Phylogenetic analysis of the composition of bacterial communities in human-exploited coastal environments from Mallorca Island (Spain)

Systematic and Applied Microbiology

Volumn 31, Issue 3, 2008, Pages 231-240

  Aguilo Ferretjans M M ^a   Bosch, R ^a   Martin Cardona C ^a   Lalucat, J ^a   Nogales, B ^a  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

Author keywords

Bacterial diversity; Coastal environments; Mallorca Island; Recreational waters

Indexed keywords

BACTERIAL DNA; CHLOROPHYLL; DNA 16S; HYDROCARBON; WATER;

ACINETOBACTER; ARTICLE; BACTERIAL COUNT; BACTERIODETE; BACTERIOPLANKTON; BACTERIUM; CLADISTICS; COASTAL WATERS; CRYOMORPHACEAE; DNA LIBRARY; GENE SEQUENCE; MARINE BACTERIUM; MICROBIAL COMMUNITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT; PHYLOGENY; PRIORITY JOURNAL; ROSEOBACTER; SEASHORE; SPAIN; WATER SAMPLING; WINTER;

BACTERIA; BATHING BEACHES; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; GENE LIBRARY; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SPAIN; SPORTS;

ACINETOBACTER; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CRYOMORPHACEAE; ROSEOBACTER;

EID: 46849116890     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2008.04.003     Document Type: Article

References (45)

