Vertical distributions of sulfate-reducing bacteria and methane-producing archaea quantified by oligonucleotide probe hybridization in the profundal sediment of a mesotrophic lake

FEMS Microbiology Ecology

Volumn 44, Issue 1, 2003, Pages 101-108

  Koizumi, Yoshikazu ^a   Takii, Susumu ^a   Nishino, Machiko ^b   Nakajima, Takuo ^b  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

^b LAKE BIWA ENVIRONMENTAL RESEARCH INSTITUTE   (Japan)

Author keywords

Mesotrophic lake; Methane producing archaea; Profundal sediment; Quantitative membrane hybridization; Small subunit rRNA distribution; Sulfate reducing bacterium

Indexed keywords

METHANE; OLIGONUCLEOTIDE; SMALL SUBUNIT RIBOSOMAL RNA; SULFATE; WATER;

BACTERIUM; FRESHWATER SEDIMENT; MESOTROPHIC ENVIRONMENT; PROBE; SULFATE-REDUCING BACTERIUM; VERTICAL DISTRIBUTION;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL METABOLISM; BACTERIAL SURVIVAL; BACTERIUM; BIOGEOGRAPHY; CONCENTRATION (PARAMETERS); DESULFOBACTER LATTUS; DESULFOBACTERIUM AUTOTROPHICUM; DESULFOBULBUS PROPIONICUS; DESULFOCOCCUS MULTIVORANS; DESULFOVIBRIO; FRESHWATER ENVIRONMENT; GEOBACTERACEAE; LAKE; MEASUREMENT; METABOLIC RATE; METHANOBREVIBACTER SMITHII; METHANOCOCCUS VOLTAE; METHANOGENIUM THERMOPHILIUM; METHANOSAETA CONCILII; METHANOSARCINA; METHANOSARCINA BARKERI; NONHUMAN; OLIGONUCLEOTIDE PROBE; ORDO; PRIORITY JOURNAL; PROFUNDAL ZONE; QUANTITATIVE ANALYSIS; RNA HYBRIDIZATION; SEDIMENT; SULFATE REDUCING BACTERIUM;

ARCHAEA; BACTERIA (MICROORGANISMS); DESULFOVIBRIONACEAE; GEOBACTERACEAE; METHANOSARCINALES;

EID: 0041381031     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(02)00463-4     Document Type: Article

References (47)

