Dokument

Summary:
Methanotrophic bacteria perform a central function in our climate system representing the only biogenic sink for the greenhouse gas methane. In wetland rice fields, they function as bio-filters preventing methane produced in anoxic layers escaping into the atmosphere, attenuating the potential methane emission by up to 90%. Despite intensive studies in the past, molecular approaches have barely started to explore the full diversity of methanotrophs. Furthermore, only little is known on their ecological niche differentiation and the factors influencing their community structure. This thesis focuses on the aerobic methanotrophic communities in the wetland rice ecosystem using the pmoA gene as a functional and phylogenetic marker to detect these bacteria in the environment. A high diversity could be recorded dominated by Methylocystis and Methylosinus species (type II) and yet uncultivated bacteria grouping within type Ib methanotrophs. The rice paddy cluster 1 (RPC-1) forms the largest cluster consisting entirely of sequences obtained from paddy fields located around the world. It is only distantly related to cultivated species and might form a new genus of methanotrophs specifically adapted to wetland rice fields. Methanotrophic communities showed no large scale horizontal distribution patterns within an Italian paddy field; thus, a reduced sampling effort is sufficient to extrapolate to the field scale. However, different methanotrophic communities were detected on the rice roots compared to the field soil and the communities in different fields differed significantly. The rice roots were characterized by a high abundance of type I methanotrophs and different rice cultivars were shown to have an effect on these communities. This effect could be correlated to the plant genotype and enables to select specific cultivars for in-depth studies. Re-evaluating the pmoA gene as a phylogenetic marker for methanotrophs revealed a good correlation of the pmoA to the 16S rRNA phylogeny. Nevertheless, some exceptions suggests that methanotrophy might be evolutionary more complicated having been even exchanged between species. Furthermore, a meta-analysis of pmoA sequences from various environments revealed distinct correlations of genotypes and habitats.

Bibliographie / References

1. Trotsenko,Y.A. and Murrell,J.C. (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 63: 183-229.
2. Ogram,A., Castro,H., Stanley,E., Chen,W.W., and Prenger,J. (2006) Distribution of methanotrophs in managed and highly disturbed watersheds. Ecological Indicators 6: 631-643.
3. Rothfuss,F., Bender,M., and Conrad,R. (1997) Survival and activity of bacteria in a deep, aged lake sediment (Lake Constance). Microb. Ecol. 33: 69-77.
4. Singh,J.S., Raghubanshi,A.S., Reddy,V.S., Singh,S., and Kashyap,A.K. (1998) Methane flux from irrigated paddy and dryland rice fields, and from seasonally dry tropical forest and savanna soils of india. Soil Biol. Biochem. 30: 135-139.
5. Shrestha,M., Abraham,W.R., Shrestha,P.M., Noll,M., and Conrad,R. (2008) Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ. Microbiol. 10: 400-412.
6. Murase,J. and Frenzel,P. (2008) Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol. Ecol. 65: 408-414.
7. Wasmund,K., Kurtboke,D.I., Burns,K.A., and Bourne,D.G. (2009) Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol. Ecol. 68: 142-151.
8. Mohanty,S.R., Bodelier,P.L.E., Floris,V., and Conrad,R. (2006) Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl. Environ. Microbiol. 72: 1346-1354.
9. Zheng,Y., Zhang,L.M., Zheng,Y.M., Di,H.J., and He,J.Z. (2008) Abundance and community composition of methanotrophs in a Chinese paddy soil under long-term fertilization practices. Journal of Soils and Sediments 8: 406-414.
10. Omelchenko,M.V., Vasileva,L.V., Zavarzin,G.A., Saveleva,N.D., Lysenko,A.M., Mityushina,L.L. et al. (1996) A novel psychrophilic methanotroph of the genus Methylobacter. Microbiology 65: 339- 343.
11. MacLean,D., Jones,J.D.G., and Studholme,D.J. (2009) Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Micro 7: 287-296.
12. Urmann,K., Schroth,M.H., Noll,M., Gonzalez-Gil,G., and Zeyer,J. (2008) Assessment of microbial methane oxidation above a petroleum-contaminated aquifer using a combination of in situ techniques. Journal of Geophysical Research-Biogeosciences 113.
