Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

Conservation Genetics

Volumn 16, Issue 3, 2015, Pages 513-522

  Zhan, Aibin ^a   MacIsaac, Hugh J ^b  

^a RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^b UNIVERSITY OF WINDSOR   (Canada)

Author keywords

Biodiversity; Metabarcoding; Next generation sequencing; Rare species; Type I error; Type II error

Indexed keywords

EID: 84939977782     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-014-0678-9     Document Type: Article

References (64)

1. Barnosky AD, Matzke N, Tomiya S, Wogan GO, Swartz B, Quental TB, Marshall C, McGuire JL, Lindsey EL, Maguire KC, Mersey B, Ferrer EA (2011) Has the Earth’s sixth mass extinction already arrived? Nature 471:51–57
2. 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
3. Berry D, Mahfoudh KB, Wagner M, Loy A (2011) Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol 77:7846–7849
4. Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H (2013) ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol Ecol Resour 13:218–224
5. Boessenkool S, Epp LS, Haile J, Bellemain E (2012) Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Mol Ecol 21:1806–1815
6. Bohmann K, Evans A, Gilbert TP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29:358–367
7. Brown SP, Veach AM, Rigdon-Huss AR, Grond K, Lickteig SK, Lothamer K, Oliver AK, Jumpponen A (2014) Scraping the bottom of the barrel: are rare high throughput sequences artifacts? Fungal Ecol. doi:10.1016/j.funeco.2014.08.006
8. Carlsen T, Aas AB, Lindner D, Vrålstad T, Chumacher T, Kauserud H (2012) Don’t make a mista(g)ke: Is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecol 5:747–749
9. Chapin FS III, Zavaleta ES, Eviner VT, Naylor RL, Vitousek PM, Reynolds HL, Hooper DU, Lavorel S, Sala OE, Hobbie SE, Mack MC, Díaz S (2000) Consequences of changing biodiversity. Nature 405:234–242
10. Clarke LJ, Soubrier J, Weyrich LS, Cooper A (2014) Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Mol Ecol Resour. doi:10.1111/1755-0998.12265
11. Creer S (2010) Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Mol Ecol 19:2829–2831
12. Crooks JA, Soulé ME (1999) Lag times in population explosions of invasive species: Cases and implications. In: Sandlund OT, Schei PJ, Viken A (eds) Invasive species and biodiversity management. Kluwer Academic Publishers, Dordrecht
13. Darling JA (2014) Genetic studies of aquatic biological invasions: closing the gap between research and management. Biol Invasions. doi:10.1007/s10530-014-0726-x
14. Darling JA, Mahon AR (2011) From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environ Res 111:978–988
15. Davey ML, Kauserud H, Ohlson M (2014) Forestry impacts on the hidden fungal biodiversity associated with bryophytes. FEMS Microbiol Ecol. doi:10.1111/1574-6941.12386
16. Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol Ecol 18:2022–2038
17. Edgar RC (2013) UPARSE: highly accurate OUT sequences from microbial amplicon reads. Nat Methods 10:996–998
18. Engelbrektson A, Kunin V, Wrighton K, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4:642–647
19. Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, Hallwachs W, Hajibabaei M (2014) Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. P Natl Acad Sci USA. doi:10.1073/pnas.1406468111
20. Greenfield P, Duesing K, Papanicolaou A, Bauer DC (2014) Blue: correcting sequencing errors using consensus and context. Bioinformatics. doi:10.1093/bioinformatics/btu368
21. Hajibabaei M (2012) The golden age of DNA metasystematics. Trends Genet 28:535–537
22. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 6:e17497
23. Heo Y, Wu X, Chen D, Ma J, Hwu WM (2014) Bless: bloom filter-based error correction solution for high-thoughput sequencing reads. Bioinformatics 30:1354–1362
24. Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, Mark Welch DB (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 11:1292–1302
25. Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck 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 Microbiol Ecol 82:666–677
26. Ilie L, Fazayeli F, Ilie S (2011) HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27:295–302
27. Kao WC, Chan AH, Song YS (2011) ECHO: a reference-free short-read error correction algorithm. Genome Res 21:1181–1192
28. 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
29. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123
30. Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ (2013) A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool 10:34
31. Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H (2013) Fungal community analysis by high-throughput sequencing of amplified markers – a user’s guide. New Phytol 199:288–299
