Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

MycoKeys

Volumn 10, Issue , 2015, Pages 1-43

  Tedersoo, Leho ^a   Anslan, Sten ^b   Bahram, Mohammad ^b,c   Põlme, Sergei ^a,b   Riit, Taavi ^b   Liiv, Ingrid ^b   Kõljalg, Urmas ^c   Kisand, Veljo ^a   Nilsson, R Henrik ^d   Hildebrand, Falk ^e   Bork, Peer ^e   Abarenkov, Kessy ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b UNIVERSITY OF TARTU   (Estonia)

^c UPPSALA UNIVERSITY   (Sweden)

^d UNIVERSITY OF GOTHENBURG   (Sweden)

^e EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

High throughput sequencing; Identification bias; Illumina MiSeq sequencing; Internal transcribed spacer (ITS); Nuclear large subunit (LSU); Nuclear small subunit (SSU); Primer bias; Shotgun metagenomics; Taxonomic coverage

Indexed keywords

EID: 84940567255     PISSN: 13144057     EISSN: 13144049     Source Type: Journal    
DOI: 10.3897/mycokeys.10.4852     Document Type: Article

References (61)

1. Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Ursing B, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U (2010) The UNITE database for molecular identification of fungi - recent updates and future perspectives. New Phytologist 186: 281-285. doi: 10.1111/j.1469-8137.2009.03160.x
2. Aird D, Ross MG, Chen W-S, Danielsson M, Dennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology 12: R18. doi: 10.1186/gb-2011-12-2-r18
3. Arfi Y, Buee M, Marchand C, Levasseur A, Record E (2012) Multiple markers pyrosequencing reveals highly diverse and host specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa. FEMS Microbiology Ecology 79: 433-444. doi: 10.1111/j.1574-6941.2011.01236.x
4. Begerow D, Nilsson RH, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology 87: 99-108. doi: 10.1007/s00253-010-2585-4
5. 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. doi: 10.1186/1471-2180-10-189
6. Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH (2012) Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Research in Microbiology 163: 407-412. doi: 10.1016/j.resmic.2012.07.001
7. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, de Wit P, Sanchez-Garcia M, Ebersberger I, de Sousa F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution 4: 914-919. doi: 10.1111/2041-210X.12073
8. Bhattacharya D, Lutzoni F, Reeb V, Simon D, Nason J, Fernandez F (2000) Widespread occurrence of spliceosomal introns in the rDNA genes of Ascomycetes. Molecular Biology and Evolution 17: 1971-1984. doi: 10.1093/oxfordjournals.molbev.a026298
9. Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H (2013) ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources 13: 218-224. doi: 10.1111/1755-0998.12065
10. Blackwell M (2011) The Fungi: 1, 2, 3 ⋯ 5.1 million species? American Journal of Botany 98: 426-428. doi: 10.3732/ajb.1000298
11. Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Applied and Environmental Microbiology 66: 4356-4360. doi: 10.1128/AEM.66.10.4356-4360.2000
12. Brown SP, Veach AM, Rigdon-Huss AR, Grond K, Lickteig SK, Lothamer K, Oliver AK, Jumpponen A (2015) Scraping the bottom of the barrel: are rare high-throughput sequences artifacts? Fungal Ecology 13: 221-225. doi: 10.1016/j.funeco.2014.08.006
13. Carninci P, Shibata Y, Hayatsu N, Itoh M, Shiraki T, Hirozane T, Watahiki A, Shibata K, Konno H, Muramatsu M, Hayashizaki Y (2011) Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics 77: 79-90. doi: 10.1006/geno.2001.6601
14. Castro HF, Classen AT, Austin ET, Norby RJ, Schadt CW (2010) Soil microbial community responses ro multiple experimental climate change drivers. Applied and Environmental Microbiology 76: 999-1007. doi: 10.1128/AEM.02874-09
15. Cavender-Bares J, Hozak KH, Fine PVA, Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecology Letters 12: 693-715. doi: 10.1111/j.1461-0248.2009.01314.x
16. Colwell RK (2013) EstimateS: Statistical estimation of species richness and shared species from samples. Version 9. User's Guide and application published at: http://purl.oclc.org/estimates.
17. Daghino S, Murat C, Sizzano E, Girlanda M, Perotto S (2012) Fungal diversity is not determined by mineral and chemical differences in serpentine substrates. PLoS ONE 7: e44233. doi: 10.1371/journal.pone.0044233
18. 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
19. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 23: 3150-3152. doi: 10.1093/bioinformatics/bts565
20. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizas and rusts. Molecular Ecology 2: 113-118. doi: 10.1111/j.1365-294X.1993.tb00005.x
21. Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J (2014) LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2: 30. doi: 10.1186/2049-2618-2-30
22. Hopple JS, Vilgalys R (1994) Phylogenetic relationships among coprinoid txa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia 86: 96-107. doi: 10.2307/3760723
23. Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenk J, Strid Y, Stenlid J, Brandström-Durling M, Clemmensen KE, Lindahl BD (2012) New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 83: 666-677. doi: 10.1111/j.1574-6941.2012.01437.x
24. Ishii N, Ishida S, Kagami M (2015) PCR primers for assessing community structure of aquatic fungi including Chytridiomycota and Cryptomycota. Fungal Ecology 13: 33-43. doi: 10.1016/j.funeco.2014.08.004
25. Kanagawa T (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). Journal of Biosciences and Bioengineering 96: 317-323. doi: 10.1016/S1389-1723(03)90130-7
26. Kohout P, Sudova R, Janouskova M, Ctvrtlikova M, Hejda M, Pankova H, Slavikova R, Stajerova K, Vosatka M, Sykorova Z (2014) Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution? Soil Biology and Biochemistry 68: 482-493. doi: 10.1016/j.soilbio.2013.08.027
27. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M (2013) Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology 22: 5271-5277. doi: 10.1111/mec.12481
