Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Molecular Ecology

Volumn 22, Issue 1, 2013, Pages 87-101

  Bittner, Lucie ^a   Gobet, Angélique ^a,b   Audic, Stéphane ^a   Romac, Sarah ^a   Egge, Elianne S ^c   Santini, Sébastien ^a   Ogata, Hiroyuki ^a   Probert, Ian ^a   Edvardsen, Bente ^c   De Vargas, Colomban ^a  

^a STATION BIOLOGIQUE DE ROSCOFF   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

454 pyrosequencing; DCM; environmental genetic diversity; environmental samples; Haptophyta; LSU rDNA; LSU rRNA

Indexed keywords

PRIMER DNA; RIBOSOME DNA;

ARTICLE; BAY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HAPTOPHYTA; ITALY; MEDITERRANEAN SEA; PHYLOGENY; PLANKTON; POPULATION GENETICS;

BAYS; DNA PRIMERS; DNA, RIBOSOMAL; GENETIC VARIATION; GENETICS, POPULATION; HAPTOPHYTA; ITALY; MEDITERRANEAN SEA; PHYLOGENY; PLANKTON; SEQUENCE ANALYSIS, DNA;

CHRYSOCULTER; EUKARYOTA; HAPTOPHYCEAE; PROTISTA;

EID: 84872840566     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12108     Document Type: Article

References (70)

1. Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM, (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE, 4, e6372.
2. Barberán A, Bates ST, Casamayor EO, Fierer N, (2011) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME Journal, 6, 343-351.
3. Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T, (2010) Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environmental Microbiology, 13, 340-349.
4. Berger SA, Krompass D, Stamatakis A, (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology, 60, 291-302.
5. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knigth R, Thomas WK, (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution, 27, 233-243.
6. Bittner L, Halary S, Payri C, et al,. (2010) Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct, 5, 47.
7. Bray JR, Curtis JT, (1957) An ordination of the upland forest communities of Southern Wisconsin. Ecological Monographs, 27, 326-349.
8. Brown MV, Philip GK, Bunge JA, Smith MC, Bisset A, Lauro FM, et al,. (2009) Microbial community structure in the North Pacific Ocean. ISME Journal, 3, 1374-1386.
9. Caron DA, Countway PD, (2009) Hypotheses on the role of the protistan rare biosphere in a changing world. Aquatic Microbial Ecology, 57, 227-238.
10. Caron DA, Countway PD, Savai P, Gast RJ, et al,. (2009) Defining DNA-based operational taxonomic units for microbial eukaryote ecology. Applied Environmental Microbiology, 75, 5797-5808.
11. Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK, (2010) Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME Journal, 4, 1053-1059.
12. Clarke KR, (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 18, 117-143. (Pubitemid 24409223)
13. Cortés MY, Bollmann J, Thierstein HR, (2001) Coccolithophore ecology at the HOT station ALOHA, Hawaii. Deep-Sea Research II, 48, 1957-1981. (Pubitemid 32434582)
14. Cuvelier ML, Allen AE, Monier A, et al,. (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences of the United States of America, 17, 14679-14684.
15. Dawson SC, Hagen KD, (2009) Mapping the protistan 'rare biosphere'. Journal of Biology, 8, 105.
16. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
17. Edgcomb V, Orsi W, Bunge J, et al,. (2011) Protistan microbial observatory in the Cariaco Basin, Caribbean I. Pyrosequencing vs Sanger insights into species richness. ISME Journal, 5, 1344-1356.
18. Edvardsen B, Eikrem W, Throndsen JAS, Probert I, Medlin L, (2011) Ribosomal DNA phylogenies and a morphological revision provide the basis for a new taxonomy of Prymnesiales (Haptophyta). European Journal of Phycology, 46, 202-228.
19. Eiler A, Heinrich F, Bertilsson S, (2011) Coherent dynamics and association networks among lake bacterioplankton taxa. ISME Journal, 6, 330-342.
20. Frada MJ, Bidle KD, Probert I, Vargas C. de, (2012) In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta). Environmental microbiology, 14, 1558-1569.
21. Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF, (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 19, 245.
22. Gower JC, (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53, 325-338.
23. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704. (Pubitemid 37365050)
24. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
25. Hammer Ø, Harper DAT, Ryan PD, (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 1-9.
26. Huber JA, Mark WDB, Morrison HG, et al,. (2007) Microbial population structures in the deep marine biosphere. Science, 318, 97-100. (Pubitemid 47538040)
27. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology, 8, R143.
28. Huse SM, Dethlefsen L, Huber JA, et al,. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics, 4, e1000255.
29. Huse SM, Welch DM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology, 12, 1889-1898.
30. Katoh K, Toh H, (2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics, 9, 212-224.
31. 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.
32. Kysela DT, Palacios C, Sogin ML, (2005) Serial analysis of V6-ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environmental Microbiology, 7, 356-364. (Pubitemid 40290124)
33. Legendre P, Gallagher ED, (2001) Ecologically meaningful transformations for ordination of species data. Oecologia, 129, 271-280. (Pubitemid 32996572)
34. Liu H, Probert I, Uitz J, et al,. (2009) Extreme diversity in noncalcifying Haptophytes explains a major pigment paradox in open oceans. Proceedings of the National Academy of Sciences of the United States of America, 106, 12803-12808.
35. Logares R, Audic S, Santini S, Pernice MC, de Vargas C, Massana, (2012) Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ISME Journal, 6, 1823-1833.
36. Long JD, Smalley GW, Barsby T, Anderson JT, Hay ME, (2007) Chemical cues induce consumer-specific defenses in a bloom-forming marine phytoplankton. Proceedings of the National Academy of Sciences of the United States of America, 104, 10512-10517. (Pubitemid 47185696)
37. Malinverno E, Ziveri P, Corselli C, (2003) Coccolithophorid distribution in the Ionian Sea and its relationship to eastern Mediterranean circulation during late fall to early winter 1997. Journal of Geophysical Research, 108, 8115.
38. Man-Aharonovich D, Philosof A, Kirkup BC, et al,. (2010) Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME Journal, 4, 1044-1052.
39. Margulies M, Egholm M, Altman WE, et al,. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380. (Pubitemid 41613494)
40. Massana R, Pernice M, Bunge JA, del Campo J, (2011) Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. ISME Journal, 5, 184-195.
41. Matsen FA, Kodner RB, Armbrust EV, (2010) Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
42. McDonald SM, Sarno D, Scanlan DJ, Zingone A, (2007) Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle. Aquatic Microbial Ecology, 50, 75-89. (Pubitemid 351154593)
43. Medlin LK, Kooistra WHCF, (2010) Methods to estimate the diversity in the marine photosynthetic protist community with illustrations from case studies: a review. Diversity, 2, 973-1014.
44. Monchy S, Sanciu G, Jobard M, et al,. (2011) Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environmental Microbiology, 13, 1433-1453.
45. Nakayama T, Yoshida M, Noël M-H, Kawachi M, Inouye I, (2005) Ultrastructure and phylogenetic position of Chrysoculter rhomboideus gen. et sp. nov (Prymnesiophyceae), a new flagellate haptophyte from Japanese coastal waters. Phycologia, 44, 369-383. (Pubitemid 41099456)
46. Nebel M, Pfabel C, Stock A, Dunthorn M, Stoeck T, (2011) Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environmental Microbiology Reports, 3, 154-158.
47. Nolte V, Pandey RV, Jost S, et al,. (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology, 19, 2908-2015.
48. Not F, del Campo J, Balagué V, de Vargas C, Massana R, (2009) New insights into the diversity of marine picoeukaryotes. PLoS ONE, 4, e7143.
49. Oksanen J, Kindt R, Legendre P, O'Hara RB, (2007) vegan: community ecology package version, 1, 8-5.Available from http://r-forge.r-project.org/ projects/vegan/.
50. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stalh DA, (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annual Review of Microbiology, 40, 337-365.
51. Pawlowski J, Burki F, (2009) Untangling the Phylogeny of Amoeboid Protists. Journal of Eukaryotic Microbiology, 56, 16-25.
52. Pawlowski J, Christen R, Lecroq B, et al,. (2011) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE, 6, e18169.
53. Piganeau G, Eyre-Walker A, Grimsley N, Moreau H, (2011) How and why DNA barcodes underestimate the diversity of microbial eukaryotes. PLoS ONE, 6, e16342.
54. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256. (Pubitemid 351882013)
55. Pulsinelli GA, Temin HM, (1994) High rate of mismatch extension during reverse transcription in a single round of retrovirus replication. Proceedings of the National Academy of Sciences of the United States of America, 91, 9490-9494. (Pubitemid 24297940)
56. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ, (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
57. Roesch LF, Fulthorpe RR, Riva A, et al,. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1, 283-290. (Pubitemid 47227850)
58. Schloss PD, (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Computational Biology, 6, e1000844.
59. Schoemann V, Becquevort S, Stefels J, Rousseau V, Lancelot C, (2005) Phaeocystis blooms in the global ocean and their controlling mechanisms: a review. Journal of Sea Research, 53, 43-66. (Pubitemid 40034034)
60. Shalchian-Tabrizi K, Reier-Røberg K, Ree DK, Klaveness D, Bråte J, (2011) Marine-freshwater colonizations of Haptophytes inferred from phylogeny of environmental 18S rDNA sequences. Journal of Eukaryotic Microbiology, 58, 315-318.
61. Shannon CE, (1948) A mathematical theory of communication. Bell System Technical Journal, 27, 379-423.
62. Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D, (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE, 4, e7657.
63. Shi XL, Lepère C, Scanlan DJ, Vaulot D, (2011) Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PLoS ONE, 6, e18979.
64. Simpson EH, (1949) Measurement of diversity. Nature, 163, 688.
65. Sogin ML, Morrison HG, Huber J, et al,. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America, 103, 12115-12120. (Pubitemid 44215820)
66. Stoeck T, Behnke A, Christen R, et al,. (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology, 7, 72.
67. Stoeck T, Bass D, Nebel M, et al,. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19, 21-31.
68. Sydow JF, Cramer P, (2009) RNA polymerase fidelity and transcriptional proofreading. Current Opinion in Structural Biology, 19, 732-739.
69. Winter A, Rost B, Hilbrecht H, Elbrächter M, (2002) Vertical and horizontal distribution of coccolithophores in the Caribbean Sea. Geo-Marine Letters, 22, 150-161. (Pubitemid 36022195)
70. Woese CR, (1987) Bacterial evolution. Microbiology Review, 51, 221-271. (Pubitemid 17082512)