메뉴 건너뛰기




Volumn 17, Issue 17, 2008, Pages 3939-3951

Damage and degradation rates of extracellular DNA in marine sediments: Implications for the preservation of gene sequences

Author keywords

16S rDNA; Depurination; DNA preservation; DNases; Extracellular DNA; Marine sediments

Indexed keywords

BACTERIAL DNA; DEOXYRIBONUCLEASE; RIBOSOME DNA; RNA 16S; SEA WATER;

EID: 50049114397     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03880.x     Document Type: Article
Times cited : (158)

References (55)
  • 1
    • 0026532736 scopus 로고
    • Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms
    • Amann RI, Stromley J, Devereux R et al 1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Applied and Environmental Microbiology, 58, 614 623.
    • (1992) Applied and Environmental Microbiology , vol.58 , pp. 614-623
    • Amann, R.I.1    Stromley, J.2    Devereux, R.3    Al, E.4
  • 2
    • 0035056250 scopus 로고    scopus 로고
    • Permutation tests for univariate or multivariate analysis of variance and regression
    • Anderson MJ (2001) Permutation tests for univariate or multivariate analysis of variance and regression. Canadian Journal of Fisheries and Aquatic Sciences, 58, 626 639.
    • (2001) Canadian Journal of Fisheries and Aquatic Sciences , vol.58 , pp. 626-639
    • Anderson, M.J.1
  • 4
    • 33644781709 scopus 로고    scopus 로고
    • Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
    • Binladen J, Wiuf C, Gilbert MTP et al 2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172, 733 741.
    • (2006) Genetics , vol.172 , pp. 733-741
    • Binladen, J.1    Wiuf, C.2    Gilbert, M.T.P.3    Al, E.4
  • 5
    • 0020997753 scopus 로고
    • Binding of recA protein to single-stranded nucleic acids: Spectroscopic studies using fluorescent polynucleotides
    • Cazenave C, Toulmè JJ, Helene C (1983) Binding of recA protein to single-stranded nucleic acids: spectroscopic studies using fluorescent polynucleotides. EMBO Journal, 2, 2247 2251.
    • (1983) EMBO Journal , vol.2 , pp. 2247-2251
    • Cazenave, C.1    Toulmè, J.J.2    Helene, C.3
  • 6
    • 0037189378 scopus 로고    scopus 로고
    • Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes
    • Coolen H, Cypionka A, Sass M, Sass H, Overmann J (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science, 296, 2401 2410.
    • (2002) Science , vol.296 , pp. 2401-2410
    • Coolen, H.1    Cypionka, A.2    Sass, M.3    Sass, H.4    Overmann, J.5
  • 7
    • 0031763993 scopus 로고    scopus 로고
    • Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment
    • Coolen MJ, Overmann J (1998) Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Applied and Environmental Microbiology, 64, 4513 4521.
    • (1998) Applied and Environmental Microbiology , vol.64 , pp. 4513-4521
    • Coolen, M.J.1    Overmann, J.2
  • 8
    • 33846046530 scopus 로고    scopus 로고
    • 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment
    • Coolen MJ, Overmann J (2007) 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment. Environmental Microbiology, 9, 238 249.
    • (2007) Environmental Microbiology , vol.9 , pp. 238-249
    • Coolen, M.J.1    Overmann, J.2
  • 9
    • 2942654846 scopus 로고    scopus 로고
    • Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake
    • Coolen MJ, Muyzer G, Rijpstra WIC et al 2004) Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake. Earth and Planetary Science Letters, 223, 225 239.
    • (2004) Earth and Planetary Science Letters , vol.223 , pp. 225-239
    • Coolen, M.J.1    Muyzer, G.2    Rijpstra, W.I.C.3    Al, E.4
  • 10
    • 12244258230 scopus 로고    scopus 로고
    • Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments
    • Corinaldesi C, Danovaro R, Dell'Anno A (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Applied and Environmental Microbiology, 71, 46 50.
    • (2005) Applied and Environmental Microbiology , vol.71 , pp. 46-50
