Ni’Matuzahro N, Gilewicz M, Guliano M, Bertrand J-C (1999) In vitro
study of interaction between photo-oxidation and biodegradation of
n-methylphenanthrene by Sphyngomonas sp. 2MPII. Chemosphere
38:2501–2507
Nies L, Vogel TM (1990) Effects of organic substrates on dechlorination of Aroclor 1242 in anaerobic sediments. Appl Environ
Microbiol 56:2612–2617
Norberg P, Bergstro ¨m M, Jethava V, Dubhashi D, Hermansson M
(2011) The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination. Nat
Commun 2:268. doi:10.1038/ncomms1267
Ohtsubo Y, Kudo T, Tsuda M, Nagata Y (2004) Strategies for bioremediation of polychlorinated biphenyls. Appl Microbiol Biotechnol
65:250–258
Okuda T, Kumata H, Zakaria MF, Naroaka H, Ishiwatari R, Takada H
(2002) Source identification of Malaysian atmospheric polycyclic
aromatic hydrocarbons nearby forest fire using molecular and isotopic compositions. Atmos Environ 36:611–618
Oleszczuk P (2007) Changes of polycyclic aromatic hydrocarbons
during composting of sewage sludges with chosen physicochemical properties and PAHs content. Chemosphere 67:582–591
Oremland RS, Stolz JF (2003) The ecology of arsenic. Science
300:939–944
Otte MP, Gagnon J, Comeau Y, Matte N, Greer CW, Samson R (1994)
Activation of an indigenous microbial consortium for
bioaugmentation of pentachlorophenol-creosote contaminated
soils. Appl Microbiol Biotechnol 40:926–932
Pandey J, Chauhan A, Jain RK (2009) Integrative approaches for
assessing the ecological sustainability on in situ bioremediation.
FEMS Microbiol Rev 33:324–375
Pei XH, Zhan XH, Wang SM, Lin YS, Zhou LX (2010) Effects of a
biosurfactant and a synthetic surfactant on phenanthrene degradation by a Sphingomonas strain. Pedosphere 20:771–779
Pemberton JM, Fisher PR (1977) 2,4-D plasmids and persistence.
Nature 268:732–733
Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH
(2008) Microbial biodegradation of polyaromatic hydrocarbons.
FEMS Microbiol Rev 32:927–955
Perkovich BS (1996) Enhanced mineralization of [
14
C]atrazine in
Kochia scoparia rhizospheric soil from a pesticide-contaminated
site. Pestic Sci 46:391–396
Peters KE, Walters CC, Moldowan JM (2005) The biomarker guide,
vols 1 and 2. Cambridge University Press, Cambridge
Petric I, Bru D, Udikovic-Kolic N, Hrsak D, Philippot L, MartinLaurent F (2011) Evidence for shifts in the structure and abundance
of microbial community in a long-term PCB-contaminated soil
under bioremediation. J Hazard Mater 195:254–260
Phillips EJP, Landa E, Lovley DR (1995) Remediation of uranium
contaminated soils with bicarbonate extraction and microbial U
(VI) reduction. J Ind Microbiol 14:203–207
Pieper DH (2005) Aerobic degradation of polychlorinated biphenyls.
Appl Microbiol Biotechnol 67:170–191
Pilon-Smits E (2005) Phytoremediation. Annu Rev Plant Biol 56:15–39
Pineda-Flores G, Boll-Argu ¨ello G, Lira-Galeana C, Mesta-Howard AM
(2004) A microbial consortium isolated from a crude oil sample that
uses asphaltenes as carbon and energy source. Biodegradation
15:145–151
Piutti S, Marchand AL, Lagacherie B, Martin-Laurent F, Soulas G
(2002) Effect of successive cropping cycles with different plants
and repeated herbicide applications on the degradation of the
diclofop-methyl, bentazon, diuron, isoproturon and pendimethalin
in soil. Pest Manag Sci 58:303–312
Poelarends GJ, van Hylckama Vlieg JE, Marchesi JR, Freitas Dos
Santos LM, Janssen DB (1999) Degradation of 1,2-dibromoethane
by Mycobacterium sp. strain GP1. J Bacteriol 181(7):2050–2058
Prince RC (1993) Petroleum spill bioremediation in marine
environments. Crit Rev Microbiol 19:217–242
Prince RC (2010) Eucaryotic hydrocarbon degraders. In: Timmis KN,
Mc Genity TJ, Merr JR, Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg,
pp 2065–2078
Prince RC, Elmendorf DL, Lute JR, Hsu CS, Halth CE, Senlus JD,
Dechert GJ, Douglas GS, Butler EL (1994) 17. alpha. (H)-21. beta.
