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Volumn 104, Issue , 2014, Pages 36-42

A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample

Author keywords

Ancient DNA; EDNA; Extracellular DNA; Fossil DNA; Intracellular DNA; South Pacific Gyre

Indexed keywords

BACTERIAL DNA; CELL DNA; EXTRACELLULAR DNA; INTRACELLULAR DNA; RNA 16S; SILICON DIOXIDE; SODIUM DIHYDROGEN PHOSPHATE; UNCLASSIFIED DRUG; DNA; SOIL;

EID: 84903727543     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2014.06.009     Document Type: Article
Times cited : (51)

References (46)
  • 1
    • 0033613644 scopus 로고    scopus 로고
    • Preservation of key biomolecules in the fossil record: current knowledge and future challenges
    • Bada J.L., Wang X.Y.S., Hamilton H. Preservation of key biomolecules in the fossil record: current knowledge and future challenges. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 1999, 354:77-86.
    • (1999) Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. , vol.354 , pp. 77-86
    • Bada, J.L.1    Wang, X.Y.S.2    Hamilton, H.3
  • 2
    • 0011758177 scopus 로고
    • Cycling of organic carbon in a coastal marine system
    • Springer, New York, NY, P. Sly (Ed.)
    • Balzer W., Pollehne F., Erlenkeuser H. Cycling of organic carbon in a coastal marine system. Sediments and water interactions 1986, 325-330. Springer, New York, NY. P. Sly (Ed.).
    • (1986) Sediments and water interactions , pp. 325-330
    • Balzer, W.1    Pollehne, F.2    Erlenkeuser, H.3
  • 3
    • 84870816718 scopus 로고    scopus 로고
    • Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea
    • Bertics V.J., Löscher C.R., Salonen I., Dale A.W., Schmitz R.A., Treude T. Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea. Biogeosci. Discuss. 2012, 9:6489-6533.
    • (2012) Biogeosci. Discuss. , vol.9 , pp. 6489-6533
    • Bertics, V.J.1    Löscher, C.R.2    Salonen, I.3    Dale, A.W.4    Schmitz, R.A.5    Treude, T.6
  • 4
    • 33747038082 scopus 로고    scopus 로고
    • Bacterial extracellular DNA forming a defined network-like structure
    • Bockelmann U., et al. Bacterial extracellular DNA forming a defined network-like structure. FEMS Microbiol. Lett. 2006, 262:31-38.
    • (2006) FEMS Microbiol. Lett. , vol.262 , pp. 31-38
    • Bockelmann, U.1
  • 8
    • 0031763993 scopus 로고    scopus 로고
    • Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment
    • Coolen M.J.L., Overmann J. Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl. Environ. Microbiol. 1998, 64:4513-4521.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4513-4521
    • Coolen, M.J.L.1    Overmann, J.2
  • 9
    • 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 M.J.L., Overmann J. 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment. Environ. Microbiol. 2007, 9:238-249.
    • (2007) Environ. Microbiol. , vol.9 , pp. 238-249
    • Coolen, M.J.L.1    Overmann, J.2
  • 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. Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl. Environ. Microbiol. 2005, 71:46-50.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 46-50
    • Corinaldesi, C.1    Danovaro, R.2    Dell' Anno, A.3
  • 11
    • 50049114397 scopus 로고    scopus 로고
    • Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences
    • Corinaldesi C., Beolchini F., Dell' Anno A. Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences. Mol. Ecol. 2008, 17:3939-3951.
    • (2008) Mol. Ecol. , vol.17 , pp. 3939-3951
    • Corinaldesi, C.1    Beolchini, F.2    Dell' Anno, A.3
  • 12
    • 78751674645 scopus 로고    scopus 로고
    • Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments
    • Corinaldesi C., Barucca M., Luna G.M., Dell' Anno A. Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Mol. Ecol. 2011, 20:642-654.
    • (2011) Mol. Ecol. , vol.20 , pp. 642-654
    • Corinaldesi, C.1    Barucca, M.2    Luna, G.M.3    Dell' Anno, A.4
  • 13
    • 84893652168 scopus 로고    scopus 로고
    • Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins
    • Corinaldesi C., Tangherlini M., Luna G.M., Dell'anno A. Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins. Proc. R. Soc. B Biol. Sci. 2014, 281.
    • (2014) Proc. R. Soc. B Biol. Sci. , pp. 281
    • Corinaldesi, C.1    Tangherlini, M.2    Luna, G.M.3    Dell'anno, A.4
  • 14
    • 67650928186 scopus 로고    scopus 로고
    • Subseafloor sedimentary life in the South Pacific Gyre
    • D' Hondt S., et al. Subseafloor sedimentary life in the South Pacific Gyre. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:11651-11656.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 11651-11656
