Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon
metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem
67:225–243
Hafeez F, Spor A, Breuil MC, Schwartz C, Martin-Laurent F, Philippot
L (2012) Distribution of bacteria and nitrogen-cycling microbial
communities along constructed Technosol depth-profiles. J Hazard
Mater 231:88–97
Harayama S, Kishira H, Kasai Y, Shutsubo K (1999) Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol
1:63–70
Harker AR, Olsen RH, Seidler RJ (1989) Phenoxyacetic acid degradation by the 2,4-dichlorophenoxyacetic acid (TFD) pathway of
plasmid pJP4: mapping and characterization of the tfd regulatory
gene, tfd R. J Bacteriol 171:314–320
Harkness MR et al (1993) In situ stimulation of aerobic PCB biodegradation in Hudson river sediments. Science 259:503–507
Harwood CS, Parales RE (1996) The β-ketoadipate pathway and the
biology of self-identity. Annu Rev Microbiol 50:553–590
Hatamian-Zarmi A, Shojaosadati A, Vasheghani-Farahani E,
Hosseinkhani S, Emamzadeh A (2009) Extensive biodegradation
of highly chlorinated biphenyl and Aroclor 1242 by Pseudomonas
aeruginosa TMU56 isolated from contaminated soils. Int
Biodeterior Biodegrad 63:788–794
Head IM, Jones DM, Larter ST (2003) Biological activity in the deep
subsurface and the origin of heavy oil. Nature 426:344–352
Heider J (2007) Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr Opin Chem Biol 11:188–194
Henze M, Harremoe ¨s P, La Cour Jansen J, Arvin E (2002) Wastewater
treatment: biological and chemical processes. Springer, Berlin
Hickey WJ, Fuster DJ, Lamar RT (1994) Transformation of atrazine in
soil by Phanerochaete chrysosporium. Soil Biol Biochem
26:1665–1671
Ho C, Applegate B, Banks MK (2007) Impact of microbial/plant
interactions on the transformation of polycyclic aromatic
hydrocarbons in the rhizosphere of Festuca arundinacea. Int J
Phytoremediation 9:107–114
Hogan DA, Buckley DH, Nakatsu CH, Schmidt TM, Hausinger RP
(1997) Distribution of the tfdA gene in soil bacteria that do not
degrade 2,4- dichlorophenoxyacetic acid (2,4-D). Microb Ecol
34:90–96
Hornafius TS, Quigley DC, Luyendik BNP (1999) The world’s most
spectacular marine hydrocarbon seeps (Coil Oil Point, Santa
Barbara Channel, California): quantification and emission.
J Geophys Res 104:20703–20711
Horvath RS (1972) Microbial co-metabolism and the degradation of
organic compounds in nature. Bacteriol Rev 36:146–155
Houot S, Topp E, Yassir A, Soulas G (2000) Dependence of accelerated
degradation of atrazine on soil pH in French and Canadian soils.
Soil Biol Biochem 32:615–625
Hurlbert MH, Krawieck S (1977) Cometabolism: a critique. J Theor
Biol 69:287–291
Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD
(2002) Manual of environmental microbiology, 2nd edn. ASM
Press, Washington, DC
Husain DR, Goutx M, Bezac C, Gilewicz M, Bertrand J-C (1997)
Morphological adaptation of Pseudomonas nautica strain 617 to
growth on eicosane and modes of eicosane uptake. Lett Appl
Microbiol 24:55–58
Imai R, Nagata Y, Fukuda M, Takagi M, Yano K (1991) Molecular
cloning of a Pseudomonas paucimobilis gene encoding a
17-kilodalton polypeptide that eliminates HCl molecules from
g-hexachlorocyclohexane. J Bacteriol 173:6811–6819
Itoh K, Kanda R, Sumita Y, Kim H, Kamagata Y, Suyama K,
Yamamoto H, Hausinger RP, Tiedje JM (2002) tfdA -like genes in
2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
cluster
in
a-proteobacteria. Appl Environ Microbiol 68:3449–3454
Iwamoto T, Nasu M (2001) Current bioremediation practice and perspective. J Biosci Bioeng 92:1–8
Jensen HL (1963) Carbon nutrition of some microorganisms
decomposing halogen-substituted aliphatic acids. Acta Agr Scand
13:404–412
Johnsen AR, Karlson U (2004) Evaluation of bacterial strategies to
promote the bioavailability of polycyclic aromatic hydrocarbons.
