Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: Implications for lipid-based stable isotope Probing methods

Applied and Environmental Microbiology

Volumn 77, Issue 20, 2011, Pages 7296-7306

  Lerch, Thomas Z ^a,b   Dignac, Marie France ^a   Barriuso, Enrique ^b   Mariotti, André ^a  

^a AGROPARISTECH   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

2 ,4-DICHLOROPHENOXYACETIC ACID; 2 ,4-DICHLOROPHENOXYACETIC ACID (2 ,4-D); BATCH STUDIES; COMPLEX ENVIRONMENTS; DEGRADING BACTERIA; FATTY ACID COMPOSITION; FATTY ACID METHYL ESTER; ISOTOPIC ANALYSIS; ISOTOPIC SIGNATURES; LIPID BIOMARKERS; MICROBIAL LIPIDS; MICROBIAL POPULATIONS; NATURAL ENVIRONMENTS; STABLE-ISOTOPE PROBING; TARGET COMPOUND;

BIOMASS; DEGRADATION; GLUCOSE; HERBICIDES; INTERNET PROTOCOLS; ISOTOPES; ORGANIC POLLUTANTS;

FATTY ACIDS;

2,4 DICHLOROPHENOXYACETIC ACID; CARBON; FATTY ACID; GLUCOSE;

BIODEGRADATION; BIOMARKER; BIOMASS; FATTY ACID; GLUCOSE; HYPOTHESIS TESTING; ISOTOPIC ANALYSIS; ISOTOPIC COMPOSITION; ORGANIC POLLUTANT; PHYSIOLOGICAL RESPONSE; PROBE; STABLE ISOTOPE;

ARTICLE; BIOTRANSFORMATION; CHEMISTRY; CUPRIAVIDUS NECATOR; GROWTH, DEVELOPMENT AND AGING; ISOTOPE LABELING; METABOLISM; METHODOLOGY; MICROBIOLOGY;

2,4-DICHLOROPHENOXYACETIC ACID; BIOTRANSFORMATION; CARBON ISOTOPES; CUPRIAVIDUS NECATOR; ENVIRONMENTAL MICROBIOLOGY; FATTY ACIDS; GLUCOSE; ISOTOPE LABELING;

EID: 82955240011     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06438-11     Document Type: Article

References (60)

