EDP Sciences logo
Search
Menu
All issues Volume 6 / No 1-2 (January-June 2007) Environ. Biosafety Res., 6 1-2 (2007) 37-53 References
Open Access
Issue
Environ. Biosafety Res.
Volume 6, Number 1-2, January-June 2007
Thematic Issue on Horizontal Gene Transfer
Page(s) 37 - 53
DOI https://doi.org/10.1051/ebr:2007031
Published online 12 September 2007
  • Ahrenholtz I, Lorenz MG, Wackernagel W (1994a) A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA. Appl. Environ. Microbiol. 60: 3746–3751 [PubMed] [Google Scholar]
  • Ahrenholtz I, Lorenz MG, Wackernagel W (1994b) The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm. Arch. Microbiol. 161: 176–183 [PubMed] [Google Scholar]
  • Alvarez AJ, Yumet GM, Santiago CL, Toranzos GA (1996) Stability of manipulated plasmid DNA in aquatic environments. Environ. Toxicol. Water Qual. 11: 129–135 [CrossRef] [Google Scholar]
  • Andersen JT, Schafer T, Jørgensen PL, Møller S (2001) Using inactivated microbial biomass as fertilizer: the fate of antibiotic resistance genes in the environment. Res. Microbiol. 152: 823–833 [CrossRef] [PubMed] [Google Scholar]
  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208–218 [CrossRef] [Google Scholar]
  • Austin JJ, Smith AB, Thomas RH (1997) Palaeontology in a molecular world: the search for authentic ancient DNA. Trends Ecol. Evol. 12: 303–306 [Google Scholar]
  • Baker RT (1977) Humic acid-associated organic phosphate. New Zealand J. Sci. 20: 439–41 [Google Scholar]
  • Battista JR (1997) Against all odds: the survival strategies of Deinococcus radiodurans. Annu. Rev. Microbiol. 51: 203–224 [CrossRef] [PubMed] [Google Scholar]
  • Bauer T, Weller P, Hammes WP, Hertel C (2003) The effect of processing parameters on DNA degradation in food. Eur. Food Res. Technol. 217: 338–343 [CrossRef] [Google Scholar]
  • Bazelyan VL, Ayzatullin TA (1979) Kinetics of enzymatic hydrolysis of DNA in sea water. Oceanology 19: 30–33 [Google Scholar]
  • Beebee TJC (1993) Identification and analysis of nucleic acids in natural freshwaters. Sci. Total Environ. 135: 123–129 [CrossRef] [Google Scholar]
  • Beliaeva MI, Kapranova MN, Vitol MI, Golubenko IA, Leshchinskaia IB (1976) Nucleic acids utilized as the main source of bacterial nutrition. Mikrobiologica 45: 420–424 [Google Scholar]
  • Benedik MJ, Strych U (1998) Serratia marcescens and its extracellular nuclease. FEMS Microbiol. Lett. 165: 1–13 [CrossRef] [PubMed] [Google Scholar]
  • Bensasson D, Boore JL, Nielsen KM (2004) Genes without frontiers. Heredity 92: 483–489 [CrossRef] [PubMed] [Google Scholar]
  • Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197–201 [CrossRef] [PubMed] [Google Scholar]
  • Bertolla F, Frostegård A, Brito B, Nesme X, Simonet P (1999) During infection of its hosts, the plant pathogen Ralstonia solanacearum naturally develops a state of competence and exchanges genetic material. Mol. Plant Microb. Interact. 12: 467–472 [CrossRef] [Google Scholar]
  • Bertolla F, Pepin R, Passelegue-Robe E, Paget E, Simkon A, Nesme X, Simonet P (2000) Plant genome complexity may be a factor limiting in situ the transfer of transgenic plant genes to the phytopathogen Ralstonia solanacearum. Appl. Environ. Microbiol. 66: 4161–4167 [CrossRef] [PubMed] [Google Scholar]
  • Blum SAE, Lorenz MG, Wackernagel W (1997) Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soil. System. Appl. Microbiol. 20: 513–521 [Google Scholar]
  • Boehme J, Frischer ME, Jiang SC, Kellogg CA, Pichard S, Rose JB, Steinway C, Paul JH (1993) Viruses, bacterioplankton, and phytoplankton in the southeastern Gulf of Mexico: distribution and contribution to oceanic DNA pools. Mar. Ecol. Prog. Ser. 97: 1–10 [CrossRef] [Google Scholar]
  • Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66: 4356–4360 [CrossRef] [PubMed] [Google Scholar]
  • Burns RG (1982) Enzyme activity in soil: location and a possible role in microbial ecology. Soil Biol. Biochem. 14: 423–427 [CrossRef] [Google Scholar]
  • Carlson CA, Pierson LS, Rosen JJ, Ingraham JL (1983) Pseudomonas stutzeri and related species undergo natural transformation. J. Bacteriol. 153: 93–99 [PubMed] [Google Scholar]
  • Ceccherini M, Pote J, Kay E, Van VT, Marechal J, Pietramellara G, Nannipieri P, Vogel TM, Simonet P (2003) Degradation and transformability of DNA from transgenic leaves. Appl. Environ. Microbiol. 69: 673–678 [CrossRef] [PubMed] [Google Scholar]
  • Chiter A, Forbes JM, Blair GE (2000) DNA stability in plant tissues: implications for the possible transfer of genes from genetically modified food. FEBS Lett. 481: 164–168 [CrossRef] [PubMed] [Google Scholar]
  • Cohan FM, Roberts MS, King EC (1991) The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45: 1383–1421 [Google Scholar]
  • Coleman GS (1980) Rumen ciliate protozoa. Adv. Parasitol. 18: 121–173 [CrossRef] [PubMed] [Google Scholar]
  • Corinaldesi C, Danavaro R, Dell'Anno A (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl. Environ. Microbiol. 71: 46–50 [CrossRef] [PubMed] [Google Scholar]
  • Couteaux MM, Sarmiento L, Bottner P, Acevedo D, Thiery JM (2002) Decomposition of standard plant material along an altitudinal transect (65-3968 m) in the tropical Andes. Soil Biol. Biochem. 34: 69–78 [CrossRef] [Google Scholar]
  • Cuatrecasas P, Wilcheck M, Anfinsen CB (1969) The action of staphylococcal nuclease on synthetic substrates. Biochemistry 8: 2277–2284 [CrossRef] [PubMed] [Google Scholar]
  • Daniel R (2005) The metagenomics of soil. Nature Rev. Microbiol. 3: 470–478 [CrossRef] [Google Scholar]
  • Daniell H (1999) New tools for chloroplast genetic engineering. Nature Biotechnol. 17: 855–856 [CrossRef] [Google Scholar]
  • Deere D, Porter J, Pickup RW, Edwards C (1996) Survival of cells and DNA of Aeromonas salmonicida released into aquatic microcosms. J. Appl. Bacteriol. 81: 309–318 [PubMed] [Google Scholar]
  • DeFlaun MF, Paul JH (1989) Detection of exogenous gene sequences in dissolved DNA from aquatic environments. Microb. Ecol. 18: 21–28 [CrossRef] [PubMed] [Google Scholar]
  • DeFlaun MF, Paul JH, Davis D (1986) Simplified method for dissolved DNA determination in aquatic environments. Appl. Environ. Microbiol. 52: 654–659 [PubMed] [Google Scholar]
  • DeFlaun MF, Paul JH, Jeffrey WH (1987) Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments. Mar. Ecol. Prog. Ser. 38: 65–73 [CrossRef] [Google Scholar]
  • Degand I, Laporte J, Pussemier L (2002) Monitoring the persistence of genes deriving from genetically modified plants in the soil environment. Meded. Rijksuniv. Gent. Fak. Landbouwkd. Toegep. Biol. Wet. 67: 85–98 [Google Scholar]
  • Dell'Anno A, Corinaldesi C (2004) Degradation and turnover of extracellular DNA in marine sediments: Ecological and methodological considerations. Appl. Environ. Microbiol. 70: 4384–4386 [CrossRef] [PubMed] [Google Scholar]
  • Dell'Anno A, Danovaro R (2005) Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 309: 2179 [CrossRef] [PubMed] [Google Scholar]
  • Dell'Anno A, Bompadre S, Danovaro R (2002) Quantification, base composition, and fate of extracellular DNA in marine sediments. Limnol. Oceanogr. 47: 899–905 [CrossRef] [Google Scholar]
  • Demanèche S, Jocteur-Monrozier L, Quiquampoix H, Simonet P (2001) Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl. Environ. Microbiol. 67: 293–299 [CrossRef] [PubMed] [Google Scholar]
  • Desai NA, Shankar V (2003) Single strand specific nucleases. FEMS Microbiol. Rev. 26: 457–491 [CrossRef] [PubMed] [Google Scholar]
