Monitoring microbial community dynamics to evaluate bioremediation

Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve

Volumn , Issue , 2014, Pages 293-312

  Baldwin, Brett R ^a   Ogles, Dora ^a   Nakatsu, Cindy H ^b  

^a Microbial Insights   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

Dioxygenase; Metagenomic; Microarrays; PCR DGGE; qPCR; RT qPCR; T RFLP

Indexed keywords

EID: 84927149682     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-4-431-54520-0_15     Document Type: Chapter

References (99)

1. Abu Laban N, Selesi D, Rattei T, Tischler P, Meckenstock RU. (2010). Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture. Environ Microbiol 12(10):2783-2796. doi: 10.1111/j.1462-2920.2010.02248.x
2. Achong GR, Rodriguez AM, Spormann AM. (2001). Benzylsuccinate synthase of Azoarcus sp. strain T: cloning, sequencing, transcriptional organization, and its role in anaerobic toluene and m -xylene mineralization. J Bacteriol 183(23):6763-6770. doi: 10.1128/jb.183.23.6763-6770.2001
3. Ahn Y, Sanseverino J, Sayler GS. (1999). Analyses of polycyclic aromatic hydrocarbon-degrading bacteria isolated from contaminated soils. Biodegradation 10(2):149-157. doi: 10.1023/a: 1008369905161
4. Amann RI, Ludwig W, Schleifer KH. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143-169
5. Baldwin BR, Nakatsu CH, Nies L. (2008). Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites. Water Res 42(3):723-731. doi: 10.1016/j.watres.2007.07.052
6. Baldwin BR, Biernacki A, Blair J, Purchase MP, Baker JM, Sublette K, Davis G, Ogles D. (2010). Monitoring gene expression to evaluate oxygen infusion at a gasoline-contaminated site. Environ Sci Technol 44(17):6829-6834. doi: 10.1021/es101356t
7. Bell TH, Yergeau E, Martineau C, Juck D, Whyte LG, Greer CW. (2011). Identification of nitrogenincorporating bacteria in petroleum-contaminated Arctic soils by using (15)N DNA-based stable isotope probing and pyrosequencing. Appl Environ Microbiol 77(12):4163-4171. doi: 10.1128/aem.00172-11
8. Beller HR, Edwards EA. (2000). Anaerobic toluene activation by benzylsuccinate synthase in a highly enriched methanogenic culture. Appl Environ Microbiol 66(12):5503-5505. doi: 10.1128/aem.66.12.5503-5505.2000
9. Beller HR, Kane SR, Legler TC, Alvarez PJJ. (2002). A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ Sci Technol 36(18):3977-3984. doi: 10.1021/es025556w
10. Bertoni G, Martino M, Galli E, Barbieri P. (1998). Analysis of the gene cluster encoding toluene/o -xylene monooxygenase from Pseudomonas stutzeri OX1. Appl Environ Microbiol 64(10): 3626-3632
11. Biegert T, Fuchs G, Heider J. (1996). Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate from toluene and fumarate. Eur J Biochem 238(3):661-668. doi: 10.1111/j.1432-1033.1996.0661w.x
12. Bordenave S, Goni-Urriza MS, Caumette P, Duran R. (2007). Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 73(19): 6089-6097. doi: 10.1128/aem.01352-07
13. Busch-Harris J, Sublette K, Roberts KP, Landrum C, Peacock AD, Davis G, Ogles D, Holmes WE, Harris D, Ota C, Yang X, Kolhatkar A. (2008). Bio-traps coupled with molecular biological methods and stable isotope probing demonstrate the in situ biodegradation potential of MTBE and TBA in gasoline-contaminated aquifers. Ground Water Monit R 28(4):47-62. doi: 10.1111/j.1745-6592.2008.00216.x
14. Butler CS, Mason JR. (1996). Structure-function analysis of the bacterial aromatic ringhydroxylating dioxygenases. In: Poole RK (ed) Advances in microbial physiology, vol 38. Academic, London, pp 47-84. doi: 10.1016/s0065-2911(08)60155-1
15. Cao B, Nagarajan K, Loh K-C. (2009). Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 85(2):207-228. doi: 10.1007/s00253-009-2192-4
16. Cavalca L, DellAmico E, Andreoni V. (2004). Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes. Appl Microbiol Biotechnol 64(4):576-587. doi: 10.1007/s00253-003-1449-6
17. Cerniglia CE. (1992). Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3(2):351-368. doi: 10.1007/bf00129093
18. Da Silva MLB, Alvarez PJJ. (2004). Enhanced anaerobic biodegradation of benzene-tolueneethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol 70(8):4720-4726. doi: 10.1128/aem.70.8.4720-4726.2004
19. DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL. (2011). PCR amplifi cation-Independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol 77:6313-6322. doi: 10.1128/aem.05262-11
20. DeBruyn JM, Chewning CS, Sayler GS. (2007). Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments. Environ Sci Technol 41(15):5426-5432. doi: 10.1021/es070406c
21. De Bruyn JM, Mead TJ, Wilhelm SW, Sayler GS. (2009). PAH biodegradative genotypes in Lake Erie sediments: evidence for broad geographical distribution of pyrene-degrading Mycobacteria. Environ Sci Technol 43(10):3467-3473. doi: 10.1021/es803348g
22. Denef VJ, Park J, Rodrigues JLM, Tsoi TV, Hashsham SA, Tiedje JM. (2003). Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5(10):933-943. doi: 10.1046/j.1462-2920.2003.00490.x
23. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. (2007). High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53(3):371-383. doi: 10.1007/s00248-006-9134-9
24. Dionisi HM, Chewning CS, Morgan KH, Menn F-M, Easter JP, Sayler GS. (2004). Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments. Appl Environ Microbiol 70(7):3988-3995. doi: 10.1128/aem.70.7.3988-3995.2004
25. DiStefano TD, Gossett JM, Zinder SH. (1991). Reductive dechlorination of high concentrations of tetrachloroethene to ethene by an anaerobic enrichment culture in the absence of methanogenesis. Appl Environ Microbiol 57(8):2287-2292
26. Dominguez R, da Silva M, McGuire T, Adamson D, Newell C, Alvarez P. (2008). Aerobic bioremediation of chlorobenzene source-zone soil in flow-through columns: performance assessment using quantitative PCR. Biodegradation 19(4):545-553. doi: 10.1007/s10532-007-9160-4
27. Duarte GF, Rosado AS, Seldin L, De Araujo W, van Elsas JD. (2001). Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl Environ Microbiol 67(3):1052-1062
28. Duetz WA, De Jong C, Williams PA, van Andel JG. (1994). Competition in chemostat culture between Pseudomonas strains that use different pathways for the degradation of toluene. Appl Environ Microbiol 60(8):2858-2863
29. Erickson BD, Mondello FJ. (1993). Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59(11):3858-3862
30. Ferrero M, Llobet-Brossa E, Lalucat J, García-Valdés E, Rosselló-Mora R, Bosch R. (2002). Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region. Appl Environ Microbiol 68(2):957-962. doi: 10.1128/aem.68.2.957-962.2002
31. Field JA, Sierra-Alvarez R. (2004). Biodegradability of chlorinated solvents and related chlorinated aliphatic compounds. Rev Environ Sci Biotechnol 3(3):185-254. doi: 10.1007/s11157-004-4733-8
32. Freedman DL, Gossett JM. (1989). Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions. Appl Environ Microbiol 55(9):2144-2151
33. Gentry T, Wickham G, Schadt C, He Z, Zhou J. (2006). Microarray applications in microbial ecology research. Micro Ecol 52(2):159-175. doi: 10.1007/s00248-006-9072-6
34. Gibson DT, Parales RE. (2000). Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11(3):236-243. doi: 10.1016/s0958-1669(00)00090-2
35. Hamady M, Knight R. (2009). Microbial community profi ling for human microbiome projects: tools, techniques, and challenges. Genome Res 19(7):1141-1152. doi: 10.1101/gr.085464.108
36. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, Dhaeseleer P, Holman H-YN, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204-208. doi: 10.1126/science.1195979
37. Heider J, Spormann AM, Beller HR, Widdel F. (1998). Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol Rev 22(5):459-473. doi: 10.1111/j.1574-6976.1998.tb00381.x
38. Hendrickson ER, Payne JA, Young RM, Starr MG, Perry MP, Fahnestock S, Ellis DE, Ebersole RC. (2002). Molecular analysis of dehalococcoides 16S ribosomal DNA from chloroethenecontaminated sites throughout North America and Europe. Appl Environ Microbiol 68(2): 485-495. doi: 10.1128/aem.68.2.485-495.2002
