Skip to main content
SpringerLink
Log in

3 Environmental DNA Analysis and the Expansion of the Fungal Tree of Life

  • Chapter
  • First Online:
Book cover Evolution of Fungi and Fungal-Like Organisms

Part of the book series: The Mycota ((MYCOTA,volume 14))

Abstract

The diversity of the Fungi has been estimated to be as much as 5.1 million species, however only a small fraction of this number are currently described. Traditional methods based around culturing and microscopic analyses of specimens enable taxonomic classification and can lead to detailed phenotypic and genotypic analysis. However, these methods select for those species easily cultured in laboratory conditions or with distinctive morphologies such as multi-cellular reproductive structures. As such the uncultured majority is overlooked. Clone library construction is widely used to identify uncultured species within an environment but few environmental gene libraries are sampled to saturation and the process can often be biased towards certain groups. However, using such methods a large number of novel sequences branching with the fungi in phylogenetic analyses have been retrieved from a variety of environments including freshwater sites, marine environments, soils, and insects. In this chapter we review some of this recently discovered novel diversity and the techniques used to obtain them. We will also discuss recent advances in second generation sequencing technology and fluorescence in situ hybridisation microscopy, and what the application of such techniques could mean for our understanding of the diversity of fungi in natural environments and the fungal tree of life.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52:399–451

    Article  PubMed  Google Scholar 

  • Amaral Zettler LA, Gómez F, Zettler E, Keenan BG, Amils R and Sogin ML (2002) Microbiology: eukaryotic diversity in Spain's river of fire. Nature 417:137

    Article  PubMed  CAS  Google Scholar 

  • Amaral-Zettler LA, McCliment EA, Ducklow HW and Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 4:e6372

    Article  PubMed  CAS  Google Scholar 

  • Anderson IC and Cairney JW (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6:769–779

    Article  PubMed  CAS  Google Scholar 

  • Anderson IC, Campbell CD and Prosser JI (2003) Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ Microbiol 5:36–47

    Article  PubMed  CAS  Google Scholar 

  • Arnold AE, Maynard Z, Gilbert GS, Coley PD and Kursar TA (2000) Are tropical fungal endophytes hyperdiverse? Ecology Letters 3:267–274

    Article  Google Scholar 

  • Bartnicki-Garcia S (1987) The cell wall: a crucial structure in fungal evolution. In: Rayner ADM, Brasier CM and Moore D (ed) Evolutionary Biology of the Fungi. Cambridge University Press, Cambridge, pp

    Google Scholar 

  • Baschien C, Manz W, Neu TR and Szewzyk U (2001) Fluorescence in situ hybrization of freshwater fungi. Internat. Rev. Hydrobiol. 86:371–381

    Article  Google Scholar 

  • Bass D and Cavalier-Smith T (2004) Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 54:2393–2404

    Article  PubMed  CAS  Google Scholar 

  • Bass D, Howe A, Brown N, Barton H, Demidova M, Michelle H, Li L, Sanders H, Watkinson SC, Willcock S et al. (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc Biol Sci 274:3069–3077

    Article  PubMed  CAS  Google Scholar 

  • Behrens S, Rühland C, Inácio J, Huber H, Fonseca A, Spencer-Martins I, Fuchs BM and Amann R (2003) In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 69:1748–1758

    Article  PubMed  CAS  Google Scholar 

  • Berney C, Fahrni J and Pawlowski J (2004) How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol 2:13

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Bruns TD and Gardes M (1993) Molecular tools for the identification of ectomycorrhizal fungi-taxon-specific oligonucleotide probes for suilloid fungi. Mol Ecol 2:233–242

    Article  PubMed  CAS  Google Scholar 

  • Buchan A, Newell SY, Moreta JI and Moran MA (2002) Analysis of internal transcribed spacer regions of rRNA genes in fungal communities in a southeastern U.S. salt marsh. Microb Ecol 43:329–340

    Article  PubMed  CAS  Google Scholar 

  • Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S and Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456

    Article  PubMed  CAS  Google Scholar 

  • Burgaud G, Le Calvez T, Arzur D, Vandenkoornhuyse P and Barbier G (2009) Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ Microbiol 11:1588–1600

