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Volumn 44, Issue 1, 2006, Pages 97-103

Molecular detection of marine nematodes from environmental samples: Overcoming eukaryotic interference

Author keywords

Denaturing gradient gel electrophoresis; DGGE; Diversity; Environmental DNA; Eukaryotic interference; Marine nematodes; Ribosomal primers

Indexed keywords

EUKARYOTA; NEMATODA;

EID: 33748755966     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame044097     Document Type: Article
Times cited : (37)

References (43)
  • 1
    • 0035656060 scopus 로고    scopus 로고
    • Response of abyssal Copepoda Harpacticoida (Crustacea) and other meiobenthos to an artificial disturbance and its bearing on future mining for polymetallic nodules
    • Ahnert A, Schriever G (2001) Response of abyssal Copepoda Harpacticoida (Crustacea) and other meiobenthos to an artificial disturbance and its bearing on future mining for polymetallic nodules. Deep-Sea Res II 48:3779-3794
    • (2001) Deep-Sea Res II , vol.48 , pp. 3779-3794
    • Ahnert, A.1    Schriever, G.2
  • 3
    • 33244485954 scopus 로고    scopus 로고
    • Natural nematode communities are useful tools to address ecological and applied questions
    • Austen MC (2004) Natural nematode communities are useful tools to address ecological and applied questions. Nematol Monogr Perspect 2:1-17
    • (2004) Nematol Monogr Perspect , vol.2 , pp. 1-17
    • Austen, M.C.1
  • 4
    • 0030618465 scopus 로고    scopus 로고
    • The use of offshore meiobenthic communities in laboratory microcosm experiments: Response to heavy metal contamination
    • Austen MC, McEvoy AJ (1997) The use of offshore meiobenthic communities in laboratory microcosm experiments: response to heavy metal contamination. J Exp Mar Biol Ecol 211:247-261
    • (1997) J Exp Mar Biol Ecol , vol.211 , pp. 247-261
    • Austen, M.C.1    McEvoy, A.J.2
  • 5
    • 0024879929 scopus 로고
    • Comparison of univariate and multivariate aspects of estuarine meiobenthic community structure
    • Austen MC, Warwick RM (1989) Comparison of univariate and multivariate aspects of estuarine meiobenthic community structure. Estuar Coast Shelf Sci 29:23-42
    • (1989) Estuar Coast Shelf Sci , vol.29 , pp. 23-42
    • Austen, M.C.1    Warwick, R.M.2
  • 6
    • 1842784656 scopus 로고    scopus 로고
    • Macrofaunal mediation of effects of megafaunal bioturbation on nematode community structure
    • Austen MC, Parry DM, Widdicombe S, Somerfield PJ, Kendall MA (2003) Macrofaunal mediation of effects of megafaunal bioturbation on nematode community structure. Vie Milieu 53:201-210
    • (2003) Vie Milieu , vol.53 , pp. 201-210
    • Austen, M.C.1    Parry, D.M.2    Widdicombe, S.3    Somerfield, P.J.4    Kendall, M.A.5
  • 8
    • 0032485270 scopus 로고    scopus 로고
    • A molecular evolutionary framework for the phylum Nematoda
    • Blaxter ML, De Ley P, Garey JR, Liu LX and 8 others (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75
    • (1998) Nature , vol.392 , pp. 71-75
    • Blaxter, M.L.1    De Ley, P.2    Garey, J.R.3    Liu, L.X.4
  • 9
    • 0033151303 scopus 로고    scopus 로고
    • Nematode community structure as a bioindicator in environmental monitoring
    • Bongers T, Ferris H (1999) Nematode community structure as a bioindicator in environmental monitoring. Trends Ecol Evol 14:224-228
    • (1999) Trends Ecol Evol , vol.14 , pp. 224-228
    • Bongers, T.1    Ferris, H.2
  • 10
    • 0034473168 scopus 로고    scopus 로고
    • Nematodes as sensitive indicators of changes at dredged material disposal sites