  • DeSalle R, Gatesy J, Wheeler W, Grimaldi D (1992) DNA sequences from a fossil termite in oligo-miocene amber and their phylogenetic implications. Science 257: 1933–1936 [CrossRef] [PubMed] [Google Scholar]
  • Dillard JP, Seifert HS (2001) A variable genetic island specific for Neisseria gonorrhoeae is involved in providing DNA for genetic transformation and is found more often in disseminated infection isolates. Mol. Microbiol. 41: 263–277 [CrossRef] [PubMed] [Google Scholar]
  • Doblhoff-Dier O, Bachmayer H, Bennett A, Brunius G, Burki K, Cantley M, Collins C, Crooy P, Elmqvist A, Frontali-Botti C, Havenaar R, Haymerle H, Lelieveld H, Lex M, Mahler JL, Martinez L, Mosgaard C, Olsen L, Pazlarova J, Rudan F, Sarvas M, Stepankova H, Tzotzos G, Wagner K, Werner R (2000) DNA content of biotechnological process waste. Trends Biotechnol. 18: 141–146 [CrossRef] [PubMed] [Google Scholar]
  • Douville M, Gagne F, Blaise C, Andre C (2007) Occurrence and persistence of Bacillus thuringiensis (Bt) and transgenic Bt corn cry1Ab gene from an aquatic environment. Ecotoxicol. Environ. Safety 66: 195–203 [CrossRef] [Google Scholar]
  • Dupray E, Caprais MP, Derrien A, Fach P (1997) Salmonella DNA persistence in natural seawaters using PCR analysis. J. Appl. Microbiol. 82: 507–510 [CrossRef] [PubMed] [Google Scholar]
  • Eaves GN, Jeffries CD (1963) Isolation and properties of an extracellular nuclease of Serratia marcescens. J. Bacteriol. 85: 273–278 [PubMed] [Google Scholar]
  • England LS, Lee H, Trevors JT (1997) Persistence of Pseudomonas aureofaciens strains and DNA in soil. Soil Biol. Biochem. 29: 1521–1527 [CrossRef] [Google Scholar]
  • England LS, Pollok J, Vincent M, Kreutzweiser D, Fick W, Trevors JT, Holmes SB (2005) Persistence of extracellular baculoviral DNA in aquatic microcosms: extraction, purification, and amplification by the polymerase chain reaction (PCR). Mol. Cell. Probes 19: 75–80 [CrossRef] [PubMed] [Google Scholar]
  • Feil EJ, Spratt BG (2001) Recombination and the population structure of bacterial pathogens. Annu. Rev. Microbiol. 55: 561–590 [CrossRef] [PubMed] [Google Scholar]
  • Finkel SE, Kolter R (2001) DNA as a nutrient: novel role for bacterial competence gene homologs. J. Bacteriol. 183: 6288–6293 [CrossRef] [PubMed] [Google Scholar]
  • Friedlander AM (1975) DNA release as a direct measure of microbial killing. I. Serum bactericidal activity. J. Immunol. 115: 1404–1408 [PubMed] [Google Scholar]
  • Frostegård Å, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65: 5409–5420 [PubMed] [Google Scholar]
  • Gallori E, Bazzicalupo M, Dal Canto L, Fani R, Nannipieri P, Vettori C, Stotzky G (1994) Transformation of Bacillus subtilis by DNA bound on clay in non-sterile soil. FEMS Microbiol. Ecol. 15: 119–126 [CrossRef] [Google Scholar]
  • Garces H, Durzan D, Pedroso MC (2001) Mechanical stress elicits nitric oxide formation and DNA fragmentation in Arabidopsis thaliana. Ann. Bot. 87: 567–574 [CrossRef] [Google Scholar]
  • Gavrieli Y, Sherman Y, Ben-Sasson SA (1992) Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation. J. Cell Biol. 119: 493–501 [CrossRef] [PubMed] [Google Scholar]
  • Gebhard F, Smalla K (1999) Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and horizontal gene transfer. FEMS Microbiol. Ecol. 28: 261–272 [CrossRef] [Google Scholar]
  • Graham JB, Istock CA (1979) Gene exchange and natural selection cause Bacillus subtilis to evolve in soil culture. Science 204: 637–639 [CrossRef] [PubMed] [Google Scholar]
  • Graham JB, Istock CA (1978) Genetic exchange in Bacillus subtilis in soil. Mol. Gen. Genet. 166: 287–290 [PubMed] [Google Scholar]