    Article  PubMed  Google Scholar 

  • Cavalier-Smith T (2004) Only six kingdoms of life. Proc R Soc Lond B Biol Sci 271:1251–1262

    Article  CAS  Google Scholar 

  • Chambouvet A, Morin P, Marie D and Guillou L (2008) Control of toxic marine dinoflagellate blooms by serial parasitic killers. Science 322:1254–1257

    Article  PubMed  CAS  Google Scholar 

  • Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  PubMed  CAS  Google Scholar 

  • Damare S and Raghukumar C (2008) Fungi and macroaggregation in deep-sea sediments. Microb Ecol 56:168–177

    Google Scholar 

  • Damare S and Raghukumar C (2008) Fungi and macroaggregation in deep-sea sediments. Microb Ecol 56:168–177

    Article  PubMed  Google Scholar 

  • Dawson SC and Pace NR (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99:8324–8329

    Article  PubMed  CAS  Google Scholar 

  • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072

    Article  PubMed  CAS  Google Scholar 

  • Edgcomb VP, Kysela DT, Teske A, de Vera Gomez A and Sogin ML (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci USA 99:7658–7662

    Article  PubMed  CAS  Google Scholar 

  • Embley TM, van der Giezen M, Horner DS, Dyal PL and Foster P (2003) Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Philos Trans R Soc Lond B Biol Sci 358:191–201

    Article  PubMed  CAS  Google Scholar 

  • Fisher CR, Takai K and Le Bris N (2007) Hydrothermal vent ecosystems. Oceanography 20:14–23

    Article  Google Scholar 

  • Gage JD and Tyler PA (1991) Deep-sea biology: a natural history of organisms at the deep-sea floor. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Gardes M and Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL and Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    Article  PubMed  CAS  Google Scholar 

  • Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ and Worden AZ (2008) Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10:3349–3365

    Article  PubMed  CAS  Google Scholar 

  • Harrison KE (1990) The role of nutrition in maturation, reproduction and embryonic development of decapod crustaceans: a review. J Shellfish Res 9:1–28

    Google Scholar 

  • Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance and conservation. Mycol Res 95:641–655

    Article  Google Scholar 

  • Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432

    Article  Google Scholar 

  • Held AA (1981) Rozella and Rozellopsis: naked endoparasitic fungi which dress up as their hosts. The Botanical Review 47:451–515

    Article  Google Scholar 

  • Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509–547

    Article  PubMed  Google Scholar 

  • Hirt RP, Healy B, Vossbrinck CR, Canning EU and Embley TM (1997) A mitochondrial HSP70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria. Curr Biol 7:995–998

    Article  PubMed  CAS  Google Scholar 

  • Hirt RP, Logsdon JM, Jr., Healy B, Dorey MW, Doolittle WF and Embley TM (1999) Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA 96:580–585

    Article  PubMed  CAS  Google Scholar 

  • Horton TR and Bruns TD (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 10:1855–1871

    Article  PubMed  CAS  Google Scholar 

  • Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA and Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100

    Article  PubMed  CAS  Google Scholar 

  • Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML and Mark Welch DB (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 11:1292–1302

    Article  PubMed  CAS  Google Scholar 

  • Huber T, Faulkner G and Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319

    Article  PubMed  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM and Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  Google Scholar 

  • Hugenholtz P and Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289–293

    Article  CAS  Google Scholar 

  • James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J et al. (2006a) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822

    Article  PubMed  CAS  Google Scholar 

  • James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Porter D, Powell MJ, Griffith GW and Vilgalys R (2006b) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860–871

    Article  PubMed  Google Scholar 

  • Jebaraj CS, Raghukumar C, Behnke A and Stoeck T (2009) Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 71:399–412

    Article  PubMed  CAS  Google Scholar 

  • Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R and Richards TA (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature: Advance Online Publication, doi:10.1038/nature09984

    Google Scholar 

  • Jumpponen A and Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184:438–448

    Article  PubMed  CAS  Google Scholar 

  • Keeling PJ (2003) Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet Biol 38:298–309

    Article  PubMed  CAS  Google Scholar 

  • Kis-Papo T (2005) Marine fungal communities. In: Dighton J, White JF and Oudemans P (ed) The fungal community: Its organisation and role in the ecosystem. Taylor and Francis Group, Boca Raton, pp

