Functional genes reveal the intrinsic PAH biodegradation potential in creosote-contaminated groundwater following in situ biostimulation

Applied Microbiology and Biotechnology

Volumn 84, Issue 1, 2009, Pages 169-182

  Nyyssönen, Mari ^a   Kapanen, Anu ^a   Piskonen, Reetta ^b   Lukkari, Tuomas ^c   Itävaara, Merja ^a  

^a VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^b WSP Environmental Ltd   (Finland)

^c Ramboll Finland Oy   (Finland)

Author keywords

Air sparging; Bioremediation; Functional gene; Gene array; Nutrient infiltration; Polycyclic aromatic hydrocarbon

Indexed keywords

16S RRNA GENE; AIR SPARGING; ANOXIC GROUNDWATER; BIODEGRADATION POTENTIALS; BIOSTIMULATION; CONTAMINANT CONCENTRATIONS; CONTAMINANT PLUME; CONTAMINATED GROUNDWATER; DENITRIFYING BACTERIA; FLUORESCEIN DIACETATE; FUNCTIONAL GENE; FUNCTIONAL GENES; GENE ARRAY; HYDROCARBON BIODEGRADATION; IN-FIELD; IN-SITU; INTRINSIC BIODEGRADATION; MONITORING WELLS; NAPHTHALENE DIOXYGENASE; PILOT SCALE; POLYMERASE CHAIN REACTION; POTENTIAL TOOL; REAL-TIME PCR; SULPHATES;

AIR; AMPLIFICATION; AROMATIC HYDROCARBONS; BACTERIA; BIOCHEMISTRY; BIODEGRADABLE POLYMERS; BIOREMEDIATION; BIOTECHNOLOGY; CONTAMINATION; DEGRADATION; DENITRIFICATION; GENES; GROUNDWATER; GROUNDWATER POLLUTION; HYDROGEOLOGY; MICROBIOLOGY; NAPHTHALENE; NUTRIENTS; ORGANIC COMPOUNDS; POLLUTION; POLYCYCLIC AROMATIC HYDROCARBONS; SEEPAGE; SOIL MECHANICS; TERNARY SYSTEMS;

BIODEGRADATION;

CREOSOTE; FLUORESCEIN DIACETATE; GROUND WATER; NAPHTHALENE DERIVATIVE; NAPHTHALENE DIOXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON; RNA 16S; UNCLASSIFIED DRUG;

BIODEGRADATION; CREOSOTE; DENITRIFICATION; GENE EXPRESSION; GROUNDWATER POLLUTION; INFILTRATION; NITRIFYING BACTERIUM; PAH; POLYMERASE CHAIN REACTION;

ARTICLE; BIOREMEDIATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DENITRIFICATION; DNA HYBRIDIZATION; GENE IDENTIFICATION; MICROBIAL COMMUNITY; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PLUME; REAL TIME POLYMERASE CHAIN REACTION; SULFATE REDUCING BACTERIUM; WATER CONTAMINATION; WATER TREATMENT;

BACTERIA; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; CREOSOTE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYCYCLIC HYDROCARBONS, AROMATIC; WATER POLLUTANTS, CHEMICAL;

EID: 68349093971     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-009-2022-8     Document Type: Article

References (44)

