Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain)

Environmental Microbiology

Volumn 14, Issue 9, 2012, Pages 2445-2456

  Triadó Margarit, Xavier ^a   Casamayor, Emilio O ^a  

^a CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S;

ALVEOLATA; ARTICLE; BIODIVERSITY; CHEMISTRY; CHRYSOPHYTA; CLASSIFICATION; DNA SEQUENCE; EUKARYOTE; FUNGUS; GENETIC VARIABILITY; GENETICS; LAKE; PHYLOGENY; PLANKTON; POPULATION DENSITY; SPAIN; STRAMENOPILE;

ALVEOLATA; BIODIVERSITY; CHRYSOPHYTA; EUKARYOTA; FUNGI; GENETIC VARIATION; LAKES; PHYLOGENY; PLANKTON; POPULATION DENSITY; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA; SPAIN; STRAMENOPILES;

ALVEOLATA; CERCOMONADIDA; CHLOROPHYCEAE; CHRYSOPHYCEAE; CRYPTOPHYTA; EUGLENOZOA; EUKARYOTA; FUNGI; FUNGI/METAZOA GROUP; KATABLEPHARIDOPHYTA; OTUS; PROTISTA; RHIZARIA; STRAMENOPILES; VIRIDIPLANTAE;

EID: 84865730246     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02797.x     Document Type: Article

