Phylogenetic composition and distribution of picoeukaryotes in the hypoxic northwestern coast of the Gulf of Mexico

MicrobiologyOpen

Volumn 2, Issue 1, 2013, Pages 130-143

  Rocke, Emma ^a   Jing, Hongmei ^a   Liu, Hongbin ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Dinoflagellates; Hypoxia; MALV I and II; Picoeukaryotes; rDNA environmental sequences

Indexed keywords

SURFACE WATER;

ARTICLE; COMMUNITY ECOLOGY; CONTROLLED STUDY; DINOFLAGELLATE; DNA LIBRARY; GENETIC VARIABILITY; GULF OF MEXICO; HYPOXIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RIVER; SPECIES COMPOSITION; SPECIES DISTRIBUTION; SPECIES DIVERSITY; STRAMENOPILE; UNINDEXED SEQUENCE; UNITED STATES; WATER ANALYSIS; WATER SAMPLING;

BIOTA; EUKARYOTA; GENETIC VARIATION; GULF OF MEXICO; MOLECULAR SEQUENCE DATA; OXYGEN; PHYLOGENY; RNA, RIBOSOMAL, 18S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84897918131     PISSN: None     EISSN: 20458827     Source Type: Journal    
DOI: 10.1002/mbo3.57     Document Type: Article

References (59)