1. Alef K (1995) Estimation of the hydrolysis of fluorescein diacetate. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry, 3rd edn. Academic, London, UK, pp 232-233
2. RI Amann W Ludwig KH Schleifer 1995 Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol Rev 59 143 169
3. RT Anderson DR Lovley 1997 Ecology and biochemistry of in situ groundwater bioremediation Adv Microb Ecol 15 289 350
4. C Bakermans EL Madsen 2002 Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters Microb Ecol 44 95 106 10.1007/s00248-002-0005-8
5. C Bakermans AM Hohnstock-Ashe S Padmanabhan P Padmanabhan EL Madsen 2002 Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communities Microb Ecol 44 107 117 10.1007/s00248-002-0004-9
6. BR Baldwin CH Nakatsu L Nies 2008 Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites Water Res 42 723 731 10.1016/j.watres.2007.07.052 (Pubitemid 351625249)
7. L Cavalca E Dell'Amico V Andreoni 2004 Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes Appl Microbiol Biotechnol 64 576 587 10.1007/s00253-003-1449-6
8. CE Cerniglia 1984 Microbial metabolism of polycyclic aromatic hydrocarbons Adv Appl Microbiol 30 31 71
9. VJ Denef J Park JL Rodrigues TV Tsoi SA Hashsham JM Tiedje 2003 Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities Environ Microbiol 5 933 943 10.1046/j.1462-2920.2003.00490.x (Pubitemid 37181564)
10. TJ Gentry GS Wickham CW Schadt Z He J Zhou 2006 Microarray applications in microbial ecology research Microb Ecol 52 159 175 10.1007/s00248-006-9072-6 (Pubitemid 44392971)
11. AS Ferguson WE Huang KA Lawson R Doherty O Gibert KW Dickson AS Whiteley LA Kulakov IP Thompson RM Kalin MJ Larkin 2007 Microbial analysis of soil and groundwater from a gasworks site and comparison with a sequenced biological reactive barrier remediation process J Appl Microbiol 102 1227 1238 10.1111/j.1365-2672.2007.03398.x (Pubitemid 46633435)
12. Z He TJ Gentry CW Schadt L Wu J Liebich SC Chong Z Huang W Wu B Gu P Jardine C Criddle J Zhou 2007 GeoChip: a comprehensive microarray for investigating biochemical, ecological and environmental processes ISME J 1 67 77 10.1038/ismej.2007.2 (Pubitemid 46717133)
13. S Iwai F Kurisu H Urakawa O Yagi I Kasuga H Furumai 2008 Development of an oligonucleotide microarray to detect di- and monooxygenase genes for benzene degradation in soil FEMS Microbiol Lett 285 111 121 10.1111/j.1574-6968.2008. 01223.x (Pubitemid 352000220)
14. CO Jeon M Park HS Ro W Park EL Madsen 2006 The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control Appl Environ Microbiol 72 1086 1095 10.1128/AEM.72.2.1086-1095.2006 (Pubitemid 43271214)
15. AR Johnsen U Karlson 2005 PAH degradation capacity of soil microbial communities-does it depend on PAH exposure? Microb Ecol 50 488 495 10.1007/s00248-005-0022-5 (Pubitemid 41832715)
16. RL Kepner JR Pratt 1994 Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present Microbiol Rev 58 603 615
17. JG Leahy RR Colwell 1990 Microbial degradation of hydrocarbons in the environment Microbiol Rev 54 305 315
18. P Liao T Chen P Chung 2001 A fast algorithm for multilevel thresholding J Inf Sci Eng 17 713 727
19. G Muyzer EC de Waal AG Uitterlinden 1993 Profiling complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Appl Environ Microbiol 59 695 700
20. NRC (1993) In situ bioremediation; when does it work?. National Academy Press, Washington, DC
21. M Nyyssönen R Piskonen M Itävaara 2006 A targeted real-time PCR assay for studying naphthalene degradation in the environment Microb Ecol 52 533 543 10.1007/s00248-006-9082-4 (Pubitemid 44899546)
22. M Nyyssönen R Piskonen M Itävaara 2008 Monitoring aromatic hydrocarbon biodegradation by functional marker genes Environ Pollut 154 192 202 10.1016/j.envpol.2007.10.009 (Pubitemid 351758975)
23. WR Pearson DJ Lipman 1988 Improved tools for biological sequence comparison Proc Natl Acad Sci U S A 85 2444 2448