39. Hendrickx B, Dejonghe W, Boënne W, Brennerova M, Cernik M, Lederer T, Bucheli-Witschel M, Bastiaens L, Verstraete W, Top EM, Diels L, Springael D. (2005). Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an In situ mesocosm study. Appl Environ Microbiol 71(7):3815-3825. doi: 10.1128/aem.71.7.3815-3825.2005
40. Hendrickx B, Dejonghe W, Faber F, Boenne W, Bastiaens L, Verstraete W, Top EM, Springael D. (2006a). PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbiol Ecol 55(2):262-273. doi: 10.1111/j.1574-6941.2005.00018.x
41. Hendrickx B, Junca H, Vosahlova J, Lindner A, Rüegg I, Bucheli-Witschel M, Faber F, Egli T, Mau M, Schlömann M, Brennerova M, Brenner V, Pieper DH, Top EM, Dejonghe W, Bastiaens L, Springael D. (2006b). Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. J Microbiol Meth 64(2):250-265. doi: 10.1016/j.mimet.2005.04.018
42. Huang XJ, Lee LS, Nakatsu C. (2000). Impact of animal waste lagoon effl uents on chlorpyrifos degradation in soils. Environ Toxicol Chem 19(12):2864-2870. doi: 10.1002/etc.5620191202
43. Iwai S, Kurisu F, Urakawa H, Yagi O, Kasuga I, Furumai H. (2008). Development of an oligonucleotide microarray to detect di-and monooxygenase genes for benzene degradation in soil. FEMS Microbiol Lett 285(1):111-121. doi: 10.1111/j.1574-6968.2008.01223.x
44. Iwai S, Johnson TA, Chai B, Hashsham SA, Tiedje JM. (2011). Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Appl Environ Microbiol 77(11):3551-3557. doi: 10.1128/aem.00331-11
45. Johnson GR, Olsen RH. (1995). Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl Environ Microbiol 61(9): 3336-3346
46. Kahng H-Y, Malinverni JC, Majko MM, Kukor JJ. (2001). Genetic and functional analysis of the tbc operons for catabolism of alkyl-and chloroaromatic compounds in Burkholderia sp. Strain JS150. Appl Environ Microbiol 67(10):4805-4816. doi: 10.1128/aem.67.10.4805-4816.2001
47. Kane SR, Beller HR, Legler TC, Anderson RT. (2002). Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading, ferric iron-reducing Geobacter metallireducens. Biodegradation 13(2):149-154. doi: 10.1023/a:1020454831407
48. Kao CM, Chen CS, Tsa FY, Yang KH, Chien CC, Liang SH, Yang CA, Chen SC. (2010). Application of real-time PCR, DGGE fi ngerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume. J Hazard Mater 178(1-3):409-416. doi: 10.1016/j.jhazmat.2010.01.096
49. Kasai Y, Takahata Y, Manefield M, Watanabe K. (2006). RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline contaminated groundwater. Appl Environ Microbiol 72(5):3586-3592
50. Kazy S, Monier A, Alvarez P. (2010). Assessing the correlation between anaerobic toluene degradation activity and bssA concentrations in hydrocarbon-contaminated aquifer material. Biodegradation 21(5):793-800. doi: 10.1007/s10532-010-9344-1
51. Khan AA, Wang R-F, Cao W-W, Doerge DR, Wennerstrom D, Cerniglia CE. (2001). Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67(8):3577-3585. doi: 10.1128/aem.67.8.3577-3585.2001
52. Kniemeyer O, Fischer T, Wilkes H, Glöckner FO, Widdel F. (2003). Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 69(2):760-768. doi: 10.1128/aem.69.2.760-768.2003
53. Kong W, Nakatsu CH. (2010). Optimization of RNA extraction for PCR quantifi cation of aromatic compound degradation genes. Appl Environ Microbiol 76(4):1282-1284. doi: 10.1128/aem.01939-09
54. Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M. (2011). Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl Environ Microbiol 77(22):7962-7974. doi: 10.1128/aem.05402-11
55. Krieger CJ, Beller HR, Reinhard M, Spormann AM. (1999). Initial reactions in anaerobic oxidation of m -xylene by the denitrifying bacterium Azoarcus sp. strain T. J Bacteriol 181(20): 6403-6410
56. Kropp KG, Davidova IA, Sufl ita JM. (2000). Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl Environ Microbiol 66(12):5393-5398. doi: 10.1128/aem.66.12.5393-5398.2000
57. Laurie AD, Lloyd-Jones G. (1999). The phn Genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181(2): 531-540
58. Laurie AD, Lloyd-Jones G. (2000). Quantifi cation of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66(5):1814-1817. doi: 10.1128/aem.66.5.1814-1817.2000