    • Corinaldesi, C.1    Danovaro, R.2    Dell'Anno, A.3
  • 11
    • 34547162302 scopus 로고    scopus 로고
    • Early diagenesis and trophic role of extracellular DNA in different benthic ecosystems
    • Corinaldesi C, Dell'Anno A, Danovaro R (2007) Early diagenesis and trophic role of extracellular DNA in different benthic ecosystems. Limnology and Oceanography, 52, 1710 1717.
    • (2007) Limnology and Oceanography , vol.52 , pp. 1710-1717
    • Corinaldesi, C.1    Dell'Anno, A.2    Danovaro, R.3
  • 12
    • 3242796796 scopus 로고    scopus 로고
    • Degradation and turnover of extracellular DNA in marine sediments: Ecological and methodological considerations
    • Dell'Anno A, Corinaldesi C (2004) Degradation and turnover of extracellular DNA in marine sediments: ecological and methodological considerations. Applied and Environmental Microbiology, 70, 4384 4386.
    • (2004) Applied and Environmental Microbiology , vol.70 , pp. 4384-4386
    • Dell'Anno, A.1    Corinaldesi, C.2
  • 13
    • 25844519572 scopus 로고    scopus 로고
    • Extracellular DNA play a key role in deep-sea ecosystem functioning
    • Dell'Anno A, Danovaro R (2005) Extracellular DNA play a key role in deep-sea ecosystem functioning. Science, 309, 1497.
    • (2005) Science , vol.309 , pp. 1497
    • Dell'Anno, A.1    Danovaro, R.2
  • 14
    • 0036092095 scopus 로고    scopus 로고
    • Quantification, base composition and fate of extracellular DNA in marine sediments
    • Dell'Anno A, Bompadre S, Danovaro R (2002) Quantification, base composition and fate of extracellular DNA in marine sediments. Limnology and Oceanography, 47, 899 905.
    • (2002) Limnology and Oceanography , vol.47 , pp. 899-905
    • Dell'Anno, A.1    Bompadre, S.2    Danovaro, R.3
  • 17
    • 1342329755 scopus 로고    scopus 로고
    • Short-term impact of clam harvesting on sediments chemistry, benthic microbes and meiofauna in the Goro Lagoon (Italy)
    • Fiordelmondo C, Manini E, Gambi C, Pusceddu A (2003) Short-term impact of clam harvesting on sediments chemistry, benthic microbes and meiofauna in the Goro Lagoon (Italy). Chemistry and Ecology, 19, 173 187.
    • (2003) Chemistry and Ecology , vol.19 , pp. 173-187
    • Fiordelmondo, C.1    Manini, E.2    Gambi, C.3    Pusceddu, A.4
  • 18
    • 0032876852 scopus 로고    scopus 로고
    • Prokaryotic genome size and SSU rDNA copy number: Estimation of microbial relative abundance from a mixed population
    • Fogel GB, Collins CR, Li J, Brunk CF (1999) Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microbial Ecology, 38, 93 113.
    • (1999) Microbial Ecology , vol.38 , pp. 93-113
    • Fogel, G.B.1    Collins, C.R.2    Li, J.3    Brunk, C.F.4
  • 20
    • 33846667604 scopus 로고    scopus 로고
    • Recharacterization of ancient DNA miscoding lesions: Insights in the era of sequencing-by-synthesis
    • Gilbert MTP, Binladen J, Miller W et al 2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research, 35, 1 10.
    • (2007) Nucleic Acids Research , vol.35 , pp. 1-10
    • Gilbert, M.T.P.1    Binladen, J.2    Miller, W.3    Al, E.4
  • 21
    • 33947696774 scopus 로고    scopus 로고
    • Holocene biostratigraphy and paleoenvironmental changes in the Black Sea based on calcareous nannoplankton
    • Giunta S, Morigi C, Negri A, Guichard F, Lericolais G (2007) Holocene biostratigraphy and paleoenvironmental changes in the Black Sea based on calcareous nannoplankton. Marine Micropalentology, 63, 91 110.
    • (2007) Marine Micropalentology , vol.63 , pp. 91-110
    • Giunta, S.1    Morigi, C.2    Negri, A.3    Guichard, F.4    Lericolais, G.5
  • 23
    • 33745358864 scopus 로고    scopus 로고
    • Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments
    • Hansen AJ, Mitchell DL, Wiuf C et al 2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics, 173, 1175 1179.