13. Singh,B.K. and Tate,K. (2007) Biochemical and molecular characterization of methanotrophs in soil from a pristine New Zealand beech forest. FEMS Microbiol. Lett. 275: 89-97.
14. Kalyuzhnaya,M.G., Khmelenina,V., Eshinimaev,B., Sorokin,D., Fuse,H., Lidstrom,M., and Trotsenko,Y. (2008) Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium. Int. J. Syst. Evol. Microbiol. 58: 591-596.
15. Vigliotta,G., Nutricati,E., Carata,E., Tredici,S.M., De,S.M., Pontieri,P. et al. (2007) Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. Appl. Environ. Microbiol. 73: 3556-3565.
16. Yan,T.F., Zhou,J.Z., and Zhang,C.L.L. (2006) Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol. Ecol. 57: 251-259.
17. Newby,D.T., Reed,D.W., Petzke,L.M., Igoe,A.L., Delwiche,M.E., Roberto,F.F. et al. (2004) Diversity of methanotroph communities in a basalt aquifer. FEMS Microbiol. Ecol. 48: 333-344.
18. LEBENSLAUF Claudia Lüke | geboren am 14.06.1980 in Witten PROMOTION Seit 10/ 2006 Doktorarbeit am Max-Planck-Institut für terrestrische Mikrobiologie in Marburg/Lahn in der Arbeitsgruppe von Prof. Dr. Peter Frenzel STUDIUM 05/ 2006 Diplom 07/2005 – 05/ 2006 Diplomarbeit an der Norwegischen Universität für Naturwissenschaften und Technologie in Trondheim, Norwegen Thema: " Selection and characterisation of microorganisms capable of degrading components which contribute to the high viscosity of heavy oil " 10/1999 – 05/ 2006
19. Hery,M., Singer,A.C., Kumaresan,D., Bodrossy,L., Stralis-Pavese,N., Prosser,J.I. et al. (2008) Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. Isme Journal 2: 92-104.
20. Lüke, C. and Frenzel, P. Effect of rice cultivar and field location on methanotrophic diversity in paddy fields. BAGECO 10 Symposium, June 2009 in Uppsala, Sweden (Poster presentation).
21. Lüke, C., and Frenzel, P. Effect of rice cultivars on root-assiciated methanotrophic communities. ISME 12 Symposium, August 2008 in Cairns, Australia (Poster presentation).
22. Lüke, C. and Frenzel, P. Effect of rice varieties on diversity of methanotrophic bacteria. METHECO meeting, January 2009 in Nieuwersluis, Netherlands (Oral presentation).
23. Whittenbury,R., Davies,S.L., and Davey,J.F. (1970) Exospores and cysts formed by methane- utilizing bacteria. J. Gen. Microbiol. 61: 219-226.
24. Whitaker,R.J., Grogan,D.W., and Taylor,J.W. (2003) Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea. Science 301: 976-978.
25. Reeburgh, W.S. (2003) Global methane biogeochemistry. In Treatise on Geochemistry, Vol. 4: The Atmosphere. Keeling, R.F., Holland, H.D., and Turekian, K.K. (eds). Oxford, UK: Elsevier- Pergamon, pp. 65–89.
26. Osaka,T., Ebie,Y., Tsuneda,S., and Inamori,Y. (2008) Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing. FEMS Microbiol. Ecol. 64: 494-506.
27. Shindell,D.T., Faluvegi,G., Koch,D.M., Schmidt,G.A., Unger,N., and Bauer,S.E. (2009) Improved attribution of climate forcing to emissions. Science 326: 716-718.
28. Lüke, C., Bodrossy, L., Lupotto, E., and Frenzel, P. Methanotrophic bacteria associated to rice roots: the rice cultivar effect assessed by T-RFLP and microarray analysis. In preparation.
29. Pol,A., Heijmans,K., Harhangi,H.R., Tedesco,D., Jetten,M.S., and Op den Camp,H.J. (2007) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450: 874-878.
30. Wartiainen,I., Hestnes,A.G., McDonald,I.R., and Svenning,M.M. (2006) Methylobacter tundripaludum sp nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78° N). Int. J. Syst. Evol. Microbiol. 56: 109-113.
31. Wise,M.G., McArthur,J.V., and Shimkets,L.J. (2001) Methylosarcina fibrata gen. nov., sp nov and Methylosarcina quisquiliarum sp nov., novel type I methanotrophs. Int. J. Syst. Evol. Microbiol. 51: 611-621.
