Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov.

Applied and Environmental Microbiology

Volumn 69, Issue 6, 2003, Pages 3311-3316

  Mikucki, Jill A ^a,c   Liu, Yitai ^a   Delwiche, Mark ^b   Colwell, Frederick S ^b   Boone, David R ^a  

^a PORTLAND STATE UNIVERSITY   (United States)

^b IDAHO NATIONAL LABORATORY   (United States)

^c MONTANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MARINE APPLICATIONS; PH EFFECTS; YEAST;

DEEP MARINE SEDIMENTS;

SEDIMENTS;

ACETIC ACID; DNA; METHANE; RIBOSOME RNA;

DEEP-SEA SEDIMENT; METHANOGENIC BACTERIUM; NEW SPECIES; TAXONOMY;

ARTICLE; BACTERIAL CELL; CARBON SOURCE; CELL GROWTH; CELL MOTILITY; DNA HYBRIDIZATION; GENE SEQUENCE; JAPAN; MARINE ENVIRONMENT; METHANOBACTERIUM; METHANOCULLEUS SUBMARINUS; METHANOGEN; NONHUMAN; NUCLEOTIDE SEQUENCE; PH MEASUREMENT; PHENOTYPE; PHYLOGENY; WATER SAMPLING;

NANKAI TROUGH; PACIFIC OCEAN;

BACTERIA (MICROORGANISMS); COCCOIDEA; METHANOBACTERIUM; METHANOCULLEUS; METHANOCULLEUS MARISNIGRI; METHANOCULLEUS SUBMARINUS;

EID: 0038655470     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.6.3311-3316.2003     Document Type: Article

References (37)