    • (2006) Genetics , vol.173 , pp. 1175-1179
    • Hansen, A.J.1    Mitchell, D.L.2    Wiuf, C.3    Al, E.4
  • 25
    • 0035581087 scopus 로고    scopus 로고
    • DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
    • Hofreiter M, Jaenicke V, Serre S, von Haeseler A, Pääbo S (2001a) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793 4799.
    • (2001) Nucleic Acids Research , vol.29 , pp. 4793-4799
    • Hofreiter, M.1    Jaenicke, V.2    Serre, S.3    Von Haeseler, A.4    Pääbo, S.5
  • 28
    • 0027320435 scopus 로고
    • Synthesis and damage specificity of a novel probe for the detection of abasic sites in DNA
    • Ide H, Akamatsu JK, Kimura Y et al 1993) Synthesis and damage specificity of a novel probe for the detection of abasic sites in DNA. Biochemistry, 32, 8276 8283.
    • (1993) Biochemistry , vol.32 , pp. 8276-8283
    • Ide, H.1    Akamatsu, J.K.2    Kimura, Y.3    Al, E.4
  • 29
    • 33644505436 scopus 로고    scopus 로고
    • Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
    • Inagaki F, Nunoura T, Nakagawa S et al 2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proceedings of the National Academy of Sciences, USA, 103, 2815 2820.
    • (2006) Proceedings of the National Academy of Sciences, USA , vol.103 , pp. 2815-2820
    • Inagaki, F.1    Nunoura, T.2    Nakagawa, S.3    Al, E.4
  • 31
    • 0026754035 scopus 로고
    • A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion?
    • Kubo K, Ide H, Wallace SS, Kow JW (1992) A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion? Biochemistry, 31, 3703 3708.
    • (1992) Biochemistry , vol.31 , pp. 3703-3708
    • Kubo, K.1    Ide, H.2    Wallace, S.S.3    Kow, J.W.4
  • 32
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709 715.
    • (1993) Nature , vol.362 , pp. 709-715
    • Lindahl, T.1
  • 33
    • 0015504248 scopus 로고
    • Rate of depurination of native deoxyribonucleic acid
    • Lindahl T, Nyberg B (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry, 11, 3610 3618.
    • (1972) Biochemistry , vol.11 , pp. 3610-3618
    • Lindahl, T.1    Nyberg, B.2
  • 34
    • 0028136885 scopus 로고
    • Bacterial gene transfer by natural genetic transformation in the environment
    • Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiological Review, 58, 563 602.
    • (1994) Microbiological Review , vol.58 , pp. 563-602
    • Lorenz, M.G.1    Wackernagel, W.2
  • 35
    • 33644871362 scopus 로고    scopus 로고
    • DNA extraction procedure: A critical issue for bacterial diversity assessment in marine sediments
    • Luna GM, Dell'Anno A, Danovaro R (2005) DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environmental Microbiology, 8, 308 320.
    • (2005) Environmental Microbiology , vol.8 , pp. 308-320
    • Luna, G.M.1    Dell'Anno, A.2    Danovaro, R.3
  • 36
    • 38949113818 scopus 로고    scopus 로고
    • Subfossil 16S rRNA gene sequences of green sulfur bacteria in the Black Sea and their implications for past photic zone anoxia
    • Manske UH, Glaeser J, Overmann J (2008) Subfossil 16S rRNA gene sequences of green sulfur bacteria in the Black Sea and their implications for past photic zone anoxia. Applied and Environmental Microbiology, 74, 624 632.
    • (2008) Applied and Environmental Microbiology , vol.74 , pp. 624-632
    • Manske, U.H.1    Glaeser, J.2    Overmann, J.3
  • 38
    • 0000832946 scopus 로고
    • Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification
    • Pääbo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proceedings of the National Academy of Sciences, USA, 86, 1939 1943.
    • (1989) Proceedings of the National Academy of Sciences, USA , vol.86 , pp. 1939-1943
    • Pääbo, S.1
  • 39
    • 0002614203 scopus 로고
    • Miocene DNA sequences - A dream come true?
    • Pääbo S, Wilson AC (1991) Miocene DNA sequences - a dream come true? Current Biology, 1, 45 46.
    • (1991) Current Biology , vol.1 , pp. 45-46
