Aerobic methanol-oxidizing Bacteria in soil

FEMS Microbiology Letters

Volumn 300, Issue 1, 2009, Pages 1-10

  Kolb, Steffen ^a  

^a UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

Ecological niche; Methanol oxidation; Methylotroph; Soil

Indexed keywords

CARBON; METHANE; METHANOL; NITRATE; NITROGEN; OXYGEN;

ACTINOBACTERIA; AEROBIC BACTERIUM; ALPHAPROTEOBACTERIA; ATMOSPHERE; BACILLUS; BACTERIUM ISOLATE; BETAPROTEOBACTERIA; BIOGEOCHEMICAL CYCLE; CHEMICAL PARAMETERS; CONCENTRATION (PARAMETERS); ECOLOGICAL NICHE; ECOSYSTEM; EUKARYOTE; FIRMICUTES; GAMMAPROTEOBACTERIA; METHYLOTROPH; NONHUMAN; OSMOTIC STRESS; OXIDATION; PH; PLANT PATHOGEN INTERACTION; PRIORITY JOURNAL; PROKARYOTE; SHORT SURVEY; SOIL MICROFLORA; SOIL TEMPERATURE; SPECIES DIVERSITY;

BACTERIA, AEROBIC; BIODIVERSITY; ECOSYSTEM; METHANE; OXIDATION-REDUCTION; SOIL MICROBIOLOGY;

ACTINOBACTERIA; EUKARYOTA; FIRMICUTES; GAMMAPROTEOBACTERIA; PROKARYOTA; VERRUCOMICROBIA;

EID: 70349655605     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2009.01681.x     Document Type: Short Survey

References (105)