    Google Scholar 

  • Kohlmeyer J and Kohlmeyer E (1979) Marine mycology: the higher fungi. Academic Press, New york

    Google Scholar 

  • Kosse D, Amann RI, Ludwig W and Scherer S (1997) Identification of yoghurt-spoiling yeasts with 18S rRNA-targeted oligonucleotide probes. Syst Appl Microbiol 20:468–480

    Article  Google Scholar 

  • Kunin V, Engelbrektson A, Ochman H and Hugenholtz P (2009) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123

    Article  PubMed  CAS  Google Scholar 

  • Lara E, Moreira D and López-Garcia P (2010) The environmental clade LKM11 and Rozella form the deepest branching clade of Fungi. Protist 161:116–121

    Article  PubMed  CAS  Google Scholar 

  • Lawley B, Ripley S, Bridge P and Convey P (2004) Molecular analysis of geographic patterns of eukaryotic diversity in Antarctic soils. Appl Environ Microbiol 70:5963–5972

    Article  PubMed  CAS  Google Scholar 

  • Le Calvez T, Burgaud G, Mahé S, Barbier G and Vandenkoornhuyse P (2009) Fungal diversity in deep-sea hydrothermal ecosystems. Appl Environ Microbiol 75:6415–6421

    Article  PubMed  CAS  Google Scholar 

  • Lefèvre E, Bardot C, Noël C, Carrias JF, Viscogliosi E, Amblard C and Sime-Ngando T (2007) Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake. Environ Microbiol 9:61–71

    Article  PubMed  CAS  Google Scholar 

  • Lefèvre E, Roussel B, Amblard C and Sime-Ngando T (2008) The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton. PLoS ONE 3:e2324

    Article  PubMed  CAS  Google Scholar 

  • Lefranc M, Thénot A, Lepère C and Debroas D (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71:5935–5942

    Article  PubMed  CAS  Google Scholar 

  • Lepère C, Boucher D, Jardillier L, Domaizon I and Debroas D (2006) Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin). Appl Environ Microbiol 72:2971–2981

    Article  PubMed  CAS  Google Scholar 

  • Lesaulnier C, Papamichail D, McCorkle S, Ollivier B, Skiena S, Taghavi S, Zak D and van der Lelie D (2008) Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol 10:926–941

    Article  PubMed  CAS  Google Scholar 

  • Li S, Cullen D, Hjort M, Spear R and Andrews JH (1996) Development of an oligonucleotide probe for Aureobasidium pullulans based on the small-subunit rRNA gene. Appl Environ Microbiol 62:1514–1518

    PubMed  CAS  Google Scholar 

  • Liu Y, Steenkamp ET, Brinkmann H, Forget L, Philippe H and Lang BF (2009) Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. BMC Evol Biol 9:272

    Article  PubMed  CAS  Google Scholar 

  • López-García P, Rodriguez-Valera F, Pedrós-Alió C and Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603–607

    Article  PubMed  Google Scholar 

  • López-Garcia P, Vereshchaka A and Moreira D (2007) Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field. Environ Microbiol 9:546–454

    Article  PubMed  CAS  Google Scholar 

  • Luo Q, Krumholz LR, Najar FZ, Peacock AD, Roe BA, White DC and Elshahed M (2005) Diversity of the microeukaryotic community in sulfide-rich Zodletone Spring (Oklahoma). Appl Environ Microbiol. 71:6175–6184

    Article  PubMed  CAS  Google Scholar 

  • Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ and Woese CR (1996) The Ribosomal Database Project (RDP). Nucleic Acids Res 24:82–85

    Article  PubMed  CAS  Google Scholar 

  • Mann KH (1988) Production and use of detritus in various freshwater, estuarine, and coastal marine ecosystems. Limnology and Oceanography 33:910–930

    Article  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  • Massana R, Castresana J, Balagué V, Guillou L, Romari K, Groisillier A, Valentin K and Pedrós-Alió C (2004) Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70:3528–3534

    Article  PubMed  CAS  Google Scholar 

  • Massana R, Guillou L, Diez B and Pedrós-Alió C (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol 68:4554–4558

