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Volumn 87, Issue 2, 2014, Pages 378-389

Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches

Author keywords

Bacterial diversity; Bacterioplankton; German Bight; Metatranscriptome; Pyrotag sequencing

Indexed keywords

BACTERIAL RNA; MESSENGER RNA; METATRANSCRIPTOME; RNA 16S; SEA WATER;

EID: 84895074799     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12230     Document Type: Article
Times cited : (95)

References (53)
  • 1
    • 33846467724 scopus 로고    scopus 로고
    • Abundance and activity of major groups of prokaryotic plankton in the coastal North Sea during spring and summer
    • Alderkamp A-C, Sintes E & Herndl GJ (2006) Abundance and activity of major groups of prokaryotic plankton in the coastal North Sea during spring and summer. Aquat Microb Ecol 45: 237-246.
    • (2006) Aquat Microb Ecol , vol.45 , pp. 237-246
    • Alderkamp, A.-C.1    Sintes, E.2    Herndl, G.J.3
  • 2
    • 33749389950 scopus 로고    scopus 로고
    • Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters
    • Alonso C & Pernthaler J (2006) Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol 8: 2022-2030.
    • (2006) Environ Microbiol , vol.8 , pp. 2022-2030
    • Alonso, C.1    Pernthaler, J.2
  • 3
    • 43949120140 scopus 로고    scopus 로고
    • Diversity, ecology, and genomics of the Roseobacter clade: a short overview
    • Brinkhoff T, Giebel HA & Simon M (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 189: 531-539.
    • (2008) Arch Microbiol , vol.189 , pp. 531-539
    • Brinkhoff, T.1    Giebel, H.A.2    Simon, M.3
  • 5
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
    • (2010) Nat Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3
  • 6
    • 0347130086 scopus 로고    scopus 로고
    • Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria
    • Cho J-C & Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria. Appl Environ Microbiol 70: 432-440.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 432-440
    • Cho, J.-C.1    Giovannoni, S.J.2
  • 8
    • 68249112686 scopus 로고    scopus 로고
    • Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean
    • Giebel HA, Brinkhoff T, Zwisler W, Selje N & Simon M (2009) Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean. Environ Microbiol 11: 2164-2178.
    • (2009) Environ Microbiol , vol.11 , pp. 2164-2178
    • Giebel, H.A.1    Brinkhoff, T.2    Zwisler, W.3    Selje, N.4    Simon, M.5
  • 9
    • 78650623430 scopus 로고    scopus 로고
    • Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate
    • Giebel HA, Kalhoefer D, Lemke A, Thole S, Gahl-Janssen R, Simon M & Brinkhoff T (2011) Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate. ISME J 5: 8-19.
    • (2011) ISME J , vol.5 , pp. 8-19
    • Giebel, H.A.1    Kalhoefer, D.2    Lemke, A.3    Thole, S.4    Gahl-Janssen, R.5    Simon, M.6    Brinkhoff, T.7
  • 10
    • 84887074945 scopus 로고    scopus 로고
    • Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea
    • DOI: 10.1099/ijs.0.053249-0 [Epub ahead of print].
    • Giebel HA, Kalhoefer D, Gahl-Janssen R et al. (2013) Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea. Int J Syst Evol Microbiol, DOI: 10.1099/ijs.0.053249-0 [Epub ahead of print].
    • (2013) Int J Syst Evol Microbiol
    • Giebel, H.A.1    Kalhoefer, D.2    Gahl-Janssen, R.3
  • 11
    • 79951810312 scopus 로고    scopus 로고
    • Quantitative analysis of a deeply sequenced marine microbial metatranscriptome
    • Gifford SM, Sharma S, Rinta-Kanto JM & Moran MA (2011) Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 5: 461-472.
    • (2011) ISME J , vol.5 , pp. 461-472
    • Gifford, S.M.1    Sharma, S.2    Rinta-Kanto, J.M.3    Moran, M.A.4
  • 12
    • 84872981638 scopus 로고    scopus 로고
    • Expression patterns reveal niche diversification in a marine microbial assemblage
    • Gifford SM, Sharma S, Booth M & Moran MA (2013) Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J 7: 281-298.
