Phylogenetic and physiological comparisons of PAH-degrading bacteria from geographically diverse soils

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 71, Issue 4, 1997, Pages 329-343

  Mueller, J G ^a   Devereux, R ^b   Santavy, D L ^b   Lantz, S E ^a   Willis, S G ^c   Pritchard, P H ^d  

^a SBP Technologies Inc   (United States)

^b US EPA Natl Hlth Environ E   (United States)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

^d NAVAL RESEARCH LABORATORY   (United States)

Author keywords

16S rRNA; Biolog ; Bioremediation; Phenotype; Phospholipid ester linked fatty acid (GC FAME); Phylogeny; Polycyclic aromatic hydrocarbons (PAHs); Taxonomy

Indexed keywords

BACTERIAL RNA; CARBON; CREOSOTE; FATTY ACID; FLUORANTHENE; PHENANTHRENE; PHOSPHOLIPID; POLYCYCLIC AROMATIC HYDROCARBON; RNA 16S;

ARTICLE; BACTERIAL METABOLISM; BIODEGRADATION; BURKHOLDERIA CEPACIA; CONTROLLED STUDY; LIPID COMPOSITION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS; RNA SEQUENCE; SOIL MICROFLORA;

BACTERIAL TYPING TECHNIQUES; BIODEGRADATION, ENVIRONMENTAL; BURKHOLDERIA CEPACIA; CELL MEMBRANE; CREOSOTE; DNA, BACTERIAL; DNA, RIBOSOMAL; FLUORENES; GERMANY; MOLECULAR SEQUENCE DATA; NORWAY; PHENANTHRENES; PHENOTYPE; PHYLOGENY; POLYCYCLIC HYDROCARBONS, AROMATIC; PSEUDOMONADACEAE; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; UNITED STATES;

BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA CEPACIA; PSEUDOMONAS; SPHINGOMONAS;

EID: 0030983233     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1000277008064     Document Type: Article

References (71)