32. Tsubota,J., Eshinimaev,B.T., Khmelenina,V.N., and Trotsenko,Y.A. (2005) Methylothermus thermalis gen. nov., sp nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan. Int. J. Syst. Evol. Microbiol. 55: 1877-1884.
33. Martiny,J.B.H., Bohannan,B.J.M., Brown,J.H., Colwell,R.K., Fuhrman,J.A., Green,J.L. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Micro 4: 102-112.
34. Jessup,C.M., Forde,S.E., and Bohannan,B.J.M. (2005) Microbial experimental systems in ecology. Advances in Ecological Research, Vol. 37: Population Dynamics and Laboratory Ecology 37: 273-307.
35. Perez-Jimenez,J.R., Young,L.Y., and Kerkhof,L.J. (2001) Molecular characterization of sulfate- reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes. FEMS Microbiol. Ecol. 35: 145-150.
36. Zbinden, M., Shillito, B., LeBries, N., deVillardi deMontlaur, C., Roussel, E., Guyot, F., Gaill, F., Cambon-Bonavita, M-A. (2008) New insigths on the metabolic diversity among the epibiotic microbial communitiy of the hydrothermal shrimp Rimicaris exoculata. J. Exp. Marin. Biol. Ecol 359: 131-140
37. Zehr,J.P., Jenkins,B.D., Short,S.M., and Steward,G.F. (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5: 539-554.
38. Nold,S.C., Zhou,J., Devol,A.H., and Tiedje,J.M. (2000) Pacific Northwest Marine Sediments Contain Ammonia-Oxidizing Bacteria in the beta Subdivision of the Proteobacteria. Appl. Environ. Microbiol. 66: 4532-4257.
39. Spiridonova,E.M., Kuznetsov,B.B., Pimenov,N.V., and Tourova,T.P. (2006) Phylogenetic characterization of endosymbionts of the hydrothermal vent mussel Bathymodiolus azoricus by analysis of the 16S rRNA, cbbL, and pmoA genes. Microbiology 75: 694-701.
40. Tavormina,P.L., Ussler,W., and Orphan,V.J. (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl. Environ. Microbiol. 74: 3985-3995.
41. Lüke, C., and Frenzel, P. Rice varieties affect diversity of methanotroph in the rhizosphere. First EuroDIVERSITY annual conference, October 2007 in Paris, France (Poster presentation; Poster Award).
42. Krause, S., Lüke, C., and Frenzel, P. (2009) Spatial heterogeneity of methanotrophs: a geostatistical analysis of pmoA-based T-RFLP patterns in a paddy soil. Environ Microbiol Rep 1: 393–397.
43. Radajewski,S., Ineson,P., Parekh,N.R., and Murrell,C. (2000) Stable isotope probing as a tool in microbial ecology. Nature 403: 646-649.
44. Tsutsumi, M., Kojima, H., Uemura, S., Ono, K., Sumida, A., Hara, T., Fukui, M. (2009) Stucture and activity of soil-inhabiting methanotrophic communities in northern forest of japan. Soil Biol. Biochem. 41: 403-408
45. Studium der Biologie an der Westfälischen Wilhelms- Universität in Münster Hauptfach: Mikrobiologie Nebenfächer: Botanik, Biochemie SCHULBILDUNG 06/1999
46. Rotthauwe,J.H., Witzel,K.P., and Liesack,W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker -molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63: 4704-4712.
47. Hakemian,A.S. and Rosenzweig,A.C. (2007) The biochemistry of methane oxidation. Annual Review of Biochemistry 76: 223-241.
48. Trotsenko,Y.A. and Khmelenina,V.N. (2002) The biology and osmoadaptation of haloalkaliphilie methanotrophs [Review]. Microbiology 71: 123-132.
49. Papke,R.T. and Ward,D.M. (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48: 293-303.
50. Lüke, C, and Frenzel, P. The pmoA gene as functional and phylogenetic marker for methanotrophic bacteria: a sequence database analysis. In preparation. BEITRÄGE ZU WISSENSCHAFTLICHEN TAGUNGEN
51. Prosser,J.I., Bohannan,B.J.M., Curtis,T.P., Ellis,R.J., Firestone,M.K., Freckleton,R.P. et al. (2007) The role of ecological theory in microbial ecology. Nat Rev Micro 5: 384-392.