  • Greaves MP, Wilson MJ (1969) The adsorption of nucleic acids by montmorillonite. Soil Biol. Biochem. 1: 317–323 [CrossRef] [Google Scholar]
  • Green PJ (1994) The ribonucleases of higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45: 421–445 [CrossRef] [Google Scholar]
  • Grimont F, Grimont PAD (1991) The genus Serratia. In Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH, eds, The prokaryotes, Springer Verlag, New York, pp 2822–2849 [Google Scholar]
  • Guan J, Spencer JL, Ma BL (2005) The fate of recombinant DNA in corn during composting. J. Environ. Sci. Health. Part B. 40: 463–473 [Google Scholar]
  • Hamilton HL, Dominguez NM, Schwartz KJ, Hackett KT, Dillard JP (2005) Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system. Mol. Microbiol. 55: 1704–1721 [CrossRef] [PubMed] [Google Scholar]
  • Harter RD, Stotzky G (1971) Formation of clay-protein complexes. Soil. Sci. Soc. Amer. Proc. 35: 383–389 [CrossRef] [Google Scholar]
  • Havel L, Durzan DJ (1996) Apoptosis in plants. Botanica Acta 109: 1–10 [Google Scholar]
  • Hay I, Morency MJ, Sequin A (2002) Assessing the persistence of DNA in decomposing leaves of genetically modified poplar trees. Can. J. For. Res. 32: 977–982 [CrossRef] [Google Scholar]
  • Henschke RB, Henschke EJ, Schmidt FRJ (1991) Monitoring survival and gene transfer in soil microcosms of recombinant Escherichia coli designed to represent an industrial production strain. Appl. Microbiol. Biotechnol. 35: 247–252 [PubMed] [Google Scholar]
  • Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S (2001) Ancient DNA. Nature Genet. 2: 353–359 [Google Scholar]
  • Huang CY, Aycliffe MA, Timmis JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422: 72–76 [CrossRef] [PubMed] [Google Scholar]
  • Iudica CA, Whitten W, Williams NH (2001) Small bones from dried mammal museum specimens as a reliable source of DNA. BioTechniques 30: 732–736 [PubMed] [Google Scholar]
  • Jiang SC, Paul JH (1995) Viral contribution to dissolved DNA in the marine kingdom as determined by differential centrifugation and kingdom probing. Appl. Environ. Microbiol. 61: 317–325 [PubMed] [Google Scholar]
  • Jørgensen NOG, Jacobsen CS (1996) Bacterial uptake and utilization of dissolved DNA. Aquat. Microb. Ecol. 11: 263–270 [CrossRef] [Google Scholar]
  • Kahn MS, Maliga P (1999) Fluorescent antibiotic resistance marker for tracking plastid transformation in higher plants. Nature Biotechnol. 17: 910–915 [CrossRef] [Google Scholar]
  • Karl DM, Bailiff MD (1989) The measurement and distribution of dissolved nucleic acids in aquatic environments. Limnol. Oceanogr. 34: 543–558 [CrossRef] [Google Scholar]
  • Kay E, Vogel TM, Bertolla F, Nalin R, Simonet P (2002) In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68: 3345–3351 [CrossRef] [PubMed] [Google Scholar]
  • Kim CK, Kwak MJ, Lee SG (1996) Structural and functional stability of the genetic recombinant plasmid pCU103 in different water environments. J. Microbiol. 34: 241–247 [Google Scholar]
  • Kögel-Knabner I (2002) The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol. Biochem. 32: 139–162 [CrossRef] [Google Scholar]
  • Krause DO, Smith WJ, McSweeney CS (2001) Extraction of microbial DNA from rumen contents containing plant tannins. BioTechniques 31: 294–298 [PubMed] [Google Scholar]
  • Ladd JN (1978) Origin and range of enzymes in soil. In Burns RG, ed, Soil Enzymes, Academic Press, London, pp 51–97 [Google Scholar]
  • Ladd JN, Forster RC, Nannipieri P, Oades JM (1996) Soil structure and biological activity. In Stotzky G, Bollag J-M, eds, Soil Structure and Biological Activity, Marcel Dekker, New York, pp 23–78 [Google Scholar]