    • (2013) ISME J , vol.7 , pp. 281-298
    • Gifford, S.M.1    Sharma, S.2    Booth, M.3    Moran, M.A.4
  • 13
    • 25144486755 scopus 로고    scopus 로고
    • Molecular diversity and ecology of microbial plankton
    • Giovannoni SJ & Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437: 343-348.
    • (2005) Nature , vol.437 , pp. 343-348
    • Giovannoni, S.J.1    Stingl, U.2
  • 15
    • 77950042744 scopus 로고    scopus 로고
    • Distribution patterns and diversity of planktonic Flavobacterial clades in contrasting water masses of the North Atlantic Ocean
    • Gomez-Pereira PR, Fuchs BM, Alonso C, Oliver M, van Beusekom J & Amann R (2010) Distribution patterns and diversity of planktonic Flavobacterial clades in contrasting water masses of the North Atlantic Ocean. ISME J 4: 472-487.
    • (2010) ISME J , vol.4 , pp. 472-487
    • Gomez-Pereira, P.R.1    Fuchs, B.M.2    Alonso, C.3    Oliver, M.4    van Beusekom, J.5    Amann, R.6
  • 17
    • 84874306600 scopus 로고    scopus 로고
    • Physiological diversity of Roseobacter clade bacteria co-occurring during a phytoplankton bloom in the North Sea
    • Hahnke S, Brock NL, Zell C, Simon M, Dickschat JS & Brinkhoff T (2013) Physiological diversity of Roseobacter clade bacteria co-occurring during a phytoplankton bloom in the North Sea. Syst Appl Microbiol 36: 39-48.
    • (2013) Syst Appl Microbiol , vol.36 , pp. 39-48
    • Hahnke, S.1    Brock, N.L.2    Zell, C.3    Simon, M.4    Dickschat, J.S.5    Brinkhoff, T.6
  • 18
    • 84861204353 scopus 로고    scopus 로고
    • Genome sequence of strain HIMB55, a novel marine gammaproteobacterium of the OM60/NOR5 clade
    • Huggett MJ & Rappé MS (2012) Genome sequence of strain HIMB55, a novel marine gammaproteobacterium of the OM60/NOR5 clade. J Bacteriol 194: 2393-2394.
    • (2012) J Bacteriol , vol.194 , pp. 2393-2394
    • Huggett, M.J.1    Rappé, M.S.2
  • 19
    • 84859605518 scopus 로고    scopus 로고
    • Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean
    • Jamieson RE, Rogers AD, Billett DS, Smale DA & Pearce DA (2012) Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean. FEMS Microbiol Ecol 80: 452-468.
    • (2012) FEMS Microbiol Ecol , vol.80 , pp. 452-468
    • Jamieson, R.E.1    Rogers, A.D.2    Billett, D.S.3    Smale, D.A.4    Pearce, D.A.5
  • 20
    • 77953594953 scopus 로고    scopus 로고
    • The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
    • Kirchman DL, Cottrell MT & Lovejoy C (2010) The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ Microbiol 12: 1132-1143.
    • (2010) Environ Microbiol , vol.12 , pp. 1132-1143
    • Kirchman, D.L.1    Cottrell, M.T.2    Lovejoy, C.3
  • 21
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M & Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1.
    • (2013) Nucleic Acids Res , vol.41
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6    Glöckner, F.O.7
  • 22
    • 0000046862 scopus 로고
    • Determination of nutrients
    • (Grasshoff K, Ehrhardt M & Kremling K, eds) Verlag Chemie, Weinheim, Germany.
    • Koroleff F & Grasshoff K (1983) Determination of nutrients. Methods of Seawater Analysis, Vol. 2 (Grasshoff K, Ehrhardt M & Kremling K, eds), pp. 125-188. Verlag Chemie, Weinheim, Germany.
    • (1983) Methods of Seawater Analysis , vol.2 , pp. 125-188
    • Koroleff, F.1    Grasshoff, K.2
  • 23
    • 84871274042 scopus 로고    scopus 로고
    • The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs
    • Lesniewski RA, Jain S, Anantharaman K, Schloss PD & Dick GJ (2012) The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J 6: 2257-2268.
    • (2012) ISME J , vol.6 , pp. 2257-2268
    • Lesniewski, R.A.1    Jain, S.2    Anantharaman, K.3    Schloss, P.D.4    Dick, G.J.5
  • 24
    • 33645083462 scopus 로고    scopus 로고
    • Physical and biogeochemical controls of microaggregate dynamics in a tidally affected coastal ecosystem
