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Volumn 9, Issue 4, 2014, Pages

Toward understanding the dynamics of microbial communities in an estuarine system

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; RIVER WATER;

EID: 84899620805     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094449.g001     Document Type: Article
Times cited : (34)

References (43)
  • 1
    • 79959612555 scopus 로고    scopus 로고
    • Gene networks and metacommunities: Dispersal differences can override adaptive advantage
    • Malcom JW (2011) Gene networks and metacommunities: dispersal differences can override adaptive advantage. PloS One 6: e21541.
    • (2011) PloS One , vol.6
    • Malcom, J.W.1
  • 2
    • 38049100699 scopus 로고    scopus 로고
    • The power of species sorting: Local factors drive bacterial community composition over a wide range of spatial scales
    • Van der Gucht K, Cottenie K, Muylaert K, Vloemans N, Cousin S, et al. (2007) The power of species sorting: local factors drive bacterial community composition over a wide range of spatial scales. Proc Natl Acad Sci USA 104: 20404-20409.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 20404-20409
    • Van Der Gucht, K.1    Cottenie, K.2    Muylaert, K.3    Vloemans, N.4    Cousin, S.5
  • 3
    • 84861992014 scopus 로고    scopus 로고
    • The application of ecological theory toward an understanding of the human microbiome
    • Elizabeth K, Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, et al. (2012) The application of ecological theory toward an understanding of the human microbiome. Science 336: 1255-1262.
    • (2012) Science , vol.336 , pp. 1255-1262
    • Elizabeth, K.1    Costello, E.K.2    Stagaman, K.3    Dethlefsen, L.4    Bohannan, B.J.5
  • 4
    • 0026273197 scopus 로고
    • Metapopulation dynamics: Brief history and conceptual domain
    • Hanski I, Gilpin M (1991) Metapopulation dynamics: brief history and conceptual domain. Biol J Linn Soc Lond 42: 3-16.
    • (1991) Biol J Linn Soc Lond , vol.42 , pp. 3-16
    • Hanski, I.1    Gilpin, M.2
  • 6
    • 27444440741 scopus 로고    scopus 로고
    • Integrating environmental and spatial processes in ecological community dynamics
    • DOI 10.1111/j.1461-0248.2005.00820.x
    • Cottenie K (2005) Integrating environmental and spatial processes in ecological community dynamics. Ecol Letts 8: 1175-1182. (Pubitemid 41532401)
    • (2005) Ecology Letters , vol.8 , Issue.11 , pp. 1175-1182
    • Cottenie, K.1
  • 7
    • 77952674526 scopus 로고    scopus 로고
    • Trait plasticity in species interactions: A driving force of community dynamics
    • Berg MP, Ellers J (2010) Trait plasticity in species interactions: a driving force of community dynamics. Evol Ecol 24: 617-629.
    • (2010) Evol Ecol , vol.24 , pp. 617-629
    • Berg, M.P.1    Ellers, J.2
  • 8
    • 0035015990 scopus 로고    scopus 로고
    • Polycyclic aromatic hydrocarbons in sediments from the Pearl river and estuary, China: Spatial and temporal distribution and sources
    • Mai B, Fu J, Zhang G, Lin Z, Min Y, et al. (2001) Polycyclic aromatic hydrocarbons in sediments from the Pearl river and estuary, China: spatial and temporal distribution and sources. Appl Geochem 16:1429-1445.
    • (2001) Appl Geochem , vol.16 , pp. 1429-1445
    • Mai, B.1    Fu, J.2    Zhang, G.3    Lin, Z.4    Min, Y.5
  • 9
    • 27744449743 scopus 로고    scopus 로고
    • Polycyclic aromatic hydrocarbons in suspended particulate matter and sediments from the Pearl River Estuary and adjacent coastal areas
    • Luo XJ, Chen SJ, Mai BX, Yang QS, Sheng GY, et al. (2006) Polycyclic aromatic hydrocarbons in suspended particulate matter and sediments from the Pearl River Estuary and adjacent coastal areas. China Environ Poll 139: 9-20.
    • (2006) China Environ Poll , vol.139 , pp. 9-20
    • Luo, X.J.1    Chen, S.J.2    Mai, B.X.3    Yang, Q.S.4    Sheng, G.Y.5
  • 10
    • 0037684834 scopus 로고    scopus 로고
    • The characteristics of nutrients and eutrophication in the Pearl River estuary, South China
    • DOI 10.1016/S0025-326X(02)00474-5
    • Huang XP, Huang LM, Yue WZ (2003) The characteristics of nutrients and eutrophication in the Pearl River estuary, South China. Mar Poll Bull 47: 30-36. (Pubitemid 36627617)
    • (2003) Marine Pollution Bulletin , vol.47 , Issue.1-6 , pp. 30-36
    • Huang, X.P.1    Huang, L.M.2    Yue, W.Z.3
  • 14
    • 0242489226 scopus 로고    scopus 로고
    • Anaerobic Ammonium Oxidation Measured in Sediments along the Thames Estuary, United Kingdom
    • DOI 10.1128/AEM.69.11.6447-6454.2003
    • Trimmer M, Nicholls JC, Deflandre B (2003) Anaerobic ammonium oxidation measured in sediments along the Thames estuary, United Kingdom. Appl Environ Microbiol 69: 6447-6454. (Pubitemid 37420176)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.11 , pp. 6447-6454
