Methane turnover and temperature response of methane-oxidizing bacteria in permafrost-affected soils of northeast Siberia

Soil Biology and Biochemistry

Volumn 40, Issue 12, 2008, Pages 3004-3013

  Knoblauch, Christian ^a   Zimmermann, Uta ^a   Blumenberg, Martin ^a   Michaelis, Walter ^a   Pfeiffer, Eva Maria ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Methane oxidation; Microbial PLFA; Permafrost; Stable isotope probing; Tundra soils

Indexed keywords

BACTERIOLOGY; CHEMICAL OXYGEN DEMAND; FATTY ACIDS; INTERNET PROTOCOLS; ISOTOPES; LANDFORMS; METHANATION; METHANE; ORGANIC COMPOUNDS; OXIDATION; PERMAFROST; PHOSPHOLIPIDS; SOILS; WETLANDS;

IN SITU CONDITIONS; METHANE CONCENTRATIONS; METHANE OXIDATION; METHANE OXIDATION RATES; METHANE OXIDATIONS; METHANOTROPHIC BACTERIA; METHANOTROPHS; MICROBIAL PLFA; NATURAL WETLANDS; NORTHEAST SIBERIA; ORGANIC MATTERS; OXIDIZING BACTERIA; PHOSPHOLIPID FATTY ACIDS; RISING TEMPERATURES; SATURATED SOILS; SOIL SAMPLES; STABLE ISOTOPE PROBING; STABLE ISOTOPES; SURFACE SOILS; TEMPERATURE RESPONSES; TUNDRA SOILS; TYPE II;

SOIL POLLUTION;

BACTERIUM; CARBON ISOTOPE; METHANE; OXIDATION; PERMAFROST; PROBE; SOIL ORGANIC MATTER; TEMPERATURE EFFECT; TUNDRA SOIL; TURNOVER; WETLAND;

EURASIA; SIBERIA;

BACTERIA (MICROORGANISMS); METHYLOCOCCACEAE; METHYLOCYSTACEAE;

EID: 55349142093     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2008.08.020     Document Type: Article

References (58)