    Article  PubMed  CAS  Google Scholar 

  • Massana R and Pedrós-Alió C (2008) Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11:213–218

    Article  PubMed  Google Scholar 

  • May RM (1991) Fondness for Fungi. Nature 352:475–476

    Article  Google Scholar 

  • May RM (1994) Conceptual aspects of quantification of the extent of biological diversity. Philos Trans R Soc Lond B Biol Sci 345:13–20

    Article  PubMed  CAS  Google Scholar 

  • Moon-van der Staay SY, De Wachter R and Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607–610

    Article  PubMed  CAS  Google Scholar 

  • Moreira D and López-Garcia P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38

    Article  PubMed  CAS  Google Scholar 

  • Moter A and Göbel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85–112

    Article  PubMed  CAS  Google Scholar 

  • Mueller GM, Schmit JP, Leacock PR, Buyck B, Cifuentes J, Desjardin DE, Halling RE, Hjortstam K, Iturriaga T. Larsson KH, et al. (2007) Global diversity and distribution of macrofungi. Biodivers. Conserv. 16:37–48

    Google Scholar 

  • Muller GM and Schmit JP (2007) Fungal biodiversity: what do we know? what we can we predict. Biodivers.Conserv. 16:1–5

    Article  Google Scholar 

  • Newell SY (1996) Established and potential impacts of eukaryotic mycelial decomposers in marine/terrestrial ecotones. J Exp Mar Biol Ecol 200:187–206

    Article  Google Scholar 

  • Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N and Larsson KH (2008) Intraspecific its variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform Online 4:193–201

    PubMed  Google Scholar 

  • Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH and Kõljalg U (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1:e59

    Article  PubMed  CAS  Google Scholar 

  • Not F, Valentin K, Romari K, Lovejoy C, Massana R, Töbe K, Vaulot D and Medlin LK (2007) Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315:253–255

    Article  PubMed  CAS  Google Scholar 

  • O’brien HE, Parrent JL, Jackson JA, Moncalvo J-M and Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550

    Article  PubMed  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR and Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  PubMed  CAS  Google Scholar 

  • Olsen GJ and Woese CR (1993) Ribosomal RNA: a key to phylogeny. Faseb J. 7:113–123

    PubMed  CAS  Google Scholar 

  • Öpik M, Metsis M, Daniell TJ, Zobel M and Moora M (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol 184:424–437

    Article  PubMed  CAS  Google Scholar 

  • Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740

    Article  PubMed  CAS  Google Scholar 

  • Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257–263

    Article  PubMed  CAS  Google Scholar 

  • Pernthaler J, Glöckner FO, Schönhuber W and Rudolf A (2001) Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. In: Paul JH (ed) Marine Microbiology. Academic Press, London, pp

    Google Scholar 

  • Porter TM, Schadt CW, Rizvi L, Martin AP, Schmidt SK, Scott-Denton L, Vilgalys R and Moncalvo JM (2008) Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Mol Phylogenet Evol 46:635–644

    Article  PubMed  CAS  Google Scholar 

  • Raghukumar S (2004) The role of fungi in marine detrital processes. In: Ramaiah N (ed) Marine Microbiology: Facets & Opportunities. National Institute of Oceanography Goa, pp 91–101

    Google Scholar 

  • Richards TA and Bass D (2005) Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis. Curr Opin Microbiol 8:240–252

    Article  PubMed  CAS  Google Scholar 

  • Richards TA, Vepritskiy AA, Gouliamova D and Nierzwicki-Bauer SA (2005) The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ Microbiol 7:1413–1425

    Article  PubMed  CAS  Google Scholar 

  • Robison-Cox JF, Bateson MM and Ward DM (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl Environ Microbiol 61:1240–1245

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Seifert KA, Samson RA, Dewaard JR, Houbraken J, Lévesque CA, Moncalvo JM, Louis-Seize G and Hebert PD (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci USA 104:3901–3906

    Article  PubMed  CAS  Google Scholar 

  • Slapeta J, Moreira D and P. L-G (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc R Soc B 272:2073–2081

    Article  PubMed  CAS  Google Scholar 

  • Sogin ML, Elwood HJ and Gunderson JH (1986) Evolutionary diversity of eukaryotic small subunit rRNA genes. Proc Natl Acad Sci USA 83:1383–1387

