Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37–57
Thies JE (2007) Soil microbial community analysis using terminal restriction fragment length
polymorphisms. Soil Sci Soc Am J 71:579–591
Tiedje JM, Asuming-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box
of soil microbial diversity. Appl Soil Ecol 13:109–122
Timmons FL (1970) A history of weed control in the United States and Canada. Weed Sci
18:294–307
Toccalino PL, Gilliom RJ, Lindsey BD, Rupert MG (2014) Pesticides in groundwater of the United
States: decadal-scale changes, 1993–2011. Groundwater 52(1):112–125
Tonin C, Vandenkoornhuyse P, Joner EJ, Straczek J, Leyval C (2001) Assessment of arbuscular
mycorrhizal fungi diversity in the rhizosphere of Violoa calaminaria and effect of these fungi on
heavy metal uptake by clover. Mycorrhiza 10:161–168
Torsvik V, Sorheim R, Goksoyr J (1996) Total bacterial diversity in soil and sediment
communities–a review. J Ind Microbiol 17:170–178
Torsvik V, Daae FL, Sandaa RA, Ovreas L (1998) Review article: novel techniques for analysing
microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62
Trethewey RN (2001) Gene discovery via metabolic profiling. Curr Opin Biotechnol 12:135–138
Urbance JW, Cole J, Saxman P, Tiedje JM (2003) BSD: the Biodegradative Strain Database.
Nucleic Acids Res 31:152–155
Urgun-Demitras M, Stark B, Pagilla K (2006) Use of genetically engineered microorganisms
(GEMs) for the bioremediation of contaminants. Crit Rev Biotechnol 26:145–164
Van Elsas JD, Jansson J, Trevors JK (2007) Modern soil microbiology, 2nd edn. CRC Press,
New York, pp 387–429
Van Herwijnen R, Joffe B, Ryngaert A, Hausner M, Springael D, Govers HAJ, Wuertz S, Parsons
JR (2006) Effect of bioaugmentation and supplementary carbon sources on degradation of
polycyclic aromatic hydrocarbons by a soil derived culture. Microb Ecol 55:122–135
Vaneechoutte M, Dijkshoorn L, Tjernberg I, Elaichouni A, de Vos P, Claeys G (1995) Identification
of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J Clin
Microbiol 33:11–15
Vasseur C, Labadie J, Hebraud M (1999) Differential protein expression by Pseudomonas fragi
submitted to various stresses. Electrophoresis 0:2204–2213
Villas-Boas SG, Bruheim P (2007) The potential of metabolic tools in bioremediation studies.
OMICS: J Integr Biol 11:305–313
Wagner M, Nielsen PH, Loy A, Nielsen J, Daims H (2006) Linking microbial community structure
with function: fluorescence in situ hybridization-micro autoradiography and isotope arrays. Curr
Opin Biotechnol 17:83–91
Wang YF, Tam NF (2011) Microbial community dynamics and biodegradation of polycyclic
aromatic hydrocarbons in polluted marine sediments in Hong Kong. Mar Pollut Bull
63:424–430
Watanabe K, Kodama Y, Syutsubo K, Harayama S (2000) Molecular characterization of bacterial
populations in petroleum-contaminated groundwater discharged from underground crude oil
storage cavities. Appl Environ Microbiol 66:4803–4809
Watts JE, Wu Q, Schreier SB, May HD, Sowers KR (2001) Comparative analysis of
polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ Microbiol 3:710–719
Weidner S, Arnold W, Puhler A (1996) Diversity of uncultured microorganisms associated with the
sea grass Halophila stipulacea estimated by restriction fragment length polymorphism analysis
of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 62:766–271
Westhead DR, Parish RM, Twyman (2003) Bioinformatics–instant notes. Bios Sceintific Publisher,
Oxford
Wiechert W, Schweissgut O, Takanaga H, Frommer WB (2007) Fluxomics: mass spectrometry
