Improved Inference of Taxonomic Richness from Environmental DNA

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Morgan, Matthew J ^a   Chariton, Anthony A ^a   Hartley, Diana M ^a   Court, Leon N ^a   Hardy, Christopher M ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; AMPLICON; ARTICLE; BIODIVERSITY; DOWNSTREAM PROCESSING; HIGH THROUGHPUT SEQUENCING; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; TAXONOMY;

ANIMALS; BASE SEQUENCE; BIODIVERSITY; DNA; DNA BARCODING, TAXONOMIC; ECOSYSTEM; ENVIRONMENTAL MONITORING; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA;

EID: 84883191674     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071974     Document Type: Article

References (37)

1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
2. Chariton AA, Court LN, Hartley DM, Colloff MJ, Hardy CM, (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front Ecol Environ 8: 233-238.
3. Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun 1: 98 doi:10.1038/ncomms1095.
4. Huber JA, Mark Welch D, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
5. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH, (2012) Environmental DNA. Mol Ecol 21: 1789-1793.
6. Yoccoz NG, (2012) The future of environmental DNA in ecology. Mol Ecol 21: 2031-2038.
7. Balzer S, Malde K, Jonassen I, (2011) Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 27: I304-I309.
8. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12.
9. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
10. 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.
11. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12.
12. Reeder J, Knight R, (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669.
13. 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.
14. Schloss PD, Gevers D, Westcott SL, (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6: e27310.
15. Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW, (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods 9: 425-426.
16. Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW, (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res 40: e94.
17. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
18. Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, et al. (2012) Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 7(9): e44224.
19. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods7: 335-336.
20. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
21. Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8.
22. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
23. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.
24. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
25. Group Jumpstart Consortium Human Microbiome Project Data Generation Working Group (2012) Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One 7(6): e39315 doi:10.1371/journal.pone.0039315.
26. Rosen MJ, Callahan BJ, Fisher DS, Holmes SP, (2012) Denoising PCR-amplified metagenome data. BMC Bioinformatics 13: 283.
27. Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, et al. (2012) A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief Bioinform 13: 107-121.
28. Sheldon F, Walker KF, (1998) Spatial distribution of littoral invertebrates in the lower Murray-Darling River system, Australia. Mar Freshwater Res 49: 171-182.
29. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-U627.
30. Fuhrman JA, (2009) Microbial community structure and its functional implications. Nature 459: 193-199.
31. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C, (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A106: 22427-22432.
32. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107: 7503-7508.
33. Bowen JL, Morrison HG, Hobbie JE, Sogin ML (2012) Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J.
34. 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.
35. Zinger L, Gobet A, Pommier T, (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol 21: 1878-1896.
36. Parks DH, Beiko RG (2012) Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. ISME J.
37. Funk WC, McKay JK, Hohenlohe PA, Allendorf FW, (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 27: 489-496.