Phylogeography of sulfate-reducing bacteria among disturbed sediments, disclosed by analysis of the dissimilatory sulfite reductase genes (dsrAB)

Applied and Environmental Microbiology

Volumn 71, Issue 2, 2005, Pages 1004-1011

  Perez Jimenez J R ^a   Kerkhof, L J ^a,b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTAMINATION; CRUDE PETROLEUM; GENES; GEOGRAPHICAL REGIONS; HYDROCARBONS; MORPHOLOGY; PLANTS (BOTANY); SEDIMENTS; SULFUR COMPOUNDS;

DISTRIBUTION PATTERNS; DIVERSITY; SULFATE REDUCING BACTERIA (SRB); TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM (T-RFLP);

BACTERIA;

SULFITE REDUCTASE;

MICROBIAL COMMUNITY; PHYLOGEOGRAPHY; SEDIMENT POLLUTION; SPATIAL DISTRIBUTION; SULFATE-REDUCING BACTERIUM;

ARTICLE; BACTERIAL FLORA; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA FINGERPRINTING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; ITALY; LATVIA; MANGROVE; NONHUMAN; NUCLEOTIDE SEQUENCE; PETROCHEMICAL INDUSTRY; PHYLOGENETIC TREE; PHYLOGENY; POLLUTION; PUERTO RICO; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RESTRICTION MAPPING; SEDIMENT; SOUTH KOREA; SULFATE REDUCING BACTERIUM; UNINDEXED SEQUENCE; UNITED STATES; VENEZUELA;

EUROPE; FRESH WATER; GEOLOGIC SEDIMENTS; KOREA; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; SULFATES; SULFUR-REDUCING BACTERIA; UNITED STATES; VENEZUELA; WATER POLLUTION, CHEMICAL;

BACTERIA (MICROORGANISMS); EUKARYOTA; RHIZOPHORACEAE;

EID: 13544259591     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.2.1004-1011.2005     Document Type: Article