    • Trimmer, M.1    Nicholls, J.C.2    Deflandre, B.3
  • 16
    • 29144463361 scopus 로고    scopus 로고
    • Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time
    • DOI 10.1128/AEM.71.12.8201-8206.2005
    • Lindstrom ES, Kamst-Van Agterveld MP, Zwart G (2005) Distribution of typical fresh water bacterial groupsis associated with pH,temperature, and lake water retention time. Appl Environ Microbiol 71: 8201-8206. (Pubitemid 41803945)
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.12 , pp. 8201-8206
    • Lindstrom, E.S.1    Kamst-Van Agterveld, M.P.2    Zwart, G.3
  • 17
    • 0141816854 scopus 로고    scopus 로고
    • Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones
    • DOI 10.1128/AEM.69.9.5248-5254.2003
    • Hahn MW (2003) Isolation of strains belonging to the cosmopolitan Polynucleo bacternecessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69: 5248-5254. (Pubitemid 37150747)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.9 , pp. 5248-5254
    • Hahn, M.W.1
  • 18
    • 0344034188 scopus 로고    scopus 로고
    • Anaerolinea thermophila gen. Nov., Sp. Nov. And Caldilinea aerophila gen. Nov., Sp. Nov., Novel filamentous thermophiles that represent a previously uncultured lineage of the domain bacteria at the subphylum level
    • DOI 10.1099/ijs.0.02699-0
    • Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, et al. (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53: 1843-1851. (Pubitemid 37483841)
    • (2003) International Journal of Systematic and Evolutionary Microbiology , vol.53 , Issue.6 , pp. 1843-1851
    • Sekiguchi, Y.1    Yamada, T.2    Hanada, S.3    Ohashi, A.4    Harada, H.5    Kamagata, Y.6
  • 19
    • 33745320006 scopus 로고    scopus 로고
    • Anaerolinea thermolimosa sp. Nov., Levilinea saccharolytica gen. Nov., Sp. Nov. And Leptolinea tardivitalis gen. Nov., Sp. Nov., Novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. And Caldilineae classis nov. In the bacterial phylum Chloroflexi
    • DOI 10.1099/ijs.0.64169-0
    • Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, et al. (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56: 1331-1340. (Pubitemid 43933829)
    • (2006) International Journal of Systematic and Evolutionary Microbiology , vol.56 , Issue.6 , pp. 1331-1340
    • Yamada, T.1    Sekiguchi, Y.2    Hanada, S.3    Imachi, H.4    Ohashi, A.5    Harada, H.6    Kamagata, Y.7
  • 20
    • 84878819687 scopus 로고    scopus 로고
    • Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing
    • Ye L, Zhang T (2012) Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl Microbiol Biotechnol 97: 2681-90.
    • (2012) Appl Microbiol Biotechnol , vol.97 , pp. 2681-2690
    • Ye, L.1    Zhang, T.2
  • 21
    • 1642376424 scopus 로고    scopus 로고
    • Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time
    • DOI 10.1128/AEM.70.3.1494-1505.2004
    • Crump CB, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influence of bacterial growth and residence time. Appl Environ Microbiol 70: 1494-1505. (Pubitemid 38365131)
    • (2004) Applied and Environmental Microbiology , vol.70 , Issue.3 , pp. 1494-1505
    • Crump, B.C.1    Hopkinson, C.S.2    Sogin, M.L.3    Hobbie, J.E.4
  • 22
    • 34548418027 scopus 로고    scopus 로고
    • Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau
    • DOI 10.1111/j.1462-2920.2007.01377.x
    • Jiang H, Dong H, Yu B, Liu X, Li Y, et al. (2007) Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol 9: 2603-2621. (Pubitemid 47366670)
    • (2007) Environmental Microbiology , vol.9 , Issue.10 , pp. 2603-2621
    • Jiang, H.1    Dong, H.2    Yu, B.3    Liu, X.4    Li, Y.5    Ji, S.6    Zhang, C.L.7
  • 23
    • 84888201068 scopus 로고    scopus 로고
    • Enhancement of coulombic efficiency and salt tolerance in microbial fuel cells by graphite/alginate granules immobilization of Shewanella oneidensis MR-1
    • Yong YC, Liao ZH, Sun JZ, Zheng T, Jiang RR, et al. (2013) Enhancement of coulombic efficiency and salt tolerance in microbial fuel cells by graphite/alginate granules immobilization of Shewanella oneidensis MR-1. Process Biochemistry 48: 1947-1951.
    • (2013) Process Biochemistry , vol.48 , pp. 1947-1951
    • Yong, Y.C.1    Liao, Z.H.2    Sun, J.Z.3    Zheng, T.4    Jiang, R.R.5
  • 24
    • 84886930478 scopus 로고    scopus 로고
    • Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium
    • Li R, Zi X, Wang X, Zhang X, Gao HF, et al. (2013) Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium. SpringerPlus 2: 1-9.
    • (2013) SpringerPlus , vol.2 , pp. 1-9
    • Li, R.1    Zi, X.2    Wang, X.3    Zhang, X.4    Gao, H.F.5
  • 25
    • 84883134954 scopus 로고    scopus 로고
    • Characterization of a cold-adapted and salt-tolerant esterase from a psychrotrophic bacterium Psychrobacter pacificensis