1. Jørgensen B.B. Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature. 296:1982;643-645.
2. Schönheit P., Kristjansson J.K., Thauer R.K. Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Arch. Microbiol. 132:1982;285-288.
3. 2 under resting and growing conditions. Arch. Microbiol. 137:1984;26-32.
4. Lovley D.R., Klug M.J. Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations. Appl. Environ. Microbiol. 45:1983;187-192.
5. Winfrey M.R., Ward D.M. Substrate for sulfate reduction and methane production in intertidal sediments. Appl. Environ. Microbiol. 45:1983;193-199.
6. Widdel, F. and Bak, F. (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: The Prokaryotes, 2nd Edn. (Balows, A., Trüper, M., Dworkin, M., Harder, W. and Schleifer, K.-H., Eds.), Vol. IV, pp. 3352-3378. Springer, New York.
7. Laanbroek H.J., Pfenning N. Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments. Arch. Microbiol. 128:1981;330-335.
8. Hines M.E., Buck J.D. Distribution of methanogenic and sulfate-reducing bacteria in near-shore marine sediments. Appl. Environ. Microbiol. 43:1982;447-453.
9. Franklin M.J., Wiebe W.J., Whitman W.B. Populations of methanogenic bacteria in a Georgia salt marsh. Appl. Environ. Microbiol. 54:1988;1151-1157.
10. Bak F., Pfenning N. Sulfate-reducing bacteria in littoral sediment of Lake Constance. FEMS Microbiol. Ecol. 85:1991;43-52.
11. Amann R.I., Ludwig W., Schleifer K.-H. Phylogenic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
12. Zaiss U. Seasonal studies of methanogenesis and desulfurication in sediments of the River Saar. Zent.bl. Bakt. Hyg. Abt. Orig. C. 2:1981;76-89.
13. Schallenberg M., Jakob K., Rasmussen J.B. Solutions to problems in enumerating sediment bacteria by direct count. Appl. Environ. Microbiol. 55:1989;1214-1219.
14. Fukui M., Takii S. Seasonal variations of population density and activity of sulfate-reducing bacteria in offshore and reed sediments of a hypertrophic freshwater lake. Jpn. J. Limnol. 51:1990;63-71.
15. Takii S., Li J.-H., Hayashi H. Methane production and sulfate reduction in profundal sediments in Lake Kizaki, Japan. Jpn. J. Limnol. 58:1997;373-384.
16. Purdy K.J., Embley T.M., Takii S., Nedwell D.B. Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl. Environ. Microbiol. 62:1996;3905-3907.
17. Stahl D.A., Flesher B., Mansfield H.R., Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1988;1079-1084.
18. Raskin L., Stromley J.M., Rittmann B.E., Stahl D.A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1994;1232-1240.
19. Zheng D., Alm E.W., Stahl D.A., Raskin L. Characterization of universal small-subunit rRNA hybridization probe for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62:1996;4504-4513.
20. Devereux R., Kane M.D., Winfery J., Stahl D.A. Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15:1992;601-609.
21. Alm E.W., Stahl D.A. Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J. Microbiol. Methods. 40:2000;153-162.
22. Nishino M., Fukui M., Nakajima T. Dense mats of Thioploca, gliding filamentous sulfur-oxidizing bacteria in Lake Biwa, central Japan. Water Res. 32:1998;953-957.
23. Li J., Purdy K.J., Takii S., Hayashi H. Seasonal changes in ribosomal RNA of sulfate-reducing bacteria and sulfate-reducing activity in a freshwater lake sediment. FEMS Microbiol. Ecol. 28:1999;31-39.
24. Purdy K.J., Nedwell D.B., Embley T.M., Takii S. Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulfate-reducing bacteria in estuarine sediments. FEMS Microbiol. Ecol. 36:2001;165-168.
25. Sass H., Wieringa E., Cypionka H., Babenzien H.-D., Overmann J. High genetic and physiological diversity of sulfate-reducing bacteria isolated from an oligotrophic lake sediment. Arch. Microbiol. 170:1998;243-251.
26. Maeda H., Kawai A. Hydrogen sulfide production in bottom sediments in the northern and southern lake Biwa. Nippon Suisan Gakkaishi. 54:1988;1623-1633.
27. Sahm K., Knoblauch C., Amann R. Phylogenetic affiliation and quantification of sulfate-reducing isolates in marine arctic sediments. Appl. Environ. Microbiol. 65:1999;3976-3981.
28. Ravenschlag K., Sahm K., Pernthaler J., Amann R. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65:1999;3982-3989.
29. Devereux R., Winfery M.R., Winfrey J., Stahl D.A. Depth profile of sulfate-reducing bacteria ribosomal RNA and mercury methylation in an estuarine sediment. FEMS Microbiol. Ecol. 20:1996;23-31.
30. Maidak B.L., Larsen N., McCaughey M.J., Overbeek R., Olsen G.J., Fogel K., Blandy J., Woese C.R. The Ribosomal Database Project. Nucleic Acids Res. 22:1994;3485-3487.
31. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
32. Barns S.M., Delwiche C.F., Palmer J.D., Pace N.R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA. 93:1996;9188-9193.
33. Whitman, W.B., Bowen, T.L. and Boone, D.R. (1992) The methanogenic bacteria. In: The Prokaryotes, 2nd Edn. (Balows, A., Trüper, M., Dworkin, M., Harder, W. and Schleifer, K.-H., Eds.), Vol. IV, pp. 719-767. Springer, New York.
34. Schleper C., Holben W., Klenk H.P. Recovery of Crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl. Environ. Microbiol. 63:1997;321-323.
35. MacGregor B.J., Moser D.P., Alm E.W., Nealson K.H., Stahl D.A. Crenarchaeota in Lake Michigan sediment. Appl. Environ. Microbiol. 63:1997;1178-1181.
36. Hershberger K.L., Barns S.M., Reysenbach A.L., Dawson S.C., Pace N.R. Wide diversity of Crenarchaeota. Nature. 384:1996;420.
37. Falz K.Z., Holliger C., Großkopf R., Liesack W., Nozhevnikova A.N., Muller B., Wehrli B., Hahn D. Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl. Environ. Microbiol. 63:1999;2402-2408.
38. Go Y.-S., Han S.-K., Lee I.-G., Ahn T.-Y. Diversity of the domain Archaea as determined by 16S rRNA gene analysis in the sediments of Lake Soyang. Arch. Hydrobiol. 149:2000;459-466.
39. Großkopf R., Janssen P.H., Liesack W. 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. 64:1998;960-969.
40. Smith R.S., Mah R.A. Growth and methanogenesis by Methanosarcina strain 227 on acetate and methanol. Appl. Environ. Microbiol. 36:1978;368-371.
41. Zehnder A.J., Huser B.A., Brock T.D., Wuhrmann K. Characterization of an acetate-decarboxylating, non-hydrogen-oxidizing methane bacterium. Arch. Microbiol. 124:1980;1-11.
42. Madigan, M.T., Martinko, J.M. and Parker, J. (2000) Brock Biology of Microorganisms, 9th Edn., pp. 548-561. Prentice-Hall, Englewood Cliffs, NJ.
43. Munson M.A., Nedwell D.B., Embley T.M. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63:1997;4729-4733.
44. Molin S., Givskov M. Application of molecular tools for in situ monitoring of bacterial growth activity. Environ. Microbiol. 1:1999;383-391.
45. Sahm K., MacGregor B.J., Jørgensen B.B., Stahl D.A. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ. Microbiol. 1:1999;65-74.
46. Ravenschlag K., Sahm K., Knoblauch C., Jørgensen B.B., Amann R. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol. 66:2000;3592-3602.
47. Franklin R.B., Taylor D.R., Mills A.L. The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer. Microb. Ecol. 38:2000;377-386.