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Volumn 5, Issue 2, 2011, Pages 184-195

Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean

Author keywords

Diversity; genetic distances; microdiversity; novelty; OTUs; picoeukaryotes

Indexed keywords

RNA 18S;

EID: 78751585012     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.104     Document Type: Article
Times cited : (40)

References (55)
  • 4
    • 29344433275 scopus 로고    scopus 로고
    • Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta)
    • Alverson AJ, Kolnick L. (2005). Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). J Phycol 41: 1248-1257.
    • (2005) J Phycol , vol.41 , pp. 1248-1257
    • Alverson, A.J.1    Kolnick, L.2
  • 5
    • 68149178616 scopus 로고    scopus 로고
    • A method for studying protistan diversity using massively parrallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes
    • Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. (2009). A method for studying protistan diversity using massively parrallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 4: e6372.
    • (2009) PLoS ONE , vol.4
    • Amaral-Zettler, L.A.1    McCliment, E.A.2    Ducklow, H.W.3    Huse, S.M.4
  • 7
    • 0037841805 scopus 로고    scopus 로고
    • The deep roots of eukaryotes
    • Baldauf SL. (2003). The deep roots of eukaryotes. Science 300: 1703-1706.
    • (2003) Science , vol.300 , pp. 1703-1706
    • Baldauf, S.L.1
  • 9
    • 46949092431 scopus 로고    scopus 로고
    • Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes
    • Burki F, Schalchian-Tabrizi K, Pawlowski J. (2008). Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biology Lett 4: 366-369.
    • (2008) Biology Lett , vol.4 , pp. 366-369
    • Burki, F.1    Schalchian-Tabrizi, K.2    Pawlowski, J.3
  • 11
    • 84945495487 scopus 로고
    • Estimating the number of classes via sample coverage
    • Chao A, Lee S-M. (1992). Estimating the number of classes via sample coverage. J Amer Stat Assoc 87: 210-217.
    • (1992) J Amer Stat Assoc , vol.87 , pp. 210-217
    • Chao, A.1    Lee, S.-M.2
  • 12
    • 33751202973 scopus 로고    scopus 로고
    • Towards a conceptual and operational union of bacterial systematics, ecology, and evolution
    • Cohan FM. (2006). Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Phil Trans R Soc B 361: 1985-1996.
    • (2006) Phil Trans R Soc B , vol.361 , pp. 1985-1996
    • Cohan, F.M.1
  • 13
    • 34247859231 scopus 로고    scopus 로고
    • Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream)
    • Countway PD, Gast RJ, Dennet MR, Savai P, Rose JM, Caron DA. (2007). Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Environ Microbiol 9: 1219-1232.
    • (2007) Environ Microbiol , vol.9 , pp. 1219-1232
    • Countway, P.D.1    Gast, R.J.2    Dennet, M.R.3    Savai, P.4    Rose, J.M.5    Caron, D.A.6
  • 14
    • 0035407646 scopus 로고    scopus 로고
    • Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing
    • Díez B, Pedrós-Alió C, Massana R. (2001). Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67: 2932-2941.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 2932-2941
    • Díez, B.1    Pedrós-Alió, C.2    Massana, R.3
  • 15
    • 0020478245 scopus 로고
    • Molecular drive: A cohesive mode of species evolution
    • Dover GA. (1982). Molecular drive: a cohesive mode of species evolution. Nature 299: 111-117.
    • (1982) Nature , vol.299 , pp. 111-117
    • Dover, G.A.1
  • 16
    • 38649124950 scopus 로고    scopus 로고
    • Missing' protists: A molecular prospective
    • Epstein S, López-García P. (2008). 'Missing' protists: a molecular prospective. Biodivers Conserv 17: 261-276.
    • (2008) Biodivers Conserv , vol.17 , pp. 261-276
    • Epstein, S.1    López-García, P.2
  • 17