1. Abraham, W. R., C. Hesse, and O. Pelz. 1998. Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage. Appl. Environ. Microbiol. 64:4202-4209.
2. Alexander, M. 1994. Biodegradation and bioremediation, p. 1-7. Academic Press, San Diego, CA.
3. Baath, E., and T. H. Anderson. 2003. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol. Biochem. 35:955-963.
4. Balagué, C., N. Sturtz, R. Duffard, and A. M. E. de Duffard. 2001. Effect of 2,4-dichlorophenoxyacetic acid herbicide on Escherichia coli growth, chemical composition, and cellular envelope. Environ. Toxicol. 16:43-53.
5. Basu, A., S. K. Apte, and P. S. Phale. 2006. Preferential utilization of aromatic compounds over glucose by Pseudomonas putida CSV86. Appl. Environ. Microbiol. 72:2226-2230.
6. Bodelier, P. L. E., et al. 2009. A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME J. 3:606-617.
7. Bombach, P., et al. 2010. Enrichment and characterization of a sulfatereducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. FEMS Microbiol. Ecol. 71:237-246.
8. Boschker, H. T. S., et al. 1998. Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers. Nature 392:801-805.
9. Brinch-Iversen, J., and G. M. King. 1990. Effects of substrate concentration, growth rate, and oxygen availability on relationships among bacterial carbon, nitrogen and phospholipid phosphorus content. FEMS Microbiol. Ecol. 74: 345-356.
10. Collier, D. N., P. W. Hager, and P. V. Phibbs. 1996. Catabolite repression control in the pseudomonads. Res. Microbiol. 147:551-561.
11. Coplen, T. B. 1995. New IUPAC guidelines for the reporting of stable hydrogen, carbon, and oxygen isotope-ratio data. J. Res. Natl. Inst. Stand. Technol. 100:285.
12. Cullen, J., M. C. Phillips, and G. G. Shipley. 1971. The effects of temperature on the composition and physical properties of the lipids of Pseudomonas fluorescens. Biochem. J. 125:733-742.
13. Denich, T. J., L. A. Beaudette, H. Lee, and J. T. Trevors. 2003. Effect of selected environmental and physico-chemical factors on bacterial cytoplasmic membranes. J. Microbiol. Methods 52:149-182.
14. de Peretti, A. F., R. Duffard, and A. M. E. de Duffard. 1992. Effects of 2,4-dichlorophenoxyacetic acid on Rhizobium sp. membrane fluidity. Arch. Environ. Contam. Toxicol. 23:301-306.
15. Don, R. H., A. J. Weightman, H. J. Knackmuss, and K. N. Timmis. 1985. Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP 134 (pJP4). J. Bacteriol. 16:85-90.
16. Egli, T. 1995. The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv. Microb. Ecol. 14:305-386.
17. Egli, T. 2010. How to live at very low substrate concentration. Water Res. 44:4826-4837.
18. Evans, W. C., B. S. W. Smith, H. N. Fernley, and J. I. Davies. 1971. Bacterial metabolism of 2,4-dichlorophenoxyacetate. Biochem. J. 122:543-551.
19. Evershed, R. P., et al. 2006. C-13-labelling of lipids to investigate microbial communities in the environment. Curr. Opin. Biotechnol. 17:72-82.
20. Fang, J. S., N. Lovanh, and P. J. J. Alvarez. 2004. The use of isotopic and lipid toluene degradation to specific analysis techniques linking microorganisms: applications and limitations. Water Res. 38:2529-2536.
21. Frostegard, A., A. Tunlid, and E. Baath. 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl. Environ. Microbiol. 59:3605-3617.
22. Fukumori, F., and R. P. Hausinger. 1993. Alcaligenes-Eutrophus JMP134 2,4-dichlorophenoxyacetate monooxygenase is an alpha-ketoglutarate-dependent dioxygenase. J. Bacteriol. 175:2083-2086.
23. Görke, B., and J. Stülke. 2008. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat. Rev. Microbiol. 6:613- 624.
24. Hanson, J. R., J. L. Macalady, D. Harris, and K. M. Scow. 1999. Linking toluene degradation with specific microbial populations in soil. Appl. Environ. Microbiol. 65:5403-5408.
25. Heipieper, H. J., G. Meulenbeld, Q. VanOirschot, and J. A. M. DeBont. 1996. Effect of environmental factors on the trans/cis ratio of unsaturated fatty acids in Pseudomonas putida S12. Appl. Environ. Microbiol. 62:2773-2777.
26. Heipieper, H. J., F. J. Weber, J. Sikkema, H. Keweloh, and J. A. M. Debont. 1994. Mechanisms of resistance of whole cells to toxic organic solvents. Trends Biotechnol. 12:409-415.
27. Jehmlich, N., F. Schmidt, M. von Bergen, H. H. Richnow, and C. Vogt. 2008. Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2:1122-1133.
28. Johnsen, A. R., A. Winding, U. Karlson, and P. Roslev. 2002. Linking of microorganisms to phenanthrene metabolism in soil by analysis of C-13-labeled cell lipids. Appl. Environ. Microbiol. 68:6106-6113.
29. Kim, I. S., L. A. Beaudette, M. B. Cassidy, H. Lee, and J. T. Trevors. 2002. Alterations in fatty acid composition and fluidity of cell membranes affect the accumulation of PCB congener 2,2',5,5'-tetrachlorobiphenyl by Ralstonia eutropha H850. J. Chem. Technol. Biotechnol. 77:793-799.
30. Kim, I. S., H. Lee, and J. T. Trevors. 2001. Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. FEMS Microbiol. Lett. 200:17-24.
31. Kreuzer-Martin, H. W. 2007. Stable isotope probing: linking functional activity to specific members of microbial communities. Soil Sci. Soc. Am. J. 71:611-619.
32. Kuzyakov, Y. V. 1997. The role of amino acids and nucleic bases in turnover of nitrogen and carbon in soil humic fractions. Eur. J. Soil Sci. 48:121-130.
