The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

S. K. Schmidt; K. L. Wilson; A. F. Meyer; C. W. Schadt; T. M. Porter; J. M. Moncalvo

doi:10.1128/9781555815509.ch4

Chapter 4 : The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

Authors: S. K. Schmidt¹, K. L. Wilson², A. F. Meyer³, C. W. Schadt⁴, T. M. Porter⁵, J. M. Moncalvo⁶

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 2: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 3: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 4: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038; 5: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; 6: Department of Ecology and Evolutionary Biology, University of Toronto, and Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada

Content Type: Monograph

Publication Year: 2008

Category: Genomics and Bioinformatics; Environmental Microbiology

Book DOI: 10.1128/9781555815509

Chapter DOI: 10.1128/9781555815509.ch4

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555815509/9781555814069_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555815509/9781555814069_Chap04-2.gif

Abstract:

Molecular surveys of soil fungi have received much less attention despite the fact that fungi dominate decomposition and nutrient cycles in many soils. The ability to sequence fungal DNA from soil samples has opened up a new realm of possibilities for identifying new fungal groups. A clone library approximates a random sample of fungi in the soil, and is likely to be biased toward some groups of fungi over others based on variables in each step of the procedure used. The Assembling the Fungal Tree of Life (AFTOL) initiative has definitively clarified the phylogenetic tree for all known fungi. Three rDNA regions are commonly used to identify fungi: the 18S small subunit (SSU); the internal transcriber spacer sequences ITS-1 and ITS-2; and the 28S large subunit (LSU). This chapter reviews the new fungal lineages that have been discovered in various soil libraries over the past 10 years. Most soil libraries to date have discovered new fungi only at the genus or species level. The chapter talks about two main discoveries, Chytridiomycota and Ascomycota, after reviewing other important but unrelated clades that have also been discovered in soil libraries. It is important to flesh out the fungal family tree as quickly as possible, as it is possible that many of the missing fungi can go extinct before it is known that they ever existed.

Citation: Schmidt S, Wilson K, Meyer A, Schadt C, Porter T, Moncalvo J. 2008. The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil, p 55-66. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch4

Key Concept Ranking

Bacteria and Archaea: 0.47612295
Transmission Electron Microscopy: 0.42646083

0.47612295

Highlighted Text: Show | Hide

Full text loading...

Figures

The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-1,webId=/content/author/10.1128/9781555815509.ch04-1,properties={foaf_givenname=S. K., foaf_name=S. K. Schmidt, foaf_surname=Schmidt, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-2,webId=/content/author/10.1128/9781555815509.ch04-2,properties={foaf_givenname=K. L., foaf_name=K. L. Wilson, foaf_surname=Wilson, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-3,webId=/content/author/10.1128/9781555815509.ch04-3,properties={foaf_givenname=A. F., foaf_name=A. F. Meyer, foaf_surname=Meyer, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-4,webId=/content/author/10.1128/9781555815509.ch04-4,properties={foaf_givenname=C. W., foaf_name=C. W. Schadt, foaf_surname=Schadt, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff4]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-5,webId=/content/author/10.1128/9781555815509.ch04-5,properties={foaf_givenname=T. M., foaf_name=T. M. Porter, foaf_surname=Porter, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff5]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815509.ch04-6,webId=/content/author/10.1128/9781555815509.ch04-6,properties={foaf_givenname=J. M., foaf_name=J. M. Moncalvo, foaf_surname=Moncalvo, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815509.ch04-aff6]]}]]

/content/10.1128/9781555815509.ch04.ch04fig01

FIGURE 1

Composite tree from a Bayesian analysis of LSU rRNA genes showing the relative position of Soil Clone Group I ( Schadt et al., 2003 ; Porter et al., 2008 ) between the Taphrinomycotina and Saccharomycotina subphyla, and Groups II and III within the Pezizomycotina subphylum as reported by Schadt et al. (2003) .

10.1128/9781555815509/f0059-01_thmb.gif

10.1128/9781555815509/f0059-01.gif

FIGURE 1

/content/10.1128/9781555815509.ch04.ch04fig02

FIGURE 2

Phylogenetic tree of environmental sequences of the Chytridiomycota and Zygomycota from high-altitude soil clone libraries. This tree consists of library clones (in rectangles), nBLAST matches of the clones, and selected guide sequences, and was constructed using Bayesian methods. Clone sequences of uncultured organisms that are nBLAST matches of the high-altitude soil clones are ovals. Support values are Bayesian posterior probabilities, and bootstraps using parsimony and neighbor joining methods (Bayes/MP/NJ). Selected posterior probabilities are those greater than 95%; selected bootstraps are those recovered greater than 50%. The TAL 6 clade represents novel chytrid sequences at the ordinal level. Two other novel lineages are also shown, T3 BA7 and T3 BF2. Zygomycete clones SF1 D5 and SF1 G7, found under snow in forest soils in Colorado, are members of a recently described snow mold consortium ( Schmidt et al., 2007 , 2008).

10.1128/9781555815509/f0061-01_thmb.gif

10.1128/9781555815509/f0061-01.gif

FIGURE 2

References

/content/book/10.1128/9781555815509.ch04

1. Acinas, S. G.,, R. Sarma-Rupavtarm,, V. Klepac-Ceraj, and, M. F. Polz. 2005. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71: 8966– 8969.

2. Anderson, I. C.,, C. D. Campbell, and, J. I. Prosser. 2003a. Diversity of fungi in organic soils under a moorland—Scots pine ( Pinus sylvestris L.) gradient. Environ. Microbiol. 5: 1121– 1132.

3. Anderson, I. C.,, C. D. Campbell, and, J. I. Prosser. 2003b. 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.

4. Arnold, A. E.,, Z. Maynard,, G. S. Gilbert,, P. D. Coley, and, T. A. Kursar. 2000. Are tropical fungal endophytes hyperdiverse? Ecol. Lett. 3: 267– 274.

5. Ashelford, K. E.,, N. A. Chuzhanova,, J. C. Fry,, A. J. Jones, and, A. J. Weightman. 2005. At east 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71: 7724– 7736.

6. Ashelford, K. E.,, N. A. Chuzhanova,, J. C. Fry,, A. J. Jones, and, A. J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72: 5734– 5741.

7. Baldauf, S. L.,, and J. D. Palmer. 1993. Animal and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90: 11558– 11562.

8. Bergero, R.,, M. Girlanda,, G. C. Varese,, D. Intili, and, A. M. Luppi. 1999. Psychrooligotrophic fungi from Arctic soils of Franz Joseph Land. Polar Biol. 21: 361– 368.

9. Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21: 163– 193.

10. Berney, C.,, J. Fahrni, and, J. Pawlowski. 2004. How many novel eukaryotic ‘kingdoms’? Pitfalls and limitations of environmental DNA surveys. BMC Biology 2: 13.

11. Blackwell, M.,, and K. Jones. 1997. Taxonomic diversity and interactions of insect-associated ascomycetes. Biodiversity Conserv. 6: 689– 699.

12. Bridge, P. D.,, P. J. Roberts,, B. M. Spooner, and, G. Panchal. 2003. On the unreliability of published DNA sequences. New Phytologist 160: 43– 48.

13. Brooks, P. D.,, S. K. Schmidt, and, M. W. Williams. 1997. Winter production of CO 2 and N 2O from Alpine tundra: environmental controls and relationship to inter-system C and N fluxes. Oecologia 110: 403– 413.

14. Bullerwell, C. E.,, L. Forget, and, B. F. Lang. 2003. Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Res. 31: 1614– 1623.

15. Cavalier-Smith, T. 2004. Only six kingdoms of life. Proc. R. Soc. London, Ser. B. 271: 1251– 1262.

16. Chen, D. M.,, and J. W. G. Cairney. 2002. Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites. Mycol. Res. 106: 532– 540.

17. Cole, J. R.,, B. Chai,, T. L. Marsh,, R. J. Farris,, Q. Wang,, S. A. Kulam,, S. Chandra,, D. M. McGarrell,, T. M. Schmidt,, G. M. Garrity, and, J. M. Tiedje. 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.

18. Dawson, S. C.,, and N. R. Pace. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99: 8324– 8329.

19. Frohlich, J.,, and K. D. Hyde. 1999. Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic? Biodiversity Conserv. 8: 977– 1004.

20. Frostegard, A.,, S. Courtois,, V. Ramisse,, S. Clerc,, D. Bernillon,, F. Le Gall,, P. Jeannin,, X. Nesme, and, P. Simonet. 1999. Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65: 5409– 5420.

21. Gardes, M.,, and T. D. Bruns. 1996. Community structure of ectomycorrhizal fungi in a Pinus muricata forest: above- and below-ground views. Can. J. Bot. 74: 1572– 1583.

22. Hawksworth, D. L. 2001. The magnitude of fungal diversity: the 1.5 million species. Mycol. Res. 105: 1422– 1432.

23. He, J. Z.,, Z. H. Xu, and, J. Hughes. 2005. Analyses of soil fungal communities in adjacent natural forest and hoop pine plantation ecosystems of subtropical Australia using molecular approaches based on 18S rRNA genes. FEMS Microbiol. Lett. 247: 91– 100.

24. Hibbett, D.,, A. Lutzoni,, D. McLaughlin,, J. Spatafora, and, R. Vilgalys. 2002. Assembling the Fungal Tree of Life (AFTOL) Project Summary. http://ocid.nacse.org/research/deephyphae/htmls/AFTOL_sum_DH.html.

25. Howlett, B. J.,, B. D. Rolls, and, A. J. Cozijnsen. 1997. Organisation of ribosomal DNA in the ascomycete Leptosphaeria maculans. Microbiol. Res. 152: 261– 267.

26. Huber, T.,, G. Faulkner, and, P. Hugenholtz. 2004. Bellerophon, a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics doi: 10.1093/bioinformatics/bth226.

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

28. Ishii, K.,, and M. Fukui. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol. 67: 3753– 3755.

29. Izzo, A.,, J. Agbowo, and, T. D. Bruns. 2005. Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. New Phytologist 166: 619– 630.

30. James T. Y., D. Porter,, C. A. Leander,, R. Vilgalys, and, J. E. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78: 336– 350.

31. James, T. Y.,, F. Kauff,, C. L. Schoch,, P. B. Matheny,, V. Hofstetter,, C. J. Cox,, G. Celio,, C. Gueidan,, E. Fraker,, J. Miadlikowska,, H. T. Lumbsch,, A. Rauhut,, V. Reeb,, A. E. Arnold,, A. Amtoft,, J. E. Stajich,, K. Hosaka,, G. H. Sung,, D. Johnson,, B. O’Rourke,, M. Crockett,, M. Binder,, J. M. Curtis,, J. C. Slot,, Z. Wang,, A. W. Wilson,, A. Schussler,, J. E. Longcore,, K. O’Donnell,, S. Mozley-Standridge,, D. Porter,, P. M. Letcher,, M. J. Powell,, J. W. Taylor,, M. M. White,, G. W. Griffith,, D. R. Davies,, R. A. Humber,, J. B. Morton,, J. Sugiyama,, A. Y. Rossman,, J. D. Rogers,, D. H. Pfister,, D. Hewitt,, K. Hansen,, S. Hambleton,, R. A. Shoemaker,, J. Kohlmeyer,, B. Volkmann-Kohlmeyer,, R. A. Spotts,, M. Serdani,, P. W. Crous,, K. W. Hughes,, K. Matsuura,, E. Langer,, G. Langer,, W. A. Untereiner,, R. Lucking,, B. Budel,, D. M. Geiser,, A. Aptroot,, P. Diederich,, I. Schmitt,, M. Schultz,, R. Yahr,, D. S. Hibbett,, F. Lutzoni,, D. J. McLaughlin,, J. W. Spatafora, and, R. Vilgalys. 2006. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443: 818– 822.

32. Janssen, P. H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72: 1719– 1728.

33. Jumpponen, A.,, and L. C. Johnson. 2005. Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations— a case study from tallgrass prairie. Mycologia 97: 1177– 1194.

34. Kirk, P. M.,, P. F. Cannon, and, J. C. David (ed.). 2001. Ainsworth and Bisby’s Dictionary of the Fungi, 9th ed. CAB International, Wallingford, United Kingdom.

35. Kurata, S.,, T. Kanagawa,, Y. Magariyama,, K. Takatsu,, K. Yamada,, T. Yokomaku, and, Y. Kamagata. 2004. Reevaluation and reduction of a PCR bias caused by reannealing of templates. Appl. Environ. Microbiol. 70: 7545– 7549.

36. Landeweert, R.,, P. Leeflang,, T. W. Kuyper,, E. Hoffland,, A. Rosling,, K. Wernars, and, E. Smit. 2003. Molecular identification of ectomycorrhizal mycelium in soil horizons. Appl. Environ. Microbiol. 69: 327– 333.

37. Landvik, S.,, T. K. Schumacher,, O. E. Eriksson, and, S. T. Moss.. 2003. Morphology and ultrastructure of Neolecta species. Mycol. Res. 107: 1021– 1031.

38. Lipson, D. A.,, C. W. Schadt, and, S. K. Schmidt. 2002. Changes in soil microbial community structure and function in an alpine dry meadow following spring snowmelt. Microb. Ecol. 43: 307– 314.

39. Liu, Y. J.,, and B. D. Hall. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II, phylogeny. Proc. Natl. Acad. Sci. USA 101: 4507– 4512.

40. Longcore, J. E. 2005. Zoosporic fungi from Australian and New Zealand tree-canopy detritus. Aust. J. Bot. 53: 259– 272.

41. Lueders, T.,, and M. W. Friedrich. 2003. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol. 69: 320– 326.

42. Lutzoni, F.,, F. Kauff,, C. J. Cox,, D. McLaughlin,, G. Celio,, B. Dentinger,, M. Padamsee,, D. Hibbett,, T. Y. James,, E. Baloch,, M. Grube,, V. Reeb,, V. Hofstetter,, C. Schoch,, A. E. Arnold,, J. Miadlikowska,, J. Spatafora,, D. Johnson,, S. Hambleton,, M. Crockett,, R. Shoemaker,, G. H. Sung,, R. Lucking,, T. Lumbsch,, K. O’Donnell,, M. Binder,, P. Diederich,, D. Ertz,, C. Gueidan,, K. Hansen,, R. C. Harris,, K. Hosaka,, Y. W. Lim,, B. Matheny,, H. Nishida,, D. Pfister,, J. Rogers,, A. Rossman,, I. Schmitt,, H. Sipman,, J. Stone,, J. Sugiyama,, R. Yahr, and, R. Vilgalys. 2004. Assembling the fungal tree of life. Progress, classification and evolution of subcellular traits. Am. J. Bot. 91: 1446– 1480.

43. Lynch, M. D. J.,, and R. G. Thorn. 2006. Diversity of basidiomycetes in Michigan agricultural soils. Appl. Environ. Microbiol. 72: 7050– 7056.

44. Malosso, E.,, I. S. Waite,, L. English,, D. W. Hopkins, and, A. G. O’Donnell. 2006. Fungal diversity in maritime Antarctic soils determined using a combination of culture isolation, molecular fingerprinting and cloning techniques. Polar Biol. 29: 552– 561.

45. Menkis, A.,, R. Vasiliauskas,, A. F. S. Taylor,, J. Stenlid, and, R. Finlay. 2005. Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation. Mycorrhiza 16: 33– 41.

46. Moncalvo, J. M. 2005. Molecular systematics—major fungal phylogenetic groups and fungal species concepts. p. 1–33 In J. P. Xu (ed.), Evolutionary Genetics of Fungi. Horizon Scientific Press, Norfolk, United Kingdom.

47. Monson, R. K.,, D. L. Lipson,, S. P. Burns,, A. A. Turnipseed,, A. C. Delany,, M. W. Williams, and, S. K. Schmidt. 2006. Winter forest soil respiration controlled by climate and microbial community composition. Nature 439: 711– 714.