    • 0030464460 scopus 로고    scopus 로고
    • SEAVIEW and PHYLO-WIN: Two graphic tools for sequence alignment and molecular phylogeny
    • Galtier N, Gouy M, Gautier C. (1996). SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
    • (1996) Comput Appl Biosci , vol.12 , pp. 543-548
    • Galtier, N.1    Gouy, M.2    Gautier, C.3
  • 19
    • 55849101172 scopus 로고    scopus 로고
    • Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata)
    • Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R et al. (2008). Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10: 397-408.
    • (2008) Environ Microbiol , vol.10 , pp. 397-408
    • Guillou, L.1    Viprey, M.2    Chambouvet, A.3    Welsh, R.M.4    Kirkham, A.R.5    Massana, R.6
  • 20
    • 0000123207 scopus 로고
    • The paradox of the plankton
    • Hutchinson GE. (1961). The paradox of the plankton. Am Nat 95: 137-145.
    • (1961) Am Nat , vol.95 , pp. 137-145
    • Hutchinson, G.E.1
  • 21
    • 33750071107 scopus 로고    scopus 로고
    • Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column
    • Jeon S-O, Bunge J, Stoeck T, Barger KJA, Hong S-H, Epstein SS. (2006). Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column. Appl Environ Microbiol 72: 6578-6583.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 6578-6583
    • Jeon, S.-O.1    Bunge, J.2    Stoeck, T.3    Barger, K.J.A.4    Hong, S.-H.5    Epstein, S.S.6
  • 22
    • 84985201114 scopus 로고
    • In-situ morphology and occurrence of eucaryotic phototrophs of bacterial size in the picoplankton of estuarine and oceanic waters
    • Johnson PW, Sieburth JMcN. (1982). In-situ morphology and occurrence of eucaryotic phototrophs of bacterial size in the picoplankton of estuarine and oceanic waters. J Phycol 18: 318-327.
    • (1982) J Phycol , vol.18 , pp. 318-327
    • Johnson, P.W.1    Sieburth, J.M.C.N.2
  • 23
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • 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 Res 30: 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 24
    • 0036954513 scopus 로고    scopus 로고
    • The abundance and biomass of choanoflagellates and other nanoflagellates in waters of contrasting temperature to the north-west of South Georgia in the Southern Ocean
    • Leakey RJG, Leadbeater BSC, Mitchell E, McCready SMM, Murray AWA. (2002). The abundance and biomass of choanoflagellates and other nanoflagellates in waters of contrasting temperature to the north-west of South Georgia in the Southern Ocean. Eur J Protistol 38: 333-350.
    • (2002) Eur J Protistol , vol.38 , pp. 333-350
    • Leakey, R.J.G.1    Leadbeater, B.S.C.2    Mitchell, E.3    McCready, S.M.M.4    Murray, A.W.A.5
  • 25
    • 26844570477 scopus 로고    scopus 로고
    • Genetic diversity of small eukaryotes in lakes differing by their trophic status
    • Lefranc M, Thénot A, Lepère C, Debroas D. (2005). Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71: 5935-5942.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 5935-5942
    • Lefranc, M.1    Thénot, A.2    Lepère, C.3    Debroas, D.4
  • 26
    • 33845873289 scopus 로고    scopus 로고
    • Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
    • Letunic I, Bork P. (2007). Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 29
    • 45849119808 scopus 로고    scopus 로고
    • Unveiling new microbial eukaryotes in the surface ocean
    • Massana R, Pedrós-Alió C. (2008). Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11: 213-218.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 213-218
    • Massana, R.1    Pedrós-Alió, C.2
  • 30
    • 0035252376 scopus 로고    scopus 로고
    • Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity
    • 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.
    • (2001) Nature , vol.409 , pp. 607-610
