Advertisement

Alcanivorax borkumensis

Reference work entry

Abstract:

Alcanivorax borkumensis is a marine bacterium that uses exclusively petroleum oil hydrocarbons as sources of carbon and energy (and is therefore designated “hydrocarbonoclastic”). It is found in low numbers in all oceans of the world and becomes abundant in oil-contaminated waters. Its ubiquity, unusual physiology and demonstrated role in biodegradation show that it is globally important in the removal of hydrocarbons from polluted marine systems. Genome sequencing, extensive functional genomic analysis and genome-wide constraint-based modeling of the metabolism Alcanivorax borkumensis SK2 type strain, an outstanding paradigm of hydrocarbonoclastic bacteria, has provided substantial insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, nutrient scavenging capabilities, niche-specific stress responses and the metabolic routes and flux distributions underlying its remarkable hydrocarbon utilization abilities. The wealth of information thus far generated provides a solid knowledge-base for the understanding the physiology and ecological success of this fascinating and globally important bacterium and for the design of new strategies to mitigate the ecological damage caused by oil spills.

Keywords

Glyoxylate Bypass Alkane Hydroxylase Alkane Degradation Hydrocarbonoclastic Bacterium Hydrocarbon Utilization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Abraham WR, Meyer H, Yakimov M (1998) Novel glycine containing glucolipids from the alkane using bacterium Alcanivorax borkumensis. Biochim Biophys Acta 1393: 57–62.PubMedGoogle Scholar
  2. Berman T, Bronk DA (2003) Dissolved organic nitrogen: a dynamic participant in aquatic ecosystems. Aquat Microb Ecol 31: 279–305.CrossRefGoogle Scholar
  3. Bruns A, Berthe-Corti L (1999) Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment. Int J Syst Bacteriol 49: 441–448.PubMedCrossRefGoogle Scholar
  4. Cappello S, Denaro R, Genovese M, Giuliano L, Yakimov MM (2007) Predominant growth of Alcanivorax during experiments on “oil spill bioremediation” in mesocosms. Microbiol Res 162: 185–190.PubMedCrossRefGoogle Scholar
  5. Cases I, De Lorenzo V, Ouzounis CA (2003) Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 11: 248–253.PubMedCrossRefGoogle Scholar
  6. Fernández-Martínez J, Pujalte MJ, García-Martínez J, Mata M, Garay E, Rodríguez-Valera F (2003) Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax. Int J Syst Evol Microbiol 53: 331–338.PubMedCrossRefGoogle Scholar
  7. Galperin MY, Nikolskaya AN, Koonin EV (2001) Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett 203: 11–21.PubMedCrossRefGoogle Scholar
  8. Harayama S, Kishira H, Kasai Y, Shutsubo K (1999) Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1: 63–70.PubMedGoogle Scholar
  9. Kalscheuer R, Stöveken T, Malkus U, Reichelt R, Golyshin PN, Sabirova JS, Ferrer M, Timmis KN, Steinbüchel A (2007) Analysis of storage lipid accumulation in Alcanivorax borkumensis: evidence for alternative triacylglycerol biosynthesis routes in bacteria. J Bacteriol 189: 918–928.PubMedCrossRefGoogle Scholar
  10. Kasai Y, Kishira H, Syutsubo K, Harayama S (2001) Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ Microbiol 3: 246–255.PubMedCrossRefGoogle Scholar
  11. Kasai Y, Kishira H, Sasaki T, Syutsubo K, Watanabe K, Harayama S (2002) Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water. Environ Microbiol 4: 141–147.PubMedCrossRefGoogle Scholar
  12. Kim BH, Kim HG, Bae GI, Bang IS, Bang SH, Choi JH, Park YK (2004) Expression of cspH upon nutrient up-shift in Salmonella enterica serovar Typhimurium. Arch Microbiol 182: 37–43.PubMedCrossRefGoogle Scholar
  13. Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328–1333.PubMedCrossRefGoogle Scholar
  14. Liu C, Shao Z (2005) Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 55: 1181–1186.PubMedCrossRefGoogle Scholar
  15. Lombardot T, Bauer M, Teeling H, Amann R, Glöckner FO (2005) The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1T as revealed by whole genome comparisons. FEMS Microbiol Lett 242: 137–145.PubMedCrossRefGoogle Scholar
  16. Martínez-Bueno MA, Tobes R, Rey M, Ramos JL (2002) Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01. Environ Microbiol 4: 842–855.PubMedCrossRefGoogle Scholar
