Effects of nitrate- and sulfate-amendment on the methanogenic populations in rice root incubations

FEMS Microbiology Ecology

Volumn 43, Issue 3, 2003, Pages 309-315

  Scheid, Daniel ^a   Stubner, Stephan ^a   Conrad, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

Methanogenesis; Nitrate reduction; Rice roots; SSU rRNA; Sulfate reduction; Terminal restriction fragment length polymorphism

Indexed keywords

NITRATE; SULFATE;

METHANOGENESIS; MICROBIAL COMMUNITY; NITRATE; REDUCTION; ROOT; SULFATE;

ARTICLE; INCUBATION TIME; METHANOGENESIS; METHANOMICROBIALES; METHANOSARCINA; NONHUMAN; PLANT ROOT; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RIBOSOME; RICE; RNA SYNTHESIS;

ARCHAEA; METHANOSARCINA;

EID: 0037375289     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(02)00432-4     Document Type: Article

References (54)

1. Liesack W., Schnell S., Revsbech N.P. Microbiology of flooded rice paddies. FEMS Microbiol. Rev. 24:2000;625-645.
2. Frenzel P., Rothfuss F., Conrad R. Oxygen profiles and methane turnover in a flooded rice microcosm. Biol. Fertil. Soil. 14:1992;84-89.
3. Revsbech N.P., Pedersen O., Reichardt W., Briones A. Microsensor analysis of oxygen and pH in the rice rhizosphere under field and laboratory conditions. Biol. Fertil. Soils. 29:1999;379-385.
4. Reddy K.R., Patrick W.H. Jr., Lindau C.W. Nitrification-denitrification at the plant root-sediment interface in wetlands. Limnol. Oceanogr. 34:1989;1004-1013.
5. Wind T., Conrad R. Sulfur compounds, potential turnover of sulfate and thiosulfate, and numbers of sulfate-reducing bacteria in planted and unplanted paddy soil. FEMS Microbiol. Ecol. 18:1995;257-266.
6. Ponnamperuma F.N. The chemistry of submerged soils. Adv. Agron. 24:1972;29-96.
7. Zehnder, A.J.B. and Stumm, W. (1988) Geochemistry and biogeochemistry of anaerobic habitats. In: Biology of Anaerobic Microorganisms (Zehnder, A.J.B., Ed.), pp. 1-38. Wiley, New York.
8. Roy R., Klüber H.D., Conrad R. Early initiation of methane production in anoxic rice soil despite the presence of oxidants. FEMS Microbiol. Ecol. 24:1997;311-320.
9. Mountfort D.O., Asher R.A. Role of sulfate reduction versus methanogenesis in terminal carbon flow in polluted intertidal sediment of Waimea Inlet, Nelson, New Zealand. Appl. Environ. Microbiol. 45:1981;252-258.
10. Holmer M., Kristensen E. Coexistence of sulfate reduction and methane production in an organic-rich sediment. Mar. Ecol. Prog. Ser. 107:1994;177-184.
11. Achtnich C., Bak F., Conrad R. Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers and methanogens in anoxic paddy soil. Biol. Fertil. Soils. 19:1995;65-72.
12. Lin M., You C. Root exudates of rice (Oryza sativa L.) and its interaction with Alcaligenes faecalis. Sci. Agric. Sin. 22:1989;6-12.
13. Waschütza S., Hofmann N., Niemann E.G., Fendrik I. Investigations on root exudates of Korean rice. Symbiosis. 13:1992;181-189.
14. Dannenberg S., Conrad R. Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biogeochemistry. 45:1999;53-71.
15. Conrad R., Klose M. Anaerobic conversion of carbon dioxide to methane, acetate and propionate on washed rice roots. FEMS Microbiol. Ecol. 30:1999;147-155.
16. Groβkopf R., Stubner S., Liesack W. Novel euryarchaeotal lineages detected on rice roots and in anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64:1998;4983-4989.
17. 2-dependent methanogenesis on washed rice roots. Environ. Microbiol. 1:1999;159-166.
18. Wind T., Stubner S., Conrad R. Sulfate-reducing bacteria in rice field soil and on rice roots. Syst. Appl. Microbiol. 22:1999;269-279.
19. Scheid D., Stubner S. Structure and diversity of gram-negative sulfate-reducing bacteria on rice roots. FEMS Microbiol. Ecol. 36:2001;175-183.
20. Arth I., Frenzel P., Conrad R. Denitrification coupled to nitrification in the rhizosphere of rice. Soil Biol. Biochem. 30:1998;509-515.
21. Schütz H., Holzapfel-Pschorn A., Conrad R., Rennenberg H., Seiler W. A 3-year continuous record on the influence of daytime, season, and fertilizer treatment on methane emission rates from an Italian rice paddy. J. Geophys. Res. 94:1989;16405-16416.
22. Schütz H., Seiler W., Conrad R. Processes involved in formation and emission of methane in rice paddies. Biogeochemistry. 7:1989;33-53.