1. Anthony C (1982) The Biochemistry of Methylotrophs. Academic Press, New York.
2. Arfman N, Watling EM, Clement W, Watling EM, Clement W, Vanoosterwijk RJ, Devries GE, Harder W, Attwood MM Dijkhuizen L (1989) Methanol metabolism in thermotolerant methylotrophic Bacillus strains involving a novel catabolic NAD-dependent methanol dehydrogenase as a key enzyme. Arch Microbiol 152 : 280 288.
3. Arfman N, Hektor HJ, Bystrykh LV, Govorukhina NI, Dijkhuizen L Frank J (1997) Properties of an NAD(H)-containing methanol dehydrogenase and its activator protein from Bacillus methanolicus. Eur J Biochem 244 : 426 433.
4. Balk M, Weijma J Stams AJM (2002) Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor. Int J Syst Evol Micr 52 : 1361 1368.
5. Balk M, Weijma J, Friedrich MW Stams AJM (2003) Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp. nov., isolated from a bioreactor. Arch Microbiol 179 : 315 320.
6. 4 mixing ratios. FEMS Microbiol Ecol 101 : 261 270.
7. Bodelier PLE Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47 : 265 277.
8. Bodelier PLE, Hahn AP, Arth IR Frenzel P (2000a) Effects of ammonium-based fertilisation on microbial processes involved in methane emission from soils planted with rice. Biogeochemistry 51 : 225 257.
9. 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.
10. Borodina E, Cox MJ, McDonald IR Murrell JC (2005) Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil. Environ Microbiol 7 : 1318 1328.
11. Boulygina ES, Kuznetov BB, Marusina AI, Kuznetov BB, Marusina AI, Tourova TP, Kravchenko IK, Bykova SA, Kalganova TV Galchenko VF (2002) A study of nucleotide sequences of nifH genes of some methanotrophic bacteria. Microbiology 71 : 500 508.
12. Brune A, Frenzel P Cypionka H (2000) Life at the oxic-anoxic interface: microbial activities and adaptations. FEMS Microbiol Rev 24 : 691 710.
13. Buckley DH, Huangyutitham V, Nelson TA, Rumberger A Thies JE (2006) Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Appl Environ Microb 72 : 4522 4531.
14. 2 reveals novel noncultivated diazotrophs in soil. Appl Environ Microb 73 : 3196 3204.
15. 2-DNA-stable isotope probing of diazotrophic methanotrophs in soil. Soil Biol Biochem 40 : 1272 1283.
16. Bull ID, Parekh NR, Hall GH, Ineson P Evershed RP (2000) Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405 : 175 178.
17. Bystrykh LV, Vonck J, Vanbruggen EFJ, Vanbeeumen J, Samyn B, Govorukhina NI, Arfman N, Duine JA Dijkhuizen L (1993) Electron-microscopic analysis and structural characterization of novel NADP(H)-containing methanol-N,N′- dimethyl-4-nitrosoaniline oxidoreductases from the Gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J Bacteriol 175 : 1814 1822.
18. Chain PSG, Denef VJ, Konstantinidis KT et al 2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. P Natl Acad Sci USA 103 : 15280 15287.
19. 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.
20. 2O, and NO). Microbiol Rev 60 : 609 641.
21. 13-isotopic signature in anoxic rice field soil. Biogeochemistry 73 : 381 393.
22. Conrad R Frenzel P (2002) Flooded soils. Encyclopedia of Environmental Microbiology (Britton G, ed), pp. 1316 1333. Wiley, New York.
23. Dedysh SN, Ricke P Liesack W (2004) NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Microbiol-SGM 150 : 1301 1313.
24. Dedysh SN, Knief C Dunfield PF (2005a) Methylocella species are facultatively methanotrophic. J Bacteriol 187 : 4665 4670.
25. Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W Trotsenko YA (2005b) Methylotrophic autotrophy in Beijerinckia mobilis. J Bacteriol 187 : 3884 3888.
26. Denman KL, Brasseur G, Chidthaisong A et al 2007) Couplings between changes in the climate system and biogeochemistry. Climate Change 2007: The Physical Science Basis Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, Tignor M Miller HL, eds), pp. 499 587. Cambridge University Press, Cambridge, UK.
27. Donnelly MI Dagley S (1980) Production of methanol from aromatic acids by Pseudomonas putida. J Bacteriol 142 : 916 924.
28. Dumont MG, Radajewski SM, Miguez CB, McDonald IR Murrell JC (2006) Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ Microbiol 8 : 1240 1250.
29. Dunfield PF, Yuryev A, Senin P et al 2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450 : 879 U818.
30. Fall R Benson AA (1996) Leaf methanol - the simplest natural product from plants. Trends Plant Sci 1 : 296 301.
31. Ferry JG (1999) Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol Rev 23 : 13 38.
32. Galbally IE Kirstine W (2002) The production of methanol by flowering plants and the global cycle of methanol. J Atmos Chem 43 : 195 229.
33. Gonzalez JM, Mayer F, Moran MA, Hodson RE Whitman WB (1997) Sagittula stellata gen. nov, sp. nov., a lignin-transforming bacterium from a coastal environment. Int J Syst Bacteriol 47 : 773 780.
34. Gulledge J, Hrywna Y, Cavanaugh C Steudler PA (2004) Effects of long-term nitrogen fertilization on the uptake kinetics of atmospheric methane in temperate forest soils. FEMS Microbiol Ecol 49 : 389 400.
35. Heikes BG, Chang WN, Pilson MEQ et al 2002) Atmospheric methanol budget and ocean implication. Global Biogeochem Cy 16 : 1133.
