Culturable populations of Sporomusa spp. and Desulfovibrio spp. in the anoxic bulk soil of flooded rice microcosms

Applied and Environmental Microbiology

Volumn 65, Issue 8, 1999, Pages 3526-3533

  Rosencrantz, Dirk ^a   Rainey, Frederick A ^b,d   Janssen, Peter H ^a,c  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM CULTURE; BACTERIUM ISOLATION; DESULFOVIBRIO; METHANOSPIRILLUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RICE; SOIL; SOIL MICROFLORA;

DESULFOVIBRIO; METHANOSPIRILLUM HUNGATEI; SPOROMUSA;

EID: 0032812280     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.8.3526-3533.1999     Document Type: Article

References (52)

1. Beliaeff, B., and J. Y. Mary. 1993. The "most probable number" estimate and its confidence limits. Water Res. 27:799-805.
2. Bradford, M. M. 1976. A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
3. 2-utilizing methanogenic bacteria. Appl. Environ. Microbiol. 33:1162-1169.
4. Chin, K.-J., and R. Conrad. 1995. Intermediary metabolism in methanogenic paddy soil and the influence of temperature. FEMS Microbiol. Ecol. 18:85-102.
5. Chin, K.-J., and P. H. Janssen. Unpublished data.
6. Chin, K.-J., D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen. Unpublished data.
7. Cline, J. D. 1969. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14:454-458.
8. Cochran, W. G. 1950. Estimation of bacterial densities by means of the "most probable number." Biometrics 6:105-116.
9. Conrad, R. 1993. Mechanisms controlling methane emission from wetland rice fields, p. 317-355. In R. S. Oremland (ed.), Biogeochemistry of global change: radiatively active trace gases. Chapman and Hall, New York, N.Y.
10. Conrad, R., F. Bak, H. J. Seitz, B. Thebrath, H. P. Mayer, and H. Schütz. 1989. Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment. FEMS Microbiol. Ecol. 62:285-294.
11. Cord-Ruwisch, R. 1985. A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate reducing bacteria. J. Microbiol. Methods 4:33-36.
12. Cord-Ruwisch, R., H.-J. Seitz, and R. Conrad. 1988. The capacity of hydrogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor. Arch. Microbiol. 149:350-357.
13. Cote, R. J., and R. L. Gherna. 1994. Nutrition and media, p. 155-178. In P. Gerhardt, R. G. E. Murray, W. A. Wood, and N. R. Krieg (ed.), Methods for general and molecular microbiology. American Society for Microbiology, Washington, D.C.
14. 4 in atmospheric chemistry: sources, sinks and possible reductions in anthropogenic sources. Ambio 24:52-55.
15. Dalsgaard, T., and F. Bak. 1994. Nitrate reduction in a sulfate-reducing bacterium, Desulfovibrio desulfuricans, isolated from rice paddy soil: sulfide inhibition, kinetics, and regulation. Appl. Environ. Microbiol. 60:291-297.
16. De Soete, G. 1983. A least squares algorithm for fitting additive trees to proximity data. Psychometrica 48:621-626.
17. Diekert, G. 1992. The acetogenic bacteria, p. 517-533. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer, Berlin, Germany.
18. Frenzel, P., and U. Bosse. 1996. Methyl fluoride, an inhibitor of methane oxidation and methane production. FEMS Microbiol. Ecol. 21:25-36.
19. Frenzel, P., U. Bosse, and P. H. Janssen. 1998. Rice roots and methanogenesis in a paddy soil: ferric iron as an alternative electron acceptor in the rooted soil. Soil Biol. Biochem. 31:421-430.
20. Frenzel, P., F. Rothfuss, and R. Conrad. 1992. Oxygen profiles and methane turnover in a flooded rice microcosm. Biol. Fertil. Soils 14:84-89.
21. Großkopf, R., P. H. Janssen, and W. Liesack. 1998. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64:960-969.
22. Heijthuisen, J. H. F. G., and T. A. Hansen. 1986. Interspecies hydrogen transfer in co-cultures of methanol-utilizing acidogens and sulfate-reducing or methanogenic bacteria. FEMS Microbiol. Ecol. 38:57-64.
23. Hermann, M., M.-R. Popoff, and M. Sebald. 1987. Sporomusa paucivorans sp. nov., a methylotrophic bacterium that forms acetic acid from hydrogen and carbon dioxide. Int. J. Syst. Bacteriol. 37:93-101.
24. Janssen, P. H., and B. Schink. 1995. Catabolic and anabolic enzyme activities and energetics of acetone metabolism of the sulfate-reducing bacterium Desulfococcus biacutus. J. Bacteriol. 177:277-282.
25. Janssen, P. H., W. Liesack, C. Kluge, S. Seeliger, B. Schink, and C. G. Harfoot. 1996. Sodium-dependent succinate decarboxylation by a new anaerobic bacterium belonging to the genus Peptostreptococcus. Antonie Leeuwenhoek 70:11-20.