    • Wu G, Wu G, Zhan T,Shao Z, Liu Z (2013) Characterization of a cold-adapted and salt-tolerant esterase from a psychrotrophic bacterium Psychrobacter pacificensis. Extremophiles 17: 809-819.
    • (2013) Extremophiles , vol.17 , pp. 809-819
    • Wu, G.1    Wu, G.2    Zhan, T.3    Shao, Z.4    Liu, Z.5
  • 27
    • 0030576557 scopus 로고    scopus 로고
    • The 1994 QUASTIMEME Laboratory Performance Study: Nutrients in seawater and standard solutions
    • DOI 10.1016/0025-326X(96)00076-8
    • Kirkwood DS, Aminot A, Carlberg SR (1996) The 1994 quasimeme laboratory performance study: nutrients in seawater and standard solutions. Mar Poll Bull 32: 640-645. (Pubitemid 26340508)
    • (1996) Marine Pollution Bulletin , vol.32 , Issue.8-9 , pp. 640-645
    • Kirkwood, D.S.1    Aminot, A.2    Carlberg, S.R.3
  • 28
    • 0031736602 scopus 로고    scopus 로고
    • Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria
    • Weinbauer MG, Beckman C, Höfle MG (1998) Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl Environ Microbiol 64: 5000-5003. (Pubitemid 28557872)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.12 , pp. 5000-5003
    • Weinbauer, M.G.1    Beckmann, C.2    Hofle, M.G.3
  • 29
    • 66249094531 scopus 로고    scopus 로고
    • Inter-and intraspecific variations of bacterial communities associated with marine sponges from San Juan Island, Washington
    • Lee OO, Wong YH, Qian PY (2009) Inter-and intraspecific variations of bacterial communities associated with marine sponges from San Juan Island, Washington. Appl Environ Microbiol 75: 3513-3521.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 3513-3521
    • Lee, O.O.1    Wong, Y.H.2    Qian, P.Y.3
  • 30
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain-specific 16S primers
    • DOI 10.1016/j.mimet.2003.08.009
    • Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domainspecific 16S primers. J Microb Methods 55: 541-555. (Pubitemid 37357207)
    • (2003) Journal of Microbiological Methods , vol.55 , Issue.3 , pp. 541-555
    • Baker, G.C.1    Smith, J.J.2    Cowan, D.A.3
  • 32
    • 77956304094 scopus 로고    scopus 로고
    • Rapid denoising of pyrosequencing amplicon data: Exploiting the rank-abundance distribution
    • Reeder J, Knight R (2010) Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nat Methods 7: 668-669.
    • (2010) Nat Methods , vol.7 , pp. 668-669
    • Reeder, J.1    Knight, R.2
  • 33
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 34
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 36
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504
    • (2011) Genome Res , vol.21 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3    Feldgarden, M.4    Ward, D.V.5
  • 37
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • DOI 10.1128/AEM.00062-07
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Näve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl Environ Microbiol 73: 5261-5267. (Pubitemid 47326658)
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 38
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35: 7188-7196.
    • (2007) Nucl Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5
  • 39
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • DOI 10.1128/AEM.71.12.8228-8235.2005
    • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235. (Pubitemid 41803949)
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.12 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 40
    • 0003426018 scopus 로고
    • SYSTAT for Windows: Statistics, graphics, data, getting started, version 5
    • Wilkinson L (1992) SYSTAT for Windows: statistics, graphics, data, getting started, version 5. Systat.
    • (1992) Systat
    • Wilkinson, L.1
  • 41
    • 3142756502 scopus 로고    scopus 로고
    • Open source clustering software
    • DOI 10.1093/bioinformatics/bth078
    • de Hoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20: 1453-1454. (Pubitemid 38931415)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1453-1454
    • De Hoon, M.J.L.1    Imoto, S.2    Nolan, J.3    Miyano, S.4
  • 42
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview - Extensible visualization of microarray data
    • DOI 10.1093/bioinformatics/bth349
    • Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248. (Pubitemid 39619217)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3246-3248
    • Saldanha, A.J.1
  • 43
    • 34748886657 scopus 로고    scopus 로고
    • PAST: Paleontological statistics software package for education and data analysis
    • Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4: 1-9.
    • (2001) Palaeontologia Electronica , vol.4 , pp. 1-9
    • Hammer, Ø.1    Harper, D.A.T.2    Ryan, P.D.3


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