59. Leahy JG, Olsen RH. (1997). Kinetics of toluene degradation by toluene-oxidizing bacteria as a function of oxygen concentration, and the effect of nitrate. FEMS Microbiol Ecol 23(1):23-30. doi: 10.1111/j.1574-6941.1997.tb00387.x
60. Lee PKH, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L. (2012). Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ Sci Technol 46(2):1044-1054. doi: 10.1021/es203005k
61. Liu WT, Marsh TL, Cheng H, Forney LJ. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11):4516-4522
62. Lloyd-Jones G, Laurie AD, Hunter DWF, Fraser R. (1999). Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29(1):69-79. doi: 10.1111/j.1574-6941.1999.tb00599.x
63. Lu X, Wilson JT, Kampbell DH. (2006). Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at fi eld scale. Water Res 40(16):3131-3140. doi: 10.1016/j.watres.2006.05.030
64. Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee Y-J, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, DHaeseleer P, Hazen TC, Zhou J. (2011). Microbial gene functions enriched in the deepwater horizon deep-sea oil plume. ISME J 6(2):451-460. doi: 10.1038/ismej.2011.91
65. Maymó-Gatell X, Anguish T, Zinder SH. (1999). Reductive dechlorination of chlorinated ethenes and 1,2-dichloroethane by Dehalococcoides ethenogenes 195. Appl Environ Microbiol 65(7):3108-3113
66. Mohanty SR, Kollah B, Brodie EL, Hazen TC, Roden EE. (2011). 16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment. Microbes Environ 26(3):261-265. doi: 10.1264/jsme2.ME11111
67. Muyzer G, De Waal EC, Uitterlinden AG. (1993). Profi ling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplifi ed genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695-700
68. Muyzer G, Hottentrager S, Teske AP, Wawer C. (1996). Denaturing gradient gel electrophoresis of PCR-amplifi ed 16S rDNA-A new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans A, van Elsas JD, De Bruijn FJ (eds) Molecular microbial ecology manual, vol 344. Kluwer Academic Publishers, Nowell, pp 1-23
69. Nakatsu CH, Marsh TL. (2007). Analysis of microbial communities with denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism. In: Reddy CA, Beveridge TL, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. ASM, Washington, DC, pp 909-923
70. Nakatsu CH, Torsvik V, Øvreås L. (2000). Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64(4):1382-1388
71. Nakatsu CH, Carmosini N, Baldwin B, Beasley F, Kourtev P, Konopka A. (2005). Soil microbial community responses to additions of organic carbon substrates and heavy metals (Pb and Cr). Appl Environ Microbiol 71(12):7679-7689. doi: 10.1128/aem.71.12.7679-7689.2005
72. Nebe J, Baldwin BR, Kassab RL, Nies L, Nakatsu CH. (2009). Quantifi cation of aromatic oxygenase genes to evaluate enhanced bioremediation by oxygen releasing materials at a gasolinecontaminated site. Environ Sci Technol 43(6):2029-2034. doi: 10.1021/es900146f
73. Níchadhain SM, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ. (2006). Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72(6):4078-4087. doi: 10.1128/aem.02969-05
74. Ogino A, Koshikawa H, Nakahara T, Uchiyama H. (2001). Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses. J Appl Microbiol 91(4):625-635. doi: 10.1046/j.1365-2672.2001.01424.x
75. Ogram A, Sun W, Brockman FJ, Fredrickson JK. (1995). Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl Environ Microbiol 61(2):763-768
76. Pandey J, Chauhan A, Jain RK. (2009). Integrative approaches for assessing the ecological sustainability of in situ bioremediation. FEMS Microbiol Rev 33(2):324-375. doi: 10.1111/j.1574-6976.2008.00133.x
77. Parales RE, Resnick SM, Yu C-L, Boyd DR, Sharma ND, Gibson DT. (2000). Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the a subunit. J Bacteriol 182(19):5495-5504. doi: 10.1128/jb.182.19.5495-5504.2000
78. Park J-W, Crowley D. (2006). Dynamic changes in nahAc gene copy numbers during degradation of naphthalene in PAH-contaminated soils. Appl Microbiol Biotech 72(6):1322-1329. doi: 10.1007/s00253-006-0423-5
79. Rhee S-K, Liu X, Wu L, Chong SC, Wan X, Zhou J. (2004). Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70(7):4303-4317. doi: 10.1128/aem.70.7.4303-4317.2004
