Culture-independent analysis of bacterial fuel contamination provides insight into the level of concordance with the standard industry practice of aerobic cultivation

Applied and Environmental Microbiology

Volumn 77, Issue 13, 2011, Pages 4527-4538

  White, Judith ^a   Gilbert, Jack ^b,c   Hill, Graham ^d   Hill, Edward ^d   Huse, Susan M ^e   Weightman, Andrew J ^a   Mahenthiralingam, Eshwar ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d ECHA Microbiology Ltd   (United Kingdom)

^e MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; 16S RRNA GENE; AEROBIC CULTIVATION; AEROBIC CULTURES; BACTERIAL DIVERSITY; BETAPROTEOBACTERIA; BURKHOLDERIA; CONTAMINATED FUELS; DENATURING GRADIENT GEL ELECTROPHORESIS; FIRMICUTES; FUEL CONTAMINATION; FUEL SAMPLES; GAMMAPROTEOBACTERIA; GENOTYPING; HALOMONAS; INDUSTRIAL SITES; INDUSTRY PRACTICES; MARINOBACTER; PROTEOBACTERIA; PSEUDOMONAS SP; PYROSEQUENCING;

AUTOMOBILE FUEL TANKS; BACTERIA; BACTERIOLOGY; CONTAMINATION; DIESEL FUELS; ELECTROPHORESIS; FUELS; GENES; IMPURITIES; INDUSTRIAL MANAGEMENT; INDUSTRY; RNA;

FUEL TANKS;

BACTERIAL DNA; FOSSIL FUEL; RIBOSOME DNA; RNA 16S;

BACTERIUM; DIESEL; DOMINANCE; ELECTROKINESIS; FUEL; GENETIC ANALYSIS; GENOTYPE; IDENTIFICATION METHOD; INDUSTRIAL PRACTICE; MICROBIAL COMMUNITY; OXIC CONDITIONS; SPECIES DIVERSITY;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BACTERIA; BACTERIOLOGICAL TECHNIQUES; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FOSSIL FUELS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

ACHROMOBACTER; BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; BURKHOLDERIA; BURKHOLDERIA VIETNAMIENSIS; CLOSTRIDIA; DELTAPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; HALOMONAS; MARINOBACTER; PROTEOBACTERIA; PSEUDOMONAS; PSEUDOMONAS SP.;

EID: 79960098229     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02317-10     Document Type: Article

References (51)