    • Moon-Van Der Staay, S.Y.1    De Wachter, R.2    Vaulot, D.3
  • 31
    • 33846502698 scopus 로고    scopus 로고
    • Picobiliphytes: A marine picoplanktonic algal group with unknown affinities to other eukaryotes
    • Not F, Valentin K, Romari K, Lovejoy C, Massana R, Töbe K et al. (2007). Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315: 252-254.
    • (2007) Science , vol.315 , pp. 252-254
    • Not, F.1    Valentin, K.2    Romari, K.3    Lovejoy, C.4    Massana, R.5    Töbe, K.6
  • 32
    • 53349168564 scopus 로고    scopus 로고
    • Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes
    • Not F, Latasa M, Scharek R, Viprey M, Karleskind P, Balagué V et al. (2008). Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes. Deep Sea Res I 55: 1456-1473.
    • (2008) Deep Sea Res I , vol.55 , pp. 1456-1473
    • Not, F.1    Latasa, M.2    Scharek, R.3    Viprey, M.4    Karleskind, P.5    Balagué, V.6
  • 33
    • 0022265348 scopus 로고
    • Marinephytoplankton distributions measured using shipboard flow-cytometry
    • Olson RJ, Vaulot D, Chisholm SW. (1985). Marinephytoplankton distributions measured using shipboard flow-cytometry. Deep Sea Res 32: 1273-1280.
    • (1985) Deep Sea Res , vol.32 , pp. 1273-1280
    • Olson, R.J.1    Vaulot, D.2    Chisholm, S.W.3
  • 34
    • 33846591068 scopus 로고    scopus 로고
    • Dipping into the rare biosphere
    • Pedrós-Alió C. (2007). Dipping into the rare biosphere. Science 315: 192-193.
    • (2007) Science , vol.315 , pp. 192-193
    • Pedrós-Alió, C.1
  • 35
    • 62549131197 scopus 로고    scopus 로고
    • RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communitites
    • Pommier T, Canbäck B, Lundberg P, HagströmA° , Tunlind A. (2009). RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communitites. Bioinformatics 25: 736-742.
    • (2009) Bioinformatics , vol.25 , pp. 736-742
    • Pommier, T.1    Canbäck, B.2    Lundberg, P.3    Hagströmä4    Tunlind, A.5
  • 36
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada D, Crandall KA. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 37
    • 20444449887 scopus 로고    scopus 로고
    • The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages
    • Richards TA, Vepritskiy AA, Gouliamova DE, Nierzwicki- Bauer SA. (2005). The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ Microbiol 7: 1413-1425.
    • (2005) Environ Microbiol , vol.7 , pp. 1413-1425
    • Richards, T.A.1    Vepritskiy, A.A.2    Gouliamova, D.E.3    Nierzwicki-Bauer, S.A.4
  • 38
    • 0242507644 scopus 로고    scopus 로고
    • Are planktonic naked amoebae predominantly floc associated or free in the water column?
    • Rogerson A, Anderson OR, Vogel C. (2003). Are planktonic naked amoebae predominantly floc associated or free in the water column? J Plankton Res 25: 1359-1365.
    • (2003) J Plankton Res , vol.25 , pp. 1359-1365
    • Rogerson, A.1    Anderson, O.R.2    Vogel, C.3
  • 39
    • 0037704805 scopus 로고    scopus 로고
    • Why plankton communities have no equilibrium: Solutions to the paradox
    • Scheffer M, Rinaldi S, Huisman J, Weissing FJ. (2003). Why plankton communities have no equilibrium: solutions to the paradox. Hydrobiologia 491: 9-18.
    • (2003) Hydrobiologia , vol.491 , pp. 9-18
    • Scheffer, M.1    Rinaldi, S.2    Huisman, J.3    Weissing, F.J.4
  • 40
    • 15444362001 scopus 로고    scopus 로고
    • Introducing DOTUR, a computer program for defining Operational Taxonomic Units and estimating especies richness
    • Schloss PD, Handelsman J. (2005). Introducing DOTUR, a computer program for defining Operational Taxonomic Units and estimating especies richness. Appl Environ Microbiol 71: 1501-1506.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 42
    • 0041813265 scopus 로고    scopus 로고
