The use of DGGE analyses to explore eastern Mediterranean and Red Sea marine picophytoplankton assemblages

Environmental Microbiology

Volumn 6, Issue 5, 2004, Pages 528-534

  Zeidner, Gil ^a   Béjà, Oded ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

PHOTOSYSTEM II, PSBA SUBUNIT; SEA WATER;

ANIMAL; ARTICLE; CLASSIFICATION; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; GREEN ALGA; INDIAN OCEAN; MEDITERRANEAN SEA; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHOTOSYSTEM II; PHYLOGENY; PHYTOPLANKTON; POLYACRYLAMIDE GEL ELECTROPHORESIS;

ALGAE, GREEN; ANIMALS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENETIC TECHNIQUES; INDIAN OCEAN; MEDITERRANEAN SEA; MOLECULAR SEQUENCE DATA; PHOTOSYSTEM II PROTEIN COMPLEX; PHYLOGENY; PHYTOPLANKTON; SEAWATER; VARIATION (GENETICS); WATER MICROBIOLOGY;

ALGAE; ANIMALIA; CHLOROPHYTA; CYANOBACTERIA; EUKARYOTA; PRASINOPHYCEAE;

EID: 1942539920     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00599.x     Document Type: Article

References (35)

1. Béjà, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., et al. (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2: 516-529.
2. Biegala, I.C.F.N., Vaulot, D., and Simon, N. (2003) Quantitative assessment of picoeukaryotes in the natural environment by using taxon-specific oligonucleotide probes in association with tyramide signal amplification- fluorescence in situ hybridization and flow cytometry. Appl Environ Microbiol 69: 5519-5529.
3. Courties, C., Vaquer, A., Troussellier, M., Lautier, J., Chrétiennot-Dinet, M.J., Neveux, J., et al. (1994) Smallest eukaryotic organism. Nature 370: 255.
4. Dahllöf, I., Baillie, H., and Kjelleberg, S. (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66: 3376-3380.
5. Dutton, C.M., Paynton, C., and Sommer, S.S. (1993) General method for amplifying regions of very high G+C content. Nucleic Acids Res 21: 2953-2954.
6. Fuller, N.J., Marie, D., Partensky, F., Vaulot, D., Post, A.F., and Scanlan, D.J. (2003) Clade-specific 16S ribosomal DNA oligonucleotldes reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl Environ Microbiol 69: 2430-2443.
7. Karl, D.M. (2002) Hidden in a sea of microbes. Nature 415: 590-591.
8. Lovell, C.R., Friez, M.J., Longshore, J.W., and Bagwell, C.E. (2001) Recovery and phylogenetic analysis of nifH sequences from diazotrophic bacteria associated with dead aboveground biomass of Spartina alterniflora. Appl Environ Microbiol 67: 5308-5314.
9. Mann, N.H., Cook, A., Millard, A., Bailey, S., and Clokie, M. (2003) bacterial photosynthesis genes in a virus. Nature 424: 741.
10. Moore, L.R., Rocap, G., and Chisholm, S.W. (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393: 464-467.
11. Morden, C.W., and Golden, S.S. (1989) psbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337: 382-385.
12. Morden, C.W., Delwiche, C.F., Kuhsel, M., and Palmer, J.D. (1992) Gene phylogenies and the endosymbiotic origin of plastids. Biosystems 28: 75-90.
13. Muyzer, G., and Smalla, K. (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73: 127-141.
14. Oved, T., Shaviv, A., Goldrath, T., Mandelbaum, R.T., and Minz, D. (2001) Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 67: 3426-3433.
15. Pace, N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
16. Palenik, B., Brahamsha, B., Larimer, F.W., Land, M., Hauser, L., Chain, P., et al. (2003) The genome of a motile marine Synechococcus. Nature 424: 1037-1042.
17. Rappé, M.S., Kemp, P.F., and Giovannoni, S.J. (1997) Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 42: 811-826.
18. Rappé, M.S., Suzuki, M.T., Vergin, K.L., and Giovannoni, S.J. (1998) Phylogenetic diversity of ultraplankton plastid small-subunit rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States. Appl Environ Microbiol 64: 294-303.
19. Reysenbach, A.L., Giver, L.J., Wickham, G.S., and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58: 3417-3418.
20. Rocap, G., Distel, D.L., Waterbury, J.B., and Chisholm, S.W. (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68: 1180-1191.
21. Rosado, A.S., Duarte, G.F., Seldin, L., and Van Elsas, J.D. (1998) Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Appl Environ Microbiol 64: 2770-2779.
22. Scherer, S., Herrmann, G., Hirschberg, J., and Boger, P. (1991) Evidence for multiple xenogenous origins of plastids: comparison of psbA-genes with a xanthophyte sequence. Curr Genet 19: 503-507.
23. Sommer, U., Berninger, U.G., Böttger-Schnack, R., Cornils, A., Hagen, W., Hansen, T., et al. (2002) Grazing during early spring in the Gulf of Aqaba and the northern Red Sea. Mar Ecol Prog Series 239: 251-261.
24. Steglich, C., Post, A.F., and Hess, W.R. (2003) Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences. Environ Microbiol 5: 681-690.
25. Swofford, D.L. (2002) paup*. Phylogenetic Analysis Using Parsimony. Sunderland, MA: Sinauer Associates.
26. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
27. Toledo, G., and Palenik, B. (2003) A Synechococcus serotype is found preferentially in surface marine waters. Limnol Oceanogr 48: 1744-1755.
28. Urbach, E., and Chisholm, S.W. (1998) Genetic diversity in Prochlorococcus populations flow cytometrically sorted from the Sargasso Sea and the Gulf Stream. Limnol Oceanogr 43: 1615-1630.
29. Urbach, E., Scanlan, D.J., Distel, D.L., Waterbury, J.B., and Chisholm, S.W. (1998) Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria). J Mol Evol 46: 188-201.
30. Wawer, C., and Muyzer, G. (1995) Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments. Appl Environ Microbiol 61: 2203-2210.
31. West, N.J., and Scanlan, D.J. (1999) Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean. Appl Environ Microbiol 65: 2585-2591.
32. West, N.J., Schonhuber, W.A., Fuller, N.J., Amann, R.I., Rippka, R., Post, A.F., and Scanlan, D.J. (2001) Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology 147: 1731-1744.
33. Yoon, H.S., Hackett, J.D., and Bhattacharya, D. (2002) A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proc Natl Acad Sci USA 99: 11724-11729.
34. Zeidner, G., Preston, C.M., Delong, E.F., Massana, R., Post, A.F., Scanlan, D.J., and Béjà, O. (2003) Molecular diversity among marine picophytoplankton as revealed by psbA analyses. Environ Microbiol 5: 212-216.
35. Zhang, Z., Green, B.R., and Cavalier-Smith, T. (2000) Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: a possible common origin for sporozoan and dinoflagellate plastids. J Mol Evol 51: 26-40.