Assessment of the microbiological potential for the natural attenuation of petroleum hydrocarbons in a shallow aquifer system

Microbial Ecology

Volumn 36, Issue 3, 1998, Pages 349-361

  Stapleton, R D ^a   Sayler, G S ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RDNA; ALKANE HYDROXYLASE; AQUIFER; CATECHOL 2,3 DIOXYGENASE; CONTAMINATION; DNA DNA HYBRIDIZATION; DNA PROBE; JET FUEL; MICROBIAL ACTIVITY; NAPHTHALENE DIOXYGENASE; OLIGONUCLEOTIDE PROBE; PETROLEUM DERIVATIVE; RIBOSOMAL DNA; SPREAD PLATE ANALYSIS; TOLUENE DIOXYGENASE; TOLUENE MONOOXYGENASE; XYLENE MONOOXYGENASE;

AQUIFER; BIOREMEDIATION; MICROBIAL ACTIVITY; PETROLEUM HYDROCARBON;

EID: 0032412432     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002489900121     Document Type: Article

References (62)

1. Amman RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
2. Applegate BM, Matrabutham U, Sanseverino J, Sayler GS (1995) Biodegradation genes as marker genes in microbial ecosystems. Molecular Microbial Ecology Manual 6.1.8:1-14
3. Baker KH, Herson DS (1991) In situ bioremediation of contaminated aquifers and subsurface soils. Geomicrobiol J 8: 133-146
4. Balkwill DL (1989) Numbers, diversity, and morphological characteristics of aerobic chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina. Geomicrobiol J 7:33-52
5. Balkwill DL, Rucinsky TE, Casida LE (1977) Release of microorganisms from soil with respect to transmission electron microscopy viewing and plate counts. Antonie van Leeuwenhoek 43:73-87
6. Barker JF, Patrick GC, Major D (1987) Natural attenuation of aromatic hydrocarbons in a shallows and aquifer. Ground Water Monit Rev 7:64-71
7. Boggs JM, Young SC, Bemton DJ, Chung YC (1990) Hydrogeologic characterization of the MADE site. EPRI Report EN-6915, Project 2485-05. Electric Power Research Institute, Palo Alto, CA
8. Boggs JM, Young SC, Beard LM, Gelhar LW, Rehfeldt KR, Adams EE (1992) Field study of dispersion in a coarse-granular aquifer 1. Overview and site description. Water Res Res 28:3281-3291
9. Boggs JM, Beard LM, Waldrop WR, Stauffer TB, MacIntyre WG, Antworth CP (1993) Transport of tritium and four organic compounds during a natural gradient experiment (MADE-2). EPRI Report TR-101998, Project 2485-05. Electric Power Research Institute, Palo Alto, CA
10. Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81:1991-1995
11. Davis JW, Klier NJ, Carpenter CL (1994) Natural biological attenuation of benzene in groundwater beneath a manufacturing facility. Groundwater 32:215-226
12. Flemming JT, Sanseverino J, Sayler GS (1993) Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ Sci Technol 27:1068-1074
13. Fredrickson JK, Balkwill DM, Zachara JM, Li SW, Brockman FJ, Simmons MA (1991) Physiological diversity and distributions of heterotrophic bacteria in deep Cretaceous sediments in the Atlantic coastal plain. Appl Environ Microbiol 57:402-411
14. Fredrickson JK, Garland TR, Hicks RJ, Thomas JM, Li SW, McFadden KM (1989) Lithotrophic and heterotrophic bacteria in deep subsurface sediments and their relation to sediment properties. Geomicrobiol J 7:53-66
15. Ghiorse WC, Balkwill DL (1983) Enumeration and morphological characterization of bacteria indigenous to subsurface environments. Dev Ind Microbiol 24:213-227
16. Ghosal D, You I, Gunsalus IC (1987) Nucleotide sequence and expression of gene nahH of plasmid NAH7 and homology with gene xylE of TOL pWWO. Gene 55:19-28
17. Hales BA, Edwards C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668-675
18. Herbes SE, Schwall LR (1978) Microbial transformation of polycyclic aromatic hydrocarbons in pristine and petroleum contaminated sediments. Appl Environ Microbiol 35:306-316
19. Herrick JB, Madsen EL, Batt CA, Ghiorse WC (1993) Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bac-teria. Appl Environ Microbiol 59:687-696
20. Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL (1997) Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar contaminated field site. Appl Environ Microbiol 63:2330-2337
21. Holben WE, Schroeter BM, Calabrese VGM, Olsen RH, Kukor JK, Bierderbeck VO, Smith AE, Tiedje JM (1992) Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid. Appl Environ Microbiol 58:3941-3948
22. Holmes DS, Quigley CM (1981) A rapid boiling method for preparation of bacterial plasmids. Anal Biochem 114:193-197
23. Johnston WH, Stapleton RD, Sayler GS (1996) Direct extraction of microbial DNA from soils and sediments. Molecular Microbial Ecology Manual 1.3.2:1-9
24. Jablonski PE, Ferry JG (1992) Reductive declorination of trichloroethylene by the CO-reduced CO dehydrogenase enzyme complex from Methanosarcina thermophila FEMS Microbiol Lett. 95:55-60
25. Jones JG, Edington MA (1968) An ecological survey of hydrocarbon-oxidizing microorganisms. J Gen Microbiol 52:381-390
26. Klecka GM, Davis JW, Gray DR, Madsen SS (1994) Natural bioremediation of organic contaminants in groundwater: Cliffs-Dow Superfund Site. Groundwater 28:534-543
27. Kok M, Oldenhuis R, van der Linden MPG, Raatjes P, Kingma J, van Lelyveld PH, Witholt B (1989) The Pseudomonas oleovorans alkane hydroxylase gene: sequence and expression. J Biol Chem 264:5435-5441