80. Rodríguez-Martínez E, Pérez E, Schadt C, Zhou J, Massol-Deyá A. (2006). Microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (Vega Baja, Puerto Rico). Int J Environ Res Public Health 3(3):292-300
81. Roling WFM, Milner MG, Jones DM, Fratepietro F, Swannell RPJ, Daniel F, Head IM. (2004). Bacterial community dynamics and hydrocarbon degradation during a fi eld-scale evaluation of bioremediation on a mudfl at beach contaminated with buried oil. Appl Environ Microbiol 70(5):2603-2613
82. Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU. (2010). Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol 192(1):295-306. doi: 10.1128/jb.00874-09
83. Shendure J, Ji HL. (2008). Next-generation DNA sequencing. Nat Biotechnol 26(10):1135-1145. doi: 10.1038/nbt1486
84. Spormann AM, Widdel F. (2000). Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11(2):85-105. doi: 10.1023/a:1011122631799
85. Staley JT, Konopka A. (1985). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321-346
86. Stephen JR, Chang YJ, Gan YD, Peacock A, Pfi ffner SM, Barcelona MJ, White DC, Macnaughton SJ. (1999). Microbial characterization of a JP-4 fuel-contaminated site using a combined lipid biomarker/polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)-based approach. Environ Microbiol 1(3):231-241
87. Sublette K, Peacock A, White D, Davis G, Ogles D, Cook D, Kolhatkar R, Beckmann D, Yang X. (2006). Monitoring subsurface microbial ecology in a sulfate-amended, gasoline-contaminated aquifer. Ground Water Monit R 26(2):70-78. doi: 10.1111/j.1745-6592.2006.00072.x
88. Taylor PM, Janssen PH. (2005). Variations in the abundance and identity of class II aromatic ring-hydroxylating dioxygenase genes in groundwater at an aromatic hydrocarboncontaminated site. Environ Microbiol 7(1):140-146. doi: 10.1111/j.1462-2920.2004.00679.x
89. Taylor PM, Medd JM, Schoenborn L, Hodgson B, Janssen PH. (2002). Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria. FEMS Microbiol Lett 216(1):61-66. doi: 10.1111/j.1574-6968.2002.tb11415.x
90. Tuomi PM, Salminen JM, Jørgensen KS. (2004). The abundance of nahAc genes correlates with the 14 C-naphthalene mineralization potential in petroleum hydrocarbon-contaminated oxic soil layers. FEMS Microbiol Ecol 51(1):99-107. doi: 10.1016/j.femsec.2004.07.011
91. Widada J, Nojiri H, Kasuga K, Yoshida T, Habe H, Omori T. (2002a). Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol 58(2):202-209. doi: 10.1007/s00253-001-0880-9
92. Widada J, Nojiri H, Omori T. (2002b). Recent developments in molecular techniques for identification and monitoring of xenobiotic-degrading bacteria and their catabolic genes in bioremediation. Appl Microbiol Biotechnol 60:45-59. doi: 10.1007/s00253-002-1072-y
93. Wilson MS, Bakermans C, Madsen EL. (1999). In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl Environ Microbiol 65(1):80-87
94. Winderl C, Schaefer S, Lueders T. (2007). Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 9(4):1035-1046. doi: 10.1111/j.1462-2920.2006.01230.x
95. Winderl C, Anneser B, Griebler C, Meckenstock RU, Lueders T. (2008). Depth-resolved quantifi cation of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl Environ Microbiol 74(3):792-801. doi: 10.1128/aem.01951-07
96. Witzig R, Junca H, Hecht H-J, Pieper DH. (2006). Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases. Appl Environ Microbiol 72(5):3504-3514. doi: 10.1128/aem.72.5.3504-3514.2006
97. Yagi JM, Madsen EL. (2009). Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer. Appl Environ Microbiol 75(20):6478-6487. doi: 10.1128/aem.01091-09
98. Yeates C, Holmes AJ, Gillings MR. (2000). Novel forms of ring-hydroxylating dioxygenases are widespread in pristine and contaminated soils. Environ Microbiol 2(6):644-653. doi: 10.1046/j.1462-2920.2000.00147.x
99. Yergeau E, Arbour M, Brousseau R, Juck D, Lawrence JR, Masson L, Whyte LG, Greer CW. (2009). Microarray and real-time PCR analyses of the responses of high-Arctic soil bacteria to hydrocarbon pollution and bioremediation treatments. Appl Environ Microbiol 75(19):6258-6267. doi: 10.1128/aem.01029-09