Successional changes in the genetic diversity of a marine bacterial assemblage during confinement

Archives of Microbiology

Volumn 173, Issue 2, 2000, Pages 138-145

  Schäfer, Hendrik ^a,c   Servais, Pierre ^b   Muyzer, Gerard ^a,c  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

16S rRNA; Alteromonas; Bacterial diversity; Cloning Grazing; Mesocosm; Polymerase chain reaction denaturing gradient gel electrophoresis

Indexed keywords

ARTICLE; GEL ELECTROPHORESIS; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; LEGIONELLA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ANIMALS; BACTERIA; COLONY COUNT, MICROBIAL; ECOSYSTEM; ELECTROPHORESIS; GENES, RRNA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTOZOA; RNA, RIBOSOMAL, 16S; SEAWATER; VARIATION (GENETICS); WATER MICROBIOLOGY;

EID: 0033950632     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002039900121     Document Type: Article

References (36)

1. Acinas SG, Anton J, Rodriguez-Valera F (1999) Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol 65:514-522
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Buchholz-Cleven BEE, Rattunde B, Straub KL (1997) Screening for the genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst Appl Microbiol 20:301-309
4. Chou Q (1992) Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucleic Acids Res 20:1717-1723
5. Del Giorgio PA, Gasol JM, Vaque D, Mura P, Agusti S, Duarte CM (1996) Bacterioplankton community structure: Protists control net production and the proportion of active bacteria in a coastal marine community. Limnol Oceanogr 41:1169-1179
6. Duarte CM, Gasol JM, Vaque D (1997) Role of experimental approaches in marine microbial ecology. Aquat Microb Ecol 13:101-111
7. Ferguson RL, Buckley EN, Palumbo AV (1984) Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol 47:49-55
8. Garcia-Pichel F, Nübel U, Muyzer G (1998) The phylogeny of unicellular, extremely halotolerant cyanobacteria. Arch Microbiol 169:469-482
9. Gauthier G, Gauthier M, Christen R (1995) Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. Int J Syst Bacteriol 45:755-761
10. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
11. González JM, Moran MA (1997) Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbiol 63:4237-4242
12. González JM, Sherr EB, Sherr BF (1990) Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56:583-589
13. Hedlund BP, Gosink JJ, Staley JT (1997) Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie Van Leeuwenhoek 72:29-38
14. Jürgens K, Güde H (1994) The potential importance of grazing-resistant bacteria in planktonic systems. Mar Ecol Prog Ser 112:169-188
15. Lebaron P, Servais P, Troussellier M, Courties C, Vives-Rego J, Muyzer G, Bernard L, Guindulain T, Schäfer H, Stackebrandt E (1999) Changes in bacterial community structure in seawater mesocosms differing in theirnutrient status. Aquat Microb. Ecol 19:255-267
16. Lee S, Fuhrman JA (1991) Species composition shift of confined bacterioplankton studied at the level of community DNA. Mar Ecol Prog Ser 79:195-201
17. Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072-5078
18. Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109-110
19. Monger BC, Landry MR (1991) Prey-size dependency of grazing by free-living marine flagellates. Mar Ecol Prog Ser 74:239-248
20. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40:148-158
21. Muyzer G, 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
22. Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165-172
23. Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1998) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual, vol. 3.4.4. Kluwer, Dordrecht, pp 1-27
24. Painting SJ, Lucas MI, Muir DG (1989) Fluctuations in heterotrophic bacterial community structure activity and production in response to development and decay of phytoplankton in a microcosm. Mar Ecol Prog Ser 53:129-142
25. Pernthaler J, Posch T, Simek K, Vrba J, Amann R, Psenner P (1997) Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl Environ Microbiol 63:596-601
26. Pukall R, Päuker O, Buntefuß D, Ulrichs G, Lebaron P, Bernard L, Guindulain T, Vives-Rego J, Stackebrandt E (1999) High sequence diversity of Alteromonas macleodii-related cloned and cellular 16S rDNAs from a Mediterranean seawater mesocosm experiment. FEMS Microbiol Ecol 28:335-344
27. Rappé MS, Kemp PF, 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
28. Rath J, Ying Wu K, Herndl GJ, DeLong EF (1998) High phylogenetic diversity in a marine-snow-associated bacterial assemblage. Aquat Microb Ecol 14:261-269
29. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491
30. Servais P, Billen G, Vives Rego J (1985) Rate of bacterial mortality in aquatic environments. Appl Environ Microbiol 49:1448-1454
31. Servais P, Billen G, Martinez J, Vives Rego J (1989) Estimating bacterial mortality by the disappearance of tritium labeled intracellular DNA. FEMS Microbiol Ecol 62:119-126
32. Servais P, Vives Rego J, Billen G (1992) Survival and mortality of bacteria in natural environments. In: Fry JD (ed) Release of genetically engineered and other micro-organisms. Cambridge University Press, Cambridge, pp 100-119
33. Sherr BF, Sherr EH, Andrew TL, Fallon RD, Newell SY (1986) Trophic interactions between heterotrophic protozoa and bacterioplankton in estuarine water analysed with selective metabolic inhibitors. Mar Ecol Prog Ser 32:169-179
34. Shiah FK, Ducklow HW (1995) Regulation of bacterial abundance and production by substrate supply and bacterivory: a mesocosm study. Microb Ecol 30:239-255
35. Suttle CA (1994) The significance of viruses to mortality in aquatic microbial communities. Microb Ecol 28:237-243
36. Teske A, Wawer C, Muyzer G, Ramsing NB (1996) Distribution of sulfate-reducing bacteria in a stratified Fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol 62:1405-1415