  17. Mohanty BK, Kushner SR (2003) Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol Microbiol 50: 645–658.PubMedCrossRefGoogle Scholar
  18. Ochsner UA, Fiechter A, Reiser J (1994) Isolation, characterization, and expression in Escherichia coli of the Pseudomonas aeruginosa rhlAB genes encoding a rhamnosyltransferase involved in rhamnolipid biosurfactant synthesis. J Biol Chem 269: 19787–19795.PubMedGoogle Scholar
  19. Reeves PR, Hobbs M, Valvano MA, Skurnik M, Whitfield C, Coplin D, Kido N, Klena J, Maskell D, Raetz CRH, Rick PD (1996) Bacterial polysaccharide synthesis and gene nomenclature. Trends Microbiol 4: 495–503.PubMedCrossRefGoogle Scholar
  20. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tümmler B, Ussery DW (2008) Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol 10: 614–625.PubMedCrossRefGoogle Scholar
  21. Rivas R, García-Fraile P, Peix A, Mateos PF, Martínez-Molina E, Velázquez E (2007) Alcanivorax balearicus sp. nov., isolated from Lake Martel. Int J Syst Evol Microbiol 57: 1331–1335.PubMedCrossRefGoogle Scholar
  22. Rocchetta HL, Burrows LL, Lam JS (1999) Genetics of O-antigen biosynthesis in Pseudomonas aeruginosa. Microbiol Mol Biol Rev 63: 523–553.PubMedGoogle Scholar
  23. Röling WFM, Milner MG, Jones DM, Lee K, Daniel F, Swannell RJP, Head IM (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68: 5537–5548.PubMedCrossRefGoogle Scholar
  24. Röling WFM, Milner MG, Jones DM, Fratepietro F, Swannell RPJ, Daniel F, Head IM (2004) Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Appl Environ Microbiol 70: 2603–2613.PubMedCrossRefGoogle Scholar
  25. Ron EZ, Rosenberg E (2001) Natural roles of biosurfactants. Environ Microbiol 3: 229–236.PubMedCrossRefGoogle Scholar
  26. Sabirova JS, Chernikova TN, Timmis KN, Golyshin PN (2008) Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2. FEMS Microbiol Lett 285: 89–96.PubMedCrossRefGoogle Scholar
  27. Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN (2006a) Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. J Bacteriol 188: 3763–3773.PubMedCrossRefGoogle Scholar
  28. Sabirova JS, Ferrer M, Lünsdorf H, Wray V, Kalscheuer R, Steinbüchel A, Timmis KN, Golyshin PN (2006b) Mutation in a “tesB-like” hydroxyacyl-coenzyme A-specific thioesterase gene causes hyperproduction of extracellular polyhydroxyalkanoates by Alcanivorax borkumensis SK2. J Bacteriol 188: 8452–8459.PubMedCrossRefGoogle Scholar
  29. Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wüthrich K, Bailey JE (1999). Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181: 6679–6688.PubMedGoogle Scholar
  30. Schneiker S, Dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24: 997–1004.PubMedCrossRefGoogle Scholar
  31. Søballe B, Poole RK (1998) Requirement for ubiquinone downstream of cytochrome(s) b in the oxygen-terminated respiratory chains of Escherichia coli K-12 revealed using a null mutant allele of ubiCA. Microbiology 144: 361–373.PubMedCrossRefGoogle Scholar
  32. Tischler AD, Camilli A (2004) Cyclic diguanylate (c-di-GMP) regulates Vibrio cholerae biofilm formation. Mol Microbiol 53: 857–869.PubMedCrossRefGoogle Scholar
  33. van Beilen JB, Marín MM, Smits THM, Röthlisberger M, Franchini AG, Witholt B, Rojo F (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 6: 264–273.PubMedCrossRefGoogle Scholar
  34. van Beilen JB, Smits THM, Roos FF, Brunner T, Balada SB, Röthlisberger M, Witholt B (2005) Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J Bacteriol 187: 85–91.PubMedCrossRefGoogle Scholar
  35. van Beilen JB, Funhoff EG, Van Loon A, Just A, Kaysser L, Bouza M, Holtackers R, Röthlisberger M, Li Z, Witholt B (2006) Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl Environ Microbiol 72: 59–65.PubMedCrossRefGoogle Scholar
  36. Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18: 257–266.PubMedCrossRefGoogle Scholar
  37. Yakimov MM, Golyshin PN, Lang S, Moore ERB, Abraham WR, Lünsdorf H, Timmis KN (1998) Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48: 339–348.PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.Systems and Synthetic Biology Research GroupHelmholtz Center for Infection ResearchBraunschweigGermany
  2. 2.Environmental Microbiology LaboratoryHelmholtz Centre for Infection ResearchBraunschweigGermany
  3. 3.School of Biological SciencesBangor UniversityGwyneddUK
  4. 4.Istituto per l’Ambiente Marino CostieroCNRMessinaItaly

Personalised recommendations