Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system

Aquatic Microbial Ecology

Volumn 31, Issue 2, 2003, Pages 163-174

  Schauer, Michael ^a,b   Balagué, Vanessa ^a   Pedrós Alió, Carlos ^a   Massana, Ramon ^a  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

16S rDNA; DGGE; Fingerprinting; Marine bacteria; Seasonal succession

Indexed keywords

ALPHAPROTEOBACTERIA; BACTEROIDES; CYANOBACTERIA; CYTOPHAGA; FLAVOBACTERIA; PRASINOPHYCEAE; PROTEOBACTERIA; ROSEOBACTER; UNCULTURED MARINE BACTERIUM;

EID: 0037435042     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame031163     Document Type: Article

References (48)

1. Acinas SG, Rodríguez-Valera F, Pedrós-Alió C (1997) Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol Ecol 24:27-40
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Bano N, Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68:505-518
4. Béjà O, Koonin EV, Aravind L, Taylor LT and 6 others (2002) Comparative genomic analysis of archaeal gentoypic variants in a single population and in two different oceanic provinces. Appl Environ Microb 68:335-345
5. Casamayor EO, Schäfer H, Bañeras L, Pedrós-Alió C, Muyzer G (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microbiol 66:499-508
6. Casamayor EO, Pedrós-Alió C, Muyzer G, Amann R (2002) Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations, Appl Environ Microbiol 68:1706-1714
7. Cottrell MT, Kirchman DL (2000a) Natural assemblages of marine Proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 66:1692-1697
8. Cottrell MT, Kirchman DL (2000b) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66:5116-5122
9. Díez B, Pedrós-Alió C, Marsh TL, Massana R (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67:2942-2951
10. Duarte CM, Agustí S, Kennedy H, Vaqué D (1999) The Mediterranean climate as a template for Mediterranean marine ecosystems: the example of the northeast Spanish littoral. Prog Oceanogr 44:245-270
11. Fandino LB, Riemann L, Steward GF, Long RA, Azam F (2001) Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquat Microb Ecol 23:119-130
12. Field KG, Gordon D, Wright T, Rappé M, Urback E, Vergin K, Giovannoni SJ (1997) Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 63:63-70
13. Gasol JM, del Giorgio PA (2000) Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities. Sci Mar 64:197-224
14. Giovannoni SJ, Rappé MS (2000) Evolution, diversity, and molecular ecology of marine prokaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, p 47-84
15. Gray ND, Head IM (2001) Linking genetic identity and function in communities of uncultured bacteria. Environ Microbiol 3:481-492
16. Jaspers E, Nauhaus K, Cypionka H, Overmann J (2001) Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol Ecol 36:153-164
17. Kelly KM, Chistoserdov AY (2001) Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol Ecol 35:85-95
18. Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91-100
19. Lindström ES (1998) Bacterioplankton community composition in a boreal forest lake. FEMS Microbiol Ecol 27: 163-174
20. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr and 6 others (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173-174
21. Masó M, Tintoré J (1991) Variability of the shelf water off the northeast Spanish coast. J Mar Syst 1:441-450
22. Massana R, DeLong EF, Pedrós-Alió C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66:1777-1787
23. Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464-467
24. Murray AE, Hollibaugh JT, Orrego C (1996) Phylogenetic composition of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 62: 2676-2680
25. Murray AE, Preston CM, Massana R, Taylor LT, Blakis A, Wu K, DeLong EF (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64:2585-2595
26. Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1997) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer Academic, Dordrecht, p 1-27
27. Nübel U, Garcia-Pichel F, Kühl M, Muyzer G (1999) Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65:422-430
28. Olsen RJ, Zettler ER, DuRand MD (1993) Phytoplankton analysis using flow cytometry. In: Kemp PF, Sherr BF, Sherr EB, Cole JJ (eds) Handbook of methods in aquatic microbial ecology. Lewis Publishers, Boca Raton, FL, p 175-186
29. Paul JH, Myers B (1982) Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258. Appl Environ Microbiol 43:1393-1399
30. Pernthaler J, Glöckner FO, Unterholzner S, Alfreider A, Psenner R, Amann R (1998) Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Appl Environ Microbiol 64:4299-4306
31. Pinhassi J, Hagström Å (2000) Seasonal succession in marine bacterioplankton. Aquat Microb Ecol 21:245-256
32. Rappé MS, Kemp PK, Giovannoni SJ (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
33. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633
34. Riemann L, Middelboe M (2002) Stability of bacterial and viral community compositions in Danish coastal waters as depicted by DNA fingerprinting techniques. Aquat Microb Ecol 27:219-232
35. Riemann L, Steward GF, Fandino LB, Campbell L, Landry MR, Azam F (1999) Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep-Sea Res 46:1791-1811
36. Schäfer H, Bernard L, Courties C, Lebaron P and 7 others (2001) Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecol 34:243-253
37. Schauer M, Massana R, Pedrós-Alió C (2000) Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular finger-printing. FEMS Microbiol Ecol 33:51-59
38. Šimek J, Kojecká P, Nedoma J, Hartman P, Vrba J, Dolan JR (1999) Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnol Oceanogr 44:1634-1644
39. Stackebrandt E, Rainey FA (1995) Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer Academic, Dordrecht, p 1-17
40. Suzuki MT (1999) Effect of protistan bacterivory on coastal bacterioplankton diversity. Aquat Microb Ecol 20:261-272
41. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
42. Suzuki MT, Rappé M, Haimberger ZW, Winfield H, Adair N, Ströbel J, Giovannoni SJ (1997) Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl Environ Microbiol 63; 983-989
43. Thingstad TF, Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 13:19-27
44. van Hannen EJ, Zwart G, van Agterveld MP, Gons HJ, Ebert J, Laanbroeck HJ (1999) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ Microbiol 65:795-801
45. Vaqué D, Blough HA, Duarte CM (1997) Dynamics of ciliate abundance, biornass and community composition in an oligotrophic coastal environment (NW Mediterranean). Aquat Microb Ecol 12:71-83
46. von Witzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples; pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229
47. Yager PL, Connelly TL, Mortazavi B, Wommack KE, Bano N, Bauer JE, Opsahl S, Hollibaugh JT (2001) Dynamic bacterial and viral response to an algal bloom at subzero temperatures. Limnol Oceanogr 46;790-801
48. Yentsch CS, Menzel DW (1963) A method for the determination of phytoplankton chlorophyll and phaeophytin by fluorescence. Deep-Sea Res 10:221-231