    • Lunau M, Lemke A, Dellwig O & Simon M (2006) Physical and biogeochemical controls of microaggregate dynamics in a tidally affected coastal ecosystem. Limnol Oceanogr 51: 847-859.
    • (2006) Limnol Oceanogr , vol.51 , pp. 847-859
    • Lunau, M.1    Lemke, A.2    Dellwig, O.3    Simon, M.4
  • 25
    • 83655169524 scopus 로고    scopus 로고
    • Genome content of uncultivated marine Roseobacters in the surface ocean
    • Luo H, Löytynoja A & Moran MA (2012) Genome content of uncultivated marine Roseobacters in the surface ocean. Environ Microbiol 14: 41-51.
    • (2012) Environ Microbiol , vol.14 , pp. 41-51
    • Luo, H.1    Löytynoja, A.2    Moran, M.A.3
  • 26
    • 78049286743 scopus 로고    scopus 로고
    • Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
    • McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW & DeLong EF (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. P Natl Acad Sci USA 107: 16420-16427.
    • (2010) P Natl Acad Sci USA , vol.107 , pp. 16420-16427
    • McCarren, J.1    Becker, J.W.2    Repeta, D.J.3    Shi, Y.4    Young, C.R.5    Malmstrom, R.R.6    Chisholm, S.W.7    DeLong, E.F.8
  • 28
    • 84895075132 scopus 로고    scopus 로고
    • DirichletReg. Available at:
    • Meier MJ (2012) DirichletReg. Available at: http://cran.r-project.org/web/packages/DirichletReg.
    • (2012)
    • Meier, M.J.1
  • 29
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3
  • 31
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • 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 coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    de Waal, E.C.2    Uitterlinden, A.G.3
  • 32
    • 79951926011 scopus 로고    scopus 로고
    • Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils
    • Nacke H, Thurmer A, Wollherr A, Will C, Hodac L, Herold N, Schoning I, Schrumpf M & Daniel R (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE 6: e17000.
    • (2011) PLoS ONE , vol.6
    • Nacke, H.1    Thurmer, A.2    Wollherr, A.3    Will, C.4    Hodac, L.5    Herold, N.6    Schoning, I.7    Schrumpf, M.8    Daniel, R.9
  • 33
    • 77952674525 scopus 로고    scopus 로고
    • Genome characteristics of a generalist marine bacterial lineage
    • Newton RJ, Griffin LE, Bowles KM et al. (2010) Genome characteristics of a generalist marine bacterial lineage. ISME J 4: 784-798.
    • (2010) ISME J , vol.4 , pp. 784-798
    • Newton, R.J.1    Griffin, L.E.2    Bowles, K.M.3
  • 34
    • 33646559677 scopus 로고    scopus 로고
    • Chlorophyllbestimmung
    • von Tuempling W & Friedrich G, eds) G Fischer, Stuttgart, Germany.
    • Nusch EA (1999) Chlorophyllbestimmung. Biologische Gewässeruntersuchung (von Tuempling W & Friedrich G, eds), pp. 368-375. G Fischer, Stuttgart, Germany.
    • (1999) Biologische Gewässeruntersuchung , pp. 368-375
    • Nusch, E.A.1
  • 36
    • 70149113077 scopus 로고    scopus 로고
    • R Development Core Team R Foundation for Statistical Computing, Vienna, Austria.
    • R Development Core Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2009) R: A Language and Environment for Statistical Computing
  • 38
    • 79956293297 scopus 로고    scopus 로고
    • Regional patterns of bacterial community composition and biogeochemical properties in the southern North Sea
    • Rink B, Seeberger S, Martens T, Duerselen C-D, Simon M & Brinkhoff T (2011) Regional patterns of bacterial community composition and biogeochemical properties in the southern North Sea. Aquat Microb Ecol 63: 207-222.
    • (2011) Aquat Microb Ecol , vol.63 , pp. 207-222
    • Rink, B.1    Seeberger, S.2    Martens, T.3    Duerselen, C.-D.4    Simon, M.5    Brinkhoff, T.6
  • 39
    • 84895073570 scopus 로고    scopus 로고
    • Ocean data view. Available at:
    • Schlitzer R (2013) Ocean data view. Available at: http://odv.awi.de.
    • (2013)
    • Schlitzer, R.1
  • 40
    • 0025860931 scopus 로고
    • Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing
    • Schmidt TM, DeLong EF & Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173: 4371-4378.