1. Appenzeller, T. 1991. Fire and ice under the deep sea floor. Science 252: 1790-1792.
2. Balch, W. E., L. J. Magrum, G. E. Fox, R. S. Wolfe, and C. R. Woese. 1977. An ancient divergence among the bacteria. J. Mol. Evol. 9:305-311.
3. Bidle, K. A., M. Kastner, and D. H. Bartlett. 1999. A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B). FEMS Microbiol. Lett. 177:101.
4. Blunier, T. 2000. Frozen methane escapes from the sea floor. Science 288: 68-69.
5. Cashion, P., M. A. Holder-Franklin, J. McCully, and M. Franklin. 1977. A rapid method for base ratio determination of bacterial DNA. Anal. Biochem. 81:461-466.
6. 2 utilization. Antonie van Leeuwenhoek 81:263-270.
7. Claypool, G. E., and K. A. Kvenvolden. 1983. Methane and other hydrocarbon gases in marine sediments. Annu. Rev. Earth Planet. Sci. 11:299-327.
8. Cragg, B. A., R. J. Parkes, J. C. Fry, A. J. Weightman, P. A. Rochelle, and J. R. Maxwell. 1996. Bacterial populations and processes in sediments containing gas hydrates (ODP leg 146: Cascadia margin). Earth Planet. Sci. Lett. 139:497-507.
9. De Ley, J., H. Cattoir, and A. Reynaerts. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12: 133-142.
10. Escara, J. F., and J. R. Hutton. 1980. Thermal stability and renaturation of DNA in dimethylsulphoxide solutions: acceleration of renaturation rate. Biopolymers 19:1315-1327.
11. Felsenstein, J. 1993. PHYLIP (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle.
12. Hungate, R. E. 1969. A roll tube method for cultivation of strict anaerobes, p. 117-132. In J. R. Norris and D. W. Ribbons (ed.), Methods in microbiology, vol. 3B. Academic Press, Inc., New York, N.Y.
13. Huss, V. A. R., H. Festl, and K. H. Schleifer. 1983. Studies on the spectrophotometric determination of DNA hybridization from renaturation rate. Syst. Appl. Microbiol. 4:184-192.
14. Jahnke, K.-D. 1992. Basic computer program for evaluation of spectroscopic DNA renaturation data from a Gilford System 2600 spectrometer on a PC/XT/AT type personal computer. J. Microbiol. Methods 15:61-73.
15. Joulian, C., B. M. Ollivier, B. K. C. Patel, and P. A. Roger. 1998. Phenotypic and phylogenetic characterization of dominant culturable methanogens isolated from ricefield soils. FEMS Microbiol. Ecol. 25:135-145.
16. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, Inc., New York, N.Y.
17. Lanoil, B. D., R. Sassen, M. T. LaDuc, S. T. Sweet, and K. H. Nealson. 2001. Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl. Environ. Microbiol. 67:5143-5153.
18. T. Int. J. Syst. Bacteriol. 41:267-274.
19. Maestrojuán, G. M., D. R. Boone, L. Xun, R. A. Mah, and L. Zhang. 1990. Transfer of Methanogenium bourgense, Methanogenium marisnigri, Methanogenium olentangyi, and Methanogenium thermophilicum to the genus Methanoculleus gen. nov., emendation of Methanoculleus marisnigri, and description of new strains of Methanoculleus bourgense and Methanoculleus marisnigri. Int. J. Syst. Bacteriol. 40:117-122.
20. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. G. M., T. M. Schimidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
21. Marchesi, J. R., A. J. Weightman, B. A. Cragg, R. J. Parkes, and J. C. Fry. 2001. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34:221-228.
22. T, and emendation of M. siciliae. Int. J. Syst. Bacteriol. 41:410-416.
23. Olsen, G. J., H. Matsuda, R. Hagstrom, and R. Overbeek. 1994. fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:41-48.
24. Page, R. D. M., and E. C. Holmes. 1998. Molecular evolution: a phylogenetic approach. Blackwell Science Ltd., Cambridge, England.
25. Powell, G. E. 1983. Interpreting gas kinetics of batch culture. Biotechnol. Lett. 5:437-440.
26. Ratkowsky, D. A., R. K. Lowry, T. A. McMeekin, A. N. Stokes, and R. E. Chandler. 1983. Model for bacterial culture growth rate throughout the entire biokinetic temperature range. J. Bacteriol. 154:1222-1226.
27. Ratkowsky, D. A., J. Olley, T. A. McMeekin, and A. Ball. 1982. Relationship between temperature and growth rate of bacterial cultures. J. Bacteriol. 149:1-5.
28. Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida, and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68:3759-3770.
29. Sloan, E. D. 1998. Clathrate hydrates of natural gases, second ed. Marcel Dekker, Inc., New York, N.Y.
30. Smith, S. W., R. Overbeek, C. R. Woese, W. Gilbert, and P. M. Gillevet. 1994. The genetic data environment: an expandable GUI for multiple sequence analysis. Comput. Appl. Biosci. 10:671-675.
31. Sowers, K. R., and K. M. Noll. 1995. Techniques for anaerobic growth, p. 15-47. In F. T. Robb, K. R. Sowers, H. J. Schreier, S. DasSarma, and E. M. Fleischmann (ed.), Archaea: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor Laboratory, N.Y.
32. Springer, E., M. S. Sachs, C. R. Woese, and D. R. Boone. 1995. Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int. J. Syst. Bacteriol. 45:554-559.
33. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
34. Valentine, D. L., and D. R. Boone. 2000. Diversity of methanogens, p. 291-302. In J. Seckbach (ed.), Microbial diversity. Kluwer Press, Dordrecht, The Netherlands.
35. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-464.
36. Wellsbury, P., K. Goodman, T. Barht, B. A. Cragg, S. P. Barnes, and R. J. Parkes. 1997. Deep marine biosphere fuelled by increasing organic matter availability during burial and heating. Nature (London) 388:573-576.
37. Zwietering, M. H., I. Jongenburger, F. M. Rombouts, and K. van't Riet. 1990. Modeling of the bacterial growth curve. Appl. Environ. Microbiol. 56:1875-1881.