36. Hektor HJ, Kloosterman H Dijkhuizen L (2002) Identification of a magnesium-dependent NAD(P)H-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus. J Biol Chem 277 : 46966 46973.
37. 4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ Micrbiol 2 : 666 679.
38. Henckel T, Jackel U, Schnell S Conrad R (2000b) Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Appl Environ Microb 66 : 1801 1808.
39. Hines ME, Crill PM, Varner RK, Talbot RW, Shorter JH, Kolb CE Harriss RC (1998) Rapid consumption of low concentrations of methyl bromide by soil bacteria. Appl Environ Microb 64 : 1864 1870.
40. Hirsch P (1989) Genus Hyphomicrobium Stutzer and Hartleb 1898. Bergey's Manual of Systematic Bacteriology, Vol. 3 (Staley JT, Bryant MP, Pfennig N Holt JG, eds), pp. 1895 1904. The Williams & Wilkins Co., Baltimore.
41. Hutchinson GE (1957) Concluding remarks. Cold Spring Harbor Symposium on Quantitative Biology, pp. 415-417.
42. Islam T, Jensen S, Reigstad LJ, Larsen O Birkeland NK (2008) Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. P Natl Acad Sci USA 105 : 300 304.
43. Ito T, Fujimura S, Uchino M et al 2007) Distribution, diversity and regulation of alcohol oxidase isozymes, and phylogenetic relationships of methylotrophic yeasts. Yeast 24 : 523 532.
44. Ivanova E, Doronina N Trotsenko Y (2007) Hansschlegelia plantiphila gen. nov sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants. Syst Appl Microbiol 30 : 444 452.
45. Jacob DJ, Field BD, Li QB et al 2005) Global budget of methanol: constraints from atmospheric observations. J Geophys Res 110 : D08303.
46. Jenni B Aragno M (1987) Xanthobacter agilis sp. nov., a motile, dinitrogen-fixing, hydrogen-oxidizing bacterium. Syst Appl Microbiol 9 : 254 257.
47. Jensen S, Holmes AJ, Olsen RA Murrell JC (2000) Detection of methane oxidizing bacteria in forest soil by monooxygenase PCR amplification. Microb Ecol 39 : 282 289.
48. Jourand P, Giraud E, Bena G et al 2004) Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Micr 54 : 2269 2273.
49. Kalyuzhnaya MG Chistoserdova L (2005) Community-level analysis: genes encoding methanopterin-dependent enzymes. Environ Microbiol 397 : 443 454.
50. Kalyuzhnaya MG, Lidstrom ME Chistoserdova L (2004) Utility of environmental primers targeting ancient enzymes: methylotroph detection in Lake Washington. Microb Ecol 48 : 463 472.
51. Kalyuzhnaya MG, Hristova KR, Lidstrom ME Chistoserdova L (2008) Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. Appl Environ Microb 190 : 3817 3823.
52. Kaszaki P, Czechowska K, Petryszak P, Miedzobrodzki J, Pawlik P Koloczek H (2006) Methylotrophic extremophilic yeast Trichosporon sp.: a soil-derived isolate with potential applications in environmental biotechnology. Acta Biochim Pol 53 : 463 473.
53. Keppler F, Eiden R, Niedan V, Pracht J Scholer HF (2000) Halocarbons produced by natural oxidation processes during degradation of organic matter. Nature 403 : 298 301.
54. Knief C Dunfield PF (2005) Response and adaptation of different methanotrophic bacteria to low methane mixing ratios. Environ Microbiol 7 : 1307 1317.
55. Knief C, Lipski A Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microb 69 : 6703 6714.
56. Knief C, Kolb S, Bodelier PLE, Lipski A Dunfield PF (2006) The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environ Microbiol 8 : 321 333.
57. Knowles R (2005) Denitrifiers associated with methanotrophs and their potential impact on the nitrogen cycle. Ecol Eng 24 : 441 446.
58. Kolb S, Knief C, Dunfield PF 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.
59. Küsel K Drake HL (1994) Acetate synthesis in soil from a Bavarian beech forest. Appl Microb Environ 60 : 1370 1373.
60. Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W Dedysh SN (2006) Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog. Int J Syst Evol Micr 56 : 1397 1402.
61. Lee JD Komagata K (1980) Pichia cellobiosa, Candida cariosilignicola, and Candida succiphila, new species of methanol-assimilating yeasts. Int J Syst Bacteriol 30 : 514 519.
62. Lejon DPH, Nowak V, Bouko S, Pascault N, Mougel C, Martins JMF Ranjard L (2007) Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination. FEMS Microbiol Ecol 61 : 424 437.
63. Lidstrom ME (2006) Aerobic methylotrophic bacteria. The Prokaryotes, Vol. 2 (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H Stackebrandt E, eds), pp. 618 634. Springer, New York.
64. Loew O (1892) Ueber einen Bacillus, welcher Ameisensäure und Formaldehyd assimiliren kann. Centralblatt Bakteriologie, Parasitenkunde, Infektionskrankheiten Hygiene, Abteilung II 12 : 462 465.
65. Lueders T, Wagner B, Claus P Friedrich MW (2004) 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.
66. Maxfield PJ, Hornibrook ERC Evershed RP (2008) Acute impact of agriculture on high-affinity methanotrophic bacterial populations. Environ Microbiol 10 : 1917 1924.
67. McDonald IR Murrell JC (1997) The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microb 63 : 3218 3224.
68. McDonald IR, Bodrossy L, Chen Y Murrell JC (2008) Molecular techniques for the study of aerobic methanotrophs. Appl Environ Microb 74 : 1305 1315.
69. Miller LG, Warner KL, Baesman SM, Oremland RS, McDonald IR, Radajewski S Murrell JC (2004) Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms. Geochim Cosmochim Ac 68 : 3271 3283.