(H)-hopane as a con- served internal marker for estimating the
biodegradation of crude oil. Environ Sci Technol 28:142–145
Prince RC, Gramain A, McGenity TJ (2010) Procaryotic hydrocarbon
degraders. In: Timmis KN, Mc Genity TJ, Merr JR, Lorenzo V (eds)
Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/
Heidelberg, pp 1671–1692
Pritchard PH, Mueller JG, Rogers JC, Kremer FV, Glaser JA (1992) Oil
spill bioremediation : experiences, lessons and results from the
Exxon Valdez oil spill in Alaska. Biodegradation 3:315–335
Quensen JF III, Boyd SA, Tiedje JM (1990) Dechlorination of four
commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Appl Environ Microbiol
56:2360–2369
Rabus R (2005) Biodegradation of hydrocarbon under anoxic
conditions. In: Ollivier B, Magot M (eds) Petroleum microbiology.
ASM Press, Washington, DC, pp 277–299
Raillard S et al (2001) Novel enzyme activities and functional plasticity
revealed by recombining highly homologous enzymes. Chem Biol
8:891–898
Ramade F (2002) Dictionnaire encyclope ´dique de l’e ´cologie et des
sciences de l’environnement, 2eth edn. Dunod, Paris
Reanney DC (1976) Extrachromosomal elements as possible agents of
adaptation and development. Bacteriol Rev 40:552–590
Rea ´tegui E, Reynolds E, Kasinkas L, Aggarwal A, Sadowsky M, Aksan
A, Wackett L (2012) Silica gel-encapsulated AtzA biocatalyst for
atrazine biodegradation. Appl Microbiol Biotechnol 96:231–240
Ripp S, Nivens DE, Ahn Y, Werner C, Jarrell J IV, Easter JP, Cox CD,
Burlage RS, Sayler GS (2000) Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation
process monitoring and control. Environ Sci Technol 34:846–853
Roanne TM, Pepper IL, Miller RM (1996) Microbial remediation of
metals. In: Crawford RL, Crawford DL (eds) Bioremediation,
principles and application. Cambridge University Press, Cambridge,
pp 312–340
Robinson JB, Tuovinen OH (1984) Mechanisms of microbial resistance
and detoxification of mercury and organomercury compounds:
physiological, biochemical, and genetic analyses. Microbiol Rev
48:95–124
Rodrigues JLM, Kachel CA, Aiello MR, Quensen JF, Maltseva OV,
Tsoi TV, Tiedje JM (2006) Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400
(ohb) and Rhodococcus sp. Strain RHA1 (fcb). Appl Environ
Microbiol 72:2476–2482
Rojo F (2009) Degradation of alkanes by bacteria. Environ Microbiol
11(10):2477–2490
Ron EZ, Rosenberg E (2002) Biosurfactants and oil bioremediation.
Curr Opin Biotechnol 13:249–252
Rontani JF, Bosser-Jpulak F, Rambeloarisoa E, Bertrand J-C, Giusti G
(1985) Analytical study of asthart crude oil: asphaltenes biodegradation. Chemosphere 14:1413–1422
Rosenberg E, Ron EZ (2000) Biosurfactant. In: Dworkin M, Falkow S,
Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes.