    • D' Hondt, S.1
  • 15
    • 50649125565 scopus 로고    scopus 로고
    • Major viral impact on the functioning of benthic deep-sea ecosystems
    • (1084-U1027)
    • Danovaro R., et al. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 2008, 454. (1084-U1027).
    • (2008) Nature , vol.454
    • Danovaro, R.1
  • 17
    • 3242796796 scopus 로고    scopus 로고
    • Degradation and turnover of extracellular DNA in marine sediments: Ecological and methodological considerations
    • Dell' Anno A., Corinaldesi C. Degradation and turnover of extracellular DNA in marine sediments: Ecological and methodological considerations. Appl. Environ. Microbiol. 2004, 70:4384-4386.
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 4384-4386
    • Dell' Anno, A.1    Corinaldesi, C.2
  • 18
    • 25844519572 scopus 로고    scopus 로고
    • Extracellular DNA plays a key role in deep-sea ecosystem functioning
    • Dell' Anno A., Danovaro R. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 2005, 309:2179-2179.
    • (2005) Science , vol.309 , pp. 2179-2179
    • Dell' Anno, A.1    Danovaro, R.2
  • 19
    • 79952085066 scopus 로고    scopus 로고
    • Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms
    • Dominiak D.M., Nielsen J.L., Nielsen P.H. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms. Environ. Microbiol. 2010, 13:710-721.
    • (2010) Environ. Microbiol. , vol.13 , pp. 710-721
    • Dominiak, D.M.1    Nielsen, J.L.2    Nielsen, P.H.3
  • 20
    • 0015469559 scopus 로고
    • Preparation of nitrogenase from nodules and separation into components
    • Academic Press, P. Anthony San (Ed.)
    • Evans H.J., Koch B., Klucas R. Preparation of nitrogenase from nodules and separation into components. Methods in Enzymology 1972, 470-476. Academic Press. P. Anthony San (Ed.).
    • (1972) Methods in Enzymology , pp. 470-476
    • Evans, H.J.1    Koch, B.2    Klucas, R.3
  • 21
    • 8844251536 scopus 로고    scopus 로고
    • Genetic response to climate change: insights from ancient DNA and phylochronology
    • Hadly E., et al. Genetic response to climate change: insights from ancient DNA and phylochronology. PLoS Biol. 2004, 2:1-10.
    • (2004) PLoS Biol. , vol.2 , pp. 1-10
    • Hadly, E.1
  • 23
    • 0023866522 scopus 로고
    • DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community
    • Holben W.E., Jansson J.K., Chelm B.K., Tiedje J.M. DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community. Appl. Environ. Microbiol. 1988, 54:703-711.
    • (1988) Appl. Environ. Microbiol. , vol.54 , pp. 703-711
    • Holben, W.E.1    Jansson, J.K.2    Chelm, B.K.3    Tiedje, J.M.4
  • 24
    • 18144401354 scopus 로고    scopus 로고
    • Microbial survival: the paleome: a sedimentary genetic record of past microbial communities
    • Inagaki F., Okada H., Tsapin A.I., Nealson K.H. Microbial survival: the paleome: a sedimentary genetic record of past microbial communities. Astrobiology 2005, 5:141-153.
    • (2005) Astrobiology , vol.5 , pp. 141-153
    • Inagaki, F.1    Okada, H.2    Tsapin, A.I.3    Nealson, K.H.4
  • 25
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • John Wiley and Sons, New York, NY, E. Stackebrandt, M. Goodfellow (Eds.)
    • Lane D.J. 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics 1991, 115-175. John Wiley and Sons, New York, NY. E. Stackebrandt, M. Goodfellow (Eds.).
    • (1991) Nucleic acid techniques in bacterial systematics , pp. 115-175
    • Lane, D.J.1
  • 26
    • 34548546604 scopus 로고    scopus 로고
    • Cycling of extracellular DNA in the soil environment
    • Levy-Booth D.J., et al. Cycling of extracellular DNA in the soil environment. Soil Biol. Biochem. 2007, 39:2977-2991.
    • (2007) Soil Biol. Biochem. , vol.39 , pp. 2977-2991
    • Levy-Booth, D.J.1
  • 27
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
    • (1993) Nature , vol.362 , pp. 709-715
    • Lindahl, T.1
  • 28
    • 80052638464 scopus 로고    scopus 로고
    • Soil-specific limitations for access and analysis of soil microbial communities by metagenomics
    • Lombard N., Prestat E., Van Elsas J.D., Simonet P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol. Ecol. 2011, 78:31-49.
    • (2011) FEMS Microbiol. Ecol. , vol.78 , pp. 31-49
    • Lombard, N.1    Prestat, E.2    Van Elsas, J.D.3    Simonet, P.4
  • 29
    • 0028136885 scopus 로고
    • Bacterial gene transfer by natural genetic transformation in the environment
    • Lorenz M.G., Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 1994, 58:563-602.
