Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys

Protist

Volumn 162, Issue 3, 2011, Pages 435-448

  del Campo, Javier ^a   Massana, Ramon ^a  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

Author keywords

18S rDNA; Bicosoecids; Choanoflagellates; Chrysophytes; Emerging diversity; Heterotrophic flagellates; Maximum likelihood phylogeny; Molecular surveys.

Indexed keywords

FRESH WATER; PROTOZOAL DNA; RIBOSOME DNA; RNA 18S; SEA WATER;

ARTICLE; BIODIVERSITY; CHEMISTRY; CHOANOFLAGELLATE; CHRYSOPHYTA; CLASSIFICATION; DNA SEQUENCE; ENVIRONMENT; GENETICS; HETEROTROPHY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL; STRAMENOPILE;

BASE SEQUENCE; BIODIVERSITY; CHOANOFLAGELLATA; CHRYSOPHYTA; DNA, PROTOZOAN; DNA, RIBOSOMAL; ENVIRONMENT; FRESH WATER; HETEROTROPHIC PROCESSES; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 18S; SEAWATER; SEQUENCE ANALYSIS, DNA; STRAMENOPILES;

BICOSOECIDA; CHOANOFLAGELLIDA; CHRYSOPHYCEAE; MASTIGOPHORA (FLAGELLATES); PROTISTA;

EID: 79958011072     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2010.10.003     Document Type: Article