  • Landweber L (1999) Something old for something new: The future of ancient DNA in conservation biology. In Landweber L, Dobson AP, eds, Genetics and the extinction of species: DNA and the conservation of biodiversity, Princeton University Press, New Jersey, USA, pp 163–186 [Google Scholar]
  • Lee GH, Stotzky G (1990) Transformation is a mechanism of gene transfer in soil. Kor. J. Microbiol. 28: 210–218 [Google Scholar]
  • Lee GH, Stotzky G (1999) Transformation and survival of donor, recipient, and transformants of Bacillus subtilis in vitro and in soil. Soil Biol. Biochem. 31: 1499–1508 [CrossRef] [Google Scholar]
  • Lindahl V, Bakken LR (1995) Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol. Ecol. 16: 135–142 [CrossRef] [Google Scholar]
  • Lorenz MG, Wackernagel W (1987) Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53: 2948–2952 [Google Scholar]
  • Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58: 563–602 [PubMed] [Google Scholar]
  • Lorenz MG, Aardema BW, Krumbein WE (1981) Interaction of marine sediment with DNA and DNA availability to nucleases. Mar. Biol. 64: 225–230 [CrossRef] [Google Scholar]
  • Lorenz MG, Gerjets D, Wackernagel W (1991) Release of transforming plasmid and chromosomal DNA from two cultured soil bacteria. Arch. Microbiol. 156: 319–326 [CrossRef] [PubMed] [Google Scholar]
  • Luna GM, Dell'Anno A, Danovaro R (2006) DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ. Microbiol. 8: 308–320 [CrossRef] [PubMed] [Google Scholar]
  • Lynch JM (1983) Soil Biotechnology. Blackwell Scientific Publications, Oxford, London, pp 42–59 [Google Scholar]
  • Maeda M, Taga N (1973) Deoxyribonuclease activity in seawater and sediment. Mar. Biol. 20: 58–63 [CrossRef] [Google Scholar]
  • Maeda M, Taga N (1974) Occurrence and distribution of deoxyribonucleic acid-hydrolyzing bacteria in seawater. J. Exp. Mar. Biol. Ecol. 14: 157–169 [CrossRef] [Google Scholar]
  • Martin-Laurent F, Phillipot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67: 2354–2359 [CrossRef] [PubMed] [Google Scholar]
  • Matsui K, Honjo M, Kawabata Z (2001) Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquat. Microb. Ecol. 26: 95–102 [CrossRef] [Google Scholar]
  • Matsui K, Ishii N, Kawabata Z (2003) Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae. Appl. Environ. Microbiol. 69: 2399–2404 [CrossRef] [PubMed] [Google Scholar]
  • Maynard Smith J, Feil EJ, Smith NH (2000) Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22: 1115–1122 [CrossRef] [PubMed] [Google Scholar]
  • Minear RA (1972) Characterization of naturally occurring dissolved organophosphorus compounds. Environ. Sci. Technol. 6: 431–437 [CrossRef] [Google Scholar]
  • Miraglia M, Berdal KG, Brera C, Corbisier P, Holst-Jensen A, Kok EJ, Marvin HJ, Schimmel H, Rentsch J, van Rie JP, Zagon J (2004) Detection and traceability of genetically modified organisms in the food production chain. Food Chem. Toxicol. 42: 1157–1180 [CrossRef] [PubMed] [Google Scholar]
  • Muela A, Arana I, Justo JI, Seco C, Barcina I (1999) Changes in DNA content and cellular death during a starvation-survival process of Escherichia coli in river water. Microb. Ecol. 37: 62–69 [CrossRef] [PubMed] [Google Scholar]
  • Nagata S (2005) DNA degradation in development and programmed cell death. Ann. Rev. Immunol. 23: 853–875 [CrossRef] [Google Scholar]
  • Nannipieri P (1994) The potential use of soil enzymes as indicators of productivity, sustainability and pollution. In Pankhurst CE, Doube BM, Gupta VVSR, Grace PR, eds, Soil biota, CSIRO, Adelaide, Australia, pp 238–244 [Google Scholar]
  • Nannipieri P, Kandeler E, Ruggiero P (2002) Enzyme activities and microbiological and biochemical processes in soil. In Burns RG, Dick R, eds, Enzymes in the Environment: Activity, Ecology, and Applications, Marcel Dekker, New York, pp 1–33 [Google Scholar]
