Direct analysis of sulfate reducing bacterial communities in gas hydrate-impacted marine sediments by PCR-DGGE

Journal of Basic Microbiology

Volumn 49, Issue SUPPL. 1, 2009, Pages

  Bagwell, Christopher E ^a   Formolo, Michael ^b   Ye, Qi ^d   Yeager, Chris M ^a   Lyons, Timothy W ^c   Zhang, Chuanlun L ^d  

^a SAVANNAH RIVER NATIONAL LABORATORY   (United States)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF GEORGIA   (United States)

Author keywords

DGGE; dsrA; Gas hydrates; PCR; Sulfate reducing bacteria

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; HYDROGEN SULFITE REDUCTASE; SULFATE;

ARTICLE; DNA SEQUENCE; GENETICS; GRAM NEGATIVE ANAEROBIC BACTERIA; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; SEDIMENT;

BACTERIAL PROTEINS; DNA, BACTERIAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GEOLOGIC SEDIMENTS; HYDROGENSULFITE REDUCTASE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SULFATES; SULFUR-REDUCING BACTERIA;

BACTERIA (MICROORGANISMS);

EID: 70349671642     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.200800278     Document Type: Article

References (31)

1. Arvidson, R.S., Morse, J.W. and Joye, S.B. 2004. The sulfur biogeochemistry of chemosynthetic cold seep communities, Gulf of Mexico, USA. Marine Chem., 87, 97-119.
2. Bahr, M., Crump, B.C., Klepac-Ceraj, V., Teske, A. et al., 2005. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ. Microbiol., 7, 1175-1185.
3. Canfield, D.E., Raiswell, R., Westrich, J.T., Reaves, C.M. and Berner, R.A. 1986, The use of chromium reduction in the analysis of reduced inorganic sulfur in sediments and shales. Chem. Geol., 54, 149-155.
4. Chang, Y.J., Peacock, A.D., Long, P.E., Stephen, J.R. et al., 2001. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol., 67, 3149-3160.
5. Dhillon, A., Teske, A., Dillon, J., Stahl, D.A. and Sogin, M.L., 2003. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microbiol., 69, 2765-2772.
6. Fishbain, S., Dillon, J.G., Gough, H.L. and Stahl, D.A. 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.
7. Formolo, M.J., Lyons, T.W., Zhang, C., Kelley, C. et al., 2004. Quantifying carbon sources in the formation of authigenic carbonates at gas hydrate sites in the Gulf of Mexico. Chem. Geol., 205, 253-264.
8. Geets, J., Borremans, B., Diels, L., Springael, D. et al., 2006. DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. J. Microbiol. Methods, 66, 194-205.
9. Girguis, P.R., Cozen, A.E. and DeLong, E.F., 2005. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuousflow bioreactor. Appl. Environ. Microbiol., 71, 3725-3733.
10. Hedges, J.I., Baldock, J.A., Gelinas, Y., Lee, C. et al., 2001. Evidence for non-selective preservation of organic matter in sinking marine particles. Nature, 409, 801-804.
11. Jørgensen, B.B., 1978. A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments. I. Measurement with radiotracer techniques. J. Geomicrobiol., 1, 11-28.
12. Joye, S.B., Boetius, A., Orcutt, B.N., Montoya, J.P. et al. 2004. The anaerobic oxidation of methane and sulphate reduction from Gulf of Mexico cold seeps. Chem. Geol., 205, 219-238.
13. Kallmeyer, J., Ferdelman, T.G., Weber, A., Fossing, H. and Jørgensen, B.B., 2004. A cold chromium distillation procedure for radiolabeled sulfide applied to sulphate reduction measurements. Limnology and Oceanography: Methods, 2, 171-180.
14. Karr, E.A., Sattley, M., Rice, M.R., Jung, D.O. et al., 2005. Diversity and distribution of sulfate-reducing bacteria in permanently frozen Lake Fryxell, McMurdo dry valleys, Antarctica. Appl. Environ. Microbiol., 71, 6353-6359.
15. Liu, X., Bagwell, C.E., Wu, L., Devol, A.H. and Zhou, J., 2003. Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats. Appl. Environ. Microbiol., 69, 6073-6081.
16. Meyer, B. and Kuever, J., 2007. Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes - origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiol., 153, 2026-2044.
17. Moran, J.J., Beal, E.J., Vrentas, J.M., Orphan, V.J. et al., 2008. Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ. Microbiol., 10, 162-173.
18. Nadkarni, M.A., Martin, F.E., Jacques, N.A. and Hunter, N., 2002. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiol., 148, 257-266.
19. Orcutt, B., Boetius, A., Elvert, M., Samarkin, V. and Joye, S.B., 2005. Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim. Cosmochim. Acta, 69, 4267-4281.
20. Orcutt, B.N., Boetius, A., Lugo, S.K., MacDonald, I.R. et al., 2004. Life at the edge of methane ice: microbial cycling of carbon and sulfur in Gulf of Mexico gas hydrates. Chem. Geol., 205, 239-251.
21. Orphan, V.J., Hinrichs, K.-U., Ussler, W., Paull, C.K. et al., 2001. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl. Environ. Microbiol., 67, 1922-1934.
22. Orphan, V.J., House, C.H., Hinrichs, K.-U., McKeegan, K.D. and DeLong, E.F., 2002. Multiple archaeal groups mediate methane oxidation in anoxic cold seeps sediments. PNAS, 99, 7663-7668.
23. Sassen, R., Joye, S., Sweet, S.T., DeFreitas, D.A. et al., 1999. Thermogenic gas hydrates and hydrocarbon gases in complex chemosynthetic communities, Gulf of Mexico continental slope. Organic Geochem., 30, 485-497.
24. Tamura, K., Dudley, J., Nei, M. and Kumar, S., 2007. MEGA 4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
25. Thomsen, T.R., Finster, K. and Ramsing, N.B., 2001. Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine setting. Appl. Environ. Microbiol., 67, 1646-1656.
26. Van der Wielen, P.W.J.J. and Heijs, S.K., Sulfate reducing prokaryotic communities in the Eastern Mediterranean Sea. Direct sequence submission to GenBank.
27. Wagner, M., Roger, A.J., Flax, J.L., Brusseau, G.A. and Stahl, D.A., 1998. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol., 180, 2975-2982.
28. Wagner, M., Loy, A., Klein, M., Lee, N. et al., 2005. Functional marker genes for identification of sulfate-reducing prokaryotes. In: Leadbetter, J.R. (ed.), Methods in Enzymology, Vol. 397 Environmental Microbiology. Elsevier Academic Press London U.K., pp. 469-489.
29. Zhang, C.L., Li, Y., Wall, J.D., Larsen, L. et al., 2002. Lipid and carbon isotopic evidence of methane-oxidizing and sulfate-reducing bacteria in association with gas hydrates from the Gulf of Mexico. Geology, 30, 239-242.
30. Zhang, C.L., Pancost, R.D., Sassen, R., Qian, Y. and Macko, S.A., 2003. Archaeal lipid biomarkers and isotopic evidence of anaerobic methane oxidation associated with gas hydrates in the Gulf of Mexico. Organic Geochem., 34, 827-836.
31. Zhang, C.L., Huang, Z., Cantu, J., Pancost, R.D. et al., 2005. Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the Gulf of Mexico. Appl. Environ. Microbiol., 71, 2106-2112.