Annual patterns of presence and activity of marine bacteria monitored by 16S rDNA-16S rRNA fingerprints in the coastal NW Mediterranean Sea

Aquatic Microbial Ecology

Volumn 54, Issue 2, 2009, Pages 199-210

  Lami, Raphaël ^a,b,c   Ghiglione, Jean François ^a,b   Desdevises, Yves ^a,b   West, Nyree J ^a,b   Lebaron, Philippe ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b CNRS   (France)

^c UNIVERSITY OF DELAWARE   (United States)

Author keywords

16S rDNA 16S rRNA; Bacteria; Bacterial activity; Canonical correspondence analysis; CE SSCP; Mediterranean Sea; Time series

Indexed keywords

BACTERIA (MICROORGANISMS); ROSEOBACTER; SYNECHOCOCCUS;

EID: 61949349707     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01264     Document Type: Article

References (48)

1. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554
2. Agawin NSR, Duarte CM, Agustí S (1998) Growth and abundance of Synechococcus sp. in a Mediterranean Bay: seasonality and relationship with temperature. Mar Ecol Prog Ser 170:45-53
3. Alonso-Saez L, Gasol JM (2007) Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in Northwestern Mediterranean coastal waters. Appl Environ Microbiol 73:3528-3535
4. Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10:257-263
5. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541-555
6. Borcard D, Legendre P, Drapeau P (1992) Partialling out the spatial component of ecological variation. Ecology 73:1045-1055
7. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107-127
8. Brown MV, Fuhrman JA (2005) Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat Microb Ecol 41:15-23
9. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7:1466-1479
10. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791
11. Cole JR, Chai B, Farris RJ, Wang Q and others (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294-D296
12. Cottrell MT, Kirchman DL (2004) Single-cell analysis of bacterial growth, cell size, and community structure in the Delaware estuary. Aquat Microb Ecol 34:139-149
13. Davis BD, Luger SM, Tai PC (1986) Role of ribosome degradation in the death of starved Escherichia coli cells. J Bacteriol 166:439-445
14. Delbès C, Godon JJ, Moletta R (1998) 16S rDNA sequence diversity of a culture-accessible part of an anaerobic digestor bacterial community. Anaerobe 4:267-275
15. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363
16. Fandino LB, Riemann L, Steward GF, Azam F (2005) Population dynamics of Cytophaga-Flavobacteria during marine phytoplankton blooms analyzed by real-time quantitative PCR. Aquat Microb Ecol 40:251-257
17. Fegatella F, Lim J, Kjelleberg S, Cavicchioli R (1998) Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol 64:4433-4438
18. Ferrera I, Massana R, Casamayor EO, Balagué V, Sánchez O, Pedrós-Alió C, Mas J (2004) High-diversity biofilm for the oxidation of sulfide-containing effluents. Appl Microbiol Biotechnol 64:726-734
19. Fuchs BM, Spring S, Teeling H, Quast C and others (2007) Characterization of a marine Gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc Natl Acad Sci USA 104:2891-2896
20. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naheem S (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci USA 103:13104-13109
21. Gentile G, Giuliano L, D'Auria G, Smedile F, Azzaro M, De Domenico M, Yakimov MM (2006) Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environ Microbiol 8:2150-2161
22. Ghiglione JF, Larcher M, Lebaron P (2005) Spatial and temporal scales of variation in bacterioplankton community structure in the NW Mediterranean Sea. Aquat Microb Ecol 40:229-240
23. Giovannoni SJ, Rappé M (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans, Wiley Liss, New York, p 47-48
24. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
25. Joux F, Agogué H, Obernosterer I, Dupuy C, Reinthaler T, Herndl GJ, Lebaron P (2006) Microbial community structure in the sea surface microlayer at two contrasting coastal sites in the northwestern Mediterranean Sea. Aquat Microb Ecol 42:91-104
26. Kemp PF, Lee S, LaRoche J (1993) Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl Environ Microbiol 59:2594-2601
27. Kerkhof L, Ward BB (1993) Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl Environ Microbiol 59:1303-1309
28. Klepac-Ceraj V, Ceraj I, Polz MF (2006). Clusterer: extendable java application for sequence grouping and cluster analyses. Online J Bioinform 7:15-21
29. Lebaron P, Parthuisot N, Catala P (1998) Comparison of blue nucleic acid dyes for flow cytometric enumeration of bacteria in aquatic systems. Appl Environ Microbiol 64:1725-1730
30. Lee S, Kemp PF (1994) Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limnol Oceanogr 39:869-879
31. Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62:3112-3120
32. Legendre L, Legendre P (1983) Numerical ecology. Elsevier Scientific Publishing, Amsterdam
33. Lemée R, Rochelle-Newall E, Van Wambeke F, Pizay MD, Rinaldi P, Gattuso JP (2002) Seasonal variation of bacterial production, respiration and growth efficiency in the open NW Mediterranean Sea. Aquat Microb Ecol 29:227-237
34. Mary I, Cummings DG, Biegala IC, Burkill PH, Archer SD, Zubkov MV (2006) Seasonal dynamics of bacterioplankton community structure at a coastal station in the western English channel. Aquat Microb Ecol 42:119-126
35. Moeseneder MM, Winter C, Herndl GJ (2001) Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnol Oceanogr 46:95-107
36. Moeseneder MM, Arrieta JM, Herndl GJ (2005) A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community. FEMS Microbiol Ecol 51:341-352
37. Moyer CL, Mortita RY (1989) Effect of growth rate and starvation-survival on cellular DNA, RNA, and protein of a psychrophilic marine bacterium. Appl Environ Microbiol 55:2710-2716
38. 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 coastal waters near Anvers Island, Antartica. Appl Environ Microbiol 64:2585-2595
39. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl Environ Microbiol 59:695-700
40. Pinhassi J, Simó R, González JM, Vila M and others (2005) Dimethylsulfoniopropionate turnover is linked to the composition and dynamics of the bacterioplankton assemblage during a microcosm phytoplankton bloom. Appl Environ Microbiol 71:7650-7660
41. Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142-160
42. Reinthaler T, Herndl GJ (2005) Seasonal dynamics of bacterial growth efficiencies in relation to phytoplankton in the southern North Sea. Aquat Microb Ecol 39:7-16
43. Schauer M, Balagué V, Pedrós-Alió C, Massana R (2003) Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system. Aquat Microb Ecol 31:163-174
44. ter Braak CJF (1987) CANOCO: a FORTRAN program for canonical community ordination by [partial] [detrended] [canonical] correspondence analysis, principal components analysis and redundancy analysis. Agricultural Mathematics Group, Wageningen
45. Troussellier M, Schäfer H, Batailler N, Bernard L and others (2002) Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat Microb Ecol 28:13-24
46. West NJ, Obernosterer I, Zemb O, Lebaron P (2008) Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean. Environ Microbiol 10:738-756
47. Zubkov MV, Fuchs BM, Archer SD, Kiene RP, Amann R, Burkill PH (2001) Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol 3:304-311
48. Zumstein E, Moletta R, Godon JJ (2000) Examination of two years of community dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single-strand conformation polymorphism analysis. Environ Microbiol 2:69-78