versus quantitative imaging. Curr Opin Plant Biol 10:323–330
18 Molecular Technologies for Assessment of Bioremediation and. . .
473
Thies JE (2007) Soil microbial community analysis using terminal restriction fragment length
polymorphisms. Soil Sci Soc Am J 71:579–591
Tiedje JM, Asuming-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box
of soil microbial diversity. Appl Soil Ecol 13:109–122
Timmons FL (1970) A history of weed control in the United States and Canada. Weed Sci
18:294–307
Toccalino PL, Gilliom RJ, Lindsey BD, Rupert MG (2014) Pesticides in groundwater of the United
States: decadal-scale changes, 1993–2011. Groundwater 52(1):112–125
Tonin C, Vandenkoornhuyse P, Joner EJ, Straczek J, Leyval C (2001) Assessment of arbuscular
mycorrhizal fungi diversity in the rhizosphere of Violoa calaminaria and effect of these fungi on
heavy metal uptake by clover. Mycorrhiza 10:161–168
Torsvik V, Sorheim R, Goksoyr J (1996) Total bacterial diversity in soil and sediment
communities–a review. J Ind Microbiol 17:170–178
Torsvik V, Daae FL, Sandaa RA, Ovreas L (1998) Review article: novel techniques for analysing
microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62
Trethewey RN (2001) Gene discovery via metabolic profiling. Curr Opin Biotechnol 12:135–138
Urbance JW, Cole J, Saxman P, Tiedje JM (2003) BSD: the Biodegradative Strain Database.
Nucleic Acids Res 31:152–155
Urgun-Demitras M, Stark B, Pagilla K (2006) Use of genetically engineered microorganisms
(GEMs) for the bioremediation of contaminants. Crit Rev Biotechnol 26:145–164
Van Elsas JD, Jansson J, Trevors JK (2007) Modern soil microbiology, 2nd edn. CRC Press,
New York, pp 387–429
Van Herwijnen R, Joffe B, Ryngaert A, Hausner M, Springael D, Govers HAJ, Wuertz S, Parsons
JR (2006) Effect of bioaugmentation and supplementary carbon sources on degradation of
polycyclic aromatic hydrocarbons by a soil derived culture. Microb Ecol 55:122–135
Vaneechoutte M, Dijkshoorn L, Tjernberg I, Elaichouni A, de Vos P, Claeys G (1995) Identification
of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J Clin
Microbiol 33:11–15
Vasseur C, Labadie J, Hebraud M (1999) Differential protein expression by Pseudomonas fragi
submitted to various stresses. Electrophoresis 0:2204–2213
Villas-Boas SG, Bruheim P (2007) The potential of metabolic tools in bioremediation studies.
OMICS: J Integr Biol 11:305–313
Wagner M, Nielsen PH, Loy A, Nielsen J, Daims H (2006) Linking microbial community structure
with function: fluorescence in situ hybridization-micro autoradiography and isotope arrays. Curr
Opin Biotechnol 17:83–91
Wang YF, Tam NF (2011) Microbial community dynamics and biodegradation of polycyclic
aromatic hydrocarbons in polluted marine sediments in Hong Kong. Mar Pollut Bull
63:424–430
Watanabe K, Kodama Y, Syutsubo K, Harayama S (2000) Molecular characterization of bacterial
populations in petroleum-contaminated groundwater discharged from underground crude oil
storage cavities. Appl Environ Microbiol 66:4803–4809
Watts JE, Wu Q, Schreier SB, May HD, Sowers KR (2001) Comparative analysis of
polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ Microbiol 3:710–719
Weidner S, Arnold W, Puhler A (1996) Diversity of uncultured microorganisms associated with the
sea grass Halophila stipulacea estimated by restriction fragment length polymorphism analysis
of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 62:766–271
Westhead DR, Parish RM, Twyman (2003) Bioinformatics–instant notes. Bios Sceintific Publisher,
Oxford
Wiechert W, Schweissgut O, Takanaga H, Frommer WB (2007) Fluxomics: mass spectrometry
versus quantitative imaging. Curr Opin Plant Biol 10:323–330
18 Molecular Technologies for Assessment of Bioremediation and. . .
473