Shi, Xiao Li, Lepère, Cécile, Scanlan, David J. and Vaulot, Daniel. (2011) Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PL o S One, Vol.6 (No.4). e18979 . ISSN 1932-6203

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Abstract

The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

Item Type:	Journal Article
Subjects:	Q Science > QK Botany
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Phytoplankton -- Genetics, Plastids, Flow cytometry
Journal or Publication Title:	PL o S One
Publisher:	Public Library of Science
ISSN:	1932-6203
Date:	28 April 2011
Volume:	Vol.6
Number:	No.4
Page Range:	e18979
Identification Number:	10.1371/journal.pone.0018979
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Natural Environment Research Council (Great Britain) (NERC), Centre national de la recherche scientifique (France) (CNRS), France. Agence nationale de la recherche (ANR), China Scholarship Council (CSC), Université Pierre et Marie Curie (UPMC), Fondation Franco-Chinoise pour la Science et ses Applications (FFCSA)
Grant number:	06-BDIV-013 (ANR), NE/C003160/1 (NERC)
References:	1. Li WKW (1994) Primary productivity of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnology and Oceanography 39: 169–175. 2. Jardillier L, Zubkov MV, Pearman J, Scanlan DJ (2010) Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME Journal 4: 1180–1192. 3. Cuvelier ML, Allen AE, Monier A, McCrow JP, Messie M, 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 107: 14679–14684. 4. Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603–607. 5. Moon-van der Staay SY, De Wachter R, Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409: 607–610. 6. Romari K, Vaulot D (2004) Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnology and Oceanography 49: 784–798. 7. Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of small eukaryotic phytoplankton (#3 mm) in marine ecosystems. FEMS Microbiology Reviews 32: 795–820. 8. Fuller NJ, Campbell C, Allen DJ, Pitt FD, Le Gall F, et al. (2006) Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using the PCR biased towards marine algal plastids. Aquatic Microbial Ecology 43: 79–93. 9. Lepe`re C, Vaulot D, Scanlan DJ (2009) Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on earth. Environmental Microbiology 11: 3105–3117. 10. Man-Aharonovich D, Philosof A, Kirkup BC, Le Gall F, Yogev T, et al. (2010) Diversity of active marine picoeukaryotes in the eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME Journal 4: 1044–1052. 11. Viprey M, Guillou L, Ferreol M, Vaulot D (2008) Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach. Environmental Microbiology 10: 1804–1822. 12. 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. 13. Marie D, Shi XL, Rigaut-Jalabert F, Vaulot D (2010) Use of flow cytometric sorting to better assess the diversity of small photosynthetic eukaryotes in the English Channel. FEMS Microbiology Ecology 72: 165–178. 14. Claustre H, Sciandra A, Vaulot D (2008) Introduction to the special section biooptical and biogeochemical conditions in the South East Pacific in late 2004: the BIOSOPE program. Biogeosciences 5: 679–691. 15. West NJ, Scanlan DJ (1999) Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean. Applied and Environmental Microbiology 65: 2585–2591. 16. West NJ, Schonhuber WA, Fuller NJ, Amann RI, Rippka R, et al. (2001) Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNAtargeted oligonucleotides. Microbiology-SGM 147: 1731–1744. 17. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, eds. Nucleic Acid Techniques in Bacterial Systematics. New York, N.Y.: John Wiley and Sons. pp 115–175. 18. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059–3066. 19. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540–552. 20. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818. 21. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and others methods). 4 ed. Sunderland, Massachusetts: Sinauer associates. 22. 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. 23. Andersen RA, Van de Peer Y, Potter D, Sexton JP, Kawachi M, et al. (1999) Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist 150: 71–84. 24. Takano Y, Hagino K, Tanaka Y, Horiguchi T, Okada H (2006) Phylogenetic affinities of an enigmatic nannoplankton, Braarudosphaera bigelowii based on the SSU rDNA sequences. Marine Micropaleontology 60: 145–156. 25. Marin B, Melkonian M (2010) Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist 161: 304–336. 26. Sipos R, Szekely AJ, Palatinszky M, Revesz S, Marialigeti K, et al. (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiology Ecology 60: 341–350. 27. Urbach E, Robertson DL, Chisholm SW (1992) Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355: 267–269. 28. Junier P, Kim OS, Hadas O, Imhoff JF, Witzel KP (2008) Evaluation of PCR primer selectivity and phylogenetic specificity by using amplification of 16S rRNA genes from betaproteobacterial ammonia-oxidizing bacteria in environmental samples. Applied and Environmental Microbiology 74: 5231–5236. 29. Le Gall F, Rigaut-Jalabert F, Marie D, Garczarek L, Viprey M, et al. (2008) Picoplankton diversity in the South-East Pacific Ocean from cultures. Biogeosciences 5: 203–214. 30. Liu H, Probert I, Uitz J, Claustre H, Aris-Brosou S, 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. 31. Zhu F, Massana R, Not F, Marie D, Vaulot D (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiology Ecology 52: 79–92. 32. Maguire MJ, Goff LJ, Coleman AW (1995) In situ plastid and mitochondrial DNA determination: Implication of the observed minimal plastid genome number. American Journal of Botany 82: 1496–1506. 33. Moon-van der Staay SY, van der Staay GWM, Guillou L, Vaulot D, Claustre H, et al. (2000) Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18S rDNA sequences. Limnology and Oceanography 45: 98–109. 34. Andersen RA, Saunders GW, Paskind MP, Sexton J (1993) Ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. and sp. nov. and the description of a new algal class, the Pelagophyceae classis nov. Journal of Phycology 29: 701–715. 35. Ras J, Claustre H, Uitz J (2008) Spatial variability of phytoplankton pigment distributions in the Subtropical South Pacific Ocean: comparison between in situ and predicted data. Biogeosciences 5: 353–369. 36. Gomez F, Claustre H, Raimbault P, Souissi S (2007) Two high-nutrient low chlorophyll phytoplankton assemblages: the tropical Central Pacific and the offshore Peru-Chile current. Biogeosciences 4: 1101–1113. 37. Grob C, Ulloa O, Claustre H, Huot Y, Alarcon G, et al. (2007) Contribution of picoplankton to the total particulate organic carbon concentration in the eastern South Pacific. Biogeosciences 4: 837–852.
URI:	http://wrap.warwick.ac.uk/id/eprint/4544

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