    • Boyd SE, Rees HL, Richardson CA (2000) Nematodes as sensitive indicators of changes at dredged material disposal sites. Estuar Coast Shelf Sci 51:805-819
    • (2000) Estuar Coast Shelf Sci , vol.51 , pp. 805-819
    • Boyd, S.E.1    Rees, H.L.2    Richardson, C.A.3
  • 11
    • 0029838624 scopus 로고    scopus 로고
    • PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases
    • Cline J, Braman JC, Hogrefe HH (1996) PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acid Res 24:3546-3551
    • (1996) Nucleic Acid Res , vol.24 , pp. 3546-3551
    • Cline, J.1    Braman, J.C.2    Hogrefe, H.H.3
  • 12
    • 19944370479 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis as a tool for the identification of marine nematodes
    • Cook AA, Bhadury P, Debenham NJ, Meldal BHM and 5 others (2005) Denaturing gradient gel electrophoresis as a tool for the identification of marine nematodes. Mar Ecol Prog Ser 291:103-113
    • (2005) Mar Ecol Prog Ser , vol.291 , pp. 103-113
    • Cook, A.A.1    Bhadury, P.2    Debenham, N.J.3    Meldal, B.H.M.4
  • 13
    • 0036421916 scopus 로고    scopus 로고
    • Present status and future of nematode systematics
    • Coomans A (2002) Present status and future of nematode systematics. Nematology 5:573-582
    • (2002) Nematology , vol.5 , pp. 573-582
    • Coomans, A.1
  • 14
    • 18044373685 scopus 로고    scopus 로고
    • Role of meiofauna in estuarine soft-bottom habitats
    • Coull BR (1999) Role of meiofauna in estuarine soft-bottom habitats. Aust Ecol 24:327-343
    • (1999) Aust Ecol , vol.24 , pp. 327-343
    • Coull, B.R.1
  • 15
    • 22044432865 scopus 로고    scopus 로고
    • Protistan diversity estimates based on 18S rRNA from seawater incubations in the Western North Atlantic
    • Countway PD, Gast RJ, Savai P, Caron DA (2005) Protistan diversity estimates based on 18S rRNA from seawater incubations in the Western North Atlantic. J Eukaryot Microbiol 52:95-106
    • (2005) J Eukaryot Microbiol , vol.52 , pp. 95-106
    • Countway, P.D.1    Gast, R.J.2    Savai, P.3    Caron, D.A.4
  • 16
    • 0035403492 scopus 로고    scopus 로고
    • Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques
    • Díez B, Pedros-Alio C, Marsh TL, Massana R, Diez B, Pedros-Alio C, Marsh TL, Massana R (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67:2942-2951
    • (2001) Appl Environ Microbiol , vol.67 , pp. 2942-2951
    • Díez, B.1    Pedros-Alio, C.2    Marsh, T.L.3    Massana, R.4    Diez, B.5    Pedros-Alio, C.6    Marsh, T.L.7    Massana, R.8
  • 17
    • 0033135245 scopus 로고    scopus 로고
    • Molecular analysis of nematode diversity
    • Dorris M, De Ley P, Blaxter M (1999) Molecular analysis of nematode diversity. Parasitol Today 15:188-193
    • (1999) Parasitol Today , vol.15 , pp. 188-193
    • Dorris, M.1    De Ley, P.2    Blaxter, M.3
  • 19
    • 0036010841 scopus 로고    scopus 로고
    • Molecular barcodes for soil nematode identification
    • Floyd R, Abebe E, Papert A, Blaxter ML (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839-850
    • (2002) Mol Ecol , vol.11 , pp. 839-850
    • Floyd, R.1    Abebe, E.2    Papert, A.3    Blaxter, M.L.4
  • 20
    • 0036213539 scopus 로고    scopus 로고
    • Development of a polymerase chain reaction-based denaturing gradient gel electrophoresis technique to study nematode species biodiversity using the 18S rDNA gene
    • Foucher A, Wilson M (2002) Development of a polymerase chain reaction-based denaturing gradient gel electrophoresis technique to study nematode species biodiversity using the 18S rDNA gene. Mol Ecol Notes 2:45-48
    • (2002) Mol Ecol Notes , vol.2 , pp. 45-48