23. Conrad R., Mayer H.P., Wüst M. Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil. FEMS Microbiol. Ecol. 62:1989;265-274.
24. Schuler S., Conrad R. Soil contain two different activities for oxidation of hydrogen. FEMS Microbiol. Ecol. 73:1990;77-84.
25. Krumböck M., Conrad R. Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment. FEMS Microbiol. Ecol. 85:1991;247-256.
26. Bak F., Scheff G., Jansen K.H. A rapid and sensitive ion chromatographic technique for the determination of sulfate and sulfate reduction rates in freshwater lake sediments. FEMS Microbiol. Ecol. 85:1991;23-30.
27. Lüdemann H., Arth I., Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66:2000;754-762.
28. Groβkopf 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.
29. Lueders T., Friedrich M.W. Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil. Appl. Environ. Microbiol. 68:2002;2484-2494.
30. Stahl, D.A. and Amann, R. (1991) Development and application of nucleic acid probes. In: Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 205-248. John Wiley and Sons, Chichester.
31. Chin K.-J., Lukow T., Conrad R. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65:1999;2341-2349.
32. Liu W.-T., Marsh T.L., Cheng H., Forney L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rDNA. Appl. Environ. Microbiol. 63:1997;4516-4522.
33. Dunbar J., Ticknor L.O., Kuske C.R. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67:2001;190-197.
34. Lueders T., Friedrich M. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 66:2000;2732-2742.
35. Ramakrishnan B., Lueders T., Dunfield P.F., Conrad R., Friedrich M. Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiol. Ecol. 37:2001;175-186.
36. Chin, K.-J., Lueders, T., Klose, M. and Conrad, R., Methanogenic pathway and methanogenic archaeal community structure on rice roots, in preparation.
37. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker - molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:1997;4704-4712.
38. Weber S., Lueders T., Friedrich M.W., Conrad R. Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiol. Ecol. 38:2001;11-20.
39. Amann R.I., Krumholtz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:1990;762-770.
40. 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.
41. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1990;1919-1925.
42. Conrad R., Klose M. Selective inhibition of reactions involved in methanogenesis and fatty acid production on rice roots. FEMS Microbiol. Ecol. 34:2000;27-34.
43. Kemp P.F., Lee S., LaRoche J. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59:1993;2594-2601.
44. Molin S., Givskov M. Application of molecular tools for in situ monitoring of bacterial growth activity. Environ. Microbiol. 1:1999;383-391.
45. 2O on methanogenesis and other redox processes in anoxic rice field soil. FEMS Microbiol. Ecol. 25:1998;301-318.
46. Lueders T., Chin K.J., Conrad R., Friedrich M. Molecular analysis of methyl-coenzyme M reductase α-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3:2001;194-204.
47. Fey A., Chin K.J., Conrad R. Thermophilic methanogens in rice field soil. Environ. Microbiol. 3:2001;295-303.
48. Garcia J.L. Taxonomy and ecology of methanogens. FEMS Microbiol. Rev. 87:1990;297-308.
49. 2O and NO). Microbiol. Rev. 60:1996;609-640.
50. Jetten M.S.M., Stams A.J.M., Zehnder A.J.B. Acetate thresholds values and acetate activating enzymes in methanogenic bacteria. FEMS Microbiol. Ecol. 73:1990;339-344.
51. Balderston W.L., Payne W.J. Inhibition of methanogenesis in salt marsh sediments and whole-cell suspensions of methanogenic bacteria by nitrogen oxides. Appl. Environ. Microbiol. 32:1976;264-269.
52. 2O on methanogenesis by Methanosarcina barkeri and Methanobacterium bryantii. FEMS Microbiol. Ecol. 25:1998;331-339.
53. Roy R., Conrad R. Effect of methanogenic precursors (acetate, hydrogen, propionate) on the suppression of methane production by nitrate in anoxic rice field soil. FEMS Microbiol. Ecol. 28:1999;49-61.
54. Muraoka Y., Hamakawa E., Toyota K., Kimura M. Observation of microbial colonization on the surface of rice roots along with their development and degradation. Soil Sci. Plant Nutr. 46:2000;491-502.