메뉴 건너뛰기




Volumn 67, Issue 1, 2009, Pages 30-42

Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea

Author keywords

16S rRNA; Bacterial diversity and activity Prochlorococcus; CE SSCP fingerprinting; Gammaproteobacteria; SAR11; Spatial distribution

Indexed keywords

BACTERIUM; COMPARATIVE STUDY; DNA; FLOW CYTOMETRY; MICROBIAL ACTIVITY; RELATIVE ABUNDANCE; RNA; SPATIAL DISTRIBUTION; SPECIES DIVERSITY;

EID: 57449090885     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2008.00591.x     Document Type: Article
Times cited : (31)

References (46)
  • 1
    • 0342506808 scopus 로고    scopus 로고
    • Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA
    • Acinas S, Rodriguez-Valera R Pedros-Alio 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.
    • (1997) FEMS Microbiol Ecol , vol.24 , pp. 27-40
    • Acinas, S.1    Rodriguez-Valera, R.2    Pedros-Alio, C.3
  • 2
    • 0032974993 scopus 로고    scopus 로고
    • Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA
    • Acinas SG, Antón J Rodríguez-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.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 514-522
    • Acinas, S.G.1    Antón, J.2    Rodríguez-Valera, F.3
  • 3
    • 34249903107 scopus 로고    scopus 로고
    • Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in Northwestern Mediterranean coastal waters
    • 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.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 3528-3535
    • Alonso-Saez, L.1    Gasol, J.M.2
  • 5
    • 0019513663 scopus 로고
    • Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli
    • 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.
    • (1981) J Mol Biol , vol.148 , pp. 107-127
    • Brosius, J.1    Dull, T.J.2    Sleeter, D.D.3    Noller, H.F.4
  • 6
    • 23944517269 scopus 로고    scopus 로고
    • Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: Development and application to a time series
    • 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.
    • (2005) Environ Microbiol , vol.7 , pp. 1466-1479
    • Brown, M.V.1    Schwalbach, M.S.2    Hewson, I.3    Fuhrman, J.A.4
  • 7
    • 17544390961 scopus 로고    scopus 로고
    • Identification of and spatio-temporal differences between microbial assemblages from two neighboring Sulfurous Lakes: Comparison by microscopy and denaturing gradient gel electrophoresis
    • Casamayor EO, Schaefer H, Baneras L, Pedros-Alio 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.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 499-508
    • Casamayor, E.O.1    Schaefer, H.2    Baneras, L.3    Pedros-Alio, C.4    Muyzer, G.5
  • 8
    • 0035208065 scopus 로고    scopus 로고
    • In situ assessment on the physiological state of purple and green sulfur bacteria through the analyses of pigment and 5S rRNA content
    • Casamayor EO, Mas J Pedros-Alio C (2001) In situ assessment on the physiological state of purple and green sulfur bacteria through the analyses of pigment and 5S rRNA content. Microb Ecol 42 : 427 437.
    • (2001) Microb Ecol , vol.42 , pp. 427-437
    • Casamayor, E.O.1    Mas, J.2    Pedros-Alio, C.3
  • 9
    • 0000601551 scopus 로고
    • Biogeochemical significance of bacterial in the ocean's euphotic zone
    • Cho BC Azam F (1990) Biogeochemical significance of bacterial in the ocean's euphotic zone. Mar Ecol Prog Ser 63 : 253 259.
    • (1990) Mar Ecol Prog Ser , vol.63 , pp. 253-259
    • Cho, B.C.1    Azam, F.2
  • 10
    • 0035003594 scopus 로고    scopus 로고
    • Bacterial and archaeal 16S rDNA and rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem
    • Delbès C, Godon JJ Moletta R (2001) Bacterial and archaeal 16S rDNA and rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem. FEMS Microbiol Ecol 35 : 19 26.
    • (2001) FEMS Microbiol Ecol , vol.35 , pp. 19-26
    • Delbès, C.1    Godon, J.J.2    Moletta, R.3
  • 11
    • 0036214336 scopus 로고    scopus 로고
    • Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient
    • Del Giorgio PA Bouvier T (2002) Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient. Limnol Oceanogr 47 : 471 486.
    • (2002) Limnol Oceanogr , vol.47 , pp. 471-486
    • Del Giorgio, P.A.1    Bouvier, T.2
  • 12
    • 0024507744 scopus 로고
    • Phylogenetic stains: Ribosomal RNA-based probes for the identification of single cells
    • DeLong EF, Wickham GS Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243 : 1360 1363.
    • (1989) Science , vol.243 , pp. 1360-1363
    • Delong, E.F.1    Wickham, G.S.2    Pace, N.R.3
  • 13
    • 31544483932 scopus 로고    scopus 로고
    • Community genomics among stratified microbial assemblages in the ocean's interior
    • DeLong EF, Preston CM, Mincer T et al 2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311 : 496 503.
    • (2006) Science , vol.311 , pp. 496-503
    • Delong, E.F.1    Preston, C.M.2    Mincer, T.3    Al, E.4
  • 14
    • 0031732597 scopus 로고    scopus 로고
    • Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints
    • Felske A, Akkermans AD De Vos WM (1998) Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64 : 4581 4587.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 4581-4587
    • Felske, A.1    Akkermans, A.D.2    De Vos, W.M.3
  • 15
    • 27844571900 scopus 로고    scopus 로고
    • Spatial and temporal scales of variation in the bacterioplankton community structure in the NW Mediterranean Sea
    • Ghiglione JF, Larcher M Lebaron P (2005) Spatial and temporal scales of variation in the bacterioplankton community structure in the NW Mediterranean Sea. Aquat Microb Ecol 40 : 229 240.
    • (2005) Aquat Microb Ecol , vol.40 , pp. 229-240
    • Ghiglione, J.F.1    Larcher, M.2    Lebaron, P.3
  • 16
    • 34547586997 scopus 로고    scopus 로고
    • Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea
    • Ghiglione JF, Mevel G, Pujo-Pay M, Mousseau L, Lebaron P Goutx M (2007) Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea. Microb Ecol 54 : 217 231.
    • (2007) Microb Ecol , vol.54 , pp. 217-231
    • Ghiglione, J.F.1    Mevel, G.2    Pujo-Pay, M.3    Mousseau, L.4    Lebaron, P.5    Goutx, M.6
  • 17
    • 33947194423 scopus 로고    scopus 로고
    • Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage
    • Hong H, Pruden A Reardon KF (2007) Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage. J Microbiol Methods 69 : 52 64.
    • (2007) J Microbiol Methods , vol.69 , pp. 52-64
    • Hong, H.1    Pruden, A.2    Reardon, K.F.3
  • 18
    • 33644963755 scopus 로고    scopus 로고
    • Distribution of picophytoplankton and bacterioplankton along a river plume gradient in the Mediterranean Sea
    • Joux F, Servais P, Naudin JJ, Lebaron P, Oriol L Courties C (2005) Distribution of picophytoplankton and bacterioplankton along a river plume gradient in the Mediterranean Sea. Vie et Milieu 55 : 197 208.
    • (2005) Vie et Milieu , vol.55 , pp. 197-208
    • Joux, F.1    Servais, P.2    Naudin, J.J.3    Lebaron, P.4    Oriol, L.5    Courties, C.6
  • 19
    • 0001169290 scopus 로고
    • Leucine incorporation as a measure of biomass production by heterotrophic bacteria
    • Kemp, P.F., Sherr, B.F., Sherr, E.B. Cole, J.J., eds), pp. Lewis Publishers, Boca Raton, FL.
    • Kirchman DL (1993) Leucine incorporation as a measure of biomass production by heterotrophic bacteria. Handbook of Methods in Aquatic Microbial Ecology (Kemp PF, Sherr BF, Sherr EB Cole JJ, eds), pp. 509 512. Lewis Publishers, Boca Raton, FL.
    • (1993) Handbook of Methods in Aquatic Microbial Ecology , pp. 509-512
    • Kirchman, D.L.1
  • 20
    • 0030754258 scopus 로고    scopus 로고
    • Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA
    • Kowalchuk GA, Gerards S Woldendorp JW (1997) Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl Environ Microbiol 63 : 858 865.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 858-865