1. Bauer JE & Capone DG (1988) Effects of co-occurring aromatic hydrocarbons on the degradation of individual polycyclic aromatic hydrocarbons in marine sediment slurries. Appl. Environ. Microbiol. 54: 1649-1655
2. Berg JD, Nesgard B, Gundersen R, Lorentsen A & Bennett TE (1993) Washing and slurry phase biotreatment of creosote-contaminated soil. In: R. Hinchee (Ed) Proceedings 2nd International Symposium on In Situ and On-Site Bioreclamation (pp 489-495) San Diego, CA
3. Bochner BR (1989) 'Breathprints' at the microbial level: An automated redox-based technology quickly identifies bacteria according to their metabolic capabilities. ASM News. 55: 536-539
4. Boivin-Jahns V, Bianchi A, Ruimy R, Garcin J, Daumas S & Christen R (1995) Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl. Environ. Microbiol. 61: 3400-3406
5. Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation. 3: 351-368
6. Cerniglia CE (1993) Biodegradation of polycyclic aromatic hydrocarbons. Curr. Opin. Biotechnol. 4: 331-338
7. Chan E-C, Kuo J, Lin H-P & Mou DG (1991) Stimulation of n-alkane conversion to dicarboxylic acid by organic-solvent- and detergent-treated microbes. Appl. Microbiol. Biotechnol. 34: 772-777
8. Difco Laboratories (1984) Difco manual: Dehydrated culture media and reagents for microbiology. (p 184) Difco Laboratories, Inc. Detroit, MI
9. Dorsch M & Stackebrandt E (1992) Some modifications in the procedure for direct sequencing of PCR amplified 16S rDNA. J. Microbiol. Methods 16: 271-279
10. Dyksterhouse SE, Gray JP, Herwig RP, Lara JC & Staley JT (1995) Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon- degrading bacterium from marine sediments. Internat. J. Systematic Bacteriol. 45: 116-123
11. Focht JM & Westlake DWS (1988) Degradation of polycyclic aromatic hydrocarbons and aromatic heterocycles by a Pseudomonas species. Can. J. Microbiol. 34: 1135-1141
12. Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB & White DC (1995) Aromatic-degrading Sphingomonas isolates from the deep surface. Appl. Environ. Microbiol. 61: 1917-1922
13. García-Valdés E, Cozar E, Rotger R, Lalucat J & Ursing J (1988) New naphthalene-degrading marine Pseudomonas strains. Appl. Environ. Microbiol. 54: 2478-2485
14. Govindaswami M, Schmidt TM, White DC & Loper JC (1993) Phylogenetic analysis of a bacterial aerobic degrader of azo dyes. J. Bacteriol. 175: 6062-6066
15. Grifoll M, Selifonov SA, Gatlin CV & Chapman PJ (1995) Actions of a versatile fluorene-degrading bacterial isolate on polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 61: 3711-3723
16. Grosser RJ, Warshawsky D & Vestal JR (1991) Indigenous and enhanced mineralization of pyrene, benzo[a]pyrene, and carbazole in soils. Appl. Environ. Microbiol. 57: 3462-3469
17. Guckert JB & White DC (1986) Phospholipid, ester-linked fatty acid analysis in microbial ecology. In: Mecusar F & Gantar M (Eds) Perspectives in Microbial Ecology (pp 455-459) Proceedings of the 4th International Symposium on Microbial Ecology. Slovene Soc. for Microbiol., Ljubljana
18. Guerin WF & Jones GE (1989) Estuarine ecology of phenanthrene-degrading bacteria. Estuarine Coastal Shelf Sci. 29: 115-130
19. Heitkamp MA & Cerniglia CE (1988) Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl. Environ. Microbiol. 54: 1612-1614
20. Ho Y & Pritchard PH (1995) Classification of PAH-degrading bacteria by PAH utilization patterns and the comparison of metabolic products. Proceed. 8th International IGT Symposium on Gas, Oil, and Environmental Biotechnology, December 11-13, Colorado Springs, CO
21. Jacobs D (1990) SAS/GRAPH software and numerical taxonomy. In: Proceedings of the 15th Annual Users Group Conference (pp 1413-1418). SAS Institute, Inc., Cary, NC
22. Karlson U, Rojo F, Elsas JDV & Moore E (1996) Genetic and serological evidence for the recognition of four pentachlorophenol-degrading bacterial strains as a species of the genus Sphingomonas. System. Appl. Microbiol. (in press)
23. Kastner M, Breuer-Jammali M & Mahro B (1994) Enumeration and characterization of the soil microflora from hydrocarbon-contaminated soil sites able to mineralize polycyclic aromatic hydrocarbons (PAH). Appl. Microbiol. Biotechnol. 41: 267-273
24. Kelley I & Cerniglia CE (1991) The metabolism of fluoranthene by a species of Mycobacterium. J. Ind. Microbiol. 7: 19-26
