélie penguins. Science 295:2270–2273

    Article  CAS  PubMed  Google Scholar 

  • Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715

    Article  CAS  PubMed  Google Scholar 

  • Lister DL, Bower MA, Howe CJ, Jones MK (2008) Extraction and amplification of nuclear DNA from herbarium specimens of emmer wheat: a method for assessing DNA preservation by maximum amplicon length recovery. Taxon 57:254–258

    Google Scholar 

  • Lumbsch HT, Huhndorf SH (2010) Myconet, vol 14. Part One. Outline of Ascomycota—2009. Fieldiana Life Earth Sci 1:1–42

    Article  Google Scholar 

  • May KJ, Ristaino JB (2002) The mitochodrial DNA haplotype of Phytophthora infestans in 19th century herbarium specimens revealed. Phytopathology 92:s53

    Google Scholar 

  • May KJ, Ristaino JB (2004) Identity of the mtDNA haplotype(s) of Phytophthora infestans in historical specimens from the Irish potato famine. Mycol Res 108:471–479

    Article  CAS  PubMed  Google Scholar 

  • McNeill J, Barrie FR, Burdet HM, Demoulin V, Hawksworth DL, Marhold K, Nicolson DH, Prado J, Silva PC, Skog JE, Wiersema JH, Turland NJ (eds) (2006) International code of botanical nomenclature (Vienna Code). A. R. G. Gantner, Ruggell

    Google Scholar 

  • Metsger DA, Byers SC (1999) Managing the modern herbarium, an interdisciplinary approach. Society of the Preservation of Natural History Collections, Washington, DC

    Google Scholar 

  • Moore S (1999) Comments on freeze-drying and storing entire mycological specimens. In: Metsger D, Byers S (eds) Managing the modern herbarium: an interdisciplinary approach. Society for the Preservation of Natural History Collections and the Royal Ontario Museum, Washington, DC, pp 368–371

    Google Scholar 

  • Mueller GM, Bills GF, Foster MS (2004) Biodiversity of fungi. Inventory and monitoring methods. Elsevier, Burlington

    Google Scholar 

  • Nakasone KK, Peterson SW, Jong S-C (2004) Preservation and distribution of fungal cultures. In: Mueller G, Bills GF, Foster MS (eds) Biodiversity of fungi. Inventory and monitoring methods. Elsevier, Burlington, pp 37–47

    Chapter  Google Scholar 

  • O’Gorman DT, Sholberg PL, Stokes SC, Ginns J (2008) DNA sequence analysis of herbarium specimens facilitates the revival of Botrytis mali, a postharvest pathogen of apple. Mycologia 100:227–235

    Article  PubMed  Google Scholar 

  • OECD (2007) OECD best practice guidelines for biological resource centres. OECD Publications, Paris

    Google Scholar 

  • Pääbo S, Pinar H, Serre D, Jaenicke-Després V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679

    Article  PubMed  Google Scholar 

  • Pertot E, Puc A, Kremser M (1977) Lyophilisation of non-sporulating strains of the fungus Claviceps. Eur J Appl Microbiol 4:289–294

    Article  CAS  Google Scholar 

  • Pyke GH, Ehrlich PR (2010) Biological collections and ecological/environmental research: a review, some observations and a look to the future. Biol Rev 85:247–266

    Article  PubMed  Google Scholar 

  • Ristaino JB (1998) The importance of archival and herbarium materials in understanding the role of oospores in late blight epidemics of the past. Phytopathology 88:1120–1130

    Article  CAS  PubMed  Google Scholar 

  • Ristaino JB (2006) Tracking the evolutionary history of the potato late blight pathogen with historical collections. Outlooks Pest Manage 17:228–232

    Article  Google Scholar 

  • Ristaino JB, Groves CT, Parra GR (2001) PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411:695–697

    Article  CAS  PubMed  Google Scholar 

  • Rossman AY (1987) The Tubeufiaceae and similar Loculoascomycetes. Mycol Pap 157:1–71

    Google Scholar 

  • Rossman AY (1996) The evolution of fungal diversity—past, present and future. In: Colwell RR, Simidu U, Ohwada K (eds) Microbial diversity in time and space. Plenum, New York, pp 33–39

    Chapter  Google Scholar 

  • Rossman A, Palm-Hernandez ME (2008) Systematics of plant pathogenic fungi: why it matters. Plant Dis 92:1376–1386

    Article  Google Scholar 

  • Rossman A, Simmons E (1999) A modified technique for making dried cultures as voucher specimens. Inoculum 50(4):3

    Google Scholar 

  • SAFRINET (1999) Collecting and preserving fungi. A manual for mycology. NCF Biodiversity Division, ARC, Pretoria

    Google Scholar 

  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354

    Article  CAS  PubMed  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    Article  CAS  PubMed  Google Scholar 

  • Sakurada M, Tsuzuki Y, Morgavi DP, Tomita Y, Onodera R (1995) Simple methods for cryopreservation of an anaerobic rumen fungus using ethylene glycol and rumen fluid. FEMS Microbiol Lett 127:171–174

    Article  CAS  PubMed  Google Scholar 

  • Savile DBO (1962) Collection and care of botanical specimens, vol 1113. Canada Department of Agriculture Research Publication, Ottawa, pp 1–124

    Google Scholar 

  • Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of novel fungal lineages in tundra soils. Science 301:1359–1361

    Article  CAS  PubMed  Google Scholar 

  • Seifert KA, Rossman AY (2010) How to describe a new fungal species. IMA Fungus 1:109–116