    • Predicting the number of new species in further taxonomic sampling
    • Shen TJ, Chao A, Lin CF. (2003). Predicting the number of new species in further taxonomic sampling. Ecology 84: 798-804.
    • (2003) Ecology , vol.84 , pp. 798-804
    • Shen, T.J.1    Chao, A.2    Lin, C.F.3
  • 44
    • 70449589699 scopus 로고    scopus 로고
    • Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean
    • 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.
    • (2009) PLoS ONE , vol.4
    • Shi, X.L.1    Marie, D.2    Jardillier, L.3    Scanlan, D.J.4    Vaulot, D.5
  • 45
    • 12544255323 scopus 로고    scopus 로고
    • The real 'kingdoms' of eukaryotes
    • Simpson AGB, Roger AJ. (2004). The real 'kingdoms' of eukaryotes. Curr Biol 14: R693-R696.
    • (2004) Curr Biol , vol.14
    • Simpson, A.G.B.1    Roger, A.J.2
  • 46
    • 0002211974 scopus 로고
    • Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies
    • Akkermans ADL, van Elsas JD, de Bruijn FJ (eds), Kluwer Academic: Dordrecht
    • Stackebrandt E, Rainey FA. (1995). Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds). Molecular Microbial Ecology Manual. Kluwer Academic: Dordrecht. pp 1-17.
    • (1995) Molecular Microbial Ecology Manual , pp. 1-17
    • Stackebrandt, E.1    Rainey, F.A.2
  • 47
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood- based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. (2006). RAxML-VI-HPC: maximum likelihood- based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 48
    • 38649123647 scopus 로고    scopus 로고
    • Protistan diversity in the Arctic: A case of paleoclimate shaping modern biodiversity?
    • Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S. (2007). Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity? PLoS ONE 2: e278.
    • (2007) PLoS ONE , vol.2
    • Stoeck, T.1    Kasper, J.2    Bunge, J.3    Leslin, C.4    Ilyin, V.5    Epstein, S.6
  • 51
    • 37249027666 scopus 로고    scopus 로고
    • Measuring rDNA diversity in eukaryotic microbial systems: How intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates
    • Thornhill DJ, Lajeunesse TC, Santos SR. (2007). Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Mol Ecol 16: 5326-5340.
    • (2007) Mol Ecol , vol.16 , pp. 5326-5340
    • Thornhill, D.J.1    Lajeunesse, T.C.2    Santos, S.R.3
  • 52
    • 49649093132 scopus 로고    scopus 로고
    • The diversity of small eukaryotic phytoplankton (p3 mm) in marine ecosystems
    • Vaulot D, Eikrem W, Viprey M, Moreau H. (2008). The diversity of small eukaryotic phytoplankton (p3 mm) in marine ecosystems. FEMS Microbiol Rev 32: 795-820.
    • (2008) FEMS Microbiol Rev , vol.32 , pp. 795-820
    • Vaulot, D.1    Eikrem, W.2    Viprey, M.3    Moreau, H.4
  • 53
    • 38649129088 scopus 로고    scopus 로고
    • Distribution and diversity of aquatic protists: And evolutionary and ecological perspective
    • Weisse T. (2008). Distribution and diversity of aquatic protists: and evolutionary and ecological perspective. Biodivers Conserv 17: 243-259.
    • (2008) Biodivers Conserv , vol.17 , pp. 243-259
    • Weisse, T.1
  • 54
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • Wintzingerode Fv, Göbel UB, Stackebrandt E. (1997). Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
    • (1997) FEMS Microbiol Rev , vol.21 , pp. 213-229
    • Fv, W.1    Göbel, U.B.2    Stackebrandt, E.3
  • 55
    • 13844317082 scopus 로고    scopus 로고
    • Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene
    • 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 Microbiol Ecol 52: 79-92.
    • (2005) FEMS Microbiol Ecol , vol.52 , pp. 79-92
    • Zhu, F.1    Massana, R.2    Not, F.3    Marie, D.4    Vaulot, D.5


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