    • Foucher, A.1    Wilson, M.2
  • 21
    • 16544394490 scopus 로고    scopus 로고
    • Characterization of protistan assemblages in the Ross Sea, Antarctica, by denaturing gradient gel electrophoresis
    • Gast RJ, Dennnett MR, Caron DA (2004) Characterization of protistan assemblages in the Ross Sea, Antarctica, by denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:2028-2037
    • (2004) Appl Environ Microbiol , vol.70 , pp. 2028-2037
    • Gast, R.J.1    Dennnett, M.R.2    Caron, D.A.3
  • 23
    • 3843078402 scopus 로고    scopus 로고
    • GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis
    • Holben WE, Feris KP, Kettunen A, Apajalahati JHA (2004) GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:2263-2270
    • (2004) Appl Environ Microbiol , vol.70 , pp. 2263-2270
    • Holben, W.E.1    Feris, K.P.2    Kettunen, A.3    Apajalahati, J.H.A.4
  • 25
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
    • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings Bioinformatics 5:150-163
    • (2004) Briefings Bioinformatics , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 26
    • 0001318827 scopus 로고
    • Sub-catastrophic sewage and industrial waste contamination as revealed by marine nematode faunal analysis
    • Lambshead PJD (1986) Sub-catastrophic sewage and industrial waste contamination as revealed by marine nematode faunal analysis. Mar Ecol Prog Ser 29:247-260
    • (1986) Mar Ecol Prog Ser , vol.29 , pp. 247-260
    • Lambshead, P.J.D.1
  • 28
    • 0025788241 scopus 로고
    • High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus
    • Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, Mathur EJ (1991) High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108:1-6
    • (1991) Gene , vol.108 , pp. 1-6
    • Lundberg, K.S.1    Shoemaker, D.D.2    Adams, M.W.3    Short, J.M.4    Sorge, J.A.5    Mathur, E.J.6
  • 30
    • 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
  • 31
    • 0022422655 scopus 로고
    • Nearby all base substitution in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis
    • Myers RM, Fischer SG, Lerman LS, Manialis T (1985) Nearby all base substitution in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3131-3145
    • (1985) Nucleic Acids Res , vol.13 , pp. 3131-3145
    • Myers, R.M.1    Fischer, S.G.2    Lerman, L.S.3    Manialis, T.4
  • 32
    • 19644369575 scopus 로고    scopus 로고
    • Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems
    • Postec A, Urios L, Lesongeur F, Ollivier B, Querellou J, Godfroy A (2005) Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems. Curr Microbiol 50:138-144
    • (2005) Curr Microbiol , vol.50 , pp. 138-144
    • Postec, A.1    Urios, L.2    Lesongeur, F.3    Ollivier, B.4    Querellou, J.5    Godfroy, A.6
  • 33
    • 0002379225 scopus 로고    scopus 로고
    • PCR-based cloning across large taxonomic distances and polymorphism detection: MHC as a case study
    • Ferraris JD, Palumbi SR (eds). John Wiley & Sons, New York
    • Potts WK (1996) PCR-based cloning across large taxonomic distances and polymorphism detection: MHC as a case study. In: Ferraris JD, Palumbi SR (eds) Molecular zoology: advances, strategies, and protocols. John Wiley & Sons, New York, p 181-194
    • (1996) Molecular Zoology: Advances, Strategies, and Protocols , pp. 181-194
    • Potts, W.K.1
  • 34
    • 0033990048 scopus 로고    scopus 로고
    • PRIMER 3 on the WWW for general users and for biologist programmers
    • Krawetz S, Misener S (eds). Humana Press, Totowa, NJ
