Advances in the research of methanotroph

Abstract

Abstract: Methanotrophs use methane as a sole carbon and energy source and play an important role in the balance of atmospheric methane. They can also degrade halogenated hydrocarbons,which has potential value in contamination bioremediation.Based on the taxonomy of methanotrophic bacteria,a preliminary conclusion was drawn on the mechanism of methane oxidation by methanotroph,its physiology and distribution in ecosystems, and methods to study methane-oxidizing bacteria,as well as potential use of methanotroph in biodegradation of toxic chemicals.In this paper we also analyzed the current problems in the studies of methanotrophs,and pointed out the directions for future research work in this field.

Key words: Natural product antifoulants, Marine natural product, Antifouling, Chemical ecology, Fouling organisms

CLC Number:

LIANG Zhanbei, SHI Yi, YUE Jin. Advances in the research of methanotroph[J]. cje, 2004, (5): 198-205.

References

[1] Amaral JA, Ekins A. 1998. Effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture[J]. Appl. Environ. Microbiol., 64:520～525.
[2] Auman AJ, Stolyar S, Anney L. 2000. Molecular characterization of methanotrophic isolates from freshwater lake sediment [ J ].Appl . Environ. Microbiol . , 66: 5259～5266.
[3] Auman AJ, Stolyer S. 1997. Molecular characterization of methanotrophic isolates from paddy soil [ J ]. Appl. Environ.Microbiol., 63: 349～357.
[4] Balkwill DL, Leach FR. 1988. Equivalence of microbial biomass measures based on membrane lipid and cell wall components,adenosine triphosphate and direct counts in subsurface aquifer sediments[ J ]. Microb. Ecol., 16:73～84.
[5] Bedard C, Knowles R. 1989. Physiology, biochemistry, and specific inhibitors of CH4, NH4+ and CO oxidation by methanotrophs and nitrifers[ J ]. Microbiol. Rev., 53: 68～84.
[6] Bender M, Conrad R. 1995. Effect of CH4 concentrations and soil conditions on the induction of CH4 oxidation activity [ J ]. Soil.Biol. Biochem . , 27:1517～1527.
[7] Blake DR, Rowland RS. 1988. Continuing worldwild increase in tropospheric methane, 1978～1987 [J]. Science, 239: 1129～1131.
[8] Bodelier PL, Frenzel EF. 1999. Contribution of methanotrophic and nitrifying bacteria to CH4 and NH4 + oxidation in the rhizosphere of rice plants as determined by new methods of discrimination[ J ]. Appl. Environ. Microbiol., 65:1826～1833.
[9] Bodelier PL, Roslev EP. 2000. Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots[J]. Nature, 403: 421～424.
[10] Bodrossy L, Holmes EM. 1997. Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thennotolerant and thermophilic methanotrophs, Methylocaldum gen. nov [ J ].Arch. Microbiol., 168: 493～503.
[11] Bosse U, Frenzel P. 1997. Activity and distribution of CH4-oxidizing bacteria in flooding rice microcosmas and in rice plants(Oryza sativa) [J]. Appl. Environ. Microbiol., 63:1199～1207.
[12] Bourne DG, Mcdonald IR. 2001. Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils[J]. Appl . Environ. Microbiol . , 67:3802～3809.
[13] Bowman DG, Sly LI. 1995. The phylogenetic position of the family Methylococcaceae [J]. Int. J. Syst . Bacteriol . , 45: 182～185.
[14] Bowman JP, Skerratt JH. 1991. Phospho-lipid fatty acid and lipopolysaccharide fatty acid signature lipida in methane-utilizing bacteria[ J ]. FEMS Microbiol. Ecol., 85:15～22.
[15] Bowman JP, McCammon SA. 1997. Methylosphaera hansonii gen. nov., a psychrophilic, group 1 methanotroph from Antarctic marine-salinity, meromictic lakes[J]. Microbiology, 143:1451 ～1459.
[16] Bowman JP. 1984. Family Methylocystaceae fam. nov[A]. In:Garrity GM. ed. Bergey's Mannul of Systematic Bacteriology (2nd ed., Vol. 2.) [ C]. New York: Springer-Verlag, 114～125.
[17] Boxrukova LV, Nikolenko YI. 1983. Comparative serological analysis of methanotrophic bacteria[ J ]. Microbiology, 52: 639～643.
[18] Brusseau GA, Tsien HC. 1990. Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity[J]. Biodegradation,1:19～29.
[19] Burrow KJ, Cornish A, Hungate JR, et al. 1984. Substrate specificities of the soluble and particulate methane monooxygenases of Methylosinus trichosporium OB3b [ J ]. J . Gen. Microbiol . , 5:335～342.