Springer, New York, pp 834–849
Rousseaux S, Hartmann A, Lagacherie B, Piutti S, Andreux F, Soulas G
(2003) Inoculation of an atrazine-degrading strain, Chelatobacter
heintzii Cit1, in four different soils: effects of different inoculum
density. Chemosphere 51:569–576
16 Applied Microbial Ecology and Bioremediation
751
study of interaction between photo-oxidation and biodegradation of
n-methylphenanthrene by Sphyngomonas sp. 2MPII. Chemosphere
38:2501–2507
Nies L, Vogel TM (1990) Effects of organic substrates on dechlorination of Aroclor 1242 in anaerobic sediments. Appl Environ
Microbiol 56:2612–2617
Norberg P, Bergstro ¨m M, Jethava V, Dubhashi D, Hermansson M
(2011) The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination. Nat
Commun 2:268. doi:10.1038/ncomms1267
Ohtsubo Y, Kudo T, Tsuda M, Nagata Y (2004) Strategies for bioremediation of polychlorinated biphenyls. Appl Microbiol Biotechnol
65:250–258
Okuda T, Kumata H, Zakaria MF, Naroaka H, Ishiwatari R, Takada H
(2002) Source identification of Malaysian atmospheric polycyclic
aromatic hydrocarbons nearby forest fire using molecular and isotopic compositions. Atmos Environ 36:611–618
Oleszczuk P (2007) Changes of polycyclic aromatic hydrocarbons
during composting of sewage sludges with chosen physicochemical properties and PAHs content. Chemosphere 67:582–591
Oremland RS, Stolz JF (2003) The ecology of arsenic. Science
300:939–944
Otte MP, Gagnon J, Comeau Y, Matte N, Greer CW, Samson R (1994)
Activation of an indigenous microbial consortium for
bioaugmentation of pentachlorophenol-creosote contaminated
soils. Appl Microbiol Biotechnol 40:926–932
Pandey J, Chauhan A, Jain RK (2009) Integrative approaches for
assessing the ecological sustainability on in situ bioremediation.
FEMS Microbiol Rev 33:324–375
Pei XH, Zhan XH, Wang SM, Lin YS, Zhou LX (2010) Effects of a
biosurfactant and a synthetic surfactant on phenanthrene degradation by a Sphingomonas strain. Pedosphere 20:771–779
Pemberton JM, Fisher PR (1977) 2,4-D plasmids and persistence.
Nature 268:732–733
Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH
(2008) Microbial biodegradation of polyaromatic hydrocarbons.
FEMS Microbiol Rev 32:927–955
Perkovich BS (1996) Enhanced mineralization of [
14
C]atrazine in
Kochia scoparia rhizospheric soil from a pesticide-contaminated
site. Pestic Sci 46:391–396
Peters KE, Walters CC, Moldowan JM (2005) The biomarker guide,
vols 1 and 2. Cambridge University Press, Cambridge
Petric I, Bru D, Udikovic-Kolic N, Hrsak D, Philippot L, MartinLaurent F (2011) Evidence for shifts in the structure and abundance
of microbial community in a long-term PCB-contaminated soil
under bioremediation. J Hazard Mater 195:254–260
Phillips EJP, Landa E, Lovley DR (1995) Remediation of uranium
contaminated soils with bicarbonate extraction and microbial U
(VI) reduction. J Ind Microbiol 14:203–207
Pieper DH (2005) Aerobic degradation of polychlorinated biphenyls.
Appl Microbiol Biotechnol 67:170–191
Pilon-Smits E (2005) Phytoremediation. Annu Rev Plant Biol 56:15–39
Pineda-Flores G, Boll-Argu ¨ello G, Lira-Galeana C, Mesta-Howard AM
(2004) A microbial consortium isolated from a crude oil sample that
uses asphaltenes as carbon and energy source. Biodegradation
15:145–151
Piutti S, Marchand AL, Lagacherie B, Martin-Laurent F, Soulas G
(2002) Effect of successive cropping cycles with different plants
and repeated herbicide applications on the degradation of the
diclofop-methyl, bentazon, diuron, isoproturon and pendimethalin
in soil. Pest Manag Sci 58:303–312
Poelarends GJ, van Hylckama Vlieg JE, Marchesi JR, Freitas Dos
Santos LM, Janssen DB (1999) Degradation of 1,2-dibromoethane
by Mycobacterium sp. strain GP1. J Bacteriol 181(7):2050–2058
Prince RC (1993) Petroleum spill bioremediation in marine
environments. Crit Rev Microbiol 19:217–242
Prince RC (2010) Eucaryotic hydrocarbon degraders. In: Timmis KN,
Mc Genity TJ, Merr JR, Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg,
pp 2065–2078
Prince RC, Elmendorf DL, Lute JR, Hsu CS, Halth CE, Senlus JD,
Dechert GJ, Douglas GS, Butler EL (1994) 17. alpha. (H)-21. beta.
