A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: A Case Study of Fungi in Indoor Dust

Microbial Ecology

Volumn 66, Issue 4, 2013, Pages 735-741

  Adams, Rachel I ^a   Amend, Anthony S ^b   Taylor, John W ^a   Bruns, Thomas D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGI; MARSHALLIA CAESPITOSA;

ARTICLE; BIODIVERSITY; CLASSIFICATION; DUST; ECOSYSTEM; FUNGUS; GENETICS; HIGH THROUGHPUT SEQUENCING; INDOOR AIR POLLUTION; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

AIR MICROBIOLOGY; AIR POLLUTION, INDOOR; BIODIVERSITY; DUST; ECOSYSTEM; FUNGI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84885910044     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-013-0266-4     Document Type: Article

References (39)

1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. doi: 10. 1038/Nature03959.
2. Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46. doi: 10. 1038/nrg2626.
3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59. doi: 10. 1038/Nature07517.
4. Clemmensen KE, Bahr A, Ovaskainen O, Dahlberg A, Ekblad A, Wallander H et al (2013) Roots and associated fungi drive long-term carbon sequestration in boreal forest. Science 339: 1615-1618. doi: 10. 1126/science. 1231923.
5. Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA (2013) Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci USA 110: 4651-4655. doi: 10. 1073/pnas. 1217767110.
6. Zimmerman NB, Vitousek PM (2012) Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proc Natl Acad Sci USA 109: 13022-13027. doi: 10. 1073/Pnas. 1209872109.
7. Huang X-F, Bakker M, Judd T, Reardon K, Vivanco J (2013) Variations in diversity and richness of gut bacterial communities of termites (Reticulitermes flavipes) fed with grassy and woody plant substrates. Microb Ecol 65: 531-536. doi: 10. 1007/s00248-013-0219-y.
8. Segata N, Haake S, Mannon P, Lemon K, Waldron L, Gevers D et al (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42.
9. Kelley ST, Gilbert JA (2013) Studying the microbiology of the indoor environment. Genome Biol 14: 202. doi: 10. 1186/gb-2013-14-2-202.
10. Meng J, Barnes CS, Rosenwasser LJ, Hlth CMCE (2012) Identity of the fungal species present in the homes of asthmatic children. Clin and Exp Allergy 42: 1448-1458. doi: 10. 1111/J. 1365-2222. 2012. 04001. X.
11. Amend AS, Seifert KA, Samson R, Bruns TD (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci USA 107: 13748-13753. doi: 10. 1073/Pnas. 1000454107.
12. Adams RI, Miletto M, Taylor JW, Bruns TD (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. doi: 10. 1038/ismej. 2013. 28.
13. Pitkaranta M, Meklin T, Hyvarinen A, Nevalainen A, Paulin L, Auvinen P et al (2011) Molecular profiling of fungal communities in moisture damaged buildings before and after remediation-a comparison of culture-dependent and culture-independent methods. BMC Microbiol 11: 235.
14. Würtz H, Sigsgaard T, Valbjørn O, Doekes G, Meyer HW (2005) The dustfall collector-a simple passive tool for long-term collection of airborne dust: a project under the Danish Mould in Buildings program (DAMIB). Indoor Air 15: 33-40. doi: 10. 1111/j. 1600-0668. 2005. 00342. x.
15. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA. doi: 10. 1073/pnas. 1117018109.
16. Gardes M, Bruns T (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118.
17. White T, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis N, Gelfand D, Sninsky J, White T (eds) PCR: protocols and applications-a laboratory manual. Academic, New York, pp 315-322.
18. 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 Microbiol 10: 189.
19. Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19: 5555-5565. doi: 10. 1111/J. 1365-294x. 2010. 04898. X.
20. 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. doi: 10. 3852/11-027.
21. Bazzicalupo AL (2013) Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities. Fungal Ecol 6: 102-109.
22. Zhou G, Whong WZ, Ong T, Chen B (2000) Development of a fungus-specific PCR assay for detecting low-level fungi in an indoor environment. Mol Cell Probes 14: 339-348.
23. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336. doi: 10. 1038/Nmeth. F. 303.
24. Reeder J, Knight R (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669. doi: 10. 1038/Nmeth0910-668b.
25. Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J et al (2010) An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecol 3: 284-287. doi: 10. 1016/J. Funeco. 2010. 05. 002.
26. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. doi: 10. 1093/Bioinformatics/Btr381.
27. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi: 10. 1093/Bioinformatics/Btq461.
28. Colwell RK (2006) EstimateS: statistical estimation of species richness and shared species from samples. http://www. purl. oclc. org/estimates. Accessed 10 Sept 2012.
29. R Development Core Team (2012) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www. R-project. org. Accessed 3 Mar 2011.
30. Abarenkov K, Nilsson RH, Larsson KH, Alexander IJ, Eberhardt U, Erland S et al (2010) The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol 186: 281-285.
31. Oksanen J, Blanchet FG, Kindt R, Legendre R, Minchin PR, O'Hara RB, et al. (2012) vegan: community ecology package.
32. Shannon CE (1948) A mathematical theory of communication. At&T Tech J 27: 623-656.
33. Gotelli NJ, Ellison AM (2004) A primer of ecological statistics. Sinauer, Sunderland.
34. Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR et al (2012) Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 7: e44224. doi: 10. 1371/journal. pone. 0044224.
35. Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-1898. doi: 10. 1111/j. 1462-2920. 2010. 02193. x.
36. Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 27: 326-349.
37. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, Freestone AL et al (2011) Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist. Ecol Lett 14: 19-28. doi: 10. 1111/j. 1461-0248. 2010. 01552. x.
38. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA 106: 22427-22432. doi: 10. 1073/Pnas. 0908284106.
39. Nazaroff WW (2004) Indoor particle dynamics. Indoor Air 14: 175-183.