Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing

FEMS Microbiology Ecology

Volumn 65, Issue 1, 2008, Pages 125-132

  Noll, Matthias ^a,b   Frenzel, Peter ^a   Conrad, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b BAM FEDERAL INSTITUTE FOR MATERIALS RESEARCH AND TESTING   (Germany)

Author keywords

Methane oxidation; Methylocaldum; Methylomicrobium; Nitrogen fertilization; Stable isotope probing; Urea

Indexed keywords

CARBON 13; ISOTOPE; METHANE; NITROGEN; RNA; UREA;

AGRICULTURAL SOIL; COMPARATIVE STUDY; FERTILIZER APPLICATION; METHANE; METHANOGENIC BACTERIUM; OXIDATION; PROBE; RICE; STABLE ISOTOPE; UREA;

ARTICLE; FERTILIZER APPLICATION; ISOTOPE ANALYSIS; ITALY; METHANOTROPH; MICROBIAL DIVERSITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RICE; RNA STABILITY; SEPARATION TECHNIQUE; SOIL; STIMULATION;

CARBON ISOTOPES; CENTRIFUGATION, ISOPYCNIC; CLONING, MOLECULAR; FERTILIZERS; METHANE; METHYLOCOCCACEAE; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; OXIDATION-REDUCTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, BACTERIAL; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; UREA;

METHYLOCALDUM; METHYLOCOCCACEAE; METHYLOMICROBIUM;

EID: 45149121427     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2008.00497.x     Document Type: Article

References (49)