33. Laura, D., G. DeSocio, R. Frassanito, and D. Rotilio. 1996. Effects of atrazine on Ochrobactrum anthropi membrane fatty acids. Appl. Environ. Microbiol. 62:2644-2646.
34. Lerch, T. Z., M. F. Dignac, E. Barriuso, G. Bardoux, and A. Mariotti. 2007. Tracing 2,4-D metabolism in Cupriavidus necator JMP134 with 13C-labelling technique and fatty acid profiling. J. Microbiol. Methods 71:162-174.
35. Lerch, T. Z., et al. 2009. Dynamics of soil microbial populations involved in 2,4-D biodegradation revealed by FAME-based stable isotope probing. Soil Biol. Biochem. 41:77-85.
36. Loos, M. A., R. N. Roberts, and M. Alexander. 1967. Phenols as intermediates in the decomposition of phenoxyacetates by an Arthrobacter species. Can. J. Microbiol. 13:679-690.
37. Lykidis, A., et al. 2010. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. Plos One 5:e9729.
38. Manefield, M., A. S. Whiteley, R. I. Griffiths, and M. J. Bailey. 2002. RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny. Appl. Environ. Microbiol. 68:5367-5373.
39. Marr, A. G., and J. L. Ingraham. 1962. Effect of temperature on the composition of fatty acids in Escherichia coli. J. Bacteriol. 84:1260-1267.
40. Mauclaire, L., O. Pelz, M. Thullner, W. R. Abraham, and J. Zeyer. 2003. Assimilation of toluene carbon along a bacteria-protist food chain determined by C-13-enrichment of biomarker fatty acids. J. Microbiol. Methods 55:635-649.
41. Monod, J. 1942. Recherches sur la croissance des cultures bactériennes. Thesis. Hermann et Cie, Paris, France.
42. Mrozik, A., Z. Piotrowska-Seget, and S. Labuzek. 2006. Cellular fatty acid patterns in Pseudomonas sp. CF600 during catechol and phenol degradation in media supplemented with glucose as an additional carbon source. Ann. Microbiol. 56:57-64.
43. Muller, R. H., and W. Babel. 1994. Phenol and its derivatives as heterotrophic substrates for microbial growth-an energetic comparison. Appl. Microbiol. Biotechnol. 42:446-451.
44. Neufeld, J. D., M. G. Dumont, J. Vohra, and J. C. Murrell. 2007. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb. Ecol. 53:435-442.
45. Oh, K. H., and O. H. Tuovinen. 1990. Degradation of 2,4-dichlorophenoxyacetic acid by mixed cultures of bacteria. J. Ind. Microbiol. 6:275-278.
46. Osterhout, G. J., J. L. Valentine, and J. D. Dick. 1998. Phenotypic and genotypic characterization of clinical strains of CDC group IVc-2. J. Clin. Microbiol. 36:2618-2622.
47. Parche, S., et al. 2006. Lactose-over-glucose preference in Bifidobacterium longum NCC2705: glcP, encoding a glucose transporter, is subject to lactose repression. J. Bacteriol. 188:1260-1265.
48. Plumeier, I., D. Perez-Pantoja, S. Heim, B. Gonzalez, and D. H. Pieper. 2002. Importance of different tfd genes for degradation of chloroaromatics by Ralstonia eutropha JMP134. J. Bacteriol. 184:4054-4064.
49. Radajewski, S., P. Ineson, N. R. Parekh, and J. C. Murrell. 2000. Stableisotope probing as a tool in microbial ecology. Nature 403:646-649.
50. Rosas, S. B., M. D. C. Secco, and N. E. Ghittoni. 1980. Effects of pesticides on the fatty acid and phospholipid composition of Escherichia coli. Appl. Environ. Microbiol. 40:231-234.
51. Sikkema, J., J. A. M. Debont, and B. Poolman. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol. Rev. 59:201-222.
52. Soltani, M., P. Metzger, and C. Largeau. 2004. Effects of hydrocarbon structure on fatty acid, fatty alcohol, and beta-hydroxy acid composition in the hydrocarbon-degrading bacterium Marinobacter hydrocarbonoclasticus. Lipids 39:491-505.
53. Soulas, G., R. Chaussod, and A. Verguet. 1984. Chloroform fumigation technique as a means of determining the size of specialized soil microbial populations: application to pesticide-degrading microorganisms. Soil Biol. Biochem. 16:497-501.
54. Soulas, G., and J. C. Fournier. 1987. Breakdown kinetics of 2,4-D and 2,4-dichlorophenol in soil, alone or in mixture, and effects on the behaviour of the respective degrading microbial biomass. Agronomie 7:193-199.
55. Vandamme, P., and T. Coenye. 2004. Taxonomy of the genus Cupriavidus: a tale of lost and found. Int. J. Syst. Evol. Microbiol. 54:2285-2289.
56. van den Bogaard, P. T. C., M. Kleerebezem, O. P. Kuipers, and W. M. de Vos. 2000. Control of lactose transport, beta-galactosidase activity, and glycolysis by CcpA in Streptococcus thermophilus: evidence for carbon catabolite repression by a non-phosphoenolpyruvate-dependent phosphotransferase system sugar. J. Bacteriol. 182:5982-5989.
57. Weber, F. J., and J. A. M. de Bont. 1996. Adaptation mechanisms of microorganisms to the toxic effects of organic solvents on membranes. Biochim. Biophys. Acta 1286:225-245.
58. Wick, L. Y., O. Pelz, S. M. Bernasconi, N. Andersen, and H. Harms. 2003. Influence of the growth substrate on ester-linked phospho- and glycolipid fatty acids of PAH-degrading Mycobacterium sp LB501T. Environ. Microbiol. 5:672-680.
59. Wick, L. Y., N. Pasche, S. M. Bernasconi, O. Pelz, and H. Harms. 2003. Characterization of multiple-substrate utilization by anthracene-degrading Mycobacterium frederiksbergense LB501T. Appl. Environ. Microbiol. 69: 6133-6142.
60. Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soils 29:111-129.