Identification of a toluene-degrading bacterium from a soil sample through H 2 18O DNA stable isotope probing

Applied and Environmental Microbiology

Volumn 77, Issue 17, 2011, Pages 5995-5999

  Woods, Angela ^a   Watwood, Maribeth ^a   Schwartz, Egbert ^a  

^a NORTHERN ARIZONA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; 16S RRNA GENE; AMPLICONS; BACTERIAL STRAINS; CESIUM CHLORIDE; DEGRADATION RATE; DIRECT SEQUENCING; DNA BANDS; METABOLIC INTERMEDIATES; OXYGEN ATOM; PCR PRODUCTS; POLLUTANT-DEGRADING BACTERIA; QUANTITATIVE REAL TIME PCR; RHODOCOCCUS; SOIL SAMPLE; STABLE-ISOTOPE PROBING;

BACTERIA; BACTERIOLOGY; BIODEGRADATION; CENTRIFUGATION; CESIUM; CESIUM COMPOUNDS; CHLORINE COMPOUNDS; CLONING; DEGRADATION; DNA; GENE ENCODING; INTERNET PROTOCOLS; ISOTOPES; OXYGEN; POLYMERASE CHAIN REACTION; RNA; SOILS;

TOLUENE;

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; TOLUENE;

BACTERIUM; CESIUM; METABOLISM; MICROBIAL ACTIVITY; NUCLEIC ACID; OXYGEN; POLYMERASE CHAIN REACTION; PROBE; QUANTITATIVE ANALYSIS; REAL TIME; SAMPLING; SOIL AMENDMENT; SOIL MICROORGANISM; STABLE ISOTOPE; TOLUENE;

ARTICLE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DENSITY GRADIENT CENTRIFUGATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; ISOTOPE LABELING; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RHODOCOCCUS;

CENTRIFUGATION, DENSITY GRADIENT; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; ISOTOPE LABELING; MOLECULAR SEQUENCE DATA; PHYLOGENY; RHODOCOCCUS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; TOLUENE;

BACTERIA (MICROORGANISMS); RHODOCOCCUS JOSTII;

EID: 80052720880     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.05689-11     Document Type: Article

References (34)

1. 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.
2. Barraclough, D., T. Kearney, and A. Croxford. 2005. Bound residues: environmental solution or future problem? Environ. Pollut. 133:85-90.
3. Boschker, J. T., et al. 1998. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392:801-805.
4. Cohn, M., and A. Hu. 1978. Isotopic (18O) shift in 31P nuclear magnetic resonance applied to a study of enzyme-catalyzed phosphate-phosphate exchange and phosphate (oxygen)-water exchange reactions. Proc. Natl. Acad. Sci. U. S. A. 75:200-203.
5. Cupples, A. M., and G. K. Sims. 2007. Identification of in situ 2,4-dichlorophenoxyacetic acid-degrading soil microorganisms using DNA-stable isotope probing. Soil Biol. Biochem. 39:232-238.
6. Dumont, M. G., and J. C. Murrell. 2005. Stable isotope probing-linking microbial identity to the function. Nat. Rev. Microbiol. 3:499-504.
7. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 29:783-791.
8. Friedrich, M. W. 2006. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr. Opin. Biotechnol. 17:59-66.
9. Gevao, B., K. T. Semple, and K. C. Jones. 2000. Bound pesticide residues in soils: a review. Environ. Pollut. 108:3-12.
10. Hackney, D. D., G. Rosen, and P. D. Boyer. 1979. Subunit interaction during catalysis: alternating site cooperativity in photophosphorylation shown by substrate modulation of (18O)ATP species formation. Proc. Natl. Acad. Sci. U. S. A. 76:3646-3650.
11. Kasho, V. N., and P. D. Boyer. 1989. Vacuolar ATPases, like F1,F0-ATPases, show a strong dependence of the reaction velocity on the binding of more than one ATP per enzyme. Proc. Natl. Acad. Sci. U. S. A. 86:8708-8711.
12. Kerkhof, L. J., and M. M. Häggblom. 2008. Detecting active bacteria involved in biodegradation in the environment, p. 55-70. In E. Diaz (ed.), Microbial biodegradation: genomics and molecular biology. Caister Academic Press, Norfolk, United Kingdom.
13. Lane, D. J., E. Stackebrandt, and M. Goodfellow. 1991. Sequencing and hybridization techniques in bacterial systematics, p. 230-270. John Wiley and Sons, New York, NY.
14. Madsen, E. L. 2006. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr. Opin. Biotechnol. 17:92-97.
15. Martínková, L., B. Uhnáková, M. Pátek, J. Nésvera, and V. Krén. 2009. Biodegradation potential of the genus Rhodococcus. Environ. Ent. 35:162-177.
16. McLeod, M. P., et al. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. U. S. A. 103:15582-15587.
17. Morris, S. A., S. Radajewski, T. W. Willison, and J. C. Murrell. 2002. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl. Environ. Microbiol. 68:1446-1453.
18. Nijenhuis, I., N. Stelzer, M. Kastner, and H. H. Richnow. 2007. Sensitive detection of anaerobic monochlorobenzene degradation using stable isotope tracers. Environ. Sci. Technol. 41:3836-3842.
19. Pelz, O., et al. 2001. Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch. Microbiol. 175:270-281.
20. Radajewski, S., P. Ineson, N. R. Parekh, and J. C. Murrell. 2000. Stableisotope probing as a tool in microbial ecology. Nature 403:646-649.
21. Rawn, D. J. 1989. Biochemistry, 1st ed. Neil Patterson Publishers, Burlington, NC.
22. Richards, O. C., and P. D. Boyer. 1966. 18O labeling of DNA during synthesis and stability of label during replication. J. Mol. Biol. 19:109-119.
23. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phyogenetic trees. Mol. Biol. Evol. 4:406-425.
24. Schwartz, E., and K. M. Scow. 1999. Using biodegradation kinetics to measure the availability of aged phenanthrene to bacteria inoculated into soil. Environ. Toxicol. Chem. 18:1742-1746.
25. 18O. Appl. Environ. Microbiol. 73:2541-2546.
26. 18O. Cold Spring Harb. Protoc. 2009: pdb.prot5341. doi:10.1101/pdb.prot5341.
27. Singleton, D. R., et al. 2005. Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl. Environ. Microbiol. 71:1202-1209.
28. Staden, R., K. F. Beal, and J. K. Bonfield. 2000. The Staden package, 1998. Methods Mol. Biol. 132:115-130.
29. Stapleton, R. D., N. G. Bright, and G. S. Sayler. 2000. Catabolic and genetic diversity of degradative bacteria from fuel-hydrocarbon contaminated aquifers. Microb. Ecol. 39:211-221.
30. Tamura, K., M. Nei, and S. Kumar. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U. S. A. 101:11030-11599.
31. 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.
32. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
33. Weissenfels, W., H. J. Klewer, and J. Langhoff. 1992. Adsorption of polycyclic aromatic hydrocarbons (PAHs) by soil particles: influence on biodegradability and biotoxicity. Appl. Microbiol. Biotechnol. 36:689-696.
34. Wellington, E. M. H., A. Berry, and M. Krsek. 2003. Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr. Opin. Microbiol. 6:295-301.