References (41)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. L. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Anbar, A. D., and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:1137-1142.
3. Annweiler, E., W., Michaelis, and R. U. Meckenstock. 2001. Anaerobic cometabolic conversion of benzothiophene by a sulfate-reducing enrichment culture and in a tar-oil-contaminated aquifer. Appl. Environ. Microbiol. 67:5077-5083.
4. Avaniss-Aghajani, E., K. Jones, D. Chapman, and C. Brunk. 1994. A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17:144-146.
5. Baker, B. J., D. P. Moser, B. J. MacGregor, S. Fishbain, M. Wagner, N. K. Fry, B. Jackson, N. Speolstra, S. Loos, K. Takai, B. S. Lollar, J. Fredrickson, D. Balkwill, T. C. Onstott, C. F. Wimpee, and D. A. Stahl. 2003. Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ. Microbiol. 5:267-277.
6. Beller, H. R., A. M. Spormann, P. K. Sharma, J. R. Cole, and M. Reinhard. 1996. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl. Environ. Microbiol. 62:1188-1196.
7. Castro, H., K. R. Reddy, and A. Ogram. 2002. Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades. Appl. Environ. Microbiol. 68:6129-6137.
8. Chang, Y. J., A. D. Peacock, P. E., Long, J. R., Stephen, J. P. McKinley, S. J., Macnaughton, A. K. Hussain, A. M. Saxton, and D. C. White. 2001. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol. 67:3149-3160.
9. Cho, J. C., and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66:5448-5456.
10. Dhillon, A., A. Teske, J. Dilon, D. A. Stahl, and M. L. Sogin. 2003. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microbiol. 69:2765-2772.
11. Eggleton, J., and K. V. Thomas. 2004. A review of factors affecting the release and bioavailability of contaminants during sediment disturbance events. Environ. Int. 30:973-980.
12. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:166-170.
13. Fishbain, S., Dillon, J. G., Gough, H. L., and D. A. Stahl. 2003. Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulfate respiration pathway. Appl. Environ. Microbiol. 69:3663-3667.
14. Fukuba, T., M. Ogawa, T. Fujii, and T. Naganuma. 2003. Phylogenetic diversity of dissimilatory sulfite reductase genes from deep-sea cold seep sediment. Mar. Biotechnol. 5:458-468.
15. Karkhoff-Schweizer, R. R., D. P. Huber, and G. Voordouw. 1995. Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl. Environ. Microbiol. 61:290-296.
16. Kitts, C. L. 2001. Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr. Issues Intest. Microbiol. 2:17-25.
17. Kleikemper, J., M. H. Schroth, W. V. Sigler, M. Schmucki, S. M. Bernasconi, and J. Zeyer. 2003. Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl. Environ. Microbiol. 68:1516-1523.
18. Magurran, A. E. 1988. Ecological diversity and its measurement. Princeton University Press, Princeton, N.J.
19. Minz, D., J. L. Flax, S. J. Green, G. Muyzer, Y. Cohen, M. Wagner, B. E. Rittmann, and D. A. Stahl. 1999. Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl. Environ. Microbiol. 65:4666-4671.
20. Murray, A. E., C. M. Preston, R. Massana, L. T. Taylor, A. Blakis, K. Wu, and E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:2585-2595.
21. Nakagawa, T., and M. Fukui. 2003. Molecular characterization of community structures and sulfur metabolism within microbial streamers in Japanese hot springs. Appl. Environ. Microbiol. 69:7044-7057.
22. Nakagawa, T., J. Ishibashi, A. Maruyama, T. Yamanaka, Y. Morimoto, H. Kimura, T. Urabe, and M. Fukui. 2004. Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. Appl. Environ. Microbiol. 70:393-403.
23. Nakagawa T., S. Nakagawa, F. Inagaki, K., Takai, and K. Horikoshi. 2004. Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures. FEMS Microbiol. Lett. 232:145-152.
24. Nakagawa, T., S. Hanada, A. Maruyama, K. Marumo, T. Urabe, and M. Fukui. 2002. Distribution and diversity of thermophilic sulfate-reducing bacteria within a Cu-Pb-Zn mine (Toyoha, Japan). FEMS Microbiol. Ecol. 1378:1-11.
25. Nealson, K. H. 1997. Sediment bacteria: who's there, what are they doing, and what's new? Annu. Rev. Earth Planet. Sci. 25:403-434.
26. Pearson, W. R., and D. L. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
27. Pérez-Jiménez, J. R. 2003. Molecular characterization of sulfidogenic communities among pristine and polluted sites based on the dissimilatory sulfite reductase genes (dsrAB). Ph.D. thesis. Rutgers University, New Brunswick, N.J.
28. Pérez-Jiménez, J. R., L. Y. Young, and L. J. Kerkhof. 2001. Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes. FEMS Microbiol. Ecol. 35:145-150.
29. Phelps, C. D. 1998. Anaerobic biodegradation of aromatic petroleum hydrocarbons. Ph.D. thesis. Rutgers University, New Brunswick, N.J.
30. Phelps, C., L. J. Kerkhof, and L. Y. Young. 1998. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol. Ecol. 27:269-279.
31. Purdy, K. J., T. M. Embley, and D. B. Nedwell. 2002. The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments. Antonie van Leeuwenhoek 81:181-187.
32. Saitou, N., and M. Nei. 1987. The neighbor joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
33. Shen, Y., R. Buick, and D. E. Canfield. 2001. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410:77-81.
34. So, C. M., and L. Y. Young. 1999. Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl. Environ. Microbiol. 65:2969-2976.
35. Stahl, D. A., S. Fishbain, M. Klein, B. J. Baker, and M. Wagner. 2002. Origins and diversification of sulfate-respiring microorganisms. Antonie Van Leeuwenhoek 81:189-195.
36. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
37. Thomsen, T. R., K. Finster, and N. B. Ramsing. 2001. Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl. Environ. Microbiol. 67:1646-1656.
38. Wagner, M., A. J. Roger, L. Flax, G. A. Brusseau, and D. A. Stahl. 1998. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol. 180:2975-2982.
39. Whitaker, R. J., D. W. Grogan, and J. W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science 301:976-978.
40. Widdel, F., and T. A. Hansen. 1999. The dissimilatory sulfate- and sulfur-reducing bacteria. In M. Dworkin, K.-H. Schleifer, and E. Stackebrandt (ed.), The prokaryotes: an evolving electronic database for the microbiological community, 3rd ed., release 3.0. [Online.]. Springer-Verlag, New York, N.Y. http://link.springer-ny.com/link/service/books/10125.
41. Zhang, X., and L. Y. Young. 1997. Carboxylation as an initial reaction in the anaerobic metabolism of naphthalene and phenanthrene by sulfidogenic consortia. Appl. Environ. Microbiol. 63:4759-4764.