1. Blumenberg M., Seifert R., Nauhaus K., Pape T., and Michaelis W. In vitro study of lipid biosynthesis in an anaerobically methane-oxidizing microbial mat. Applied and Environmental Microbiology 71 (2005) 4345-4351
2. Boike, J., Wille, C., Abnizova, A., 2008. Climatology and summer energy and water balance of polygonal tundra in the Lena River Delta, Siberia. Journal of Geophysical Research 113, G03025, doi:10.1029/2007JG000540.
3. 4 at different temperatures in landfill cover soil. FEMS Microbiology Ecology 48 (2004) 305-312
4. Boschker H.T.S., and Middelburg J.J. Stable isotopes and biomarkers in microbial ecology. FEMS Microbiology Ecology 40 (2002) 85-95
5. 13C-labelling of biomarkers. Nature 392 (1998) 801-805
6. Bowman J. The methanotrophs - the families Methylococcaceae and Methylocystaceae. In: Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., and Stackebrandt E. (Eds). The Prokaryotes (2006), Springer, New York 266-289
7. Bowman J.P., Skerratt J.P., Nichols P.D., and Sly L.I. Phospholipid fatty acid and lipopolysaccharide fatty acid signature lipids in methane-utilizing bacteria. FEMS Microbiology Ecology 85 (1991) 15-22
8. Bowman J.P., McCammon S.A., and Skerratt J.H. Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143 (1997) 1451-1459
9. Bull I.D., Parekh N.R., Hall G.H., Ineson P., and Evershed R.P. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405 (2000) 175-178
10. Cai Z., and Yan X. Kinetic model for methane oxidation by paddy soil as affected by temperature, moisture and N addition. Soil Biology & Biochemistry 31 (1999) 715-725
11. Christian R.R., and Wiebe W.J. The effects of temperature upon the reproduction and respiration of a marine obligate psychrophile. Canadian Journal of Microbiology 20 (1974) 1341-1345
12. Crossman Z.M., Abraham F., and Evershed R.P. Stable isotope pulse-chasing and compound specific stable carbon isotope analysis of phospholipid fatty acids to assess methane oxidizing bacterial populations in landfill cover soils. Environmental Science and Technology 38 (2004) 1359-1367
13. Dedysh S.N., Khmelenina V.N., Suzina N., Trotsenko Y.A., Semrau J.D., Liesack W., and Tiedje J.M. Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. International Journal of Systematic and Evolutionary Microbiology 52 (2002) 251-261
14. Dedysh S.N., Dunfield P.F., Derakshani M., Stubner S., Heyer J., and Liesack W. Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiology Ecology 43 (2003) 299-308
15. Dedysh S.N., Belova S.E., Bodelier P.L.E., Smirnova K.V., Khmelenina V.N., Chidthaisong A., Trotsenko Y.A., Liesack W., and Dunfield P.F. Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs. International Journal of Systematic and Evolutionary Microbiology 57 (2007) 472-479
16. Denman K.L., Brasseur G., Chidthaisong A., Ciais P., Cox P.M., Dickinson R.E., Hauglustaine D., Heinze C., Holland E., Jacob D., Lohmann U., Ramachandran S., Dias P.L.d.S., Wofsy S.C., and Zhang X. Couplings between changes in the climate system and biogeochemistry. In: Solomon S., Qin D., Manning M., Chen Z., Marquis M., Averyt K.B., Tignor M., and Miller H.L. (Eds). Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (2007), Cambridge University Press, Cambridge, United Kingdom/New York, NY, USA 499-588
17. Dunfield P., Knowles R., Dumont R., and Moore T.R. Methane production and consumption in temperate and subarctic peat soils: response to temperature and pH. Soil Biology & Biochemistry 25 (1993) 321-326
18. Dunfield P.F., Khmelenina V.N., Suzina N.E., Trotsenko Y.A., and Dedysh S.N. Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. International Journal of Systematic and Evolutionary Microbiology 53 (2003) 1231-1239
19. Eller G., and Frenzel P. Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Applied and Environmental Microbiology 67 (2001) 2395-2403
20. Ganzert L., Jurgens G., Münster U., and Wagner D. Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints. FEMS Microbiology Ecology (2006)
21. Gebert J., Groengroeft A., Schloter M., and Gattinger A. Community structure in a methanotroph biofilter as revealed by phospholipid fatty acid analysis. FEMS Microbiology Letters 240 (2004) 61-68
22. 4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environmental Microbiology 2 (2000) 666-679
23. Heyer J., Berger U., Hardt M., and Dunfield P.F. Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea. International Journal of Systematic and Evolutionary Microbiology 55 (2005) 1817-1826
24. Isaksen M.F., and Jørgensen B.B. Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments. Applied and Environmental Microbiology 62 (1996) 408-414
25. Kalyuzhnaya M.G., Makutina V.A., Rusakova T.G., Nikitin D.V., Khmelenina V.N., Dmitriev V.V., and Trotsenko Y.A. Methanotrophic communities in the soils of the Russian northern taiga and subarctic tundra. Microbiology 71 (2002) 227-233
26. 13C-labelled fatty acids. Environmental Microbiology 5 (2003) 1155-1167
27. Knoblauch C., and Jørgensen B.B. Effect of temperature on sulfate reduction, growth rate, and growth yield in five psychrophilic sulfate-reducing bacteria from Arctic sediments. Environmental Microbiology 1 (1999) 457-467
28. Knoblauch C., Sahm K., and Jørgensen B.B. Psychrophilic sulfate-reducing bacteria isolated from permanently cold Arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov., and Desulfotalea arctica, sp. nov. International Journal of Systematic Bacteriology 49 (1999) 1631-1643
29. Krumholz L.R., Hollenback J.L., Roskes S.J., and Ringelberg D.B. Methanogenesis and methanotrophy within Sphagnum peatland. FEMS Microbiology Ecology 18 (1995) 215-224
30. Liebner S., and Wagner D. Abundance, distribution and potential activity of methane oxidising bacteria in permafrost soils from the Lena Delta, Siberia. Environmental Microbiology 9 (2006) 107-117
31. Macalady J.L., McMillan A.M.S., Dickens A.F., Tyler S.C., and Scow K.M. Population dynamics of type I and II methanotrophic bacteria in rice soils. Environmental Microbiology 4 (2002) 148-157
32. McDonald I.R., Hall G.H., Pickup R.W., and Murrell J.C. Methane oxidation potential and preliminary analysis of methanotrophs in blanket bog peat using molecular ecology techniques. FEMS Microbiology Ecology 21 (1996) 197-211
33. Moore T.R., and Dalva M. Methane and carbon dioxide exchange potentials of peat soils in aerobic and anaerobic laboratory incubations. Soil Biology & Biochemistry 29 (1997) 1157-1164
34. Nesbit S.P., and Breitenbeck G.A. A laboratory study of factors influencing methane uptake by soils. Agriculture Ecosystems and Environment 41 (1992) 39-54
35. Nichols P.D., Guckert J.B., and White D.C. Determination of monounsaturated fatty acid double-bound position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulfide adducts. Journal of Microbiological Methods 5 (1986) 49-55
36. Omelchenko M.V., Vasileva L.V., Zavarzin G.A., Saveleva N.D., Lysenko A.M., Mityushina L.L., Khmelenina V.N., and Trotsenko Y.A. A novel psychrophilic methanotroph of the genus Methylobacter. Mikrobiologiya 65 (1996) 384-389
37. 4-production in polygonal and thermokarst lakes of the Lena Delta. Reports on Polar and Marine Research 550 (2007) 72-75
38. Popp T.J., Chanton J.P., Whiting G.J., and Grant N. Evaluation of methane oxidation in the rhizosphere of a Carex dominated fen in north central Alberta, Canada. Biogeochemistry 51 (2000) 259-281
39. Post W.M., Emanuel W.R., Zinke P.J., and Stangenberger A.G. Soil carbon pools and world life zones. Nature 298 (1982) 156-159
40. Roslev P., and King G.M. Regulation of methane oxidation in a freshwater wetland by water table changes and anoxia. FEMS Microbiology Ecology 19 (1996) 105-115
41. 4 emissions and production and oxidation potentials at microsites on an oligotrophic pine fen. Oecologia 110 (1997) 414-422
42. Sahm K., Knoblauch C., and Amann R.I. Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine Arctic sediments. Applied and Environmental Microbiology 65 (1999) 3976-3981
43. Shrestha M., Abraham W.-R., Shrestha P.M., Noll M., and Conrad R. 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. Environmental Microbiology 10 (2008) 400-412
44. Sundh I., Borgå P., Nilsson M., and Svensson B.H. Estimation of cell numbers of methanotrophic bacteria in boreal peatlands based on analysis of specific phospholipid fatty acids. FEMS Microbiology Ecology 18 (1995) 103-112
45. Sundh I., Mikkela C., Nilsson M., and Svensson B.H. Potential aerobic methane oxidation in a Sphagnum-dominated peatland-controlling factors and relation to methane emission. Soil Biology & Biochemistry 27 (1995) 829-837
46. Sundh I., Börjesson G., and Tunlid A. Methane oxidation and phospholipid fatty acid composition in a podzolic soil profile. Soil Biology & Biochemistry 32 (2000) 1025-1028
47. Trenberth K.E., Jones P.D., Ambenje P., Bojariu R., Easterling D., Tank A.K., Parker D., Rahimzadeh F., Renwick J.A., Rusticucci M., Soden B., and Zhai P. Observations: surface and atmospheric climate change. In: Solomon S., Qin D., Manning M., Chen Z., Marquis M., Averyt K.B., Tignor M., and Miller H.L. (Eds). Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (2007), Cambridge University Press, Cambridge, United Kingdom/New York, NY, USA 235-336
48. Tsubota J., Eshinimaev B.T., Khmelenina V.N., and Trotsenko Y.A. Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan. International Journal of Systematic and Evolutionary Microbiology 55 (2005) 1877-1884
49. USDA. Keys to Soil Taxonomy (2006), United States Department of Agriculture, Soil Survey Staff
50. Wagner D., Kobabe S., Pfeiffer E.-M., and Hubberten H.-W. Microbial controls on methane fluxes from a polygonal tundra of the Lena Delta, Siberia. Permafrost and Periglacial Processes 14 (2003) 173-185
51. Wagner D., Lipski A., Embacher A., and Gattinger A. Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality. Environmental Microbiology 7 (2005) 1582-1592
52. 4 oxidation in boreal soils. Soil Biology & Biochemistry 28 (1996) 1271-1281
53. Whalen S.C., and Reeburgh W.S. Methane oxidation, production, and emission at contrasting sites in a boreal bog. Geomicrobiology Journal 17 (2000) 237-251
54. White D.C., Davis W.M., Nickels J.S., King J.D., and Bobbie R.J. Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia 40 (1979) 51-62
55. Whittenbury R., Phillips K.C., and Wilkinson J.F. Enrichment, isolation and some properties of methane-utilizing bacteria. Journal of General Microbiology 61 (1970) 205-218
56. Wuebbles D.J., and Hayhoe K. Atmospheric methane and global change. Earth-Science Reviews 57 (2002) 177-210
57. Zhang T., Barry R.G., Knowles K., Hegnibottom J.A., and Brown J. Statistics and characteristics of permafrost and ground-ice distribution in the Northern Hemisphere. Polar Geography 2 (1999) 132-154
58. Zimmermann, U., 2007. Methane Oxidising Bacterial Communities in Soils and Sediments of the Siberian Permafrost. PhD thesis, University of Hamburg, Department of Earth Sciences, Hamburg, 123 pp. (in German).