Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity

Environmental Microbiology

Volumn 16, Issue 8, 2014, Pages 2491-2500

  Yamamoto, Naomichi ^a   Bibby, Kyle ^b,c  

^a Seoul National University   (South Korea)

^b University of Pittsburgh   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OTUS;

SPACER DNA;

ARTICLE; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA SEQUENCE; FUNGUS; GENETICS; PHYLOGENY; STATISTICS;

CELL NUCLEUS; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA, INTERGENIC; FUNGI; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84905384182     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12390     Document Type: Article

References (34)

1. Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013) Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7: 1262-1273.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Amend, A.S., Seifert, K.A., Samson, R., and Bruns, T.D. (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107: 13748-13753.
4. Bakker, M.G., Tu, Z.J., Bradeen, J.M., and Kinkel, L.L. (2012) Implications of pyrosequencing error correction for biological data interpretation. PLoS ONE 7: e44357. doi:10.1371/journal.pone.0044357.
5. Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S., and Martin, F. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: 449-456.
6. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., etal. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
7. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam, S.A., McGarrell, D.M., etal. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: D294-D296.
8. Dannemiller, K.C., Reeves, D., Bibby, K., Yamamoto, N., and Peccia, J. (2013) Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J Basic Microbiol. doi:10.1002/jobm.201200507.
9. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
10. Gaspar, J.M., and Thomas, W.K. (2013) Assessing the consequences of denoising marker-based metagenomic data. PLoS ONE 8: e60458. doi:10.1371/journal.pone.0060458.
11. Hawksworth, D.L. (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105: 1422-1432.
12. Koljalg, U., Nilsson, R.H., Abarenkov, K., Tedersoo, L., Taylor, A.F., Bahram, M., etal. (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22: 5271-5277.
13. Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
14. Larena, I., Salazar, O., Gonzalez, V., Julian, M.C., and Rubio, V. (1999) Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. J Biotechnol 75: 187-194.
15. Lindahl, B.D., Nilsson, R.H., Tedersoo, L., Abarenkov, K., Carlsen, T., Kjoller, R., etal. (2013) Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytol 199: 288-299.
16. Lindner, D.L., and Banik, M.T. (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.
17. Lindner, D.L., Carlsen, T., Nilsson, R.H., Davey, M., Schumacher, T., and Kauserud, H. (2013) Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecol Evol 3: 1751-1764.
18. Manter, D.K., and Vivanco, J.M. (2007) Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Methods 71: 7-14.
19. Mueller, G.M., and Schmit, J.P. (2007) Fungal biodiversity: what do we know? What can we predict? Biodivers Conserv 16: 1-5.
20. Nilsson, R.H., Ryberg, M., Kristiansson, E., Abarenkov, K., Larsson, K.-H., and Kõljalg, U. (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1: e59.
21. Nilsson, R.H., Kristiansson, E., Ryberg, M., Hallenberg, N., and 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. Evol Bioinform Online 4: 193-201.
22. Nilsson, R.H., Bok, G., Ryberg, M., Kristiansson, E., and Hallenberg, N. (2009) A software pipeline for processing and identification of fungal ITS sequences. Source Code Biol Med 4: 1.
23. O'Brien, H.E., Parrent, J.L., Jackson, J.A., Moncalvo, J.M., and Vilgalys, R. (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71: 5544-5550.
24. O'Gorman, C.M., Fuller, H., and Dyer, P.S. (2009) Discovery of a sexual cycle in the opportunistic fungal pathogen A.fumigatus. Nature 457: 471-474.
25. Quince, C., Lanzen, A., Curtis, T.P., Davenport, R.J., Hall, N., Head, I.M., etal. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
26. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
27. Reeder, J., and Knight, R. (2009) The 'rare biosphere': a reality check. Nat Methods 6: 636-637.
28. Reeder, J., and Knight, R. (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669.
29. Schmidt, P.-A., Bálint, M., Greshake, B., Bandow, C., Römbke, J., and Schmitt, I. (2013) Illumina metabarcoding of a soil fungal community. Soil Biol Biochem 65: 128-132.
30. Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., etal. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: 6241-6246.
31. Taylor, J.W. (2011) One Fungus=One Name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2: 113-120.
32. Yamamoto, N., Shendell, D.G., and Peccia, J. (2011) Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air 21: 521-530.
33. Yamamoto, N., Bibby, K., Qian, J., Hospodsky, D., Rismani-Yazdi, H., Nazaroff, W.W., and Peccia, J. (2012) Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J 6: 1801-1811.
34. Yamamoto, N., Dannemiller, K., Bibby, K., and Peccia, J. (2013) Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation. Environ Microbiol. doi:10.1111/1462-2920.12338.