    • Kowalchuk, G.A.1    Gerards, S.2    Woldendorp, J.W.3
  • 21
    • 0029786831 scopus 로고    scopus 로고
    • Non radioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation-polymorphism
    • Lee DH, Zo YG Kim SJ (1996) Non radioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation- polymorphism. Appl Environ Microbiol 62 : 3112 3120.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 3112-3120
    • Lee, D.H.1    Zo, Y.G.2    Kim, S.J.3
  • 22
    • 0026379756 scopus 로고
    • Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization
    • Lee SH Fuhrman JA (1991) Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization. Limnol Oceanogr 36 : 1277 1287.
    • (1991) Limnol Oceanogr , vol.36 , pp. 1277-1287
    • Lee, S.H.1    Fuhrman, J.A.2
  • 23
    • 0035133741 scopus 로고    scopus 로고
    • Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints
    • 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.
    • (2001) Limnol Oceanogr , vol.46 , pp. 95-107
    • Moeseneder, M.M.1    Winter, C.2    Herndl, G.J.3
  • 24
    • 12344287312 scopus 로고    scopus 로고
    • A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community
    • 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.
    • (2005) FEMS Microbiol Ecol , vol.51 , pp. 341-352
    • Moeseneder, M.M.1    Arrieta, J.M.2    Herndl, G.J.3
  • 26
    • 0031814110 scopus 로고    scopus 로고
    • Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica
    • 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.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 2585-2595
    • Murray, A.E.1    Preston, C.M.2    Massana, R.3    Taylor, L.T.4    Blakis, A.5    Wu, K.6    Delong, E.F.7
  • 27
    • 0000489265 scopus 로고
    • Spectrofluorometric determination of chlorophylls and pheophytins
    • Neveux J Panouse M (1987) Spectrofluorometric determination of chlorophylls and pheophytins. Archiv Hydrobiol 109 : 567 581.
    • (1987) Archiv Hydrobiol , vol.109 , pp. 567-581
    • Neveux, J.1    Panouse, M.2
  • 28
    • 0033009854 scopus 로고    scopus 로고
    • Prochlorococcus, a marine photosynthetic prokaryote of global significance
    • Partensky F, Hess WR Vaulot D (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63 : 106 127.
    • (1999) Microbiol Mol Biol Rev , vol.63 , pp. 106-127
    • Partensky, F.1    Hess, W.R.2    Vaulot, D.3
  • 29
    • 24944484336 scopus 로고    scopus 로고
    • Fate of heterotrophic microbes in pelagic habitats: Focus on populations
    • Pernthaler J Amann R (2005) Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol Mol Biol Rev 69 : 440 461.
    • (2005) Microbiol Mol Biol Rev , vol.69 , pp. 440-461
    • Pernthaler, J.1    Amann, R.2
  • 30
    • 0032875296 scopus 로고    scopus 로고
    • Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis
    • Piceno YM, Noble PA Lovell CR (1999) Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. Microb Ecol 38 : 157 167.
    • (1999) Microb Ecol , vol.38 , pp. 157-167
    • Piceno, Y.M.1    Noble, P.A.2    Lovell, C.R.3
  • 31
    • 0027264175 scopus 로고
    • Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms
    • Poulsen LK, Ballard G Stahl DA (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59 : 1354 1360.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 1354-1360
    • Poulsen, L.K.1    Ballard, G.2    Stahl, D.A.3
  • 32
    • 0032769414 scopus 로고    scopus 로고
    • Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rDNA
    • 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 rDNA. Deep-Sea Res II 46 : 1791 1811.
    • (1999) Deep-Sea Res II , vol.46 , pp. 1791-1811
    • Riemann, L.1    Steward, G.F.2    Fandino, L.B.3    Campbell, L.4    Landry, M.R.5    Azam, F.6
  • 33
    • 0036098886 scopus 로고    scopus 로고
    • Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus
    • Scanlan DJ West NJ (2002) Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus. FEMS Microb Ecol 40 : l 12.