52. References Baani,M. and Liesack,W. (2008) Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc. Natl. Acad. Sci. U. S. A 105: 10203-10208.
53. Pacheco-Oliver,M., McDonald,I.R., Groleau,D., Murrell,J.C., and Miguez,C.B. (2002) Detection of methanotrophs with highly divergent pmoA genes from Arctic soils. FEMS Microbiol. Lett. 209: 313-319.
54. Chen,Y., Dumont,M.G., McNamara,N.P., Chamberlain,P.M., Bodrossy,L., Stralis-Pavese,N., and Murrell,J.C. (2008) Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ. Microbiol. 10: 446-459.
55. Lüke, C., Krause, S., Cavigiolo, S., Greppi, D., Lupotto, E., and Frenzel, P. (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol. In press.
56. Nielsen,A.K., Gerdes,K., and Murrell,J.C. (1997) Copper-dependent reciprocal transcriptional regulation of methane monooxygenase genes in methylococcus capsulatus and methylosinus trichosporium. Molecular Microbiology 25: 399-409.
57. Hutchens,E., Radajewski,S., Dumont,M.G., McDonald,I.R., and Murrell,J.C. (2004) Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ. Microbiol. 6: 111- 120.
58. Bodrossy,L., Stralis-Pavese,N., Murrell,J.C., Radajewski,S., Weilharter,A., and Sessitsch,A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5: 566-582.
59. Qiu,Q., Noll,M., Abraham,W.R., Lu,Y., and Conrad,R. (2008) Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME. J. 2: 602-614.
60. Nercessian,O., Noyes,E., Kalyuzhnaya,M.G., Lidstrom,M.E., and Chistoserdova,L. (2005b) Bacterial Populations Active in Metabolism of C1 Compounds in the Sediment of Lake Washington, a Freshwater Lake. Appl. Environ. Microbiol. 71: 6885-6899.
61. Rahalkar,M. and Schink,B. (2007) Comparison of aerobic methanotrophic communities in littoral and profundal sediments of Lake Constance by a molecular approach. Appl. Environ. Microbiol. 73: 4389-4394.
62. Singh,B.K., Tate,K.R., Kolipaka,G., Hedley,C.B., Macdonald,C.A., Millard,P., and Murrell,J.C. (2007) Effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria. Appl. Environ. Microbiol. 73: 5153-5161.
63. Pruesse,E., Quast,C., Knittel,K., Fuchs,B.M., Ludwig,W., Peplies,J., and Glockner,F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35: 7188-7196.
64. Volker,H., Schweisfurth,R., and Hirsch,P. (1977) Morphology and Ultrastructure of Crenothrix- Polyspora Cohn. J. Bact. 131: 306-313
65. Pester,M., Friedrich,M.W., Schink,B., and Brune,A. (2004) pmoA-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment. Appl. Environ. Microbiol. 70: 3138-3142.
66. Holmes,A.J., Roslev,P., McDonald,I.R., Iversen,N., Henriksen,K., and Murrell,J.C. (1999) Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl. Environ. Microbiol. 65: 3312-3318.
67. Eller,G. and 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.
68. Horz,H.P., Yimga,M.T., and Liesack,W. (2001) Detection of Methanotroph Diversity on Roots of Submerged Rice Plants by Molecular Retrieval of pmoA, mmoX, mxaF, and 16S rRNA and Ribosomal DNA, Including pmoA-Based Terminal Restriction Fragment Length Polymorphism Profiling. Appl. Environ. Microbiol. 67: 4177-4185.
69. Stoecker,K., Bendinger,B., Schoning,B., Nielsen,P.H., Nielsen,J.L., Baranyi,C. et al. (2006) Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc. Natl. Acad. Sci. USA 103: 2363-2367.
70. Kolb,S., Knief,C., Dunfield,P.F., and Conrad,R. (2005) Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ. Microbiol. 7: 1150-1161.
71. Eller,G., Krüger,M., and 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.
72. Dunfield,P.F., Yuryev,A., Senin,P., Smirnova,A.V., Stott,M.B., Hou,S. et al. (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450: 879-882.
73. Bodelier,P.L.E., Roslev,P., Henckel,T., and Frenzel,P. (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403: 421-424.

Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten