Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

New Phytologist

Volumn 199, Issue 1, 2013, Pages 288-299

  Lindahl, Björn D ^a   Nilsson, R Henrik ^b   Tedersoo, Leho ^c   Abarenkov, Kessy ^c   Carlsen, Tor ^d   Kjøller, Rasmus ^e   Kõljalg, Urmas ^c   Pennanen, Taina ^f   Rosendahl, Søren ^e   Stenlid, Jan ^a   Kauserud, Håvard ^d  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c UNIVERSITY OF TARTU   (Estonia)

^d UNIVERSITY OF OSLO   (Norway)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

454 pyrosequencing; Barcoding; Bioinformatics; Environmental sequencing; Internal transcribed spacer (ITS) region; PCR

Indexed keywords

FUNGAL DNA; PRIMER DNA; SPACER DNA;

BIOINFORMATICS; COMMUNITY COMPOSITION; COMMUNITY ECOLOGY; COMMUNITY STRUCTURE; FUNGUS; MYCORRHIZA; RISK ASSESSMENT; SAPROTROPHY;

ARTICLE; BIOLOGY; BIOTA; CLASSIFICATION; FUNGUS; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MICROBIOLOGY; MYCORRHIZA; POLYMERASE CHAIN REACTION;

BIOTA; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA, FUNGAL; DNA, INTERGENIC; FUNGI; GENETIC MARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MYCORRHIZAE; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY;

EID: 84878360700     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12243     Document Type: Article

References (116)

1. Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Hoiland K, Kjøller R, Larsson E, Pennanen T et al. 2010b. The UNITE database for molecular identification of fungi - recent updates and future perspectives. New Phytologist 186: 281-285.
2. Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, Veldre V, Parmasto E, Prous M, Aan A, Ots M et al. 2010a. PlutoF - a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences. Evolutionary Bioinformatics 6: 189-196.
3. Amend AS, Seifert KA, Bruns TD. 2010. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology 19: 5555-5565.
4. Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, Zifcakova L, Snajdr J, Ridl J, Vlcek C et al. 2012. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. The ISME Journal 6: 248-258.
5. Baldrian P, Větrovský T, Cajthaml T, Dobiášová P, Petránková M, Šnajdr J, Eichlerová I. 2013. Estimation of fungal biomass in forest litter and soil. Fungal Ecology 6: 1-11.
6. Balzer S, Malde K, Jonassen I. 2011. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 27: i304-i309.
7. Bazzicalupo AL, Bálint M, Schmitt I. 2013. Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities. Fungal Ecology 6: 102-109.
8. Begerow D, Nilsson H, Unterseher M, Maier W. 2010. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology 87: 99-108.
9. Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 10: 189.
10. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH. 2011. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek 100: 471-475.
11. Berry D, Ben-Mahfoudh K, Wagner M, Loy A. 2011. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Applied and Environmental Microbiology 77: 7846-7849.
12. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. 2012. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution 27: 233-243.
13. Boddy L. 2000. Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiology Ecology 31: 185-194.
14. Bödeker ITM, Nygren CMR, Taylor AFS, Olson Å, Lindahl BD. 2009. ClassII peroxidase encoding genes are present in a wide phylogenetic range of ectomycorrhizal fungi. The ISME Journal 3: 1387-1395.
15. Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW. 2012. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods 9: 425-426.
16. Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009. 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist 184: 449-456.
17. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.
18. Carlsen T, Bjørnsgaard-Aas A, Lindner D, Vrålstad T, Schumacher T, Kauserud H. 2012. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecology 5: 747-749.
19. Christen R. 2008. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes and Environments 23: 253-268.
20. Coleman AW. 2009. Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution 50: 197-203.
21. Courty P-E, Franc A, Garbaye J. 2008. Temporal changes in the ectomycorrhizal community in two soil horizons of a temperate oak forest. Applied and Environmental Microbiology 74: 5792-5801.
22. Davey ML, Heegaard E, Halvorsen R, Ohlson M, Kauserud H. 2012. Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing. New Phytologist 195: 844-856.
23. Dickie IA. 2010. Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytologist 188: 916-918.
24. Dickie IA, Xu B, Koide RT. 2002. Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytologist 156: 527-535.
25. Douhan GW, Vincenot L, Gryta H, Selosse MA. 2011. Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions. Fungal Biology 115: 569-597.
26. Eddy SR. 2011. Accelerated Profile HMM Searches. PLoS Computational Biology 7: e1002195.
27. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
28. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P. 2010. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. The ISME Journal 4: 642-647.
29. Faircloth BC, Glenn TC. 2012. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS ONE 7: e42543.
30. Fonseca VG, Nichols B, Lallias D, Quince C, Carvalho GR, Power DM, Creer S. 2012. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research 40: e66.
31. Freeman KR, Martin AP, Karki D, Lynch RC, Mitter MS, Meyer AF, Longcore JE, Simmons DR, Schmidt SK. 2009. Evidence that chytrids dominate fungal communities in high-elevation soils. Proceedings of the National Academy of Sciences, USA 106: 18315-18320.
32. Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113-118.
33. Gazis R, Rehner S, Chaverri P. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Molecular Ecology 20: 3001-3013.
34. Gihring TM, Green SJ, Schadt CW. 2012. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environmental Microbiology 14: 285-290.
35. Glenn TC. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 11: 759-769.
36. Gobet A, Quince C, Ramette A. 2010. Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Research 38: e155.
37. Gollotte A, van Tuinen D, Atkinson D. 2004. Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment. Mycorrhiza 14: 111-117.
38. Grant S, Grant WD, Cowan DA, Jones BE, Ma YH, Ventosa A, Heaphy S. 2006. Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. Applied and Environmental Microbiology 72: 135-143.
39. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Södergren E et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 21: 494-504.
40. Hamady M, Lozupone C, Knight R. 2010. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME Journal 4: 17-27.
41. Hao X, Jiang R, Chen T. 2011. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 27: 611-618.
42. Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH. 2010. V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16 S/18 S) ribosomal RNA gene sequences. Journal of Microbiological Methods 83: 250-253.
43. Hartmann M, Howes CG, Vaninsberghe D, Yu H, Bachar D, Christen R, Nilsson RH, Hallam SJ, Mohn WW. 2012. Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. The ISME Journal 6: 2199-2218.
44. Herrera ML, Vallor AC, Gelfond JA, Patterson TF, Wickes BL. 2009. Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus. Journal of Clinical Microbiology 47: 1325-1332.
45. Hibbett DS, Gilbert LB, Donoghue MJ. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407: 506-508.
46. Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, Welch DBM. 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology 11: 1292-1302.
47. Huse SM, Welch DM, Morrison HG, Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 12: 1889-1898.
48. Huson DH, Mitra S, Weber N, Ruscheweyh H, Schuster SC. 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Research 21: 1552-1560.
49. Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, Strid Y, Stenlid J, Brandström-Durling M, Clemmensen KE et al. 2012. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 82: 666-677.
50. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J et al. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822.
51. Jumpponen A, Jones KL. 2009. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate quercus macrocarpa phyllosphere. New Phytologist 184: 438-448.
52. Kanagawa T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). Journal of Bioscience and Bioengineering 96: 317-323.
53. Kang S, Mansfield MA, Park B, Geiser DM, Ivors KL, Coffey MD, Grunwald NJ, Martin FN, Levesque CA, Blair JE. 2010. The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes. Phytopathology 100: 732-737.
54. Katoh K, Frith MC. 2012. Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics 28: 3144-3146.
55. Kauserud H, Kumar S, Brysting AK, Nordén J, Carlsen T. 2012. High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples. Mycorrhiza 22: 309-315.
56. Kebaara BW, Nielsen LE, Nickerson KW, Atkin AL. 2006. Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor. Genome 49: 894-899.
57. Kellner H, Zak DR, Vandenbol M. 2010. Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS ONE 5: e10971.
58. Kerekes J, Kaspari M, Stevenson B, Nilsson RH, Hartmann M, Amend A, Bruns TD. 2013. Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest. Molecular Ecology. doi:10.1111/mec.12259.
59. Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Müller T, Wolf M, Schultz J. 2010. The ITS2 Database III - sequences and structures for phylogeny. Nucleic Acids Research 38: D275-D279.
60. Koš M, Tollervey D. 2010. Yeast pre-rRNA processing and modification occur cotranscriptionally. Molecular Cell 37: 745-746.
61. Krüger M, Stockinger H, Krüger C, Schüssler A. 2009. DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytologist 183: 212-223.
62. Kumar S, Carlsen T, Mevik B-H, Enger P, Blaalid R, Shalchian-Tabrizi K, Kauserud H. 2011. CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics 12: 182.
63. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology 12: 118-123.
64. Kuske CR, Lindahl BD. 2013. Metagenomics for study of fungal ecology. In: Martin F, ed. Ecological genomics of the fungi. Hoboken, NJ, USA: Wiley-Blackwell.
65. Lahr DJG, Katz LA. 2009. Reducing the impact of PCR-mediated recombina-tion in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. BioTechniques 47: 857-863.
66. Lee J, Lee S, Young JPW. 2008. Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology 65: 339-349.
67. Lekberg Y, Schnoor T, Kjøller R, Gibbons SM, Hansen LH, Al-Soud WA, Sørensen SJ, Rosendahl S. 2012. 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. Journal of Ecology 100: 151-160.
68. Lennon JT. 2011. Replication, lies and lesser-known truths regarding experimental design in environmental microbiology. Environmental Microbiology 13: 1383-1386.
69. Lewis LK, Robson MH, Vecherkina Y, Ji C, Beall GW. 2010. Interference with spectrophotometric analysis of nucleic acids and proteins by leaching of chemicals from plastic tubes. BioTechniques 48: 297-302.
70. Li M, Diehl F, Dressman D, Vogelstein B, Kinzler KW. 2006. BEAMing up for detection and quantification of rare sequence variants. Nature Methods 3: 95-97.
71. Lilleskov EA, Bruns TD, Horton TR, Taylor DL, Grogan P. 2004. Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities. FEMS Microbiology Ecology 49: 319-332.
72. Lindahl BD, de Boer W, Finlay RD. 2010. Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi. The ISME Journal 4: 872-881.
73. Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Högberg P, Stenlid J, Finlay RD. 2007. Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytologist 173: 611-620.
74. Lindahl BD, Taylor AFS. 2004. N-acetylhexosaminidase coding genes in ectomycorrhizal basidiomycetes. New Phytologist 164: 193-199.
75. Lindner DL, Banik MT. 2011. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 103: 731-740.
76. Liu KL, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. 2012. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Applied and Environmental Microbiology 78: 1523-1533.
77. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
78. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G. 2001. DNA extraction from soils: old bias for new microbial diversity analysis methods. Applied and Environmental Microbiology 67: 2354-2359.
79. Mello A, Napoli C, Murat C, Morin E, Marceddu G, Bonfante P. 2011. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia 103: 1184-1193.
80. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. 2008. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics 4: 193-201.
81. Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. 2009. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters 296: 97-101.
82. Nilsson RH, Tedersoo L, Lindahl BD, Kjøller R, Carlsen T, Quince C, Abarenkov K, Pennanen T, Stenlid J, Bruns T et al. 2011. Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytologist 191: 314-318.
83. Öpik M, Metsis M, Daniell TJ, Zobel M, Moora M. 2009. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist 184: 424-437.
84. Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier U, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241.
85. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. 2007. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research 35: e130.
86. Pennanen T, Caul S, Daniell TJ, Griffiths BS, Ritz K, Wheatley RE. 2004. Community-level responses of metabolically-active soil microorganisms to the quantity and quality of substrate inputs. Soil Biology & Biochemistry 36: 841-848.
87. Petersen L, Minkkinen P, Esbensen KH. 2005. Representative sampling for reliable data analysis: theory of Sampling. Chemometrics and Intelligent Laboratory Systems 77: 261-277.
88. Pickles BJ, Genney DR, Potts JM, Lennon JJ, Anderson IC, Alexander IJ. 2010. Spatial and temporal ecology of Scots pine ectomycorrhizas. New Phytologist 186: 755-768.
89. Polz MF, Cavanaugh CM. 1998. Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology 64: 3724-3730.
90. Porter TM, Golding GB. 2012. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS ONE 7: e35749.
91. Prosser JI. 2010. Replicate or lie. Environmental Microbiology 12: 1806-1810.
92. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 35: 7188-7196.
93. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6: 639-641.
94. Quince C, Lanzen A, Turnbaugh PJ. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
95. Rajala T, Peltoniemi M, Hantula J, Mäkipää R, Pennanen T. 2011. RNA reveals a succession of active fungi during the decay of Norway spruce logs. Fungal Ecology 4: 437-444.
96. Reeder J, Knight R. 2010. Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nature Methods 7: 668-669.
97. Rosen MJ, Callahan BJ, Fisher DS, Holmes SP. 2012. Denoising PCR-amplified metagenome data. BMC Bioinformatics 13: 283.
98. Russell DJ, Way SF, Benson AK, Sayood K. 2010. A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. BMC Bioinformatics 11: 601.
99. Sanders IR, Croll D. 2010. Arbuscular mycorrhiza: the challenge to understand the genetics of the fungal partner. Annual Review of Genetics 44: 271-292.
100. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.
101. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences, USA 109: 6241-6246.
102. Shokralla S, Spall JL, Gibson JF, Hajibabaei M 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794-1805.
103. Smith ML, Bruhn JN, Anderson JB. 1992. The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nature 356: 428-431.
104. Stockinger H, Kruger M, Schussler A. 2010. DNA barcoding of arbuscular mycorrhizal fungi. New Phytologist 187: 461-474.
105. Taberlet P, Prud'homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clément J-C et al. 2012. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology 21: 1816-1820.
106. Tanner MA, Goebel BM, Dojka MA, Pace NR. 1998. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Applied and Environmental Microbiology 64: 3110-3113.
107. Tedersoo L, Abarenkov K, Nilsson RH, Schussler A, Grelet GA, Kohout P, Oja J, Bonito GM, Veldre V, Jairus T et al. 2011. Tidying up international nucleotide sequence databases: ecological, geographical, and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLoS ONE 6: e24940.
108. Tedersoo L, Jairus T, Horton BM, Abarenkov K, Suvi T, Saar I, Kõljalg U. 2008. Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytologist 180: 479-490.
109. Tedersoo L, May TW, Smith ME. 2010b. Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20: 217-263.
110. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. 2010a. 454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291-301.
111. Toju H, Tanabe AS, Yamamoto S, Sato H. 2012. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS ONE 7: e40863.
112. van Tuinen D, Jacquot E, Zhao B, Gollotte A, Gianinazzi-Pearson V. 1998. Charecterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR. Molecular Ecology 7: 879-887.
113. Wallander H, Johansson U, Sterkenburg E, Brandström-Durling M, Lindahl BD. 2010. Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests. New Phytologist 187: 1124-1134.
114. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73: 5261-5267.
115. White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfland DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego, CA, USA: Academic Press, 315-322.
116. Wilson IG. 1997. Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology 63: 3741-3751.