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References
Ahn J, Daidou T, Tsuneda S, Hirata A (2002) Characterization of denitrifying phosphate-accumulating organisms cultivated under different electron acceptor conditions using polymerase chain reaction-denaturing gradient gel electrophoresis ASSA Water Res 6:403–412
Battin TJ, Wille A, Sattler B, Psenner R (2001) Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl Environ Microbiol 67:799–807
Berthelet M, Whyte LG, Greer CW (1996) Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett 138:17–22
Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–82
Bonin PC, Michotey VD, Mouzdahir A, Rontani J-F (2002) Anaerobic biodegradation of squalene: Using DGGE to monitor the isolation of denitrifying bacteria taken from enrichment cultures. FEMS Microbiol Ecol 42:37–49
Evans FF, Seldin L, Sebastian GV, Kjelleberg S, Holmstrom C, Rosado AS (2004) Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE. Lett Appl Microbiol 38:93–98
Eyers L, George I, Schuler L, Stenuit B, Agathos SN, El Fantroussi S (2004) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Microbiol Biotechnol 66:123–130
Fisher SG, Lerman LS (1979) Length-independent separation of DNA restriction fragments in two dimensional gel electrophoresis. Cell 16:191–200
Ford JE, McHeyzer-Williams MG, Lieber, MR (1994) Chimeric molecules created by geneamplification interfere with the analysis of somatic hypermutation of murine immunoglobulin genes. Gene 142:279–283
Fortin N, Beaumier D, Lee K, Greer CW (2004) Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. J Microbiol Meth 56:181–191
Fortin N, Fulthorpe RR, Allen DG, Greer CW (1998) Molecular analysis of bacterial isolates and total community DNA from Kraft pulp mill effluent treatment systems. Can J Microbiol 44:537–546
Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4:634–643
Greer CW, Whyte LG, Lawrence JR, Masson L, Brousseau R (2001) Current and future impact of genomics-based technologies on environmental science. Environ Sci Technol 35:360A–366A
Ibekwe AM, Kennedy AC, Frohne PS, Papiernik SK, Yang C-H, Crowley DE (2002) Microbial diversity along a transect of agronomic zones. FEMS Microbiol Ecol 39:183–191
Juck D, Charles T, Whyte LG, Greer CW (2000) Polyphasic microbial community analysis of petroleum hydrocarbon contaminated soils originating from 2 northern Canadian communities. FEMS Microbiol Ecol 33:241–249
Kauffmann IM, Schmitt J, Schmid RD. (2004) DNA isolation from soil samples for cloning in different hosts. Appl Microbiol Biotechnol 64:665–70
Kreader CA (1996) Relief of amplification in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106
Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material from an Australian terrestrial environment. J Bacteriol 174:5072–5078
Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microb Ecol 21:191–198
Liu W-T, Chanc O-C, Fang HP (2002) Characterization of microbial community in granular sludge treating brewery wastewater. Water Res 36:1767–1775
Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081
Luz AP, Pellizari VH, Whyte L. G, Greer CW (2004) A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil. Can J Microbiol 50:323–333
Macnaughton S, Stephen JR, Chang YG, Peacock A, Flemming AM, Leung KT, White DC (1999) Characterization of metal-resistant soil eubacteria by polymerase chain reaction in denaturing gradient gel electrophoresis with isolation of resistant strains. Can J Microbiol 45:116–124
Margesin R, Labbé D, Schinner F, Greer CW, Whyte LG (2003) Characterization of hydrocarbon-degradative microbial populations in contaminated and pristine alpine soils. Appl Environ Microbiol 69:3985–3092
Martin-Laurent F, Philippot 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
Massol-Deya A, Weller R, Rios-Hernandez L, Zhou Z, Hickey RF, Tiedje JM (1997) Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl Environ Microbiol 63:270–276
Meyerhans A, Vartanian JP, Wain-Hobson SW (1990) DNA recombination during PCR Nucleic Acids Res 18: 1697–1691
Miller KM, Ming TJ, Schulze AD, Withler RE (1999) Denaturing gradient gel electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. Bio Techniques 27:1016–1024
Mills DK, Fitzgerald K, Litchfield CD, Gillevet PM (2003) A comparison of DNA profiling techniques for monitoring nutrient impacton microbial community composition during bioremediation of petroleum-contaminated soils. J Microbiol Methods 54:57–74
Mumy KL, Findlay RH (2004) Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. J Microbiol Methods 57:259–68
Murray AE, Preston CM, Massana R, Taylor LT, Blakis A, Wu K, DeLong EF (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64:2585–95
Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) inmicrobial ecology. Antonie van Leeuwenhoek 73:127–141
Muyzer G, Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Myers RM, Fischer SG, Lerman LS, Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3131–3145
Nakagawa T, Fukui M (2002) Phylogenic characterization of microbial mats and streamers from a Japanese alkaline hot spring with a thermal gradient. J Gen Appl Microbiol 48:211–222
Nübel U, Garcia-Pichel F, Muyzer G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63:3327–3332
Paabo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–4721
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547
Sambrook J, Russell DW (2001) Molecular Cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, New York
Schneegurt MA, Dore SY, Kulpa CF Jr. (2003) Direct extraction of DNA from soils for studies in microbial ecology. Curr Issues Mol Biol 5:1–8
Soloway DA, Nahir M, Billowits ME, Whyte LG (2001) In-situ bioremediation of diesel-contaminated soil in Canada’s Arctic territory: a case study at the Whitehorse International Airport, Yukon Territory. Polar Record 202:267–272
Stahl DA (2004) High-throughput techniques for analyzing complex bacterial communities. Adv Exp Med Biol 547:5–17
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229
Wang GC, Wang Y (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142:1107–1114
Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis for microorganisms as they occur in nature. Adv Microbiol Ecol 12:219–286
Whyte LG, Bourbonniere L, Bellerose C, Greer CW (1999) Bioremediation assessment of hydrocarbon-contaminated soils from the high Arctic. Bioremediation J 3:69–79
Whyte LG, Goalen B, Hawari J, Labbé D, Greer CW, Nahir M (2001) Bioremediation treatability assessment of hydrocarbon contaminated soils from Eureka, Nunavut. Cold Regions Sci Technol 32:121–132
Whyte LG, Labbé D, Goalen B, Buchko J, Nahir M, Billowits M, Greer CW (2003) In situ bioremediation of hydrocarbon contaminated soils in the high Arctic. ARCSACC Conference. Edmonton, May 4–6, pp 245–256
Whyte LG, Schultz A, van Beilen JB, Luz AP, Pellizari D, Labbé D, Greer CW (2002) Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine Soils. FEMS Microbiol Ecol 41:141–150
Zhou J, Thompson, DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207
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Whyte, L.G., Greer, C.W. (2005). Molecular Techniques for Monitoring and Assessing Soil Bioremediation. In: Monitoring and Assessing Soil Bioremediation. Soil Biology, vol 5. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-28904-6_10
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DOI: https://doi.org/10.1007/3-540-28904-6_10
Publisher Name: Springer, Berlin, Heidelberg
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