High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters

Journal of Phycology

Volumn 50, Issue 5, 2014, Pages 960-965

  Taylor, Joe D ^a   Cunliffe, Michael ^a  

^a THE LABORATORY   (United Kingdom)

Author keywords

18S rRNA gene; Coastal; Fungi; Neuston; Plankton; Protist

Indexed keywords

EUKARYOTA; FUNGI; PROTISTA;

EID: 84908554622     PISSN: 00223646     EISSN: 15298817     Source Type: Journal    
DOI: 10.1111/jpy.12228     Document Type: Article

References (28)

1. Agogue, H., Casamayor, E. O., Joux, F., Obernosterer, I., Dupuy, C., Lantoine, F., Catala, P., Weinbauer, M. G., Reinthaler, T., Herndl, G. J. & Lebaron, P. 2004. Comparison of samplers for the biological characterization of the sea surface microlayer. Limnol. Oceanogr. Methods 2:213-25.
2. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N. et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-6.
3. Crow, S. A., Ahern, D. G., Cook, W. L. & Bourquin, A. W. 1975. Densities of bacteria and fungi in coastal surface films as determined by a membrane-adsorption procedure. Limnol. Oceanogr. 20:644-6.
4. Cunliffe, M., Engel, A., Frka, S., Gašparović, B., Guitart, C., Murrell, J. C., Salter, M., Stolle, C., Upstill-Goddard, R. & Wurl, O. 2013. Sea surface microlayers: a unified physicochemical and biological perspective of the air-ocean interface. Prog. Oceanogr. 109:104-16.
5. Cunliffe, M. & Murrell, J. C. 2010. Eukarya 18S rRNA gene diversity in the sea surface microlayer: insights on the structure of the neustonic microbial loop. ISME J. 4:455-8.
6. Cunliffe, M., Schafer, H., Harrison, E., Cleave, S., Upstill-Goddard, R. C. & Murrell, J. C. 2008. Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary. ISME J. 2:776-89.
7. Cunliffe, M., Upstill-Goddard, R. C. & Murrell, J. C. 2011. Microbiology of aquatic surface microlayers. FEMS Microbiol. Rev. 35:233-46.
8. Cunliffe, M., Whiteley, A. S., Schäfer, H., Newbold, L., Oliver, A. & Murrell, J. C. 2009. Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm. Appl. Environ. Microbiol. 75:7173-81.
9. De Souza Limaa, Y. & Chretiennot-Dinet, M. J. 1984. Measurements of biomass and activity of neustonic microorganisms. Est. Coast. Shelf Sci. 19:167-80.
10. Dunthorn, M., Klier, J., Bunge, J. & Stoeck, T. 2012. Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity. J. Eukaryot. Microbiol. 59:185-7.
11. Gao, Z., Johnson, Z. I. & Wang, G. 2010. Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. ISME J. 4:111-20.
12. Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597-604.
13. Hadziavdic, K., Lekang, K., Lanzen, A., Jonassen, I., Thompson, E. M. & Troedsson, C. 2014. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS ONE 9:e87624.
14. Hardy, J. T. & Apts, C. W. 1984. The sea-surface microlayer: phytoneuston productivity and effects of atmospheric particulate matter. Mar. Biol. 82:293-300.
15. Hardy, J. T. & Apts, C. W. 1989. Photosynthetic carbon reduction: high rates in the sea surface microlayer. Mar. Biol. 101:411-7.
16. Hardy, J. T. & Valett, M. 1981. Natural and microcosm phytoneuston communities of Sequim Bay, Washington. Est. Coast. Shelf Sci. 12:3-12.
17. Joux, F., Agogue, H., Obernosterer, I., Dupuy, C., Reinthaler, T., Herndl, G. J. & Lebaron, P. 2006. Microbial community structure in the sea surface microlayer at two contrasting coastal sites in the northwestern Mediterranean Sea. Aquat. Microb. Ecol. 42:91-104.
18. Lane, D. J. 1991. 16S/23S rRNA sequencing. In Stackebrandt, E. & Goodfellow, M. [Eds.] Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons, Chichester, UK, pp. 115-75.
19. Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-9.
20. Montes-Hugo, M. A. & Alvarez-Borrego, S. 2007. Differences in photosynthetic pigment signatures between phytoneuston and phytoplankton communities in a coastal lagoon of Baja California. Mar. Biol. 151:1225-36.
21. Naumann, E. 1917. Beiträge zur kenntnis des teichnanoplanktons. II. Über das neuston des süßwasser. Biol. Zentbl. 37:98-106.
22. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. & Glöckner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-6.
23. Richards, T. A., Jones, M. D. M., Leonard, G. & Bass, D. 2012. Marine fungi: their ecology and molecular diversity. Ann. Rev. Mar. Sci. 4:495-522.
24. Southward, A. J., Langmead, O., Hardman-Mountford, N. J., Aiken, J., Boalch, G. T., Dando, P. R., Genner, M. J. et al. 2005. Long-term oceanographic and ecological research in the Western English Channel. Adv. Mar. Biol. 47:1-105.
25. Stolle, C., Labrenz, M., Meeske, C. & Jürgens, K. 2011. The bacterioneuston community structure of the southern Baltic Sea and its dependence on meteorological conditions. Appl. Environ. Microbiol. 77:3726-33.
26. Taylor, J. D., Cottingham, S. D., Billinge, J. & Cunliffe, M. 2014. Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. ISME J. 8:245-8.
27. Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., Allcock, R. & O'Donnell, A. 2012. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) platform. J. Microbiol. Methods 91:80-8.
28. Widdicombe, C. E., Eloire, D., Harbour, D., Harris, R. P. & Somerfield, P. J. 2010. Long-term phytoplankton community dynamics in the Western English Channel. J. Plankton Res. 32:643-55.