48. Nishida, H.,, and J. Sugiyama. 1994. Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 35: 361– 366.

49. O’Brien, H. E.,, J. L. Parrent,, J. A. Jackson,, J.- M. Moncalvo, and, R. Vilgalys. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Appl. Environ. Microbiol. 71: 5544– 5550.

50. Polz, M. F.,, and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64: 3724– 3730.

51. Porter, T. M.,, C. W. Schadt,, L. Rizvi,, A. P. Martin,, S. K. Schmidt,, L. Scott-Denton,, R. Vilgalys, and, J.- M. Moncalvo. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Mol. Phylogenet. Evol., in press.

52. Pringle, A.,, J.- M. Moncalvo, and, R. Vilgalys. 2000. High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica. Mycologia 92: 259– 268.

53. Rappé, M. S.,, and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369– 394.

54. Robertson, C. E.,, J. K. Harris,, J. R. Spear, and, N. R. Pace. 2005. Phylogenetic diversity and ecology of environmental archaea. Curr. Opin. Microbiol. 8: 638– 642.

55. Rosling, A.,, R. Landeweert,, B. D. Lindahl,, K.- H. Larsson,, T. W. Kuyper,, A. F. S. Taylor, and, R. D. Finlay. 2003. Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytologist 159: 775– 783.

56. Schadt, C. W.,, A. P. Martin,, D. A. Lipson, and, S. K. Schmidt. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301: 1359– 1361.

57. Schloss, P. D.,, and J. Handelsman. 2006. Toward a census of bacteria in soil. PloS Comp. Biol. 2: 786– 793.

58. Schmidt, S. K.,, E. K. Costello,, D. R. Nemergut,, C. C. Cleveland,, S. C. Reed,, M. N. Weintraub,, A. F. Meyer, and, A. M. Martin. 2007. Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology 88: 1379– 1385.

59. Schmidt, S. K.,, K. L. Wilson,, M. M. Gebauer,, A. F. Meyer, and, A. J. King. Phylogeny and ecophysiology of opportunistic “snow molds” from a subalpine forest ecosystem. Microb. Ecol., in press.

60. Schübler, A.,, D. Schwarzott, and, C. Walker. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol. Res. 105: 1413– 1421.

61. Selbmann, L.,, G. S. de Hoog,, A. Mazzaglia,, E. I. Friedmann, and, S. Onofri. 2005. Fungi at the edge of life: cryptoendolithic black fungi from Antarctic desert. Stud. Mycol. 51: 1– 32.

62. Simmons, D. R. 2007. Systematics of the Lobulomycetales, a new order within the Chytridiomycota. University of Maine, Orono, ME.

63. Taylor, L.,, I. C. Harriott,, J. Long, and, K. O’Neill. 2007. TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction. Environ. Microbiol. doi:10.1111/j:1462-2920.

64. Ustinova, I.,, L. Krienitz, and, V. A. R. Huss. 2000. Hyaloraphidium curvatum is not a green alga, but a lower fungus; Amoebidium parasiticum is not a fungus, but a member of the DRIPs. Protist 151: 253– 262.

65. Vandenkoornhuyse, P.,, S. L. Baldauf,, C. Leyval,, J. Straczek, and, J. P. W. Young. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.

66. Vilgalys, R. 2003. Taxonomic misidentification in public DNA databases. New Phytologist 160: 4– 5.

67. von Wintzingerode, F.,, U. B. Gobel, and, E. Stacke-brandt. 1997. Determination of microbial diversity in environmental samples/ pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21: 213– 229.

68. Wynn-Williams, D. D. 1996. Antarctic microbial diversity: the basis of polar ecosystem processes. Biodiversity Conserv. 5: 1271– 1293.

Tables

The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

/content/10.1128/9781555815509.ch04.ch04tab01

TABLE 1

Biogeographic distribution of SCGI in rDNA clone libraries of soils a

TABLE 1

Biogeographic distribution of SCGI in rDNA clone libraries of soils a