24. R Piskonen M Itävaara 2004 Evaluation of chemical pretreatment of contaminated soil for improved PAH bioremediation Appl Microbiol Biotechnol 65 627 634 10.1007/s00253-004-1679-2 (Pubitemid 39410071)
25. R Piskonen M Nyyssönen M Itävaara 2005 Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry Biodegradation 16 127 134 10.1007/s10532-004-4893-9
26. R Piskonen M Nyyssönen M Itävaara 2008 Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes Biodegradation 19 883 895 10.1007/s10532-008-9190-6
27. T Pulli M Höyhtyä H Söderlund K Takkinen 2005 One-step homogeneous immunoassay for small analytes Anal Chem 77 2637 2642 10.1021/ac048379l (Pubitemid 40562768)
28. SK Rhee X Liu L Wu SC Chong X Wan J Zhou 2004 Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays Appl Environ Microbiol 70 4303 4317 10.1128/AEM.70.7.4303-4317.2004 (Pubitemid 38969779)
29. Riser-Roberts E (1998) Remediation of petroleum contaminated soils: biological, physical, and chemical processes. CRC, New York
30. DB Ringelberg JW Talley EJ Perkins SG Tucker RG Luthy EJ Bouwer HL Fredrickson 2001 Succession of phenotypic, genotypic, and metabolic community characteristics during in vitro bioslurry treatment of polycyclic aromatic hydrocarbon-contaminated sediments Appl Environ Microbiol 67 1542 1550 10.1128/AEM.67.4.1542-1550.2001 (Pubitemid 33644921)
31. AI Saeed V Sharov J White J Li W Liang N Bhagabati J Braisted M Klapa T Currier M Thiagarajan A Sturn M Snuffin A Rezantsev D Popov A Ryltsov E Kostukovich I Borisovsky Z Liu A Vinsavich V Trush J Quackenbush 2003 TM4: a free, open-source system for microarray data management and analysis Biotechniques 34 374 8
32. JM Salminen PM Tuomi KS Jørgensen 2008 Functional gene abundances (nahAc, alkB, xylE) in the assessment of the efficacy of bioremediation Appl Biochem Biotechnol 151 638 652 10.1007/s12010-008-8275-3
33. SFS (1979) Determination of pH-value of water. Finnish Standards Association, SFS 3021, Helsinki
34. SFS (1980) Metal content of water, sludge and sediment determined by atomic absorption spectroscopy, atomization in flame. Special guidelines for lead, iron, cadmium, cobalt, copper, nickel and zinc. Finnish Standards Association, SFS 3047, Helsinki
35. SFS (1994) Water quality. Determination of electrical conductivity (ISO 7888:1985). Finnish Standards Association, SFS 27888, Helsinki
36. SFS (1997) Water analysis. Guidelines for the determination of total organic carbon (TOC) and dissolved organic carbon (DOC). Finnish Standards Association, SFS 1484, Helsinki
37. JR Stephen YJ Chang YD Gan A Peacock SM Pfiffner MJ Barlecona DC White SJ Macnaughton 1999 Microbial characterization of a JP-4 fuel contaminated site using a combined lipid biomarker/PCR-DGGE based approach Environ Microbiol 1 231 41 10.1046/j.1462-2920.1999.00030.x
38. S Stübner T Wind R Conrad 1998 Sulfur oxidation of in rice field soil: activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria Syst Appl Microbiol 21 569 578
39. MT Suzuki SJ Giovannoni 1996 Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR Appl Environ Microbiol 62 625 630
40. T Tolker-Nielsen UC Brinch PC Ragas JB Andersen CS Jacobsen S Molin 2000 Development and dynamics of Pseudomonas sp. biofilms J Bacteriol 182 6482 6489
41. 14C-naphthalene mineralization potential in petroleum hydrocarbon-contaminated oxic soil layers FEMS Microbiol Ecol 51 99 107 10.1016/j.femsec.2004.07.011 (Pubitemid 39647643)
42. MS Wilson C Bakermans EL Madsen 1999 In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxyegnase mRNA transcripts from groundwater Appl Environ Microbiol 65 80 87
43. L Wu X Liu CW Schadt J Zhou 2006 Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification Appl Environ Microbiol 72 4931 4941 10.1128/AEM.02738-05 (Pubitemid 44078823)
44. NY Zhou SL Fuenmayor PA Williams 2001 nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism J Bacteriol 183 700 708 10.1128/JB.183.2.700-708.2001 (Pubitemid 32048130)