25. Kiyohara H, Nagao K & Yana K (1981) Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbiol. 43: 454-457
26. Komukai S, Iwabuchi T, Ogawa H, Yamasoto K & Harayama S (1995) Proceed. Pseudomonas 95 Conf., Tsukuba City, Japan (p 141)
27. Krieger J (1992) Technique identifies bacteria that degrade wastes. Chemical and Engineering News, July27, p. 36
28. Laha S & Luthy RG (1991) Inhibition of phenanthrene mineralization by nonionic surfactants in soil-water systems. Environ. Sci. Technol. 25: 1920-1930
29. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E & Goodfellow M (Eds) Nucleic Acid Techniques in Bacterial Systematics (p 115-147). John Wiley & Sons, Chichester
30. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML & Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82: 6955-6959
31. Lantz SE, Lin J-E, Mueller JG & Pritchard PH (1995) Effects of surfactants on fluoranthene mineralization by Sphingomonas paucimobilis strain EPA505. In: Hinchee RE, Vogel cm, Brockman FJ (Eds) Microbial Processes for Bioremediation (pp 7-14). Battelle Press, Columbus, OH
32. Lantz SE, Montogomery MT, Schultz WW, Pritchard PH, Spargo BJ, & Mueller JG (1996) Constituents of organic wood preservatives that inhibit the fluoranthene-degrading activity of Sphingomonas paucimobilis strain EPA 505. Submitted to Environ Sci Tech.
33. Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbees R, Macke TJ, Marsh TL & Woese CR (1993) Nucleic Acids Res. 21: 3021-3023
34. Magurran AE (1988) Ecological diversity and its measurement. Princeton University Press, Princeton, NJ. 179 pp.
35. Menn F-M, Applegate BM & Sayler GS (1993) NAH plasmid- mediated catabolism of anthracene and phenanthrene to naphthoic acids. Appl. Environ. Microbiol. 59: 1938-1942
36. MIDI, Inc. (1993) Microbial identification system operating manual. Version 4. MIDI, Inc., Newark, NJ.
37. Moore ERB, Wittich R-M, Fortnagel P & Timmis KN (1993) 16S ribosomal RNA gene sequence characterization and phylogenetic analysis of a dibenzo-p-dioxin-degrading isolate within the new genus Sphingomonas. Lett. Appl. Microbiol. 17: 115-118
38. Mueller JG, Chapman PJ & Pritchard PH (1989) Action of a fluoranthene-utilizing bacterial community on polycyclic aromatic hydrocarbon components of creosote. Appl. Environ. Microbiol. 55: 3085-3090
39. Mueller JG, Chapman PJ, Blattmann BO & Pritchard PH (1990) Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl. Environ. Microbiol. 56: 1079-1086
40. Mueller JG, Lantz SE, Blattmann BO & Chapman PJ (1991a) Benchscale evaluation of alternative biological treatment processes for the remediation of pentachlorophenol- and creosote-contaminated materials: Solid-phase bioremediation. Environ. Sci. Technol. 25: 1045-105
41. - (1991b) Bench-scale evaluation of alternative biological treatment processes for the remediation of pentachlorophenol- and creosote-contaminated materials: Slurry-phase bioremediation. Environ. Sci. Technol. 25: 1055-1061
42. Mueller JG, Resnick SM, Shelton ME, & Pritchard PH (1992) Effect of inoculation of the biodegradation of weathered Prudhoe Bay crude oil. J. Indust. Microbiol. 10: 95-105
43. Mueller JG, Lantz SE, Colvin RJ, Ross D, Middaugh DP & Pritchard PH (1993) Strategy using bioreactors and specially-selected microorganisms for bioremediation of ground water contaminated with creosote and pentachlorophenol. Environ. Sci. Technol. 27: 691-698
44. Mueller JG, Lantz SE, Devereux R, Berg JD & Pritchard PH (1994) Studies on the microbial ecology of PAH biodegradation. In: Hinchee RE, Leeson A, Semprini L & Ong SK (Eds) Bioremediation of Chlorinated and Polycyclic Aromatic Hydrocarbon Compounds (pp 218-230) Lewis Publishers, Boca Raton, FL
45. Mueller JG, Cerniglia CE & Pritchard PH (1996) Bioremediation of environments contaminated by polycyclic aromatic hydrocarbons. In: Crawford R & Crawford D (Eds) Bioremediation: Principles and Applications. Chapter 5. Cambridge University Press
46. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR & Stahl DA (1986) Microbial ecology and evolution: A ribosomal RNA approach. Annu. Rev. Microbiol. 40: 57-263
47. Okpokwasili GC, Somerville CC, Grimes DJ & Colwell RR (1986) Plasmid-associated phenanthrene degradation by Chesapeake Bay sediment bacteria. A. Colloq. Inst. Fran. Rech. Exploit. Mer 3:601-610