  • Nielsen KM, Townsend JP (2004) Monitoring and modeling horizontal gene transfer. Nature Biotechnol. 22: 1110–1114 [Google Scholar]
  • Nielsen KM, van Weerelt MDM, Berg TN, Bones AM, Hagler AN, van Elsas JD (1997a) Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63: 1945–1952 [Google Scholar]
  • Nielsen KM, Bones AM, van Elsas JD (1997b) Induced natural transformation of Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63: 3972–3977 [Google Scholar]
  • Nielsen KM, Smalla K, van Elsas JD (2000) Natural transformation of Acinetobacter sp. strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens and Burkholderia cepacia in soil microcosms. Appl. Environ. Microbiol. 66: 206–212 [Google Scholar]
  • Nielsen KM, van Elsas JD, Smalla K (2001) Dynamics, horizontal transfer and selection of novel DNA in the phytosphere of transgenic plants. Ann. Microbiol. 51: 79–94 [Google Scholar]
  • Nielsen KM, Calamai L, Pietramellara G (2006) Stabilization of extracellular DNA and proteins by transient binding to various soil components. In Nannipieri P, Smalla K, eds, Soil Biology, Vol. 8, Nucleic acids and proteins in soil, Springer Verlag, Heidelberg, Germany, pp 141–157 [Google Scholar]
  • Nielsen KM, Johnsen P, van Elsas JD (2007) Gene transfer and micro-evolution in soil. In van Elsas JD, Janssen JK, Trevors J, eds, Modern Soil Microbiology, 2nd edn, CRC Press, pp 55–81 [Google Scholar]
  • Niemeyer J, Gessler F (2002) Determination of free DNA in soils. J. Plant Nutr. Soil Sci. 165: 121–124 [Google Scholar]
  • Novitsky JA (1986) Degradation of dead microbial biomass in a marine sediment. Appl. Environ. Microbiol. 52: 504–509 [Google Scholar]
  • Nygaard I (1983) Utilization of preformed purine bases and nucleosides. In Munch-Pedersen A, ed, Metabolism of nucleosides and nucleobases in microorganisms, Academic press, London, pp 27–93 [Google Scholar]
  • Oades JM (1988) The retention of organic matter in soils. Biogeochemistry 5: 35–70 [CrossRef] [Google Scholar]
  • Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J. Microbiol. Meth. 7: 57–66 [CrossRef] [Google Scholar]
  • Paget E, Simonet P (1994) On the track of natural transformation in soil. FEMS Microbiol. Ecol. 15: 109–118 [CrossRef] [Google Scholar]
  • Paget E, Lebrun M, Freyssinet G, Simonet P (1998) The fate of recombinant plant DNA in soil. Eur. J. Soil Biol. 34: 81–88 [Google Scholar]
  • Palmen R, Hellingwerf KJ (1995) Acinetobacter calcoaceticus liberates chromosomal DNA during induction of competence by cell lysis. Curr. Microbiol. 30: 7–10 [Google Scholar]
  • Palmen R, Hellingwerf KJ (1997) Uptake and processing of DNA by Acinetobacter calcoaceticus – a review. Gene 192: 179–190 [Google Scholar]
  • Palmer CJ, Tsai YL, Paszko-Kolva C, Mayer C, Sangeramo LR (1993) Detection of Legionella species in sewage and ocean water by polymerase chain reaction, direct fluorescent-antibody, and plate culture methods. Appl. Environ. Microbiol. 59: 3618–3624 [PubMed] [Google Scholar]
  • Paul JH, Myers B (1982) Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258. Appl. Environ. Microbiol. 43: 1393–1399 [PubMed] [Google Scholar]
  • Paul JH, Jeffrey WH, DeFlaun MF (1987) Dynamics of extracellular DNA in the marine environment. Appl. Environ. Microbiol. 53: 170–179 [Google Scholar]
  • Paul JH, Jeffrey WH, David AW, DeFlaun MF, Cazares LH (1989) Turnover of extracellular DNA in eutrophic and oligotrophic environments of southwest Florida. Appl. Environ. Microbiol. 55: 1823–1828 [Google Scholar]
  • Paul JH, Jeffrey WH, Cannon JP (1990) Production of dissolved DNA, RNA, and protein by microbial populations in a Florida reservoir. Appl. Environ. Microbiol. 56: 2957–2962 [Google Scholar]