[20] Cai ZC, Yan XY. 1999. Kinetic model for methane oxidation by paddy soil as affected by temperature, moisture and N addition [J]. Soil. Biol. Biochem., 31: 715～725.
[21] Cheng YS, Halsey J L. 1999. Detection of methanotrophs in groundwater by PCR[ J ]. Appl . Environ. Microbiol . , 65: 648～651.
[22] Cicerone RJ, Oremland RS. 1998. Biogeochemical aspects of atmospheric methane [J]. Global. Biogeochem. Cycles, 2: 299～327.
[23] Collins MLP, Bucholzl LA. 1991. Effect of copper on Methylosinus albus BG8 [ J ]. Appl. Environ. Microbiol., 57: 1261 ～1264.
[24] Conrad R. 1984. Capacity of aerobic microorganisms to utilize and grow on atmospheric trace gases[A]. In: Klug MG, eds.Current Perspectives in Microbial Ecology [ C ]. Washington DC:American Society for Microbiology, 461～467.
[25] Conrad R. 1999. Soil microorganisms oxidizing atmospheric trace gases (CH4, CO, H2, NO)[J]. Indian J. Microbiol., 39:193～203.
[26] Dalton H, Leak DJ. 1985. Methane oxidation by microorganisms [A]. In: Poole RK, eds. Microbial Gas Metabolism: Mechanistic, Metabolic and Biotechnological Aspects [ C]. London: Academic Press, Inc. Ltd., 173～200.
[27] De Angelis MA, Baross JA. 1991. Enhanced microbial methane oxidation in water from a deep-sea hydrothermal vent field at simulated in situ hydrostatic pressures[J ]. Limnol. Oceanogr.,36: 570～577.
[28] De Angelis MA. 1989. Studies of microbial methane oxidation in deep-sea hydrothermal plumes[ J ]. Limnol. Oceanogr, 33: 34 ～56.
[29] Dedysh SN, Derakshani M. 2001. Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of a newly developed oligonucleotide probe for Methylocella palustris [J ]. Appl.Environ. Microbiol., 67: 4850～4857.
[30] Dedysh SN, Derakshani M. 2000. Phospholipid and lipopolysaccharide normal and hydroxy fatty acids as potential signatures for methaneoxidizing bacteria[ J ]. Appl. Environ. Microbiol . , 66:547～553.
[31] Dedysh SN . 1996. Enrichment, isolation and some properties of methane utilizing bacteria [ J ]. Soil. Biol. Biochem., 98: 101 ～108.
[32] Dedysh SN, Panikov NS. 1998. Isolation of acidophilic methaneoxidizing bacteria from northern peat werlands [J ]. Science,282: 281～284.
[33] Dispirito AA, Gulledge J. 1992 . Trichloroethylene oxidation by the membrane associated methane monooxygenase in type Ⅰ,type Ⅱ, and type X methanotrophs [J]. Biodegradation., 2:151～164.
[34] Dunfield PF, Liesack W. 1999. High-affinity methane oxidation by a soil enrichment culture containing a type Ⅱ methanotroph [J]. Appl . Environ. Microbiol . , 65:1009～1014.
[35] Duxbury JM, Mosier AR. 1993. Status and issues concerning agricultural emissions of greenhouse gases[A]. In: Drennen TE,eds. Agricultual Dimensions of Global Climate Change[ C]. Delray Beach, Fla: St. Lucie Press, 229～258.
[36] Eller G, Frenzel P. 2001. Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice[ J ]. Appl. Environ. Microbiol., 67: 2395～2403.
[37] Fang JS, Barcelona MJ. 2000. Cheracterization of methanotrophic bacteria on the basis of intact phospholipid profiles [ J ]. FEMS Microbiol. Lett. , 189:67～72.
[38] Frans-Jaco WA. 1997. Spatial distribution and inhibition by ammonium of methane oxidation in intertidal freshwater marshes [ J ]. Appl. Environ. Microbiol., 63: 4734～4740.
[39] Fuse H, Ohta M. 1998. Oxidation of trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing soluble methane monooxygenase[ J ].Biosci.Biotechnol. Biochem., 62:1925～1931.
[40] Gilbert B, Mcdonald IR. 2000. Molecular analysis of the pmo (particulate methane monooxygenase)operons from two type Ⅱmethanotrophs[ J ]. Appl. Environ. Microbiol., 66: 966～975.
[41] Gilbert B, Assmus B. 1998. In situ localization of two methanotrophic strains in the rhizosphere of rice plants[J]. FEMS Microbiol . Ecol., 25:117～128.
[42] Gilbert B, Frenzel H. 1995. Methanotrophic bacteria in the rhizosphere of rice microcosms and their effect on porewater methane concentration and methane emission[J]. Biol. Fertil. Soils, 20:93～100.
[43] Gilbert B, Frenzel P. 1998. Rice roots and CH4 oxidation the activity of bacteria, their distribution and the microenvironment [J]. Soil. Biol. Biochem . , 30:1903～1916.
