Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: A test for freshwater diatoms

Molecular Ecology Resources

Volumn 13, Issue 4, 2013, Pages 607-619

  Kermarrec, L ^a,b,c   Franc, A ^d,e   Rimet, F ^a,b   Chaumeil, P ^d,e   Humbert, J F ^f   Bouchez, A ^a,b  

^a UMR CARRTEL   (France)

^b UNIVERSITÉ DE SAVOIE   (France)

^c Asconit Consultants   (France)

^d UMR 1202 BIOGECO   (France)

^e UNIVERSITÉ DE BORDEAUX   (France)

^f UPMC University Paris 06   (France)

Author keywords

Benthic diatom diversity; Environmental communities; High throughput sequencing; Molecular ecology; Species inventories

Indexed keywords

CYTOCHROME C OXIDASE; FRESH WATER; MITOCHONDRIAL DNA; RBCL PROTEIN, PLASTID; RIBOSOME DNA; RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA 18S;

ARTICLE; CHEMISTRY; CLASSIFICATION; DIATOM; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOME; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

DIATOMS; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; ELECTRON TRANSPORT COMPLEX IV; FRESH WATER; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; MOLECULAR SEQUENCE DATA; RIBULOSE-BISPHOSPHATE CARBOXYLASE; RNA, RIBOSOMAL, 18S;

BACILLARIOPHYTA; EUKARYOTA;

EID: 84879420877     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12105     Document Type: Article

References (45)

1. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Applied and environmental Microbiology, 71, 8966-8969.
2. Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology, 19, 5555-5565.
3. Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T (2011) Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environmental Microbiology, 13, 340-349.
4. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution, 27, 233-243.
5. Bornet B, Antoine E, Bardouil M, Marcaillou-Le Baut C (2004) ISSR as new markers for genetic characterization and evaluation of relationships among phytoplankton. Journal of Applied Phycology, 16, 285-290.
6. Bruder K, Medlin LK (2007) Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis. Nova Hedwigia, 85, 331-352.
7. CEN (2004) EN 14407, Water quality - guidance standard for the identification, enumeration and interpretation of benthic diatom samples from running waters. European Committee of Standardization, 1-13.
8. Daugbjerg N, Andersen RA (1997) A molecular phylogeny of the Heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. Journal of Phycology, 33, 1031-1041.
9. Ehara M, Inagaki Y, Watanabe KI, Ohama T (2000) Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolution. Current Genetics, 37, 29-33.
10. Engelbrektson A, Kunin V, Wrighton KC et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME Journal, 4, 642-647.
11. Evans KM, Wortley AH, Mann DG (2007) An assessment of potential diatom barcode genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist, 158, 349-364.
12. Evans KM, Wortley AH, Simpson GE, Chepurnov VA, Mann DG (2008) A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta). Journal of Phycology, 44, 215-231.
13. Feinstein LM, Sul WJ, Blackwood CB (2009) Assessment of bias associated with incomplete extraction of microbial DNA from soil. Applied and Environmental Microbiology, 75, 5428-5433.
14. Gardner TA, Barlow J, Araujo IS et al. (2008) The cost-effectiveness of biodiversity surveys in tropical forests. Ecology Letters, 11, 139-150.
15. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12, 245.
16. Gusfield D (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York, 534 p.
17. Hajibabaei M, deWaard JR, Ivanova NV et al. (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1959-1967.
18. 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.
19. Hammer Ã, Harper DAT, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 9.
20. Hamsher SE, Evans KM, Mann DG, Poulíčková A, Saunders GW (2011) Barcoding diatoms: exploring alternatives to COI-5P. Protist, 162, 405-422.
21. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B, 270, 313-321.
22. Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, Welch DBM (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology, 11, 1292-1302.
23. Kermarrec L (2012) Contribution of molecular biology tools for using diatoms as bioindicators of the quality of lotic aquatic ecosystems and for the study of their taxonomy. PhD thesis, University of Grenoble, France.
24. Kermarrec L, Chaumeil P, Rimet F, Frigerio JM, Bouchez A, Franc A (2011) metaMatch: a tool for barcoding in metagenomics. Technical Report - KCRFBF 2011
25. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12, 118-123.
26. MacGillivary ML, Kaczmarska I (2011) Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms. Journal of Eukaryotic Microbiology, 58, 529-536.
27. Mandelik Y, Roll U, Fleischer A (2010) Cost-efficiency of biodiversity indicators for Mediterranean ecosystems and the effects of socio-economic factors. Journal of Applied Ecology, 47, 1179-1188.
28. Mann DG, Sato S, Trobajo R, Vanormelingen P, Souffreau C (2010) DNA barcoding for species identification and discovery in diatoms. Cryptogamie Algologie, 31, 557-577.
29. Mariette J, Noirot C, Klopp C (2011) Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Research Notes, 4, 149.
30. Medlin LK, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71, 491-499.
31. Moniz MBJ, Kaczmarska I (2009) Barcoding diatoms: is there a good marker? Molecular Ecology Resources, 9, 65-74.
32. Pilgrim EM, Jackson SA, Swenson S et al. (2011) Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. Journal of the North American Benthological Society, 30, 217-231.
33. Porazinska DL, Sung W, Giblin-Davis RM, Thomas WK (2010) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Molecular Ecology Resources, 10, 666-676.
34. Quince C, Lanzén A, Curtis TP et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6, 639-641.
35. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. Journal of Molecular Biology, 147, 195-197.
36. Soininen J (2012) Macroecology of unicellular organisms - patterns and processes. Environmental Microbiology Reports, 4, 10-22.
37. Stegen JC, Hurlbert AH (2011) Inferring ecological processes from taxonomic, phylogenetic and functional trait β-diversity. PLoS ONE, 6, e20906.
38. Sweeney BW, Battle JM, Jackson JK, Dapkey T (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? Journal of the North American Benthological Society, 30, 195-216.
39. Tedersoo L, Nilsson RH, Abarenkov K et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist, 188, 291-301.
40. Trobajo R, Mann DG, Clavero E, Evans KM, Vanormelingen P, McGregor RC (2010) The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae). European Journal of Phycology, 45, 413-425.
41. Villeneuve A, Montuelle B, Bouchez A (2010) Influence of slight differences in environmental conditions (light, hydrodynamics) on the structure and function of the periphyton. Aquatic Sciences, 72, 33-44.
42. Wilson J, Rougerie R, Schonfeld J et al. (2011) When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths. BMC Ecology, 11, 18.
43. Wittebolle L, Marzorati M, Clement L et al. (2009) Initial community evenness favours functionality under selective stress. Nature, 458, 623-626.
44. Zimmermann J, Jahn R, Gemeinholzer B (2011) Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Organisms Diversity and Evolution, 11, 173-192.
45. Zinger L, Gobet A, Pommier T (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Molecular Ecology, 21, 1878-1896.