Appl Microbiol Biotechnol 63:452–459
Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAHdegradation in soil. Environ Pollut 133:71–84
Joner EJ, Leyval C (2003) Phytoremediation of organic pollutants using
mycorrhizal plants; a new aspect of rhizosphere interactions.
Agronomie 23:495–502
Julsing MK, Schrewe M, Cornelissen S, Hermann I, Schmid A, Bu ¨hler
B (2012) Outer membrane protein AlkL boosts biocatalytic
oxyfunctionalization of hydrophobic substrates in Escherichia
coli. Appl Environ Microbiol 78:5724–5733
Kalin N, Wheeler WN, Meinrath G (2005) The removal of uranium
form mining waste water using algal/microbial biomass. J Environ
Radioact 78:151–177
Khelifi N, Grossi V, Hamdi M, Dolla A, Tholozan J-L, Ollivier B,
Hirschler-Re ´a A (2010) Anaerobic oxidation of fatty acids and
alkenes by the hyperthermophilic sulfate-reducing archaeon
Archaeoglobus fulgidus. Appl Environ Microbiol 76:3057–3060
Kim E-J, Oh JE, Chang Y-S (2003) Effects of forest fire on the level and
distribution of PCDD/Fs and PAHs in soil. Sci Total Environ
311:177–189
Kim DU, Kim MS, Lim JS, Ka JO (2013) Widespread occurrence of the
tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1
and p712. Plasmid 69:243–248
Klein B, Grossi V, Bouriat P, Goulas P, Grimaud R (2008) Cytoplasmic
wax ester accumulation during biofilm-driven substrate assimilation
at the alkane-water interface by Marinobacter hydrocarbonoclasticus SP17. Res Microbiol 159:137–144
Knackmus HJ (1981) Degradation of halogenated and sulfonated
hydrocarbons. In: Leisinger T, Cook AM, Mu ¨ller R, Nu ¨sch J (eds)
Microbial degradation of xenobiotic and recalcitrant compounds.
Academic, London, pp 189–212
Kolic NU, Hrsak D, Begonja Kolar A, Petric I, Stipicevic S, Soulas G,
Martin-Laurent F (2007) Combined metabolic activity within an
atrazine-mineralizing community enriched from agrochemical factory soil. Int Biodeter Biodegr 60:299–307
Konhauser K (2007) Biomineralisation. In: Kohnhauser K (ed) Introduction to geomicrobiology. Blackwell, Oxford, pp 139–191
Kunapuli U, Griehler C, Beller HR, Meckenstock RU (2008) Identification of intermediates formed during anaerobic benzene degradation by iron-reducing enrichment culture. Environ Microbiol
10:1703–1712
La Farge B (1995) Le biogaz. Masson, Paris/Milan/Barcelona
Laemmli CM, Leveau JHJ, Zehnder AJB, van der Meer JR (2000)
Characterization of a second tfd gene cluster for chlorophenol and
chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha
JMP134 (pJP4). J Bacteriol 82:165–4172
Lajoie CA, Zylstra CJ, DeFlaun MF, Strom PF (1993) Development of
field application vectors for remediation of soils contaminated with
polychlorinated biphenyls. Appl Environ Microbiol 59:1735–1741
Lal R, Dogra C, Malhotra S, Sharma P, Pal R (2006) Diversity, distribution and divergence of lin genes in hexachlorocyclohexanedegrading sphingomonads. Trends Biotechnol 24:121–130
Lawniczak L, Marecik R, Chrzanowski L (2013) Contributions of
biosurfactants to natural or induced bioremediation. Appl Microbiol
Biotechnol 97:2327–2339
16 Applied Microbial Ecology and Bioremediation
749
metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem
67:225–243
Hafeez F, Spor A, Breuil MC, Schwartz C, Martin-Laurent F, Philippot
L (2012) Distribution of bacteria and nitrogen-cycling microbial
communities along constructed Technosol depth-profiles. J Hazard
Mater 231:88–97