    • (1994) Microbiol. Rev. , vol.58 , pp. 563-602
    • Lorenz, M.G.1    Wackernagel, W.2
  • 30
    • 33644871362 scopus 로고    scopus 로고
    • DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments
    • Luna G.M., Dell' Anno A., Danovaro R. DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ. Microbiol. 2006, 8:308-320.
    • (2006) Environ. Microbiol. , vol.8 , pp. 308-320
    • Luna, G.M.1    Dell' Anno, A.2    Danovaro, R.3
  • 31
    • 0021086732 scopus 로고
    • Changes in antibiotic sensitivity and cell surface hydrophobicity in Escherichia coli injured by heating, freezing, drying or gamma radiation
    • Mackey B.M. Changes in antibiotic sensitivity and cell surface hydrophobicity in Escherichia coli injured by heating, freezing, drying or gamma radiation. FEMS Microbiol. Lett. 1983, 20:395-399.
    • (1983) FEMS Microbiol. Lett. , vol.20 , pp. 395-399
    • Mackey, B.M.1
  • 32
    • 0038820050 scopus 로고    scopus 로고
    • Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure
    • Molin S., Tolker-Nielsen T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 2003, 14:255-261.
    • (2003) Curr. Opin. Biotechnol. , vol.14 , pp. 255-261
    • Molin, S.1    Tolker-Nielsen, T.2
  • 33
    • 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 E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 34
    • 84870754855 scopus 로고    scopus 로고
    • Characterization of microbial activity in pockmark fields of the SW-Barents Sea
    • Nickel J.C., Di Primio R., Mangelsdorf K., Stoddart D., Kallmeyer J. Characterization of microbial activity in pockmark fields of the SW-Barents Sea. Mar. Geol. 2012, 332:152-162.
    • (2012) Mar. Geol. , vol.332 , pp. 152-162
    • Nickel, J.C.1    Di Primio, R.2    Mangelsdorf, K.3    Stoddart, D.4    Kallmeyer, J.5
  • 36
    • 12744281935 scopus 로고
    • The Extraction and Purification of Microbial DNA from Sediments
    • Ogram A., Sayler G.S., Barkay T. The Extraction and Purification of Microbial DNA from Sediments. J. Microbiol. Methods 1987, 7:57-66.
    • (1987) J. Microbiol. Methods , vol.7 , pp. 57-66
    • Ogram, A.1    Sayler, G.S.2    Barkay, T.3
  • 38
    • 0028072252 scopus 로고
    • On the track of natural transformation in soil
    • Paget E., Simonet P. On the track of natural transformation in soil. FEMS Microbiol. Ecol. 1994, 15:109-117.
    • (1994) FEMS Microbiol. Ecol. , vol.15 , pp. 109-117
    • Paget, E.1    Simonet, P.2
  • 39
    • 0026793353 scopus 로고
    • Adsorption of DNA on clay minerals: protection against DNaseI and influence on gene transfer
    • Paget E., Monrozier L.J., Simonet P. Adsorption of DNA on clay minerals: protection against DNaseI and influence on gene transfer. FEMS Microbiol. Lett. 1992, 97:31-39.
    • (1992) FEMS Microbiol. Lett. , vol.97 , pp. 31-39
    • Paget, E.1    Monrozier, L.J.2    Simonet, P.3
  • 41
    • 0029663543 scopus 로고    scopus 로고
    • Amino acid racemization and the preservation of ancient DNA
    • Poinar H.N., Hoss M., Bada J.L., Paabo S. Amino acid racemization and the preservation of ancient DNA. Science 1996, 272:864-866.
    • (1996) Science , vol.272 , pp. 864-866
    • Poinar, H.N.1    Hoss, M.2    Bada, J.L.3    Paabo, S.4
  • 44
    • 0025329372 scopus 로고
    • Detection of Horizontal Gene-Transfer by Natural Transformation in Native and Introduced Species of Bacteria in Marine and Synthetic Sediments
    • Stewart G.J., Sinigalliano C.D. Detection of Horizontal Gene-Transfer by Natural Transformation in Native and Introduced Species of Bacteria in Marine and Synthetic Sediments. Appl. Environ. Microbiol. 1990, 56:1818-1824.
    • (1990) Appl. Environ. Microbiol. , vol.56 , pp. 1818-1824
    • Stewart, G.J.1    Sinigalliano, C.D.2
  • 45
    • 84881020568 scopus 로고    scopus 로고
    • Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil
    • Wagner D., Schirmack J., Ganzert L., Morozova D., Mangelsdorf K. Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil. Int. J. Syst. Evol. Microbiol. 2013, 63:2986-2991.
    • (2013) Int. J. Syst. Evol. Microbiol. , vol.63 , pp. 2986-2991
    • Wagner, D.1    Schirmack, J.2    Ganzert, L.3    Morozova, D.4    Mangelsdorf, K.5
  • 46
    • 79551494878 scopus 로고    scopus 로고
    • Methanogenic Archaea Isolated from Taiwan's Chelungpu Fault
    • Wu S.-Y., Lai M.-C. Methanogenic Archaea Isolated from Taiwan's Chelungpu Fault. Appl. Environ. Microbiol. 2011, 77:830-838.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 830-838
    • Wu, S.-Y.1    Lai, M.-C.2


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