1. Allsopp, D., K. Seal, and C. C. Gaylarde. 2004. Introduction to biodeterioration, 2nd ed. Cambridge University Press, Cambridge, United Kingdom.
2. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Baldwin, A., et al. 2005. Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J. Clin. Microbiol. 43:4665-4673.
4. Biddick, R., T. Spilker, A. Martin, and J. J. LiPuma. 2003. Evidence of transmission of Burkholderia cepacia, Burkholderia multivorans and Burkholderia dolosa among persons with cystic fibrosis. FEMS Microbiol. Lett. 228:57-62.
5. Brown, L. M., et al. 2010. Community dynamics and phylogenetics of bacteria fouling Jet A and JP-8 aviation fuel. Int. Biodeterior. Biodeg. 64:253- 261.
6. Campbell, M., E. Mahenthiralingam, and D. P. Speert. 2000. Evaluation of random amplified polymorphic DNA typing of Pseudomonas aeruginosa. J. Clin. Microbiol. 38:4614-4615.
7. Chao, A., and J. Bunge. 2002. Estimating the number of species in a stochastic abundance model. Biometrics 58:531-539.
8. Clarke, K. R. 1993. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18:117-143.
9. Clarke, K. R., and R. M. Warwick. 1999. The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Mar. Ecol. Prog. Ser. 184:21-29.
10. Coenye, T., P. Vandamme, J. R. Govan, and J. J. LiPuma. 2001. Taxonomy and identification of the Burkholderia cepacia complex. J. Clin. Microbiol. 39:3427-3436.
11. Cole, J. R., et al. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35:D169-D172.
12. DeMello, J. A., et al. 2007. Biodegradation and environmental behavior of biodiesel mixtures in the sea: an initial study. Mar. Pollut. Bull. 54:894-904.
13. Gauthier, M. J., et al. 1992. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int. J. Syst. Bacteriol. 42:568-576.
14. Gaylarde, C. C., F. J. Bento, and J. Kelly. 1999. Microbial contamination of stored hydrocarbon fuels and its control. Rev. Microbiol. 30:1-10. (In Spanish.)
15. Gerdes, B., R. Brinkmeyer, G. Dieckmann, and E. Helmke. 2005. Influence of crude oil on changes of bacterial communities in Arctic sea-ice. FEMS Microbiol. Ecol. 53:129-139.
16. Gilbert, J. A., et al. 2009. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11:3132-3139.
17. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
18. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
19. Hareland, W. A., R. L. Crawford, P. J. Chapman, and S. Dagley. 1975. Metabolic function and properties of 4-hydroxyphenylacetic acid 1-hydroxylase from Pseudomonas acidovorans. J. Bacteriol. 121:272-285.
20. Huber, J. A., et al. 2007. Microbial population structures in the deep marine biosphere. Science 318:97-100.
21. Huse, S. M., et al. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255.
22. Huse, S. M., D. M. Welch, H. G. Morrison, and M. L. Sogin. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12:1889-1898.
23. Huu, N. B., E. B. Denner, D. T. Ha, G. Wanner, and H. Stan-Lotter. 1999. Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Int. J. Syst. Bacteriol. 49:367-375.
24. Institute of Petroleum. 1999. Determination of the viable aerobic microbial content of fuels and fuel components, p. 385.1-385.7. In Standard methods for the analysis and testing of petroleum products and British standard 2000 Parts. Energy Institute, London, United Kingdom.
25. Institute of Petroleum. 2007. Guidelines for the investigation of the microbial content of petroleum fuels and for the implementation of avoidance and remedial strategy, 2nd ed. The Energy Institute, London, United Kingdom.
26. International Air Transport Association. 2005. Guidance on microbiological contamination in aircraft fuel tanks, 2nd ed. International Air Transport Association, Montreal, Canada.
27. Kim, B. S., et al. 2008. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J. Microbiol. 46:357-363.
28. Larkin, M. A., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
29. Mahenthiralingam, E., A. Baldwin, and C. G. Dowson. 2008. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J. Appl. Microbiol. 104:1539-1551.
30. Mahenthiralingam, E., M. E. Campbell, D. A. Henry, and D. P. Speert. 1996. Epidemiology of Burkholderia cepacia infection in patients with cystic fibrosis: analysis by randomly amplified polymorphic DNA fingerprinting. J. Clin. Microbiol. 34:2914-2920.
31. Margulies, M., et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376-380.
32. Mehdi, H., and E. Giti. 2008. Investigation of alkane biodegradation using the microtiter plate method and correlation between biofilm formation, biosurfactant production and crude oil biodegradation. Int. Biodeterior. Biodegrad. 62:170-178.
33. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of 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.
34. Muyzer, G., and A. J. M. Stams. 2008. The ecology and biotechnology of sulphate-reducing bacteria. Nat. Rev. Microbiol. 6:441-454.
35. O'Sullivan, L. A., and E. Mahenthiralingam. 2005. Biotechnological potential within the genus Burkholderia. Lett. Appl. Microbiol. 41:8-11.
36. O'Sullivan, L. A., G. Webster, J. C. Fry, R. J. Parkes, and A. J. Weightman. 2008. Modified linker-PCR primers facilitate complete sequencing of DGGE DNA fragments. J. Microbiol. Methods 75:579-581.
37. O'Sullivan, L. A., et al. 2007. Identifying the genetic basis of ecologically and biotechnologically useful functions of the bacterium Burkholderia vietnamiensis. Environ. Microbiol. 9:1017-1034.
38. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
39. Rahman, K. S. M., T. Rahman, P. Lakshmanaperumalsamy, and I. M. Banat. 2002. Occurrence of crude oil degrading bacteria in gasoline and diesel station soils. J. Basic Microbiol. 42:284-291.
40. Rajasekar, A., B. Anandkumar, S. Maruthamuthu, Y. P. Ting, and P. K. S. M. Rahman. 2010. Characterization of corrosive bacterial consortia isolated from petroleum-product-transporting pipelines. Appl. Microbiol. Biotech. 85:1175-1188.
41. Rauch, M. E., et al. 2006. Characterization of microbial contamination in United States Air Force aviation fuel tanks. J. Ind. Microbiol. Biotech. 33:29-36.
42. Roesch, L. F., et al. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. Int. Soc. Microb. Ecol. J. 1:283-290.
43. Sogin, M. L., et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
44. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
45. Vandamme, P., et al. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407-438.
46. Van Hamme, J. D., A. Singh, and O. P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol. Mol. Biol. Rev. 67:503-549.
47. Webster, G., C. J. Newberry, J. C. Fry, and A. J. Weightman. 2003. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J. Microbiol. Methods 55: 155-164.
48. Webster, G., et al. 2006. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol. Ecol. 58:65-85.
49. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
50. Yemashova, N. A., et al. 2007. Biodeterioration of crude oil and oil derived products: a review. Rev. Environ. Sci. Biotech. 6:315-337.
51. Zhou, H. W., et al. 2009. Polycyclic aromatic hydrocarbon-induced structural shift of bacterial communities in mangrove sediment. Microb. Ecol. 58:153- 160.