48. Page AL, Miller RH & Keeney DR (1982) Methods of Soil Analysis: Part 2, Chemical and Microbiological Properties, 2nd ed. American Society of Agronomy, Madison, WI, 1159 pp
49. Palleroni NJ (1992) Introduction to the family Pseudomonadaceae. In: Balows A, Trüper HG, Dworkon M, Harder W & Schleifer K-H (Eds) The Prokaryotes, 2nd ed. (pp 3071-3085). Springer-Verlag, New York
50. Palleroni NJ, Kunisawa R, Contpoulou R & Doudoroff M (1973) Nucleic acid homologies in the genus Pseudomonas. Int. J. Syst. Bacteriol. 23: 333-339
51. Petrasek AC, IJ Kugelman, BM Austern, TA Pressley, LA Winslow & Wise RH (1983) Fate of toxic organic compounds in wastewater treatment plants. Journal WPCF 55: 1286-1296
52. Phillips I (1977) Pseudomonas paucimobilis, new species isolated from human clinical specimens in the hospital environment and other sources. Int. J. Syst. Bact. 27: 133-146
53. Pritchard PH, Lantz SE, Lin J-E & Mueller JG (1994) Metabolic and ecological factors affecting the bioremediation of PAH- and creosote-contaminated soil and water. In: U.S. EPA Annual Symposium on Bioremediation of Hazardous Wastes: Research, Development and Field Evaluations. San Francisco, CA, June 28-30 (pp 129-138). EPA/600/R-94/075
54. Pritchard PH, Mueller JG, Lantz SE & Santavy DL (1995) The potential importance of biodiversity in environmental biotechnology applications: Bioremediation of PAH-contaminated soils and sediments, Chapter 9. In: Allsopp D, Hawksworth EL & Colwell RR (Eds) Microbial Diversity and Ecosystem Function. CAB International
55. Resnick SM & Chapman PJ (1994) Physiological properties and substrate specificity of a pentachlorophenol-degrading Pseudomonas species. Biodegradation. 5: 47-54
56. Schocken MJ & Gibson DT (1984) Bacterial oxidation of the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene. Appl. Environ. Microbiol. 48: 10-16
57. Senoo K, Nishiyama M, Wada H & Matsumoto S (1992) Differences in dynamics between indigenous and inoculated Sphingomonas paucimobilis strain SS86 in soils. FEMS Microbial Ecol. 86: 311-320
58. Sneath PHA & Sokal RR (1973) Numerical taxonomy. W.H. Freeman and Co., San Francisco, CA 573 pp.
59. Stackebrandt E, Murray RGE & Trüper HG (1988) Proteobacteria classis nov., a name for the phylogenetic taxon that includes the 'purple bacteria and their relatives.' Int. J. Syst. Bacteriol. 3: 321-325
60. Takeuchi M, Sawada H, Oyaizu H & Yokota A (1994) Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria. Int. J. Syst. Bacteriol. 44: 308-314
61. Tiehm A (1994) Degradation of polycyclic aromatic hydrocarbons in the presence of synthetic surfactants. Appl. Environ. Microbiol. 60:258-263
62. Tonso NL, Matheson VG & Holben WE (1995) Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4-D. Microbial Ecology 30: 3-24
63. van Bruggen AHC, Jochimsen KN, Steinberger EM, Segers P & Gillis M (1993) Classification of Rhizomonas suberifaciens, an unnamed Rhizomonas species, and Sphingomonas spp. in rRNA superfamily IV. Int. J. Syst. Bacteriol. 43: 1-7
64. Vestal JR & White DC (1989) Lipid analysis in microbial ecology. BioScience. 39: 535-541
65. Walter U, Beyer M, Klein J, Rehm HJ (1991) Degradation of pyrene by Rhodococcus sp. UW1. Appl. Microbiol. Biotechnol. 34: 671-676
66. Weisburg WG, Barnes SM, Pelleteir DA & Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703
67. Weissenfels WD, Beyer M & Klein J (1990) Degradation of phenanthrene, fluorene and fluoranthene by pure bacterial cultures. Appl. Microbiol. Biotechnol. 32: 479-484
68. West PA, Okpokwasili GC, Brayton PR, Grimes DJ & Colwell RR (1984) Numerical taxonomy of phenanthrene-degrading bacteria isolated from the Chesapeake Bay. Appl. Environ. Microbiol. 48: 988-993
69. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T & Yamamoto H (1990) Proposals of Sphingomonas paucimobilis gen. nov. and comb, nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34: 99-119
70. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T & Arakawa M (1992) Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes, 1981) comb. nov. Microbiol. Immunol. 36: 1251-1275
71. Zylstra GJ & Gibson DT (1991) Aromatic hydrocarbon degradation: A molecular approach. In: Setlow JK (Ed) Genetic Engineering: Principles and Methods, Vol. 13 (pp 183-203). Plenum Press, New York