  • Pettersen AK, Primicero R, Bøhn T, Nielsen KM (2005) Modeling suggest frequency estimates are not informative for predicting the long-term effect of horizontal gene transfer in bacteria. Environ. Biosafety Res. 4: 222–233 [Google Scholar]
  • Pietramellara G, Canto L, Vettori C, Gallori E, Nannipieri P (1997) Effects of air-drying and wetting cycles on the transforming abiliting of DNA bound on clay minerals. Soil Biol. Biochem. 29: 55–61 [CrossRef] [Google Scholar]
  • Pillai TVN, Ganguly AK (1970) Nucleic acids in the dissolved constituents of seawater. Curr. Sci. 22: 501–504 [Google Scholar]
  • Pillai TVN, Ganguly AK (1972) Nucleic acids in the dissolved constituents of seawater. J. Mar. Biol. Ass. India 14: 384–390 [Google Scholar]
  • Puyet A, Greenberg B, Lacks SA (1990) Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae. J. Mol. Biol. 213: 727–738 [CrossRef] [PubMed] [Google Scholar]
  • Rangarajan ES, Shankar V (2001) Sugar non-specific endonucleases. FEMS. Microb. Rev. 25: 583–613 [CrossRef] [Google Scholar]
  • Recorbet G, Picard C, Normand P, Simonet P (1993) Kinetics of persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59: 4289–4294 [Google Scholar]
  • Ricchetti M, Fairhead C, Dujon B (1999) Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402: 96–100 [CrossRef] [PubMed] [Google Scholar]
  • Richards BN (1987) Microbiology of the rhizosphere. Longman Science & Technology, Essex, England, pp 222–254 [Google Scholar]
  • Rizzi AL, Panebianco D, Giacca, Sorlini C, Daffonchio D (2003) Stability and recovery of maize DNA during food processing. Italian J. Food Sci. 15: 499–510 [Google Scholar]
  • Robe P, Nalin R, Capellano C, Vogel TM, Simonet P (2003) Extraction of DNA from soil. Eur. J. Soil Biol. 39: 183–190 [Google Scholar]
  • Romanowski G, Lorenz MG, Sayler G, Wackernagel W (1992) Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl. Environ. Microbiol. 58: 3012–3019 [Google Scholar]
  • Romanowski G, Lorenz MG, Wackernagel W (1993) Plasmid DNA in a groundwater aquifer microcosm – adsorption, DNase resistance and natural genetic transformation of Bacillus subtilis. Mol. Ecol. 2: 171–181 [CrossRef] [PubMed] [Google Scholar]
  • Ruiz TR, Andrews S, Smith GB (2000) Identification and characterization of nuclease activities in anaerobic environmental samples. Can. J. Microbiology 46: 736–740 [CrossRef] [Google Scholar]
  • Ryerson DE, Heath MC (1996) Cleavage of nuclear DNA into oligonucleosomal fragments during cell death induced by fungal infection or by abiotic treatments. Plant Cell 8: 393–402 [CrossRef] [PubMed] [Google Scholar]
  • Saano A, Kajialainen S, Lindstrom K (1993) Inhibition of DNA mobilization to nylon membrane by soil compounds. Microb. Releases 2: 153–160 [Google Scholar]
  • Selenska S, Klingmüller W (1991) DNA recovery and direct detection of Tn5 sequences from soil. Lett. Appl. Microbiol. 13: 21–24 [CrossRef] [PubMed] [Google Scholar]
  • Selenska S, Klingmüller W (1992) Direct recovery and molecular analysis of DNA and RNA from soil. Microb. Releases 1: 41–46 [Google Scholar]
  • Sikorski J, Graupner S, Lorenz MG, Wackernagel W (1998) Natural genetic transformation of Pseudomonas stutzeri in a non-sterile soil. Microbiology 144: 569–76 [Google Scholar]
  • Siuda W, Gude H (1996) Determination of dissolved deoxyribonucleic acid concentration in lake water. Aquat. Microb. Ecol. 11: 193–202 [CrossRef] [Google Scholar]
  • Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K (1999) Analysis of fungal diversity on the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 2614–2621 [Google Scholar]
  • Steinberger RE, Holden PA (2005) Extracellular DNA in single-and multiple-species unsaturated biofilms. Appl. Environ. Microbiol. 71: 5404–5410 [Google Scholar]