    • (2002) FEMS Microb Ecol , vol.40
    • Scanlan, D.J.1    West, N.J.2
  • 34
    • 0033914764 scopus 로고    scopus 로고
    • Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting
    • Schauer M, Massana R Pedrós-Alió C (2000) Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting. FEMS Microbiol Ecol 33 : 51 59.
    • (2000) FEMS Microbiol Ecol , vol.33 , pp. 51-59
    • Schauer, M.1    Massana, R.2    Pedrós-Alió, C.3
  • 35
    • 15444362001 scopus 로고    scopus 로고
    • Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
    • Schloss PD Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71 : 1501 1506.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 37
    • 0033538855 scopus 로고    scopus 로고
    • Estimating the abundance and single-cell characteristics of respiring bacteria via the redox dye CTC
    • Sherr BF, Del Giorgio PA Sherr EB (1999) Estimating the abundance and single-cell characteristics of respiring bacteria via the redox dye CTC. Aquat Microb Ecol 18 : 117 131.
    • (1999) Aquat Microb Ecol , vol.18 , pp. 117-131
    • Sherr, B.F.1    Del Giorgio, P.A.2    Sherr, E.B.3
  • 38
    • 0001123060 scopus 로고
    • A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine
    • Smith DC Azam F (1992) A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Microb Food Webs 6 : 107 114.
    • (1992) Mar Microb Food Webs , vol.6 , pp. 107-114
    • Smith, D.C.1    Azam, F.2
  • 39
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 : 4876 4882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 41
    • 0030698675 scopus 로고    scopus 로고
    • Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs
    • Vallaeys T, Topp E, Muyzer G, Macheret V, Laguerre G, Rigaud A Soulas G (1997) Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol Ecol 24 : 279 285.
    • (1997) FEMS Microbiol Ecol , vol.24 , pp. 279-285
    • Vallaeys, T.1    Topp, E.2    Muyzer, G.3    MacHeret, V.4    Laguerre, G.5    Rigaud, A.6    Soulas, G.7
  • 42
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • Venter JC, Remington K, Heidelberg JF et al 2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 : 66 74.
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1    Remington, K.2    Heidelberg, J.F.3    Al, E.4
  • 43
    • 38549100034 scopus 로고    scopus 로고
    • Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean
    • 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.
    • (2008) Environ Microbiol , vol.10 , pp. 738-756
    • West, N.J.1    Obernosterer, I.2    Zemb, O.3    Lebaron, P.4
  • 44
    • 4143072557 scopus 로고    scopus 로고
    • Diel cycles in viral infection of bacterioplankton in the North Sea
    • Winter C, Herndl G Weinbauer MG (2004) Diel cycles in viral infection of bacterioplankton in the North Sea. Aquat Microb Ecol 35 : 207 216.
    • (2004) Aquat Microb Ecol , vol.35 , pp. 207-216
    • Winter, C.1    Herndl, G.2    Weinbauer, M.G.3
  • 45
    • 34548270865 scopus 로고    scopus 로고
    • Safum: Statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators
    • Zemb O, Haegeman B, Delgenes JP, Lebaron P Godon JJ (2007) Safum: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators. Mol Ecol Notes 7 : 767 770.
    • (2007) Mol Ecol Notes , vol.7 , pp. 767-770
    • Zemb, O.1    Haegeman, B.2    Delgenes, J.P.3    Lebaron, P.4    Godon, J.J.5
  • 46
    • 8144219976 scopus 로고    scopus 로고
    • Depth related amino acid uptake by Prochlorococcus cyanobacteria in the Southern Atlantic tropical gyre
    • Zubkov MV, Tarran GA, Bernhard M Fuchs BM (2004) Depth related amino acid uptake by Prochlorococcus cyanobacteria in the Southern Atlantic tropical gyre. FEMS Microbiol Ecol 50 : 153 161.
    • (2004) FEMS Microbiol Ecol , vol.50 , pp. 153-161
    • Zubkov, M.V.1    Tarran, G.A.2    Bernhard, M.3    Fuchs, B.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.