1. Auman AJ, Speake CC Lidstrom ME (2001) nifH sequences and nitrogen fixation in type I and type II methanotrophs. Appl Environ Microbiol 67: 4009.
2. Bodelier PLE Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47: 265 277.
3. Bodelier PLE, Hahn AP, Arth I Frenzel P (2000a) Effects of ammonium-based fertilisation on microbial processes involved in methane emission from soils planted with rice. Biogeochemistry 51: 225 257.
4. Bodelier PLE, Roslev P, Henckel T Frenzel P (2000b) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403: 421 424.
5. Bodrossy L, Stralis-Pavese N, Konrad-Koszler M, Weilharter A, Reichenauer TG, Schofer D Sessitsch A (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72: 1672 1676.
6. Bowman J (2000) The Methanotrophs. The Families Methylococcaceae and Methylocystaceae. The Prokaryotes (Dworkin M, ed pp. 266 289. Springer, New York.
7. Cassman KG, Peng S, Olk DC, Ladha JK, Reichardt W, Dobermann A Singh U (1998) Opportunities for increased nitrogen-use efficiency from improved resource management in irrigated rice systems. Field Crops Res 56: 7 39.
8. Cebron A, Bodrossy L, Stralis-Pavese N, Singer AC, Thompson IP, Prosser JI Murrell JC (2007) Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity. Appl Environ Microbiol 73: 798 807.
9. Chen Y, Dumont MG, McNamara NP, Chamberlain PM, Bodrossy L, Stralis-Pavese N Murrell JC (2008) Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ Microbiol 10: 446 459.
10. Corbin JL (1984) Liquid-chromatographic fluorescence determination of ammonia from nitrogenase reactions: a 2-min assay. Appl Environ Microbiol 47: 1027 1030.
11. Dedysh SN, Ricke P Liesack W (2004) NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Microbiology 150: 1301 1313.
12. Dedysh SN, Knief C Dunfield PF (2005) Methylocella species are facultatively methanotrophic. J Bact 187: 4665 4670.
13. Denier van der Gon HAC Neue HU (1996) Oxidation of methane in the rhizosphere of rice plants. Biol Fertil Soils 22: 359 366.
14. Dunfield P Knowles R (1995) Kinetics of inhibition of methane oxidation by nitrate, nitrite, and ammonium in a humisol. Appl Environ Microbiol 61: 3129 3135.
15. Eller G Frenzel P (2001) Changes in activity and community structure of methane oxidising bacteria over the growth period of rice. Appl Environ Microbiol 67: 2395 2403.
16. Eller G, Krüger M Frenzel P (2005) Comparing field and microcosm experiments: a case study on methano- and methylotrophic bacteria in paddy soil. FEMS Microbiol Ecol 51: 279 291.
17. Frenzel P (2000) Plant-associated methane oxidation in rice fields and wetlands. Adv Microb Ecol 16: 85 114.
18. Garrity GM, Winters M Searles DB (2001) Taxonomic outline of the prokaryotic genera. Bergey's Manual of Systematic Bacteriology (Garrity GM, Boone DR Castenholz RW, eds pp. 1 39. Springer-Verlag, New York, NY.
19. Glibert P, Harrison J, Heil C Seitzinger S (2006) Escalating worldwide use of urea: a global change contributing to coastal eutrophication. Biogeochemistry 77: 441 463.
20. Graham DW, Chaudhary JA, Hanson RS Arnold RG (1993) Factors affecting competition between type-I and type-II methanotrophs in 2-organism, continuous-flow reactors. Microb Ecol 25: 1 17.
21. Hanson RS Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60: 439.
22. Holzapfel-Pschorn A, Conrad R Seiler W (1986) Effects of vegetation on the emission of methane from submerged paddy soil. Plant Soil 92: 223 233.
23. Intergovernmental Panel on Climate Change (2007) Climate Change 2007: The Physical Science Basis. Summary for Policymakers. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Summary for Policymakers formally approved at the 10th Session of Working Group I of the IPCC, Paris.
24. Kindt R Coe R (2005) Tree Diversity Analysis. World Agroforestry Centre, Nairobi, Kenya. ISBN 92 9059 179 X.
25. King GM Schnell S (1994) Ammonium and nitrite inhibition of methane oxidation by Methylobacter albus BG8 and Methylosinus trichosporium OB3b at low methane concentrations. Appl Environ Microbiol 60: 3508 3513.
26. 4 emissions from microcosms and rice fields. Global Change Biol 9: 773 784.
27. Krüger M, Frenzel P Conrad R (2001) Microbial processes influencing methane emission from rice fields. Global Change Biol 7: 49 63.
28. 4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors. Global Change Biol 8: 265 280.
29. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E Goodfellow M, eds), pp. 115 175. John Wiley and Sons, Chichester, UK.
30. Ludwig W, Strunk O, Westram R et al 2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363 1371.
31. Lueders T, Manefield M Friedrich MW (2004a) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73 78.
32. Lueders T, Wagner B, Claus P Friedrich MW (2004b) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6: 60 72.
33. Manefield M, Whiteley AS, Griffiths RI Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367 5373.
34. McCune B Grace JB (2002) Analysis of Ecological Communities. MjM Software Design, Gleneden Beach, OR.
35. Mohanty SR, Bodelier PLE, Floris V Conrad R (2006) Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 72: 1346 1354.
36. Morris SA, Radajewski S, Willison TW Murrell JC (2002) Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol 68: 1446 1453.
37. Murase J Frenzel P (2007) A methane-driven microbial food web in a wetland rice soil. Environ Microbiol 9: 3025 3034.
38. Murase J, Noll M Frenzel P (2006) The impact of protists on activity and structure of the bacterial community in a rice field soil. Appl Environ Microbiol 72: 5436 5444.
39. Murrell JC Dalton H (1983) Nitrogen fixation in obligate methanotrophs. J Gen Microbiol 129: 3481 3486.
40. Noll M, Matthies D, Frenzel P, Derakshani M Liesack W (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7: 382 395.
41. Radajewski S, Ineson P, Parekh NR Murrell C (2000) Stable isotope probing as a tool in microbial ecology. Nature 403: 646 649.
42. R Development Core Team (2007) R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL.
43. Reeburgh WS, Whalen SC Alperin MJ (1993) The role of methylotrophy in the global methane budget. Microbial Growth on C-1 Compounds (Murrell JC Kelly DP, eds), pp. 1 14. Intercept, Andover.
44. Schmidt HA, Strimmer K, Vingron M von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502 504.
45. Schnell S King GM (1994) Mechanistic analysis of ammonium inhibition of atmospheric methane consumption in forest soils. Appl Environ Microbiol 60: 3514 3521.
46. Soh KG (2001) Global Supply and Demand for Urea. Mitco Marketing & Trading Forum, Bangi, Malaysia.
47. Steudler PA, Bowden RD, Melillo JM Aber JD (1989) Influence of nitrogen fertilization on methane uptake in temperate forest soils. Nature 341: 314 316.
48. Theisen AR Murrell JC (2005) Facultative methanotrophs revisited. J Bact 187: 4303 4305.
49. Whittenbury R, Philips KC Wilkinson JF (1970) Enrichment, isolation, and some properties of methane-utilizing bacteria. J Gen Microbiol 61: 205 218.