28. Korsakovsky Pond S, Wadhawan S, Chairomonte F, Ananda G, Chung W-Y, Taylor J, Nekrutenko A, The Galaxy Team (2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research 19: 2144-2153. doi: 10.1101/gr.094508.109
29. Kopylova E, Noé L, Touzet H (2012) SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28: 3211-3217. doi: 10.1093/bioinformatics/bts611
30. Livermore JA, Mattes TE (2013) Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets. Environmental Microbiology 15: 2333-2341. doi: 10.1111/1462-2920.12106
31. Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingkamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG (2014) Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology 16: 2659-2671. doi: 10.1111/1462-2920.12250
32. Martin KJ, Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiology 5: 28. doi: 10.1186/1471-2180-5-28
33. Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD (2012) PANDAseq: PAired-eND Assembler for Illumina sequences. BMC Bioinformatics 13: 31. doi: 10.1186/1471-2105-13-31
34. 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. doi: 10.1111/j.1574-6968.2009.01618.x
35. Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson K-H, Kõljalg U, Edgar RC, Abarenkov K(in press) A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments. doi: 10.1264/jsme2.ME14121
36. Oja J, Bahram M, Tedersoo L, Kull T, Kõljalg U (2015) Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing. New Phytologist 205: 1608-1618. doi: 10.1111/nph.13223
37. Olesen JM, Jordano P (2002) Geographic patterns in plant-pollinator mutualistic networks. Ecology 83: 2416-2424. doi: 10.2307/3071803
38. Op De Beeck M, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV (2014) Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS ONE 9: e97629. doi: 10.1371/journal.pone.0097629
39. Põlme S, Bahram M, Kõljalg U, Tedersoo L (2014) Global biogeography of Alnus-associated Frankia Actinobacteria. New Phytologist 204: 979-988. doi: 10.1111/nph.12962
40. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596. doi: 10.1093/nar/gks1219
41. Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301: 1359-1361. doi: 10.1126/science.1086940
42. Schadt CW, Rosling A (in press) Global diversity and geography of soil fungi: minus one widespread group. Science.
43. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JS, Strez B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing Mothur: open-source, platform-independent community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541. doi: 10.1128/AEM.01541-09
44. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera G, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul T, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schussler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiss M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D (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. doi: 10.1073/pnas.1117018109
45. Taylor DL, Hollingsworth TN, McFarland JW, Lennon NJ, Nussbaum C, Ruess RW (2014) A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecological Monographs 84: 3-20. doi: 10.1890/12-1693.1
46. Taylor DL, McCormick MK (2008) Internal transcribed spacer primers and sequences for improved characterization of basidomycetous orchid mycorrhizas. New Phytol. 177: 1020-1033. doi: 10.1111/j.1469-8137.2007.02320.x
47. Tedersoo L, Bahram M, Cajthaml T, Põlme S, Hiiesalu I, Anslan S, Harend H, Buegger F, Pritsch K, Koricheva J, Abarenkov K (2015a) Tree diversity and species identity effects on soil fungi, protists and animals are context-dependent. The ISME Journal. [in press]
48. Tedersoo L, Bahram M, Põlme S, Anslan S, Riit T, Kõljalg U, Nilsson RH, Hildebrand F, Abvarenkov K (2015b) Analytical biases in microbial diversity studies. Science. [in press]
49. Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Villarreal-Ruiz L, Vasco-Palacios A, Quang Thu P, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Ratkowsky D, Pritsch K, Riit T, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo L, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K (2014) Global diversity and geography of soil fungi. Science 346: 1078. doi: 10.1126/science.1256688
50. 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. doi: 10.1111/j.1469-8137.2008.02561.x
51. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291-301. doi: 10.1111/j.1469-8137.2010.03373.x
52. Tedersoo L, Smith ME (2013) Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground. Fungal Biology Reviews 27: 83-99. doi: 10.1016/j.fbr.2013.09.001
53. 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. doi: 10.1371/journal.pone.0040863
54. Turenne CY, Sanche SS, Hoban DJ, Karlowsky JA, Kabani AM (1999) Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. Journal of Clinical Microbiology 37: 1846-1851.
55. Turner S, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. Journal of Eukaryote Microbiology 46: 327-338. doi: 10.1111/j.1550-7408.1999.tb04612.x
56. 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. doi: 10.1128/AEM.00062-07
57. Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q (2015) ITS1: a DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources 15: 573-586. doi: 10.1111/1755-0998.12325
58. Waud M, Busschaert P, Ruyters S, Jacquemyn H, Lievens B (2014) Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing. Molecular Ecology Resources 14: 679-699. doi: 10.1111/1755-0998.12229
59. White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (Eds) PCR Protocols: A Guide to Methods and Applications. Academic Press, New York, 315-322. doi: 10.1016/B978-0-12-372180-8.50042-1
60. Zhou J, He Z, Deng Y, Tringe SG, Alvarez-Cohen L (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 6: e02288-14. doi: 10.1128/mBio.02288-14
61. Zhou X, Li Y, Liu S, Yang Q, Su X, Zhou L, Tang M, Fu R, Li J, Huang Q (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Giga Science 2: 4. doi: 10.1186/2047-217X-2-4