Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

ISME Journal

Volumn 6, Issue 10, 2012, Pages 1823-1833

  Logares, Ramiro ^a   Audic, Stephane ^b,c   Santini, Sebastien ^d   Pernice, Massimo C ^a   De Vargas, Colomban ^c   Massana, Ramon ^a  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b STATION BIOLOGIQUE DE ROSCOFF   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d CNRS Aix Marseille University   (France)

Author keywords

Diversity; Heterotrophic flagellates; MAST; Pyrosequencing; Stramenopiles

Indexed keywords

RNA 18S; SEA WATER;

BODY SIZE; EVOLUTIONARY BIOLOGY; FLAGELLATE; HETEROTROPHY; MARINE ECOSYSTEM; MOLECULAR ANALYSIS; PHYLOGENETICS; SPECIES DIVERSITY; TAXONOMY; TROPHIC LEVEL;

ARTICLE; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; GENETICS; HETEROTROPHY; MICROBIOLOGY; PHYLOGENY; PLANKTON; STRAMENOPILE;

BIODIVERSITY; HETEROTROPHIC PROCESSES; PHYLOGENY; PLANKTON; RNA, RIBOSOMAL, 18S; SEAWATER; SEQUENCE ANALYSIS, DNA; STRAMENOPILES;

EUROPE;

ARCHAEA; BACTERIA (MICROORGANISMS); MASTIGOPHORA (FLAGELLATES); STRAMENOPILES;

EID: 84867740787     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.36     Document Type: Article

References (41)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Baldauf SL. (2003). The deep roots of eukaryotes. Science 300: 1703-1706.
3. Caron D, Countway P, Jones A, Kim D, Schnetzer A. (2012). Marine protistan diversity. Ann Rev Mar Sci 4:6.1-6.27.
4. Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 460-2461.
5. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
6. Faith D. (1992). Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
7. Gomez F, Moreira D, Benzerara K, Lopez-Garcia P. (2011). Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3. Environ Microbiol 13: 193-202.
8. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G et al. (2011). Chimeric 16S r RNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
9. Hamady M, Lozupone C, Knight R. (2010). Fast Uni Frac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrose-quencing and Phylo Chip data. ISMEJ4: 17-27.
10. Han MV, Zmasek CM. (2009). Phylo XML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10: 356.
11. Jardillier L, Zubkov MV, Pearman J, Scanlan DJ. (2010). Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISMEJ4: 1180-1192.
12. Jurgens K, Massana R. (2008). Protistan Grazing on Marine Bacterioplankton, 2nd edn. Wiley-Blackwell: Hoboken, NJ.
13. Koski LB, Golding GB. (2001). The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52: 540-542.
14. Lopez-Garcia P, Moreira D. (2008). Tracking microbial biodiversity through molecular and genomic ecology. Res Microbiol 159: 67-73.
15. Martin AP. (2002). Phylogenetic approaches for describing and comparing the diversity of microbial commu-nities. Appl Environ Microbiol 68: 3673-3682.
16. Massana R. (2011). Eukaryotic picoplankton in surface oceans. Ann Rev Microbiol 65: 91-110.
17. Massana R, Castresana J, Balague V, Guillou L, Romari K, Groisillier A et al. (2004). Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70: 3528-3534.
18. Massana R, Terrado R, Forn I, Lovejoy C, Pedros-Alio C. (2006). Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environ Microbiol 8: 1515-1522.
19. Massana R, Unrein F, Rodriguez-Martinez R, Forn I, Lefort T, Pinhassi J et al. (2009). Grazing rates and functional diversity of uncultured heterotrophic flagellates. ISMEJ3: 588-596.
20. Matsen FA, Kodner RB, Armbrust EV. (2010). pplacer: linear time maximum-likelihood and Bayesian phylo-genetic placement of sequences onto a fixed reference tree. BMCBioinformatics 11: 538.
21. Not F, del Campo J, Balague V, de Vargas C, Massana R. (2009). New insights into the diversity of marine picoeukaryotes. PloS One 4: e7143.
22. Not F, Latasa M, Scharek R, Viprey M, Karleskind P, Balague V et al. (2008). Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes. Deep Sea Res Part I Oceanogr Res Papers 55: 1456-1473.
23. Orsi W, Edgcomb V, Jeon S, Leslin C, Bunge J, Taylor GT et al. (2011). Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. ISME J 5: 1357-1373.
24. Pedrós-Alió C. (2006). Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263.
25. Piwosz K, Pernthaler J. (2010). Seasonal population dynamics and trophic role of planktonic nanoflagel-lates in coastal surface waters of the Southern Baltic Sea. Environ Microbiol 12: 364-377.
26. Porter TM, Golding GB. (2011). Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metage-nomic amplicons? New Phytologist 192: 775-782.
27. Prokopowich CD, Gregory TR, Crease TJ. (2003). The correlation between r DNA copy number and genome size in eukaryotes. Genome 46: 48-50.
28. R-Development-Core-Team. (2008). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria.
29. Richards TA, Bass D. (2005). Molecular screening of free-living microbial eukaryotes: diversity and distri-bution using a meta-analysis. Curr Opin Microbiol 8: 240-252.
30. Riisberg I, Orr RJ, Kluge R, Shalchian-Tabrizi K, Bowers HA, Patil V et al. (2009). Seven gene phylogeny of heterokonts. Protist 160: 191-204.
31. Rodriguez-Martinez R, Labrenz M, del Campo J, Forn I, Jurgens K, Massana R. (2009). Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real time quantitative PCR. Environ Microbiol 11: 397-408.
32. Rodriguez-Martinez R, Rocap G, Logares R, Romac S, Massana R. (2012). Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Mol Biol Evol (in press).
33. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
34. Sherr E, Sherr B. (2008). Understanding roles of microbes in marine pelagic food webs: a brief history. In: Kirchman DL (ed.). Microbial Ecology of the Oceans. Wiley-Blackwell: Hoboken, NJ, pp 27-44.
35. Stamatakis A. (2006). RAx ML-VI-HPC: maximum like-lihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
36. Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW et al. (2010). Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19(Suppl 1): 21-31.
37. Suttle CA. (2005). Viruses in the sea. Nature 437: 356-361.
38. Takishita K, Miyake H, Kawato M, Maruyama T. (2005). Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine caldera floor based on the small-subunit r DNA phylogeny. Extremophiles 9: 185-196.
39. Takishita K, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T. (2007). Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles 11: 563-576.
40. Tsui CK, Marshall W, Yokoyama R, Honda D, Lippmeier JC, Craven KD et al. (2009). Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding. Mol Phylogenet Evol 50: 129-140.
41. Zhu F, Massana R, Not F, Marie D, Vaulot D. (2005). Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S r RNA gene. FEMS Microbiol Ecol 52: 79-92.