(H)-hopane as a con- served internal marker for estimating the
biodegradation of crude oil. Environ Sci Technol 28:142–145
Prince RC, Gramain A, McGenity TJ (2010) Procaryotic hydrocarbon
degraders. In: Timmis KN, Mc Genity TJ, Merr JR, Lorenzo V (eds)
Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/
Heidelberg, pp 1671–1692
Pritchard PH, Mueller JG, Rogers JC, Kremer FV, Glaser JA (1992) Oil
spill bioremediation : experiences, lessons and results from the
Exxon Valdez oil spill in Alaska. Biodegradation 3:315–335
Quensen JF III, Boyd SA, Tiedje JM (1990) Dechlorination of four
commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Appl Environ Microbiol
56:2360–2369
Rabus R (2005) Biodegradation of hydrocarbon under anoxic
conditions. In: Ollivier B, Magot M (eds) Petroleum microbiology.
ASM Press, Washington, DC, pp 277–299
Raillard S et al (2001) Novel enzyme activities and functional plasticity
revealed by recombining highly homologous enzymes. Chem Biol
8:891–898
Ramade F (2002) Dictionnaire encyclope ´dique de l’e ´cologie et des
sciences de l’environnement, 2eth edn. Dunod, Paris
Reanney DC (1976) Extrachromosomal elements as possible agents of
adaptation and development. Bacteriol Rev 40:552–590
Rea ´tegui E, Reynolds E, Kasinkas L, Aggarwal A, Sadowsky M, Aksan
A, Wackett L (2012) Silica gel-encapsulated AtzA biocatalyst for
atrazine biodegradation. Appl Microbiol Biotechnol 96:231–240
Ripp S, Nivens DE, Ahn Y, Werner C, Jarrell J IV, Easter JP, Cox CD,
Burlage RS, Sayler GS (2000) Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation
process monitoring and control. Environ Sci Technol 34:846–853
Roanne TM, Pepper IL, Miller RM (1996) Microbial remediation of
metals. In: Crawford RL, Crawford DL (eds) Bioremediation,
principles and application. Cambridge University Press, Cambridge,
pp 312–340
Robinson JB, Tuovinen OH (1984) Mechanisms of microbial resistance
and detoxification of mercury and organomercury compounds:
physiological, biochemical, and genetic analyses. Microbiol Rev
48:95–124
Rodrigues JLM, Kachel CA, Aiello MR, Quensen JF, Maltseva OV,
Tsoi TV, Tiedje JM (2006) Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400
(ohb) and Rhodococcus sp. Strain RHA1 (fcb). Appl Environ
Microbiol 72:2476–2482
Rojo F (2009) Degradation of alkanes by bacteria. Environ Microbiol
11(10):2477–2490
Ron EZ, Rosenberg E (2002) Biosurfactants and oil bioremediation.
Curr Opin Biotechnol 13:249–252
Rontani JF, Bosser-Jpulak F, Rambeloarisoa E, Bertrand J-C, Giusti G
(1985) Analytical study of asthart crude oil: asphaltenes biodegradation. Chemosphere 14:1413–1422
Rosenberg E, Ron EZ (2000) Biosurfactant. In: Dworkin M, Falkow S,
Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes.
Springer, New York, pp 834–849
Rousseaux S, Hartmann A, Lagacherie B, Piutti S, Andreux F, Soulas G
(2003) Inoculation of an atrazine-degrading strain, Chelatobacter
heintzii Cit1, in four different soils: effects of different inoculum
density. Chemosphere 51:569–576
16 Applied Microbial Ecology and Bioremediation
751