28. Layton AC, Lajoie CA, Easter JP, Jernigan R, Sanseverino J, Sayler GS (1994) Molecular diagnostics and chemical analysis for assessing biodegradation of polychlorinated biphenyls in contaminated soils. J Ind Microbiol 13:392-401
29. Lee MD, Ward CH (1985) Biological methods for the restoration of contaminated aquifers. Environ Tox Chem 4:743-750
30. Lee MD, Thomas JM, Borden RC, Bedient PB, Ward CH, Wilson JT (1988) Biorestoration of aquifers contaminated with organic compounds. CRC Crit Rev Environ Control 18:29-89
31. Lovell CR, Piceno Y (1994) Purification of DNA from estuarine sediments. J Microbiol Meth 20:161-174
32. Lovell CR, Hui Y (1991) Design and testing of a functional group-specific DNA probe for the study of natural populations of acetogenic bacteria. Appl Environ Microbiol 57:2602-2609
33. MacIntyre WG, Antworth CP, Stauffer TB, Young RG (1997) Heterogeneity of sorption and transport related properties in a sand-gravel aquifer at Columbus, Mississippi. J Cont Hydrol (in press)
34. Madsen EL, Sinclair JL, Ghiorse WG (1991) In situ biodegradation: microbiological patterns in a contaminated aquifer. Science 252:830-833
35. National Research Council (1993) In Situ Bioremediation: When Does It Work? National Academy Press, Washington DC
36. Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Meth 7:57-66
37. Ogram A, Sayler GS (1988) The use of gene probes in the rapid analysis of natural microbial communities. J Ind Microbiol 3:281-292
38. Peterson SO, Klug MJ (1994) Effects of sieving, storage, and incubation temperature on the phospholipid fatty acid profile of a soil microbial community. Appl Environ Microbiol 60: 2421-2430
39. Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25:943-948
40. Phelps TJ, Rainone G, White DC, Fliermans CB (1989) Microbial activities in deep subsurface sediments. Geomicrobiol J 7:79-91
41. Promega (1992) Promega Technical Bulletin 009. Promega, Madison, WI
42. nd ed, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
43. Sanger F, Coulson AR, Hong GF, Hill DF, Peterson GB (1982) Nucleotide sequence of bacteriophage λ DNA. Mol Biol 162: 729-733
44. Sanseverino J, Werner C, Flemming J, Applegate B, King JMH, Sayler GS (1993) Molecular diagnostics of polycyclic aromatic hydrocarbon biodegradation in manufactured gas plant soils. Biodegradation 4:303-321
45. Sayler GS, Shields MS, Tedford ET, Breen A, Hooper SW, Sirotkin KM, Davis JW (1985) Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Appl Environ Microbiol 49:1295-1303
46. Sayler GS, Layton AC (1990) Environmental application of nucleic acid hybridization. Ann Rev Microbiol 44:625-648
47. Simon MJ, Osslund TD, Saunders R, Ensley BD, Suggs S, Harcourt A, Suen W, Cruden WL, Gibson DT, Zylstra GJ (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31-37
48. Smith GB, Tiedje JM (1992) Isolation and characterization of a nitrate reductase gene and its use as a probe for denitrifying bacteria. Appl Environ Microbiol 58:376-384
49. Song H-G, Bartha R (1990) Effects of jet fuel spills on the microbial community of soil. Appl Environ Microbiol 56:646-651
50. Song H-G, Wang X, Bartha R (1990) Bioremediation potential of terrestrial fuel spills. Appl Environ Microbiol 56:652-656
51. Spain JC, van Veld PA (1983) Adaptation of natural microbial communities to degradation of xenobiotic compounds: effects of concentration, exposure time, inoculum, and chemical structure. Appl Environ Microbiol 45:428-435
52. Stahl DA, Flescher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54: 1079-1084
53. Stapleton RD, Ripp S, Jimenez L, Koh SC, Fleming JT, Gregory IR, Sayler GS (1997) Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J Microbiol Meth 2:165-178
54. Stauffer TB, Boggs JM, MacIntyre WG (1997) Ten years of research in groundwater transport studies at Columbus Air Force Base, Mississippi. In: Gayler GS, Sanseverino J, Davis K (eds) Biotechnology in the Sustainable Environment. Plenum Press, New York, pp 85-96
55. Suzuki M, Hayakawa T, Shaw JP, Rekik M, Harayama S (1991) Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J Bacteriol 173:1690-1695
56. Thomas JM, Lee MD, Scott MJ, Ward CH (1989) Microbial ecology of the subsurface at an abandoned creosote waste site. J Ind Microbiol 4:109-120
57. Torsvik VL, Goksoyr J (1978) Determination of bacterial DNA in soil. Soil Biol Biochem 10:7-12
58. Voordouw G, Niviere V, Ferris FG, Fedorak PM, Westlake DWS (1990) Distribution of hydrogenase genes in Desulfovibrio spp. and their use in identification of species from the oil field environment. Appl Environ Microbiol 56:3748-3754
59. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured inhabitants in a natural community. Nature 345:63-65
60. Wilson JT, Mcnabb JF, Balkwill DL, Ghiorse WC (1983) Enumeration and characterization of bacteria indigenous to a shallow water-table aquifer. Groundwater 21:134-142
61. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316-322
62. Zylstra GJ, Gibson DT (1989) Toluene degradation by Pseudomonas putida F1. J Biol Chem 264:14940-14946