32. Liu S, Li Y, Lu J, Su X, Tang M, Zhang R, Zhou L, Zhou C, Yang Q, Ji Y, Yu DW, Zhou X (2013) SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods Ecol Evol 4:1142–1150
33. Machida RJ, Knowlton N (2012) PCR Primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PLoS One 7:e46180
34. Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, De Santis TZ, Brodie EL, Malamud D, Poles MA, Pei Z (2010) Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroentero 16:4135–4144
35. Ojaveer H, Galil BS, Minchin D, Olenin S, Amorim A, Canning-Clode J, Chainho P, Copp GH, Collasch S, Jelmert A, Lehtiniemi M, McKenzie C, Mikušm J, Miossecn L, Occhipinti-Ambrogio A, Pećarevićm M, Pedersonp J, Quilez-Badiaq G, Wijsmanr JWM, Zenetoss A (2013) Ten recommendations for advancing the assessment and management of non-indigenous species in marine ecosystems. Mar Policy 44:1–6
36. Ovaskainen O, Schigel D, Ali-Kovero H, Auvinen P, Paulin L, Nordén B, Nordén J (2013) Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi. ISME J 7:1696–1709
37. Pedrós-Alió C (2012) The rare bacterial biosphere. Annu Rev Mar Sci 4:449–466
38. Pimm SL, Russell GJ, Gittleman JL, Brooks TM (1995) The future of biodiversity. Science 269:347–350
39. Pochon X, Bott NJ, Smith KF, Wood SA (2013) Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS One 8:e73935
40. Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6:639–641
41. Reeder J, Knight R (2009) The ‘rare biosphere’: a reality check. Nat Methods 6:636–637
42. Salmela L (2010) Correction of sequencing errors in a mixed set of reads. Bioinformatics 26:1284–1290
43. Salmela L, Schröder J (2011) Correcting errors in short reads by multiple alignments. Bioinformatics 27:1455–1461
44. Schmieder R, Edwards R (2011) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288
45. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci USA 109:6241–6246
46. Srivathsan A, Sha JCM, Vogler AP, Meier R (2014) Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus). Mol Ecol Resour. doi:10.1111/1755-0998.12302
47. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Mol Ecol 21:1789–1793
48. Tang CQ, Leasi F, Obertegger U, Kieneke A, Barraclough TG, Fontaneto D (2012) The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. P Natl Acad Sci USA 109:16208–16212
49. Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573
50. 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
51. van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, Poel Hvd, Oeveren Jv, Verstege H, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJT (2007) Complexity reduction of polymorphic sequences (CRoPS™): A novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2:e1172
52. van Velzen R, Weitschek E, Felici G, Bakker FT (2012) DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One 7:e30490
53. Westra H-J, Jansen RC, Fehrmann RSN, te Meerman GJ, van Heel D, Wijmenga C, Franke L (2011) MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics 27:2104–2111
54. Wilson HB, Joseph LN, Moore AL, Possingham HP (2011) When should we save the most endangered species? Ecol Lett 14:886–890
55. Yang X, Dorman KS, Aluru S (2010) Reptile: representative tiling for short read error correction. Bioinformatics 26:2526–2533
56. Yang X, Chockalingam SP, Aluru S (2013) A survey of error-correction methods for next-generation sequencing. Brief Bioinform 14:56–66
57. Zhan A, Hulák M, Sylvester F, Huang X, Adebayo AA, Abbott CL, Adamowicz SJ, Heath DD, Cristescu ME, MacIsaac HJ (2013) High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol Evol 4:558–565
58. Zhan A, Bailey SA, Heath DD, MacIsaac HJ (2014a) Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Mol Ecol Resour 14:1049–1059
59. Zhan A, He S, Brown EA, Chain FJJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME, MacIsaac HJ (2014b) Reproducibility of pyrosequencing data for biodiversity assessment in complex communities. Methods Ecol Evol 5:881–890
60. Zhan A, Xiong W, He S, MacIsaac HJ (2014c) Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing. PLoS One 9:e96928
61. Zhou J, Wu L, Deng Y, Zhi X, Jiang Y, Tu Q, Xie J, Van Nostrand JD, He Z, Yang Y (2011) Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5:1303–1313
62. Zhou X, Li Y, Liu S, Yang Q, Su X, Zhou L, Tang M, Fu R, Li J, Huang Q (2013a) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience 2:4
63. Zhou J, Jiang Y, Deng Y, Shi Z, Zhou B, Xue K, Wu L, He Z, Yang Y (2013b) Random sampling process leads to overestimation of β-diversity of microbial communities. mBio 4:e00324
64. Zimmerman N, Izard J, Klatt C, Zhou J, Aronson E (2014) The unseen world: environmental microbial sequencing and identification methods for ecologists. Front Ecol Environ 12:224–231