    Article  PubMed  CAS  Google Scholar 

  • Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM and Herndl GJ (2006) Microbial diversity in the deep-sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120

    Article  PubMed  CAS  Google Scholar 

  • Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW and Richards TA (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19 Suppl 1:21–31

    Article  PubMed  CAS  Google Scholar 

  • Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W and Edgcomb VP (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol 7:72

    Article  PubMed  CAS  Google Scholar 

  • Stoeck T and Epstein S (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69:2657–2663

    Article  PubMed  CAS  Google Scholar 

  • Stoeck T, Hayward B, Taylor GT, Varela R and Epstein SS (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31–43

    Article  PubMed  CAS  Google Scholar 

  • Suh SO, McHugh JV, Pollock DD and Blackwell M (2005) The beetle gut: a hyperdiverse source of novel yeasts. Mycol Res 109:261–265

    Article  PubMed  CAS  Google Scholar 

  • Takishita K, Tsuchiya M, Reimer JD and Maruyama T (2006) Molecular evidence demonstrating the basidiomycetous fungus Cryptococcus curvatus is the dominant microbial eukaryote in sediment at the Kuroshima Knoll methane seep. Extremophiles 10:165–169

    Article  PubMed  CAS  Google Scholar 

  • Van de Peer Y, Jansen J, De Rijk P and De Wachter R (1997) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res 25:111–116

    Article  PubMed  Google Scholar 

  • van der Giezen M, Slotboom DJ, Horner DS, Dyal PL, Harding M, Xue GP, Embley TM and Kunji ER (2002) Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. Embo J 21:572–579

    Article  PubMed  Google Scholar 

  • Van Dover CL, Ward ME, Scott JL, Underdown J, Andersen B, Gustafson C, Whalen M and Carnegia RB (2007) A fungal epizootic in mussels at a deep-sea hydrothermal vent. Marine Ecology 28:54–62

    Article  CAS  Google Scholar 

  • van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ and Laanbroek HJ (1999) Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478–2484

    PubMed  Google Scholar 

  • Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J and Young JPW (2002) Extensive fungal diversity in plant roots. Science 295:2051

    Article  PubMed  Google Scholar 

  • Vilgalys R (2003) Taxonomic misidentification in public DNA databases. New Phyt. 160:4–5

    Article  CAS  Google Scholar 

  • von der Heyden S, Chao EE and Cavalier-Smith T (2004) Genetic diversity of goniomonads: an ancient divergence between marine and freshwater species. Eur J Phycol 39:343–350

    Article  CAS  Google Scholar 

  • White TJ, Bruns TD, Lee IY and Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies. In: Innis MA, Gelfand DH, Sninsky JJ and White T (ed) PCR protocols: a guide to methods and amplifications. Academic Press, San Diego, pp

    Google Scholar 

  • Winker S and Woese CR (1991) A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. Syst Appl Microbiol 14:305–310

    Google Scholar 

  • Winker S and Woese CR (1991) A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. Syst Appl Microbiol 14:305–310

    Article  PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O and Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  PubMed  CAS  Google Scholar 

  • Wuyts J, De Rijk P, Van de Peer Y, Pison G, Rousseeuw P and De Wachter R (2000) Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res 28:4698–4708

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Natural History Museum, Cromwell Road, London, SW7 5BD, UK

    Meredith D. M. Jones & Thomas A. Richards

Authors
  1. Meredith D. M. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thomas A. Richards
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Meredith D. M. Jones .

Editor information

Editors and Affiliations

  1. , Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany

    Stefanie Pöggeler

  2. , Institut für Allgemeine Mikrobiologie, Friedrich-Schiller-Universität Jena, Neugasse 24, Jena, 07743, Germany

    Johannes Wöstemeyer

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Jones, M.D.M., Richards, T.A. (2011). 3 Environmental DNA Analysis and the Expansion of the Fungal Tree of Life. In: Pöggeler, S., Wöstemeyer, J. (eds) Evolution of Fungi and Fungal-Like Organisms. The Mycota, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19974-5_3

Download citation

Publish with us

Policies and ethics

Search

Navigation