70. 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 Microb 72 : 1346 1354.
71. Mohanty SR, Bodelier PLE Conrad R (2007) Effect of temperature on composition of the methanotrophic community in rice field and forest soil. FEMS Microbiol Ecol 62 : 24 31.
72. Murase J Frenzel P (2007) A methane-driven microbial food web in a wetland rice soil. Environ Microbiol 9 : 3025 3034.
73. Murase J Frenzel P (2008) Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol Ecol 65 : 408 414.
74. Nercessian O, Kalyuzhnaya MG, Joye SB, Lidstrom ME Chistoserdova L (2005) Analysis of fae and fhcD genes in Mono Lake, California. Appl Environ Microb 71 : 8949 8953.
75. Neufeld JD, Schafer H, Cox MJ, Boden R, McDonald IR Murrell JC (2007) Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J 1 : 480 491.
76. Neufeld JD, Chen Y, Dumont MG Murrell JC (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10 : 1526 1535.
77. L and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins. Biochemistry-US 45 : 3481 3492.
78. Noll M, Frenzel P Conrad R (2008) Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiol Ecol 65 : 125 132.
79. Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MSM den Camp HJMO (2007) Methanotrophy below pH1 by a new Verrucomicrobia species. Nature 450 : 874 U817.
80. Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable isotope probing. Microbiol-SGM 148 : 2331 2342.
81. Raghoebarsing AA, Smolders AJP, Schmid MC et al 2005) Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436 : 1153 1156.
82. Rahalkar M, Bussmann I Schink B (2007) Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance. Int J Syst Evol Micr 57 : 1073 1080.
83. Raj HD (1989) Oligotrophic methylotrophs - Ancylobacter (Basonym Microcyclus Orskov) Raj gen. nov. Crit Rev Microbiol 17 : 89 106.
84. Redeker KR, Wang NY, Low JC, McMillan A, Tyler SC Cicerone RJ (2000) Emissions of methyl halides and methane from rice paddies. Science 290 : 966 969.
85. T: a classic process for an atypical symbiont. Soil Biol Biochem 40 : 1404 1412.
86. Rhew RC Abel T (2007) Measuring simultaneous production and consumption fluxes of methyl chloride and methyl bromide in annual temperate grasslands. Environ Sci Technol 41 : 7837 7843.
87. Schäfer H (2007) Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. Appl Environ Microb 73 : 2580 2591.
88. Schink B Zeikus JG (1980) Microbial methanol formation - a major end product of pectin metabolism. Curr Microbiol 4 : 387 389.
89. Schink B, Ward JC Zeikus JG (1981) Microbiology of wetwood - importance of pectin degradation and Clostridium species in living trees. Appl Environ Microb 42 : 526 532.
90. Seghers D, Siciliano SD, Top EM Verstraete W (2005) Combined effect of fertilizer and herbicide applications on the abundance, community structure and performance of the soil methanotrophic community. Soil Biol Biochem 37 : 187 193.
91. Semrau JD, DiSpirito AA Murrell JC (2008) Life in the extreme: thermoacidophilic methanotrophy. Trends Microbiol 16 : 190 193.
92. Sexstone AJ, Parkin TB Tiedje JM (1985) Temporal response of soil denitrification rates to rainfall and irrigation. Soil Sci Soc Am J 49 : 99 103.
93. Singh H, Chen Y, Tabazadeh A et al 2000) Distribution and fate of selected oxygenated organic species in the troposphere and lower stratosphere over the Atlantic. J Geophys Res 105 : 3795 3805.
94. Sy A, Giraud E, Jourand P et al 2001) Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183 : 214 220.
95. Tie X, Guenther A Holland E (2003) Biogenic methanol and its impacts on tropospheric oxidants. Geophys Res Lett 30 : 1881.
96. Tiedje JM, Sexstone AJ, Parkin TB, Revsbech NP Shelton DR (1984) Anaerobic processes in soil. Plant Soil 76 : 197 212.
97. Trotsenko YA Murrell JC (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63 : 183 229.
98. von Kuhlmann R, Lawrence MG, Crutzen PJ Rasch PJ (2003) A model for studies of tropospheric ozone and nonmethane hydrocarbons: model description and ozone results. J Geophys Res 108 : 4294.
99. Vorholt JA, Kalyuzhnaya MG, Hagemeier CH, Lidstrom ME Chistoserdova L (2005) MtdC, a novel class of methylene tetrahydromethanopterin dehydrogenases. J Bacteriol 187 : 6069 6074.
100. Ward N, Larsen O, Sakwa J et al 2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2 : 1616 1628.
101. Warneke C, Karl T, Judmaier H, Hansel A, Jordan A, Lindinger W Crutzen PJ (1999) Acetone, methanol, and other partially oxidized volatile organic emissions from dead plant matter by abiological processes: significance for atmospheric HOx chemistry. Global Biogeochem Cy 13 : 9 17.
102. Warwick NJ, Pyle JA Shallcross DE (2006) Global modelling of the atmospheric methyl bromide budget. J Atmos Chem 54 : 133 159.
103. 3 in the upper troposphere. Science 279 : 49 53. (Pubitemid 28079149)
104. Zausig J, Stepniewski W Horn R (1993) Oxygen concentration and redox potential gradients in unsaturated model soil aggregates. Soil Sci Soc Am J 57 : 908 916.
105. Zhang GS, Tian JQ, Jiang N, Guo XP, Wang YF Dong XZ (2008) Methanogen community in Zoige wetland of Tibetan plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I. Environ Microbiol 10 : 1850 1860.