References (62)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Auguet, J.C., Barberán, A., and Casamayor, E.O. (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182-190.
3. Baldauf, S.L. (2003) The deep roots of eukaryotes. Science 300: 1703-1706.
4. Barberán, A., and Casamayor, E.O. (2010) Global phylogenetic community structure and beta-diversity patterns of surface bacterioplankton metacommunities. Aquat Microb Ecol 59: 1-10.
5. Barberán, A., Fernández-Guerra, A., Auguet, J.C., Galand, P.E., and Casamayor, E.O. (2011) Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol Ecol 20: 1988-1996.
6. Battarbee, R.W., Carvalho, L., Jones, V.J., Flower, R.J., Cameron, N.G., Bennion, H., and Juggins, S. (2001) Diatoms. In Tracking Environmental Change Using Lake Sediments, Volume 3: Terrestrial, Algal, and Siliceous Indicators. Smol, J., Last, W., and Birks, H.J.B. (eds). Dordrecht, The Netherlands: Kluwer Academic Publishers, pp. 155-202.
7. Buchaca, T., and Catalan, J. (2009) Factors influencing the variability of pigments in the surface sediments of mountain lakes. Fresh Biol 52: 1365-1379.
8. Butinar, L., Spencer-Martins, I., and Gunde-Cimerman, N. (2007) Yeasts in high Arctic glaciers: the discovery of a new habitat for eukaryotic microorganisms. Anton Leeuw Int J G 91: 277-289.
9. Caron, D.A., Countway, P.D., Savai, P., Gast, R.J., Schnetzer, A., Moorthi, S.D., etal. (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75: 5797-5808.
10. Catalan, J., Ballesteros, E., Camarero, L., Felip, M., and Gacia, E. (1992) Limnology in the Pyrenean Lakes. Limnetica 8: 27-38.
11. Catalan, J., Camarero, L., Felip, M., Pla, S., Ventura, M., Buchaca, T., etal. (2006) High mountain lakes: extreme habitats and witnesses of environmental changes. Limnetica 25: 551-584.
12. Chen, M., Chen, F., Yu, Y., Ji, J., and Kong, F. (2008) Genetic diversity of eukaryotic microorganisms in Lake Taihu, a large shallow subtropical lake in china. Microb Ecol 56: 572-583.
13. Countway, P.D., Gast, R.J., Dennett, M.R., Savai, P., Rose, J.M., and Caron, D.A. (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. Del Campo, J., and Massana, R. (2011) Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys. Protist 162: 435-448.
15. Demergasso, C., Escudero, L., Casamayor, E.O., Chong, G., Balague, V., and Pedros-Alio, C. (2008) Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama). Extremophiles 12: 491-504.
16. Díez, B., Pedros-Alio, C., and 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.
17. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
18. Elwood, H.J., Olsen, G.J., and Sogin, M.L. (1985) The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol Evol 2: 399-410.
19. Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
20. Felip, M., Bartumeus, F., Halac, S., and Catalan, J. (1999) Microbial plankton assemblages, composition and biomass, during two ice-free periods in a deep high mountain lake (Estany Redó, Pyrenees). J Limnol 58: 193-202.
21. Finlay, B. (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.
22. Finlay, B.J., and Clarke, K.J. (1999) Ubiquitous dispersal of microbial species. Nature 400: 828.
23. Freeman, K.R., Martin, A.P., Karki, D., Lynch, R.C., Mitter, M.S., Meyer, A.F., etal. (2009) Evidence that chytrids dominate fungal communities in high-elevation soils. Proc Natl Acad Sci USA 106: 18315-18320.
24. Gonzalez, J.M., Zimmermann, J., and Saiz-Jimenez, C. (2005) Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-337.
25. Guillou, L., Moon-van der Staay, S.Y., Claustre, H., Partensky, F., and Vaulot, D. (1999) Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl Environ Microbiol 65: 4528-4536.
26. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
27. Helmus, M.R., Bland, T.J., Williams, C.K., and Ives, A.R. (2007) Phylogenetic measures of biodiversity. Am Nat 169: e68-e83.
28. Hoef-Emden, K., and Melkonian, M. (2003) Revision of the genus Cryptomonas (Cryptophyceae): a combination of molecular phylogeny and morphology provides insights into a long-hidden dimorphism. Protist 154: 371-409.
29. Huber, T., Faulkner, G., and Hugenholtz, P. (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
30. Klaveness, D., Shalchian-Tabrizi, K., Thomsen, H.A., Eikrem, W., and Jakobsen, K.S. (2005) Telonema antarcticum sp. nov., a common marine phagotrophic flagellate. Int J Syst Evol Microbiol 55: 2595-2604.
31. Lefèvre, E., Bardot, C., Noel, C., Carrias, J.F., Viscogliosi, E., Amblard, C., and Sime-Ngando, T. (2007) Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake. Environ Microbiol 9: 61-71.
32. Lefèvre, E., Roussel, B., Amblard, C., and Sime-Ngando, T. (2008) The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton. PLoS ONE 3: e2324.
33. Lefranc, M., Thenot, A., Lepere, C., and Debroas, D. (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71: 5935-5942.
34. Lepère, C., Domaizon, I., and Debroas, D. (2008) Unexpected importance of potential parasites in the composition of the freshwater small-eukaryote community. Appl Environ Microbiol 74: 2940-2949.
35. Logares, R., Braate, J., Bertilsson, S., Clasen, J.L., Shalchian-Tabrizi, K., and Rengefors, K. (2009) Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol 17: 414-422.
36. Lozupone, C., Hamady, M., and Knight, R. (2006) UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
37. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, etal. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
38. Luo, W., Bock, C., Li, H.R., Padisak, J., and Krienitz, L. (2011) Molecular and microscopic diversity of planktonic eukaryotes in the oligotrophic Lake Stechlin (Germany). Hydrobiologia 661: 133-143.
39. McArdle, B.H., and Anderson, M.J. (2001) Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82: 290-297.
40. Margalef, R. (1983) Limnologia. Ed. Omega S.A. Barcelona, Spain: Omega.
41. Massana, R. (2011) Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol 65: 91-110.
42. Massana, R., Guillou, L., Diez, B., and Pedros-Alio, C. (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol 68: 4554-4558.
43. Massana, R., Balague, V., Guillou, L., and Pedros-Alio, C. (2004) Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 50: 231-243.
44. Medlin, L., Elwood, H.J., Stickel, S., and Sogin, M.L. (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-499.
45. Mladenov, N., Sommaruga, R., Morales-Baquero, R., Laurion, I., Camarero, L., Dieguez, M.C., etal. (2011) Dust inputs and bacteria influence dissolved organic matter in clear alpine lakes. Nat Commun 2: 405-412.
46. Monchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chabé, M., etal. (2011) Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environ Microbiol 13: 1433-1453.
47. Not, F., Gausling, R., Azam, F., Heidelberg, J.F., and Worden, A.Z. (2007) Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ Microbiol 9: 1233-1252.
48. Not, F., del Campo, J., Balague, V., de Vargas, C., and Massana, R. (2009) New insights into the diversity of marine picoeukaryotes. PLoS ONE 4: e7143.
49. Oksanen, J., Blanchet, G., Kindt, R., Legendre, P., Minchin, P.R., O'Hara, R.B., etal. (2011) Vegan: Community Ecology Package version 2.0-0. [WWW document]. URL http://vegan.r-forge.r-project.org/
50. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glockner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
51. Richards, T.A., Vepritskiy, A.A., Gouliamova, D.E., and Nierzwicki-Bauer, S.A. (2005) The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ Microbiol 7: 1413-1425.
52. Sanders, R.W. (2009) Protists. In Encyclopedia of Inland Waters. Likens, G.E. (ed.). Oxford, UK: Elsevier, pp. 252-260.
53. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., etal. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
54. Shalchian-Tabrizi, K., Bråte, J., Logares, R., Klaveness, D., Berney, C., and Jakobsen, K.S. (2008) Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol 10: 2635-2644.
55. Sherr, E., and Sherr, B. (1988) Role of microbes in pelagic food webs - a revised concept. Limnol Oceanogr 33: 1225-1227.
56. Singleton, D.R., Furlong, M.A., Rathbun, S.L., and Whitman, W.B. (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-4376.
57. Slapeta, J., Moreira, D., and Lopez-Garcia, P. (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc Biol Sci 272: 2073-2081.
58. Stoeck, T., Bruemmer, F., and Foissner, W. (2007) Evidence for local ciliate endemism in an alpine anoxic lake. Microb Ecol 54: 478-486.
59. Thornhill, D.J., LaJeunesse, T.C., and Santos, S.R. (2007) Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Mol Ecol 16: 5326-5340.
60. Vishniac, H.S., and Hempfling, W.P. (1979) Cryptococcus vishniacii sp-nov, an Antarctic yeast. Int J Syst Bacteriol 29: 153-158.
61. Weisse, T. (2008) The meaning of protist diversity: ecology meets taxonomy. Denisia 23: 297-306.
62. Wetzel, R.G. (2001) Limnology: Lake and River Ecosystems, 3rd edn. San Diego, CA, USA: Academic Press.