    • Pääbo, S.1    Wilson, A.C.2
  • 41
    • 33846847656 scopus 로고    scopus 로고
    • Modern sediment accumulation on the Po shelf, Adriatic Sea
    • Palinkas CM, Nittrouer CA (2007) Modern sediment accumulation on the Po shelf, Adriatic Sea. Continental Shelf Research, 27, 489 505.
    • (2007) Continental Shelf Research , vol.27 , pp. 489-505
    • Palinkas, C.M.1    Nittrouer, C.A.2
  • 42
    • 0036667310 scopus 로고    scopus 로고
    • The genetic secrets some fossils hold
    • Poinar HN (2002) The genetic secrets some fossils hold. Accounts of Chemical Research, 35, 676 684.
    • (2002) Accounts of Chemical Research , vol.35 , pp. 676-684
    • Poinar, H.N.1
  • 43
    • 85023036487 scopus 로고    scopus 로고
    • The top 10 list: Criteria of authenticity for DNA from ancient and forensic samples
    • Poinar HN (2003) The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. International Congress Series, 1239, 575 579.
    • (2003) International Congress Series , vol.1239 , pp. 575-579
    • Poinar, H.N.1
  • 44
    • 0029663543 scopus 로고    scopus 로고
    • Amino acid racemization and the preservation of ancient DNA
    • Poinar HN, Höss M, Bada JL, Pääbo S (1996) Amino acid racemization and the preservation of ancient DNA. Science, 272, 864 866.
    • (1996) Science , vol.272 , pp. 864-866
    • Poinar, H.N.1    Höss, M.2    Bada, J.L.3    Pääbo, S.4
  • 46
    • 33745121530 scopus 로고    scopus 로고
    • Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR
    • Schippers A, Neretin LN (2006) Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environmental Microbiology, 8, 1251 1260.
    • (2006) Environmental Microbiology , vol.8 , pp. 1251-1260
    • Schippers, A.1    Neretin, L.N.2
  • 47
  • 48
    • 0035848873 scopus 로고    scopus 로고
    • Neanderthal DNA. Not just old but old and cold?
    • Smith CI, Chamberlain AT, Riley MS et al 2001) Neanderthal DNA. Not just old but old and cold? Nature, 410, 771 772.
    • (2001) Nature , vol.410 , pp. 771-772
    • Smith, C.I.1    Chamberlain, A.T.2    Riley, M.S.3    Al, E.4
  • 49
    • 50049086099 scopus 로고    scopus 로고
    • Biogeochemical processes in sediments of the Manfredonia Gulf (Southern Adriatic Sea): Early diagenesis of carbon and nutrient and benthic exchange
    • Spagnoli F, Bartolini G, Marini M et al 2004) Biogeochemical processes in sediments of the Manfredonia Gulf (Southern Adriatic Sea): early diagenesis of carbon and nutrient and benthic exchange. Biogeosciences Discussions, 1, 803 823.
    • (2004) Biogeosciences Discussions , vol.1 , pp. 803-823
    • Spagnoli, F.1    Bartolini, G.2    Marini, M.3    Al, E.4
  • 50
    • 0033766069 scopus 로고    scopus 로고
    • Rapid detection and quantification of members of the archaeal community by quantitative pcr using fluorogenic probes
    • Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative pcr using fluorogenic probes. Applied and Environmental Microbiology, 66, 5066 5072.
    • (2000) Applied and Environmental Microbiology , vol.66 , pp. 5066-5072
    • Takai, K.1    Horikoshi, K.2
  • 52
    • 0346051368 scopus 로고    scopus 로고
    • Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records
    • Willerslev E, Hansen AJ, Brand TB et al 2003) Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records. Science, 300, 792 795.
    • (2003) Science , vol.300 , pp. 792-795
    • Willerslev, E.1    Hansen, A.J.2    Brand, T.B.3    Al, E.4
  • 55
    • 34447337482 scopus 로고    scopus 로고
    • Ancient biomolecules from deep ice cores reveal forested southern Greenland
    • Willerslev E, Cappellini E, Boomsma W (2007) Ancient biomolecules from deep ice cores reveal forested southern Greenland. Science, 317, 111 114.
    • (2007) Science , vol.317 , pp. 111-114
    • Willerslev, E.1    Cappellini, E.2    Boomsma, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.