26. Janssen, P. H., A. Schuhmann, E. Mörschel, and F. A. Rainey. 1997. Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl. Environ. Microbiol. 63:1382-1388.
27. 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, New York, N.Y.
28. Kappler, O., P. H. Janssen, J.-U. Kreft, and B. Schink. 1997. Effects of alternative methyl group acceptors on the growth energetics of the O-demethylating anaerobe Holophaga foetida. Microbiology 143:1105-1114.
29. 2 concentrations in methanogenic environments with a gas diffusion probe. FEMS Microbiol. Ecol. 12:149-158.
30. Krumböck, M., and R. Conrad. 1991. Metabolism of position-labeled glucose in anoxic methanogenic paddy soil and lake sediment. FEMS Microbiol. Ecol. 85:247-256.
31. Kuhner, C. H., C. Frank, A. Greißhammer, M. Schmittroth, G. Acker, A. Gößner, and H. L. Drake. 1997. Sporomusa silvacetica sp. nov., an acetogenic bacterium isolated from aggregated forest soil. Int. J. Syst. Bacteriol. 47:352-358.
32. Küsel, K., and H. L. Drake. 1995. Effects of environmental parameters on the formation and turnover of acetate by forest soils. Appl. Environ. Microbiol. 61:3667-3675.
33. Liesack, W., P. H. Janssen, F. A. Rainey, N. L. Ward-Rainey, and E. Stackebrandt. 1997. Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques, p. 375-439. In J. D. van Elsas, J. T. Trevors, and E. M. H. Wellington (ed.), Modern soil microbiology. Marcell Dekker, New York, N.Y.
34. Lovell, C. R., and Y. Hui. 1991. Design and testing of a functional group-specific DNA probe for the study of natural populations of acetogenic bacteria. Appl. Environ. Microbiol. 57:2602-2609.
35. Lovley, D. R., and M. J. Klug. 1986. Model for the distribution of sulfate reduction and methanogenesis in freshwater sediments. Geochim. Cosmochim. Acta 50:11-18.
36. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22:3485-3487.
37. Minami, K., and H.-U. Neue. 1994. Rice paddies as a methane source. Clim. Change 27:13-26.
38. 12-requiring member of the family Rhodospirillaceae. Int. J. Syst. Bacteriol. 28:283-288.
39. Pfennig, N., and S. Wagener. 1986. An improved method for preparing wet mounts for photomicrographs of microorganisms. J. Microbiol. Methods 4:303-306.
40. Postgate, J. R. 1959. A diagnostic reaction of Desulphovibrio desulphuricans. Nature 183:481-482.
41. Rainey, F. A., N. Ward-Rainey, R. M. Kroppenstedt, and E. Stackebrandt. 1996. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int. J. Syst. Bacteriol. 46:1088-1092.
42. 4 production in a flooded Italian rice field. Biogeochemistry 18:137-152.
43. Schink, B. 1994. Diversity, ecology, and isolation of acetogenic bacteria, p. 197-235. In H. L. Drake (ed.), Acetogenesis. Chapman and Hall, New York, N.Y.
44. Süßmuth, R., J. Eberspächer, R. Haag, and W. Springer. 1987. Biochemischmikrobiologishes Praktikum. Thieme, Stuttgart, Germany.
45. Thebrath, B., H. P. Mayer, and R. Conrad. 1992. Bicarbonate dependent production and methanogenic consumption of acetate in anoxic paddy soil. FEMS Microbiol. Ecol. 86:295-302.
46. Tilman, D. 1994. Competition and biodiversity in spatially structured habitats. Ecology 75:2-16.
47. Wagner, C., A. Greißhammer, and H. L. Drake. 1996. Acetogenic capacities and the anaerobic turnover of carbon in a Kansas prairie soil. Appl. Environ. Microbiol. 62:494-500.
48. Widdel, F., and F. Bak. 1992. Gram-negative mesophilic sulfate-reducing bacteria, p. 3352-3378. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer, Berlin, Germany.
49. Willems, A., and M. D. Collins. 1996. Phylogenetic relationships of the genera Acetobacterium and Eubacterium sensu stricto and reclassification of Eubacterium alactolyticum as Pseudoramibacter alactolyticus gen. nov., comb. nov. Int. J. Syst. Bacteriol. 46:1083-1087.
50. Wind, T., and R. Conrad. 1995. Sulfur compounds, potential turnover of sulfate and thiosulfate, and numbers of sulfate-reducing bacteria in planted and unplanted paddy soil. FEMS Microbiol. Ecol. 18:257-266.
51. Wind, T., and R. Conrad. 1997. Localization of sulfate reduction in planted and unplanted rice field soil. Biogeochemistry 37:253-278.
52. Wood, H. G., and L. G. Ljungdahl. 1991. Autotrophic character of the acetogenic bacteria, p. 201-250. In J. M. Shively and L. L. Barton (ed.), Variations in autotrophic life. Academic Press, New York, N.Y.