1. Arndt, H. 2000. Functional diversity of heterotrophic flagellates in aquatic systems. Pp. 240-268 in B. S. C. Leadbeater and J. C. Green, eds. The flagellates: unity, diversity and evolution. Taylor & Francis Press, London, U.K.
2. Bass, D., and T. Cavalier-Smith. 2004. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int. J. Syst. Evol. Microbiol. 54:2393-2404.
3. 2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl. Environ. Microbiol. 72:3626-3636.
4. Bianchi, T. S., R. L. Cook, E. M. Perdue, P. E. Kolic, N. Green, Y. Zhang, et al. 2011. Impacts of diverted freshwater on dissolved organic matter and microbial communities in Barataria Bay, Louisiana, U.S.A. Mar. Environ. Res. 72:248-257.
5. Boström, K. H., K. Simu, Å. Hagstrom, and L. Riemann. 2004. Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol. Oceanogr. Methods 2:365-373.
6. Caron, D., and P. Countway. 2009. Hypotheses on the role of the protistan rare biosphere in a changing world. Aquat. Microb. Ecol. 57:227-238.
7. Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int. J. Syst. Evol. Microbiol. 52:7-76.
8. Chambouvet, A., M. Laabir, M. Sengco, A. Vaquer, and L. Guillou. 2011. Genetic diversity of Amoebophryidae (Syndiniales) during Alexandrium catenella/tamarense (Dinophyceae) blooms in the Thau lagoon (Mediterranean Sea, France). Res. Microbiol. 162:959-968.
9. Coats, D. W. 1999. Parasitic life styles of marine dinoflagellates. J. Eukaryot. Microbiol. 46:402-409.
10. Coats, D. W., and K. R. Bockstahler. 1994. Occurrence of the parasitic dinoflagellate Amoebophrya ceratii in Chesapeake Bay populations of Gymnodinium sanguineum. J. Eukaryot. Microbiol. 41:586-593.
11. Coats, D. W., and M. G. Park. 2002. Parasitism of phytosynthetic dinoflagellates by three strains of Amoebophrya (Dinophyta): parasite survival, infectivity, generation. J. Phycol. 38:520-528.
12. Countway, P. D., R. J. Gast, P. Savai, and D. A. Caron. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J. Eukaryot. Microbiol. 52:95-106.
13. Countway, P. D., R. J. Gast, M. R. Dennett, P. Savai, J. M. Rose, and D. A. Caron. 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.
14. Dawson, S. C., and N. R. Pace. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99:8324-8329.
15. Diaz, R. J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. Science 321:926-929.
16. Diez, B., C. Pedrós-alió, R. Massana, C. Pedro, and B. Di. 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.
17. Edgcomb, V., W. Orsi, J. Bunge, S. Jeon, R. Christen, C. Leslin, et al. 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J. 5:1344-1356.
18. Epstein, S., and P. Lopez-Garcia. 2008. "Missing" protists: a molecular perspective. Biodivers. Conserv. 17:261-276.
19. Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5:163-166.
20. Fenchel, T., L. D. Kristensen, and L. Rasmussen. 1990. Water column anoxia: vertical zonation of planktonic protozoa. Mar. Ecol. Prog. Ser. 62:1-10.
21. Fenchel, T., and B. Finlay. 2008. Oxygen and the spatial structure of microbial communities. Biol. Rev. Camb. Philos. Soc. 83:553-569.
22. Fenchel, T. 1986. The ecology of heterotrophic microflagellates. Adv. Microb. Ecol. 9:57-97.
23. Green, R. E., T. S. Bianchi, M. J. Dagg, N. D. Walker, and G. A. Breed. 2006. An organic carbon budget for the Mississippi River turbidity plume, and plume contributions to air-sea CO2 fluxes and bottom water hypoxia. Estuaries 29:579-597.
24. Guillou, L., M. Viprey, A. Chambouvet, R. M. Welsh, A. R. Kirkham, R. Massana, et al. 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ. Microbiol. 10:3349-3365.
25. Hall, T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41:95-98.
26. Helm, K. P., N. L. Bindoff, and J. A. Church. 2011. Observed decreases in oxygen content of the global ocean. Geophys. Res. Lett. 38:L23602.
27. Hoback, W. W., and M. C. Barnhart. 1996. Lethal limits and sublethal effects of hypoxia on the amphipod Gammarus pseudolimnaeus. J. North Am. Bentholog. Soc. 15:117-126.
28. Jeong, H. J., Y. D. Yoo, J. S. Kim, K. A. Seong, N. S. Kang, and T. H. Kim. 2010. Growth, feeding and ecological roles of the mixotrophic and heterotrophic dinoflagellates in marine planktonic foodwebs. Ocean Sci. J. 45:65-91.
29. Johansson, M., and D. Coats. 2002. Ciliate grazing on the parasite Amoebophrya sp. decreases infection of the red-tide dinoflagellate Akashiwo sanguinea. Aquat. Microb. Ecol. 28:69-78.
30. Liu, H., and M. Dagg. 2003. Interactions between nutrients, phytoplankton growth, and micro- and mesozooplankton grazing in the plume of the Mississippi River. Mar. Ecol. Prog. Ser. 258:31-42.
31. Loeblich, A. R. 1976. Dinoflagellate evolution: speculation and evidence. J. Protozool. 23:13-28.
32. López-García, P., F. Rodríguez-Valera, C. Pedrós-Alió, and D. Moreira. 2001. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603-607.
33. Lovejoy, C., R. Massana, and C. Pedro. 2006. Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl. Environ. Microbiol. 72:3085-3095.
34. Massana, R., L. Guillou, B. Díez, and C. Pedro. 2002. Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl. Environ. Microbiol. 68:4554-4558.
35. Massana, R., J. Castresana, V. Balagué, K. Romari, A. Groisillier, K. Valentin, et al. 2004. Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 70:3528-3534.
36. Medlin, L. K., K. Metfies, H. Mehl, K. Wiltshire, and K. Valentin. 2006. Picoeukaryotic plankton diversity at the Helgoland time series site as assessed by three molecular methods. Microb. Ecol. 52:53-71.
37. Moon-van der Staay, S. Y., R. De Wachter, and D. Vaulot. 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607-610.
38. Moreira, D., and P. López-García. 2002. The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol. 10:31-38.
39. Morquecho, L., and C. H. Lechuga-Deveze. 2003. Dinoflagellate cysts in recent sediments from Bahía Concepción, Gulf of California. Bot. Mar. 46:132-141.
40. Nolte, V., R. V. Pandey, S. Jost, R. Medinger, B. Ottenwalder, J. Boenigk, et al. 2010. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol. Ecol. 19:2908-2915.
41. Not, F., R. Gausling, F. Azam, J. F. Heidelberg, and A. Worden. 2007. Vertical distribution of picoeukaryote diversity in the Sargasso Sea. Environ. Microbiol. 9:1233-1252.
42. Not, F., D.-C. Javier, V. Balague, C. de Vargas, and R. Massana. 2009. New insights into the diversity of marine picoeukaryotes. Plos One 4:e7143.
43. Orsi, W., Y. C. Song, S. Hallam, and V. Edgecomb. 2012. Effect of oxygen minimum zone formation on communities of marine protists. ISME J. 6:1586-1601.
44. Rabalais, N. N., and E. R. Turner. 2001. Hypoxia in the northern Gulf of Mexico: description, causes, and change. Pp. 1-36 in Coastal and Estuarine Studies ed. Coastal hypoxia: consequences for living resources and ecosystems. American Geophysical Union, 2000 Florida Ave., Washington, DC.
45. Rabalais, N. N., R. J. Diaz, L. A. Levin, R. E. Turner, D. Gilbert, and J. Zhang. 2010. Dynamics and distribution of natural and human-caused hypoxia. Biogeosciences 7:585-619.
46. Romari, K., D. Vaulot, M. Curie, and R. Cedex. 2004. Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol. Oceanogr. 49:784-798.
47. Schloss, P. D., and J. Handelsman. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68:686-691.
48. Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, et al. 2009. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
49. Stoeck, T., and S. Epstein. 2003. Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl. Environ. Microbiol. 69:2657-2663.
50. Stoeck, T., B. Hayward, G. T. Taylor, R. Varela, and S. S. Epstein. 2006. A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31-43.
51. Stoeck, T., D. Bass, M. Nebel, R. Christen, M. D. M. Jones, H.-W. Breiner, et al. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol. 19:21-31.
52. Takishita, K., N. Yubuki, N. Kakizoe, Y. Inagaki, and T. Maruyama. 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.
53. Tester, P. A., and K. A. Steidinger. 1997. Gymnodinium breve red tide blooms: initiation, transport, and consequences of surface circulation. Limnol. Oceanogr. 42:1039-1051.
54. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
55. Vaulot, D., W. Eikrem, M. Viprey, and H. Moreau. 2008. The diversity of small eukaryotic phytoplankton (< or =3 micron) in marine ecosystems. FEMS Microbiol. Rev. 32:795-820.
56. Weckström, K., and S. Juggins. 2005. Coastal diatom-environment relationships from the Gulf of Finland, Baltic sea. J. Phycol. 42:21-35.
57. Wylezich, C., and K. Jurgens. 2011. Protist diversity in suboxic and sulfidic waters of the Black Sea. Environ. Microbiol. 13:2939-2956.
58. Zhang, J., D. Gilbert, A. J. Gooday, L. Levin, W. A. Naqvi, J. J. Middelburg, et al. 2010. Natural and human-induced hypoxia and consequences for coastal areas: synthesis and future development. Biogeosciences 7:1443-1467.
59. Zuendorf, A., J. Bunge, A. Behnke, K. J. Barger, and T. Stoeck. 2006. Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol. Ecol. 58:476-491.