    • Rozen S, Skaletsky H (2000) PRIMER 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Methods and protocols. Bioinformatics. Humana Press, Totowa, NJ, p 365-368 (also available at: http://Fokker.wi.mit.edu/primer3)
    • (2000) Methods and Protocols. Bioinformatics , pp. 365-368
    • Rozen, S.1    Skaletsky, H.2
  • 35
    • 4444293563 scopus 로고    scopus 로고
    • Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods
    • Savin MC, Martin JL, LeGresley M, Giewat M, Rooney-Varga J (2004) Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods. Microb Ecol 48:51-65
    • (2004) Microb Ecol , vol.48 , pp. 51-65
    • Savin, M.C.1    Martin, J.L.2    LeGresley, M.3    Giewat, M.4    Rooney-Varga, J.5
  • 36
    • 0034530892 scopus 로고    scopus 로고
    • Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: Changes in the genetic diversity of bacterial populations
    • Schafer H, Bernard L, Courties C, Lebaron P and 7 others (2001) Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecol 34:243-253
    • (2001) FEMS Microbiol Ecol , vol.34 , pp. 243-253
    • Schafer, H.1    Bernard, L.2    Courties, C.3    Lebaron, P.4
  • 37
    • 0001977561 scopus 로고    scopus 로고
    • Ribosomal DNA probes and primers
    • Karp A, Esaac PG, Ingram DS (eds). Chapman & Hall, London
    • Schlötterer C (1998) Ribosomal DNA probes and primers. In: Karp A, Esaac PG, Ingram DS (eds) Molecular tools for screening biodiversity, plant and animals. Chapman & Hall, London, p 265-276
    • (1998) Molecular Tools for Screening Biodiversity, Plant and Animals , pp. 265-276
    • Schlötterer, C.1
  • 38
    • 0000023099 scopus 로고
    • Attachment of a 40-base-pair G + C rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes
    • Sheffield VC, Cox DR, Lerman LS, Myers RM (1989) Attachment of a 40-base-pair G + C rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci USA 86:232-236
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 232-236
    • Sheffield, V.C.1    Cox, D.R.2    Lerman, L.S.3    Myers, R.M.4
  • 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
  • 40
    • 0021283758 scopus 로고
    • The use of free-living nematodes as a bioassay for estuarine sediments
    • Tietjen JH, Lee JH (1984) The use of free-living nematodes as a bioassay for estuarine sediments. Mar Environ Res 11:233-251
    • (1984) Mar Environ Res , vol.11 , pp. 233-251
    • Tietjen, J.H.1    Lee, J.H.2
  • 41
    • 10744225768 scopus 로고    scopus 로고
    • Design and evaluation of nematode 18S rRNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA
    • Waite IS, O'Donnell AG, Harrison A, Davies JT and 11 others (2003) Design and evaluation of nematode 18S rRNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA. Soil Biol Biochem 35:1165-1173
    • (2003) Soil Biol Biochem , vol.35 , pp. 1165-1173
    • Waite, I.S.1    O'Donnell, A.G.2    Harrison, A.3    Davies, J.T.4
  • 42
    • 0001376085 scopus 로고
    • Ecological and metabolic studies on free-living nematodes from an estuarine mud-flat
    • Warwick RM, Price R (1979) Ecological and metabolic studies on free-living nematodes from an estuarine mud-flat. Estuar Coast Mar Sci 9:257-271
    • (1979) Estuar Coast Mar Sci , vol.9 , pp. 257-271
    • Warwick, R.M.1    Price, R.2
  • 43
    • 0002590294 scopus 로고
    • Nematodes in decomposition
    • Freckman DW (ed). University of Texas, Austin, TX
    • Yeates GW, Coleman DC (1982) Nematodes in decomposition. In: Freckman DW (ed) Nematodes in soil ecosystems. University of Texas, Austin, TX, p 55-80
    • (1982) Nematodes in Soil Ecosystems , pp. 55-80
    • Yeates, G.W.1    Coleman, D.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.