References (52)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
2. Amaral-Zettler L.A., McCliment E.A., Ducklow H.W., Huse S.M. A method for studying protistan diversity using massively parrallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 2009, 4:e6372.
3. Andersen R.A., van de Peer Y., Potter D., Sexton J.P., Kawachi M., LaJeunesse T. Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist 1999, 150:71-84.
4. Arndt H, Dietrich D, Auer B, Cleven EJ, Gräfenhan T, Weitere M, Mylnikov AP (2000) Functional Diversity of Heterotrophic Flagellates in Aquatic Ecosystems. In Leadbeater BSC, Green JC (eds) The Flagellates: Unity, Diversity and Evolution. Taylor & Francis Press, London, pp 240-268.
5. Bass D., Cavalier-Smith C. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 2004, 54:2393-2404.
6. Brandt S.M., Sleigh M.A. The quantitative occurrence of different taxa of heterotrophic flagellates in Southampton water, U.K. Estuar Coast Shelf Sci 2000, 51:91-102.
7. Caron D.A., Countway P.D., Brown M.V. The growing contributions of molecular biology and immunology to protistan ecology: Molecular signatures as ecological tools. J Eukaryot Microbiol 2004, 51:38-48.
8. Carr M., Leadbeater B.S.C., Hassan R., Nelson M., Baldauf S.L. Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proc Natl Acad Sci USA 2008, 105:16641-16646.
9. Carrias J.F., Amblard C., Quiblier-Lloberas C., Bourdier G. Seasonal dynamics of free and attached heterotrophic nanoflagellates in an oligomesotrophic lake. Freshwat Biol 1998, 39:91-101.
10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552.
11. Cavalier-Smith T., Chao E.E. Phylogeny and megasystematics of phagotrophic heterokonts (Kingdom Chromista). J Mol Evol 2006, 62:388-420.
12. Chambouvet A., Morin P., Marie D., Guillou L. Control of toxic marine dinoflagellate blooms by serial parasitic killers. Science 2008, 322:1254-1257.
13. Fenchel T. Ecology of heterotrophic microflagellates. IV. Quantitative occurrence and importance as bacterial consumers. Mar Ecol Prog Ser 1982, 9:35-42.
14. Fenchel T., Patterson D.J. Cafeteria roenbergensis nov. gen., nov. sp., a heterotrophic microflagellate from marine plankton. Mar Microb Food Webs 1988, 3:9-19.
15. Fuller N.J., Campbell C., Allen D.J., Pitt F.D., Zwirglmaier K., LeGall F., Vaulot D., Scanlan D.J. Analysis of photosynthetic picoeukaryotic diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids. Aquat Microb Ecol 2006, 43:79-93.
16. Galtier N., Gouy M., Gautier C. SeaView and Phylo_Win, two graphic tools for sequence alignment and molecular phylogeny. Comput Applic Biosci 1996, 12:543-548.
17. Guillou L., Viprey M., Chambouvet A., Welsh R.M., Kirkham A.R., Massana R., Scanlan D.J., Worden A.Z. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 2008, 10:397-408.
18. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinfomatics 2001, 17:754-755.
19. Jürgens K, Massana R (2008) Protistan Grazing on Marine Bacterioplankton. In Kirchman, DL (ed) Microbial Ecology of the Oceans, Second Edition. John Wiley & Sons, Inc., New York, USA, pp 383-441.
20. Katoh K., Misawa K., Kuma L., Miyata Y. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30:3059-3066.
21. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, M Marr M, et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783-788.
22. Könneke M., Bernhard A.E., de la Torre J.R., et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437:543-546.
23. Leadbeater BSC (1991) Choanoflagellate Organization with Special Reference to the Loricate Taxa. In Patterson DJ, Larson J (eds) The Biology of the Free-living Heterotrophic Flagellates. Clarendon Press, Oxford, pp 241-258.
24. Leakey R.J.G., Leadbeater B.S.C., Mitchell E., Mccready S.M.M., Murray A.W.A. 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 2002, 38:333-350.
25. Lee JJ, Leedale GF, Bradbury P (2000) The Illustrated Guide to the Protozoa, 2nd ed. Lawrence: Society of Protozoologists.
26. Lefranc M., Thénot A., Lepère C., Debroas D. Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 2005, 71:5935-5942.
27. Leipe D.D., Winright P.O., Gunderson J.H., Porter D., Patterson D.J., Valois F. 16S-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 1994, 33:369-377.
28. Lim E.L., Dennet M.R., Caron D.A. The ecology of Paraphysomonas imperforata based on studies employing oligonucleotide probe identification in coastal water samples and enrichment cultures. Limnol Oceanogr 1999, 44:37-51.
29. Logares R., Shalchian-Tabrizi K., Boltovskoy A., Rengefors K. Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions. Mol Phylogen Evol 2007, 45:887-903.
30. Marin B., Melkonian M. Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist 2010, 161:304-336.
31. Massana R., Pedrós-Alió C. Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 2008, 11:213-218.
32. Massana R., Balagué V., Guillou L., Pedrós-Alió C. Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 2004, 50:231-243.
33. Massana R., del Campo J., Dinter C., Sommaruga R. Crash of a population of the marine heterotrophic flagellate Cafeteria roenbergensis by viral infection. Environ Microbiol 2007, 9:2660-2669.
34. Massana R, Pernice M, Bunge J, del Campo J (2010) Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. ISME J doi:10.1038/ismej.2010.104.
35. Massana R., Guillou L., Terrado R., Forn I., Pedrós-Alió C. Growth of uncultured heterotrophic flagellates in unamended seawater incubations. Aquat Microb Ecol 2006, 45:171-180.
36. Not F., Latasa M., Scharek R., Viprey M., Karleskind P., Balagué V., Ontoria-Oviedo I., Cumino A., Goetze E., Vaulot D., Massana R. Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes. Deep Sea Res Part I 2008, 55:1456-1473.
37. Not F, del Campo J., Balagué V., de Vargas C., Massana R. New insights into the diversity of marine picoeukaryotes. PLoS ONE 2009, 4:e7143.
38. Patterson DJ, Lee WJ (2000) Geographic Distribution and Diversity of Free-Living Heterotrophic Flagellates. In Leadbeater BSC, Green JC (eds) The Flagellates: Unity, Diversity and Evolution. Taylor & Francis Press, London, pp 269-287.
39. Pernthaler J. Predation on prokaryotes in the water column and its ecological implications. Nature Rev Microbiol 2005, 3:537-546.
40. Preisig HR, Vørs N, Hällfors G (1991) Diversity of Heterotrophic Heterokont Flagellates. In Patterson DJ, Larson J (eds) The Biology of the Free-living Heterotrophic Flagellates. Clarendon Press, Oxford, pp 361-399.
41. Rappé M.S., Connon S.A., Vergin K.L., Giovannoni S.J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 2002, 418:630-633.
42. Richards T.A., Vepritskiy A.A., Gouliamova D.E., Nierzwicki-Bauer S.A. The molecular diversity of freshwater picoeukaryotes from oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ Microbiol 2005, 7:1413-1425.
43. Rusch D.B, Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., Beeson K., et al. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology 2007, 5:398-431.
44. Sherr E.B., Sherr B.F. Significance of predation by protists in aquatic microbial food webs. Antonie van Leeuwenhoek 2002, 81:293-308.
45. Shi X.L., Marie D., Jardillier L., Scanlan D.J., Vaulot D. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE 2009, 4:e7657.
46. Šlapeta J., Moreira D., López-García P. The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc Biol Sci 2005, 272:2073-2083.
47. Stamatakis A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
48. Stoeck T., Behnke A., Christen R., Amaral-Zettler L., Rodriguez-Mora M.J., Chistoserdov A., Orsiand W., Edgcomb V.P. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology 2009, 7:72.
49. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, Mass.
50. von Wintzingerode F., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997, 21:213-229.
51. Zhu F., Massana R., Not F., Marie D., Vaulot D. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 2005, 52:79-92.
52. Zuendorf A., Bunge J., Behnke A., Barger K.J.A., Stoeck T. Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol Ecol 2006, 58:476-491.