Harayama S, Kishira H, Kasai Y, Shutsubo K (1999) Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol
1:63–70
Harker AR, Olsen RH, Seidler RJ (1989) Phenoxyacetic acid degradation by the 2,4-dichlorophenoxyacetic acid (TFD) pathway of
plasmid pJP4: mapping and characterization of the tfd regulatory
gene, tfd R. J Bacteriol 171:314–320
Harkness MR et al (1993) In situ stimulation of aerobic PCB biodegradation in Hudson river sediments. Science 259:503–507
Harwood CS, Parales RE (1996) The β-ketoadipate pathway and the
biology of self-identity. Annu Rev Microbiol 50:553–590
Hatamian-Zarmi A, Shojaosadati A, Vasheghani-Farahani E,
Hosseinkhani S, Emamzadeh A (2009) Extensive biodegradation
of highly chlorinated biphenyl and Aroclor 1242 by Pseudomonas
aeruginosa TMU56 isolated from contaminated soils. Int
Biodeterior Biodegrad 63:788–794
Head IM, Jones DM, Larter ST (2003) Biological activity in the deep
subsurface and the origin of heavy oil. Nature 426:344–352
Heider J (2007) Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr Opin Chem Biol 11:188–194
Henze M, Harremoe ¨s P, La Cour Jansen J, Arvin E (2002) Wastewater
treatment: biological and chemical processes. Springer, Berlin
Hickey WJ, Fuster DJ, Lamar RT (1994) Transformation of atrazine in
soil by Phanerochaete chrysosporium. Soil Biol Biochem
26:1665–1671
Ho C, Applegate B, Banks MK (2007) Impact of microbial/plant
interactions on the transformation of polycyclic aromatic
hydrocarbons in the rhizosphere of Festuca arundinacea. Int J
Phytoremediation 9:107–114
Hogan DA, Buckley DH, Nakatsu CH, Schmidt TM, Hausinger RP
(1997) Distribution of the tfdA gene in soil bacteria that do not
degrade 2,4- dichlorophenoxyacetic acid (2,4-D). Microb Ecol
34:90–96
Hornafius TS, Quigley DC, Luyendik BNP (1999) The world’s most
spectacular marine hydrocarbon seeps (Coil Oil Point, Santa
Barbara Channel, California): quantification and emission.
J Geophys Res 104:20703–20711
Horvath RS (1972) Microbial co-metabolism and the degradation of
organic compounds in nature. Bacteriol Rev 36:146–155
Houot S, Topp E, Yassir A, Soulas G (2000) Dependence of accelerated
degradation of atrazine on soil pH in French and Canadian soils.
Soil Biol Biochem 32:615–625
Hurlbert MH, Krawieck S (1977) Cometabolism: a critique. J Theor
Biol 69:287–291
Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD
(2002) Manual of environmental microbiology, 2nd edn. ASM
Press, Washington, DC
Husain DR, Goutx M, Bezac C, Gilewicz M, Bertrand J-C (1997)
Morphological adaptation of Pseudomonas nautica strain 617 to
growth on eicosane and modes of eicosane uptake. Lett Appl
Microbiol 24:55–58
Imai R, Nagata Y, Fukuda M, Takagi M, Yano K (1991) Molecular
cloning of a Pseudomonas paucimobilis gene encoding a
17-kilodalton polypeptide that eliminates HCl molecules from
g-hexachlorocyclohexane. J Bacteriol 173:6811–6819
Itoh K, Kanda R, Sumita Y, Kim H, Kamagata Y, Suyama K,
Yamamoto H, Hausinger RP, Tiedje JM (2002) tfdA -like genes in
2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
cluster
in
a-proteobacteria. Appl Environ Microbiol 68:3449–3454
Iwamoto T, Nasu M (2001) Current bioremediation practice and perspective. J Biosci Bioeng 92:1–8
Jensen HL (1963) Carbon nutrition of some microorganisms
decomposing halogen-substituted aliphatic acids. Acta Agr Scand
13:404–412
Johnsen AR, Karlson U (2004) Evaluation of bacterial strategies to
promote the bioavailability of polycyclic aromatic hydrocarbons.