1. Acinas S.G., Rodríguez-Valera F., and Pedrós-Alió C. Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol. Ecol. 24 (1997) 27-40
2. Alonso C., Warnecke F., Amann R., and Pernthaler J. High local and global diversity of Flavobacteria in marine plankton. Environ. Microbiol. 9 (2007) 1253-1266
3. Alonso-Sáez L., Balagué V., Sà E.L., Sánchez O., González J.M., Pinhassi J., Massana R., Pernthaler J., Pedrós-Alió C., and Gasol J.M. Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol. Ecol. 60 (2007) 98-112
4. Amann R.I., Binde B.J., Olson R.J., Chisholm S.W., Devereux R., and Stahl D. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56 (1990) 1919-1925
5. Buchan A., González J.M., and Moran M.A. Overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71 (2005) 5665-5677
6. Cole J.R., Chai B., Marsh T.L., Farris R.J., Wang Q., Kulam S.A., Chandra D., McGarrell M., Schmidt T.M., Garrity G.M., and Tiedje J.M. The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31 (2003) 442-443
7. Connon S.A., and Giovannoni S.J. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68 (2002) 3878-3885
8. Cottrell M.T., and Kirchman D.L. Natural assemblages of marine Proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66 (2000) 1692-1697
9. DeLong E.F., Franks D.G., and Alldredge A.L. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol. Oceanogr. 38 (1993) 924-934
10. Eilers H., Pernthaler J., Peplies J., Glöckner F.O., Gerdts G., and Amann R. Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface bacterioplankton. Appl. Environ. Microbiol. 67 (2001) 5134-5142
11. Gentile G., Giuliano L., D'Auria G., Smedile F., Azzaro M., De Domenico M., and Yakimov M.M. Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environ. Microbiol. 8 (2006) 2150-2161
12. Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D., Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappé M.S., Short J.M., Carrington J.C., and Mathur E.J. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309 (2005) 1242-1245
13. Glöckner F.O., Amann R., Alfreider A., Pernthaler J., Psenner R., Trebesius K., and Schleifer K.H. An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst. Appl. Microbiol. 19 (1996) 403-406
14. González J.M., and Moran M.A. Numerical dominance of a group of marine bacteria in the α-subclass of the Class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63 (1997) 4237-4242
15. Good I.L. The population frequencies of species and the estimation of population parameters. Biometrika 40 (1953) 237-264
16. Hahn M.W., Stadler P., Wu Q.L., and Pöckl M. The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J. Microbiol. Meth. 57 (2004) 379-390
17. Hammer Ø., Harper D.A.T., and Ryan P.D. PAST: paleontological statistics software package for education and data analysis. Paleontol. Electron. 4 (2001) 1-9
18. Islam M.S., and Tanaka M. Impacts of pollution on coastal and marine ecosystems including coastal and marine fisheries and approach for management: a review and synthesis. Mar. Pollut. Bull. 48 (2004) 624-649
19. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.N. (Ed). Mammalian Protein Metabolism (1969), Academic Press, New York 21-132
20. Kelly K.M., and Chistoserdov A.Y. Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol. Ecol. 35 (2001) 85-95
21. Kirchman D.L., Yu L., and Cottrell M.T. Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware estuary. Appl. Environ. Microbiol. 69 (2003) 6587-6596
22. Kulikova T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., Castro M., Cochrane G., Duggan K., Eberhardt R., Faruque N., Hoad G., Kanz C., Lee C., Leinonen R., Lin Q., Lombard V., Lopez R., Lorenc D., McWilliam H., Mukherjee G., Nardone F., García-Pastor M.P., Plaister S., Sobhany S., Stoehr P., Vaughan R., Wu D., Zhu W., and Apweiler R. EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35 (2007) D16-D20
23. Lane D.J. 16S/23S rRNA sequencing. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic Acid Techniques in Bacterial Systematics (1991), Wiley, Chichester 115-175
24. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüßmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., and Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Res. 32 (2004) 1363-1371
25. Marchesi J.R., Sato T., Weightman A.J., Martin T.A., Fry J.C., Hiom S.J., Dymock D., and Wade W.G. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 63 (1998) 795-799
26. Nogales B., Aguiló-Ferretjans M.M., Martín-Cardona C., Lalucat J., and Bosch R. Bacterial diversity, composition and dynamics in and around recreational coastal areas. Environ. Microbiol. 9 (2007) 1913-1929
27. O'Sullivan L.A., Fuller K.E., Thomas E.M., and Turley C.M. Distribution and culturability of the uncultivated "AGG58" cluster of the Bacteroidetes phylum in aquatic environments. FEMS Microbiol. Ecol. 47 (2004) 359-370
28. Orphan V.J., Taylor L.T., Hafenbradl D., and DeLong E.F. Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl. Environ. Microbiol. 66 (2000) 700-711
29. Osborn A.M., Moore E.R.B., and Timmis K.N. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2 (2000) 39-50
30. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85 (1988) 2444-2448
31. Pinhassi J., Sala M.M., Havskum H., Peters F., Guadayol O., Malits A., and Marrase C. Changes in bacterioplankton composition under different phytoplankton regimens. Appl. Environ. Microbiol. 70 (2004) 6753-6766
32. Pinhassi J., Simó R., González J.M., Vila M., Alonso-Sáez L., Kiene R.P., Moran M.A., and Pedros-Alió C. Dimethylsulfoniopropionate turnover is linked to the composition and dynamics of the bacterioplankton assemblage during a microcosm phytoplankton bloom. Appl. Environ. Microbiol. 71 (2005) 7650-7660
33. Radwan S.S., Al-Hasan R.H., Al-Awadhi H., Salamah S., and Abdullah H.M. Higher oil biodegradation potential at the Arabian Gulf coast than in the water body. Mar. Biol. 135 (1999) 741-745
34. Rappé M.S., Kemp P.F., and Giovannoni S.J. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42 (1997) 811-826
35. Rappé M.S., Gordon D.A., Vergin K.L., and Giovannoni S.J. Phylogeny of Actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Syst. Appl. Microbiol. 22 (1999) 106-112
36. Rappé M.S., Vergin K., and Giovannoni S.J. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater communities. FEMS Microbiol. Ecol. 33 (2000) 219-232
37. Riemann L., Steward G.F., and Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66 (2000) 578-587
38. Rooney-Varga J.N., Giewat M.W., Savin M.C., Sood S., LeGresley M., and Martin J.L. Links between phytoplankton and bacterial community dynamics in a coastal marine environment. Microb. Ecol. 49 (2005) 163-175
39. 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., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F., Utterback T., Rogers Y.H., Falcón L.I., Souza V., Bonilla-Rosso G., Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K., Friedman R., Frazier M., and Venter J.C. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern tropical Pacific. PLOS Biol. 5 (2007) 398-431
40. Saitou N., and Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
41. Singleton D.R., Furlong M.A., Rathbun S.L., and Whitman W.B. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67 (2001) 4374-4376
42. Suzuki M.T., Béjà O., Taylor L.T., and DeLong E.F. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ. Microbiol. 3 (2001) 323-331
43. Vieira R.P., Gonzalez A.M., Cardoso A.M., Oliveira D.N., Albano R.M., Clementino M.M., Martins O.B., and Paranhos R. Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro. Environ. Microbiol. 10 (2008) 189-199
44. Warnecke F., Amann R., and Pernthaler J. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ. Microbiol. 6 (2004) 242-253
45. Zhang R., Liu B., Lau S.C.K., Ki J.S., and Qian P.Y. Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong. FEMS Microbiol. Ecol. 61 (2007) 496-508