    Article  PubMed Central  PubMed  Google Scholar 

  • Smith D (1983) Cryoprotectants and the cryopreservation of fungi. Trans Br Mycol Soc 80:360–363

    Article  Google Scholar 

  • Smith D, Coulson GE, Morris GJA (1986) A comparative study of the morphology and viability of hyphae of Penicillium expansum and Phytophthora nicotiana during freezing and thawing. J Gen Microbiol 132:2013–2021

    CAS  PubMed  Google Scholar 

  • Smith D, Onions AHS (1994) The preservation and maintenance of living fungi, 2nd edn. CAB International, Wallingford

    Google Scholar 

  • Sokolski S, Piché Y, Bérubé JA (2004) Lophodermium macci sp. nov., a new species on senesced foliage of five-needle pines. Mycologia 96:1261–1267

    Article  CAS  PubMed  Google Scholar 

  • Souzu H (1987) Freezing damage in microorganisms. In: Sakai A (ed) Cryopreservation. Asakura Shoten, Tokyo, pp 23–29

    Google Scholar 

  • Spooner B, Cannon P (2010) World’s largest collection of fungi held at Kew Gardens. Mycol News 2010(1):8–9

    Google Scholar 

  • Stalpers JA, De Hoog A, Vlug IJ (1987) Improvement of the straw technique for the preservation of fungi in liquid nitrogen. Mycologia 79:82–88

    Article  Google Scholar 

  • Stielow JB, Vaas LAI, Göker M, Hoffmann P, Klenk H-P (2012) Charcoal filter paper improves the viability of cryopreserved filamentous ectomycorrhizal and saprotrophic Basidiomycota and Ascomycota. Mycologia 104:324–330

    Article  PubMed  Google Scholar 

  • Tan CS (1997) Preservation of fungi. Crypt Mycol 18:157–163

    Google Scholar 

  • Tan CS (2011) Freeze-drying of filamentous fungi and yeasts. PhD thesis, Utrecht University, the Netherlands

    Google Scholar 

  • Tan CS, Stalpers JA (1996) Vitrification of fungi. In: Cimerman A, Gunde-Cimerman N (eds) Biodiversity. International biodiversity seminar ECCO XIV. Meeting. National Institute of Chemistry, Ljubljana, pp 189–193

    Google Scholar 

  • Tan CS, Stalpers JA, van Ingen CW (1991) Freeze-drying of fungal hyphae. Mycologia 83:654–657

    Article  Google Scholar 

  • Tan CS, Vlug IJA, Stalpers JA, van Ingen CW (1994) Microscopical observations on the influence of the cooling rate during freeze-drying of conidia. Mycologia 86:281–289

    Article  Google Scholar 

  • Tan CS, van Ingen CW, Talsma H, Miltenburg JC, Steffensen CL, Vlug IJA, Stalpers JA (1995) Freeze-drying of fungi: influence of composition and glass transition temperature of the protectant. Cryobiology 32:60–67

    Article  Google Scholar 

  • Taylor JW, Swann EC (1994) Dried samples: soft tissues, DNA from herbarium specimens. In: Herrmann B, Hummel S (eds) Ancient DNA. Springer, Berlin, pp 166–181

    Chapter  Google Scholar 

  • Telle S, Thines M (2008) Amplification of cox2 (~620 bp) from 2 mg of up to 129 year old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS One 3:e3584

    Article  PubMed Central  PubMed  Google Scholar 

  • Thevelein JM (1984) Regulation of trehalose mobilization in fungi. Microbiol Rev 48:42–59

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wiemken A (1990) Trehalose in yeasts, stress protectant rather than reserve carbohydrate. Antonie Van Leeuwenhoek 58:209–217

    Article  CAS  PubMed  Google Scholar 

  • Wood EW, Eriksson T, Donoghue MJ (1999) Guidelines for the use of herbarium materials in molecular research. In: Metsger DA, Byers SC (eds) Managing the modern herbarium, an interdisciplinary approach. Society of the Preservation of Natural History Collections, Washington, DC, pp 265–275

    Google Scholar 

  • Wu Q, Thiers BM, Pfister DH (2004) Preparation, preservation, and use of fungal specimens in herbaria. In: Mueller GM, Bills GF, Foster MS (eds) Biodiversity of fungi: inventory and monitoring methods. Elsevier, Amsterdam, pp 23–36

    Chapter  Google Scholar 

  • Zischler H, Hoss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J (1995) Detecting dinosaur DNA. Science 268:1192–1193

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Collections Manager Shannon Dominick is thanked for her useful comments on best herbarium practices as well as her conscientious management of the U.S. National Fungus Collections (BPI). Pedro W. Crous is kindly acknowledged for commenting on the manuscript.

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Authors and Affiliations

  1. CBS Biodiversity Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands

    Gerard J. M. Verkley

  2. Systematic Mycology & Microbiology Laboratory, USDA-ARS, Rm. 246, B010A 10300 Baltimore Ave., Beltsville, MD, 20705, USA

    Amy Rossman & Jo Anne Crouch

Authors
  1. Gerard J. M. Verkley
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  2. Amy Rossman
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  3. Jo Anne Crouch
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Correspondence to Gerard J. M. Verkley .

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Editors and Affiliations

  1. Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA

    David J. McLaughlin

  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA

    Joseph W. Spatafora

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Verkley, G.J.M., Rossman, A., Crouch, J.A. (2015). 8 The Role of Herbaria and Culture Collections. In: McLaughlin, D., Spatafora, J. (eds) Systematics and Evolution. The Mycota, vol 7B. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-46011-5_8

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