Appl Microbiol Biotechnol 63:452–459
Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAHdegradation in soil. Environ Pollut 133:71–84
Joner EJ, Leyval C (2003) Phytoremediation of organic pollutants using
mycorrhizal plants; a new aspect of rhizosphere interactions.
Agronomie 23:495–502
Julsing MK, Schrewe M, Cornelissen S, Hermann I, Schmid A, Bu ¨hler
B (2012) Outer membrane protein AlkL boosts biocatalytic
oxyfunctionalization of hydrophobic substrates in Escherichia
coli. Appl Environ Microbiol 78:5724–5733
Kalin N, Wheeler WN, Meinrath G (2005) The removal of uranium
form mining waste water using algal/microbial biomass. J Environ
Radioact 78:151–177
Khelifi N, Grossi V, Hamdi M, Dolla A, Tholozan J-L, Ollivier B,
Hirschler-Re ´a A (2010) Anaerobic oxidation of fatty acids and
alkenes by the hyperthermophilic sulfate-reducing archaeon
Archaeoglobus fulgidus. Appl Environ Microbiol 76:3057–3060
Kim E-J, Oh JE, Chang Y-S (2003) Effects of forest fire on the level and
distribution of PCDD/Fs and PAHs in soil. Sci Total Environ
311:177–189
Kim DU, Kim MS, Lim JS, Ka JO (2013) Widespread occurrence of the
tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1
and p712. Plasmid 69:243–248
Klein B, Grossi V, Bouriat P, Goulas P, Grimaud R (2008) Cytoplasmic
wax ester accumulation during biofilm-driven substrate assimilation
at the alkane-water interface by Marinobacter hydrocarbonoclasticus SP17. Res Microbiol 159:137–144
Knackmus HJ (1981) Degradation of halogenated and sulfonated
hydrocarbons. In: Leisinger T, Cook AM, Mu ¨ller R, Nu ¨sch J (eds)
Microbial degradation of xenobiotic and recalcitrant compounds.
Academic, London, pp 189–212
Kolic NU, Hrsak D, Begonja Kolar A, Petric I, Stipicevic S, Soulas G,
Martin-Laurent F (2007) Combined metabolic activity within an
atrazine-mineralizing community enriched from agrochemical factory soil. Int Biodeter Biodegr 60:299–307
Konhauser K (2007) Biomineralisation. In: Kohnhauser K (ed) Introduction to geomicrobiology. Blackwell, Oxford, pp 139–191
Kunapuli U, Griehler C, Beller HR, Meckenstock RU (2008) Identification of intermediates formed during anaerobic benzene degradation by iron-reducing enrichment culture. Environ Microbiol
10:1703–1712
La Farge B (1995) Le biogaz. Masson, Paris/Milan/Barcelona
Laemmli CM, Leveau JHJ, Zehnder AJB, van der Meer JR (2000)
Characterization of a second tfd gene cluster for chlorophenol and
chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha
JMP134 (pJP4). J Bacteriol 82:165–4172
Lajoie CA, Zylstra CJ, DeFlaun MF, Strom PF (1993) Development of
field application vectors for remediation of soils contaminated with
polychlorinated biphenyls. Appl Environ Microbiol 59:1735–1741
Lal R, Dogra C, Malhotra S, Sharma P, Pal R (2006) Diversity, distribution and divergence of lin genes in hexachlorocyclohexanedegrading sphingomonads. Trends Biotechnol 24:121–130
Lawniczak L, Marecik R, Chrzanowski L (2013) Contributions of
biosurfactants to natural or induced bioremediation. Appl Microbiol
Biotechnol 97:2327–2339
16 Applied Microbial Ecology and Bioremediation
749