    • (1991) J Bacteriol , vol.173 , pp. 4371-4378
    • Schmidt, T.M.1    DeLong, E.F.2    Pace, N.R.3
  • 41
    • 0842285837 scopus 로고    scopus 로고
    • A newly discovered Roseobacter cluster in temperate and polar oceans
    • Selje N, Simon M & Brinkhoff T (2004) A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427: 445-448.
    • (2004) Nature , vol.427 , pp. 445-448
    • Selje, N.1    Simon, M.2    Brinkhoff, T.3
  • 42
    • 4444344357 scopus 로고    scopus 로고
    • Oligotrophic bacterioplankton with a novel single-cell life strategy
    • Simu K & Hagström Å (2004) Oligotrophic bacterioplankton with a novel single-cell life strategy. Appl Environ Microbiol 70: 2445-2451.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 2445-2451
    • Simu, K.1    Hagström, A.2
  • 43
    • 84871997292 scopus 로고    scopus 로고
    • Temporal dynamics in the free-living bacterial community composition in the coastal North Sea
    • Sintes E, Witte H, Stodderegger K, Steiner P & Herndl GJ (2013) Temporal dynamics in the free-living bacterial community composition in the coastal North Sea. FEMS Microbiol Ecol 83: 413-424.
    • (2013) FEMS Microbiol Ecol , vol.83 , pp. 413-424
    • Sintes, E.1    Witte, H.2    Stodderegger, K.3    Steiner, P.4    Herndl, G.J.5
  • 44
    • 84866017371 scopus 로고    scopus 로고
    • Differential effects of hydrographic and biogeochemical properties on the SAR11 clade and Roseobacter RCA cluster in the North Sea
    • Sperling M, Giebel HA, Rink B, Grayek S, Staneva J, Stanev E & Simon M (2012) Differential effects of hydrographic and biogeochemical properties on the SAR11 clade and Roseobacter RCA cluster in the North Sea. Aquat Microb Ecol 67: 25-34.
    • (2012) Aquat Microb Ecol , vol.67 , pp. 25-34
    • Sperling, M.1    Giebel, H.A.2    Rink, B.3    Grayek, S.4    Staneva, J.5    Stanev, E.6    Simon, M.7
  • 45
    • 34247488726 scopus 로고    scopus 로고
    • The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin
    • Stingl U, Desiderio RA, Cho JC, Vergin KL & Giovannoni SJ (2007) The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol 73: 2290-2296.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 2290-2296
    • Stingl, U.1    Desiderio, R.A.2    Cho, J.C.3    Vergin, K.L.4    Giovannoni, S.J.5
  • 46
    • 84860488672 scopus 로고    scopus 로고
    • Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom
    • Teeling H, Fuchs BM, Becher D et al. (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608-611.
    • (2012) Science , vol.336 , pp. 608-611
    • Teeling, H.1    Fuchs, B.M.2    Becher, D.3
  • 47
    • 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
  • 48
    • 84863403687 scopus 로고    scopus 로고
    • Community analysis of high- and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing
    • Vila-Costa M, Gasol JM, Sharma S & Moran MA (2012) Community analysis of high- and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing. Environ Microbiol 14: 1390-1402.
    • (2012) Environ Microbiol , vol.14 , pp. 1390-1402
    • Vila-Costa, M.1    Gasol, J.M.2    Sharma, S.3    Moran, M.A.4
  • 49
    • 0036199576 scopus 로고    scopus 로고
    • Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses
    • Weinbauer MG, Fritz I, Wenderoth DF & Höfle MG (2002) Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses. Appl Environ Microbiol 68: 1082-1087.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 1082-1087
    • Weinbauer, M.G.1    Fritz, I.2    Wenderoth, D.F.3    Höfle, M.G.4
  • 50
    • 84871419499 scopus 로고    scopus 로고
    • RNA-based assessment of diversity and composition of active archaeal communities in the German Bight
    • Wemheuer B, Wemheuer F & Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012: 695826.
    • (2012) Archaea , vol.2012 , pp. 695826
    • Wemheuer, B.1    Wemheuer, F.2    Daniel, R.3
  • 51
    • 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


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