  • Stewart GJ, Sinigalliano CD, Garko KA (1991) Binding of exogenous DNA to marine sediments and the effect of DNA/sediment binding on natural transformation of Pseudomonas stutzeri strain Zobell in sediment columns. FEMS Microbiol. Ecol. 85: 1–8 [CrossRef] [Google Scholar]
  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59: 2657–2665 [Google Scholar]
  • Thomas CM, Nielsen KM (2005) Mechanisms and barriers to horizontal gene transfer between bacteria. Nature Rev. Microbiol. 3: 711–721 [Google Scholar]
  • Thomas H, Stoddart J (1980) Leaf senescence. Annu. Rev. Plant Physiol. 31: 83–111 [CrossRef] [Google Scholar]
  • Thorsness PE, White KH, Fox D (1993) Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 5418–5426 [Google Scholar]
  • Torsvik VL, Goksøyr J (1978) Determination of bacterial DNA in soil. Soil Biol. Biochem. 10: 7–12 [CrossRef] [Google Scholar]
  • Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782–787 [Google Scholar]
  • Trevors JT, van Elsas JD, eds (1995) Nucleic acids in the environment, Springer Verlag, Berlin-Heidelberg [Google Scholar]
  • Tsai YL, Olson BH (1992) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58: 754–757 [Google Scholar]
  • Turk V, Rehnstam AS, Lundberg E, Hagstrøm Å (1992) Release of bacterial DNA by marine nanoflagellates, an intermediate step in phosphorous regeneration. Appl. Environ. Microbiol. 58: 3744–3750 [PubMed] [Google Scholar]
  • van Elsas JD, Duarte GF, Keijzer-Wolters A, Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J. Microbiol. Meth. 43: 133–151 [Google Scholar]
  • Vaneechoutte M, Young DM, Ornston LN, De Baere T, Nemec A, Van Der Reijden T, Carr E, Tjernberg I, Dijkshoorn L (2006) Naturally transformable Acinetobacter sp. strain ADP1 belongs to the newly described species Acinetobacter baylyi. Appl. Environ. Microbiol. 72: 932–936 [Google Scholar]
  • Vincent RD, Hofmann TT, Zassenhaus HP (1988) Sequence and expression of NUC1, the gene encoding the mitochondrial nuclease in Saccharomyces cerevisiae. Nucleic Acids Res. 16: 3297–3312 [CrossRef] [PubMed] [Google Scholar]
  • Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS (2002) Extracellular DNA required for bacterial biofilm formation. Science 295: 1497 [Google Scholar]
  • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571–1577 [CrossRef] [PubMed] [Google Scholar]
  • Widmer F, Seidler RJ, Watrud LS (1996) Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol. Ecol. 5: 603–613 [CrossRef] [Google Scholar]
  • Widmer F, Seidler RJ, Donegan KK, Reed GL (1997) Quantification of transgenic plant marker gene persistence in the field. Mol. Ecol. 6: 1–7 [CrossRef] [Google Scholar]
  • Woodhouse HW (1982) Leaf senescence. In Smith H, Grierson D, eds, The molecular biology of plant development, Blackwell, Oxford, pp 256–281 [Google Scholar]
  • Yin X, Stotzky G (1997) Gene transfer among bacteria in natural environments. Adv. Appl. Microbiol. 45: 153–212 [Google Scholar]
  • Yonemura K, Matsumoto K, Maeda H (1983) Isolation and characterization of nucleases from a clinical isolate of Serratia marcescens kums 3958. J. Biochem. 93: 1287–1295 [PubMed] [Google Scholar]
  • Yu X, Gabriel A (1999) Patching broken chromosomes with extranuclear cellular DNA. Mol. Cell. 4: 873–881 [Google Scholar]
  • Zawadzki P, Cohan FM (1995) The size and continuity of DNA segments integrated in Bacillus transformation. Genetics 141: 1231–1243 [PubMed] [Google Scholar]
  • Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316–322 [Google Scholar]
  • Zweifel UL, Hagstrøm A (1995) Total counts of marine bacteria include a large fraction of nun-nucleoid-containing bacteria (ghosts). Appl. Environ. Microbiol. 61: 2180–2185 [Google Scholar]