[44] Green PN. 1992. Taxonomy of methylotrophic bacteria[A]. In:Murrel JC, eds. Microbial Growth on C1 Compounds [ C ]. London: Intercept Press Ltd., 23～84.
[45] Gucker JB, Ringleberg DB. 1991. Membrane fatty acids as phenotypic markers for the polyphasic approach to taxonomy of methylotrophs within the Proteobacteria [ J ]. J. Gen. Microbiol., 137:2631 ～2641.
[46] Gulledge J, Ahmad R, Gilbert NA. 2001. Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria[J]. Appl. Environ. Microbiol., 67:4726～4733.
[47] Hanson RS. 1992. Introduction[A]. In: Murrell JC, eds. Methane and Methanol Utilizers[C]. New York:Plenum Press, 1～22.
[48] Hanson RS, Netrusov AI. 1991. The obligate methanotrophic bacteria Meth ylococ cus , Meth ylomonas , Meth ylosinus and related bacteria [ A]. In: Balows A, eds. The Prokaryotes [ C ]. New York: Springer Verlag, 2350～2365.
[49] Hanson RS, Hanson TE. 1996. Methanotrophic bacteria[J ]. Microbiol . Rev., 60:439～471.
[50] Hazen T. 1992. Test plan for in situ bioremediation demonstration of the Savannah River[A]. In: Aiken SC, eds. Integrated Demonstration[project DOE/OTD TTP no. SR 0566 -01(u)].Aiken SC:Westinghouse Savannah River Co., 152～164.
[51] Henckel T, Roslev P. 2000. Effect of O2 and CH4 on prersence and activity of the indigenous methanotrophic community in rice field soil[J]. Appl . Environ. Microbiol . , 2: 666 ～679.
[52] Henckel T, Jackel U. 2000. Melocular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane[ J ]. Appl. Environ. Microbiol., 66:1801～1808.
[53] Hoehler TM, Alperin MJ. 1994. Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium[J]. Global Biogeochem.Cycle., 8:451 ～463.
[54] Holmes AJ, Costello A. 1995. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related[J ]. FEMS Microbiol. Lett., 132:203～208.
[55] Jensen S, Priame A. 1998. Methanol improves methane uptake in starved methanotrophic microorganisms [ J ]. Appl. Environ.Microbiol., 64:1143～1146.
[56] King GM, Schnell S. 1994. Ammonium and nitrite inhibition of methane oxidation by Methylobacter albus BG8 and Methylosinus trichosporium OB3b at low methane concentrations[ J ]. Appl. Environ. Microbiol . , 60: 3508～3513.
[57] Leak DJ, Dalton H. 1986. Growth yields of methanotrophs. 1.Effect of copper on the energetics of methane oxidation[J]. Appl. Microbiol . Biotechnol . , 23: 470～476.
[58] Leak DJ. 1992. Biotechnological and applied aspect of methane and methanol utilizer [ A]. In: Murrell JC, eds. Methane and Methanol Utilizers[ C]. New York :Plenum Press, 245～282.
[59] LeMer J, Escoffier S. 1996. Microbiological aspects of methane emission by a ricefield soil from the Camargue (France)2.Methanotrophy and related microflora[J]. Eur. J. Soil. Biol.,32:71～80.
[60] Lipscomb JD. 1994. Biochemistry of the soluble methane monoxygenase[J]. Annu . Rev. Microbiol . , 48: 371～399.
[61] Little CK, Palumbo AV. 1988. Trichloroethylene biodegradation by a methane-oxidizing bacterium[J]. Appl. Environ. Microbiol., 45: 371～399.
[62] Mandernack KW, Kinney KM. 2000. The biogeochemical controls of N2O production and emission in landfill cover soils: the role of methanotrophs in the nitrogen cycle[J]. Environ. Microbiol., 2:298～309.
[63] Mcdonald IR. 1997. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs[J ]. Appl. Environ. Microbiol., 63:3218～3224.
[64] Mcfarland MJ, Vogel CM. 1992. Methanotrophic cometabolism of trichloroethylene(TCE) in a two stage bioreator system[J].Water Res., 26: 259～265.
[65] Megraw SR, Knowles R. 1989. Effect of picolinic acid (2-pyridine carboxylic acid) on the oxidation of methane and ammonia in soil and in liquid culture[J]. Soil. Biol. Biochem., 89:11 ～20.
[66] Mikal GW, Mc Arthur JV, Shimkets LJ. et al. 1999. Methanotroph diversity in landfill soil: Isolation of novel type I methanotrpohs whose presence was suggested by culture-independent 16S Ribosomal DNA analysis[J]. Appl. Environ. Microbiol.,65(11) :4887-4897.
[67] Mosier A, Schimel D. 1991. Methane and nitrous oxide fluxes in native, fertilized and cultivated grasslands [ J ]. Nature ( London), 350: 330～332.
[68] Murrel JC, Gilbert B. 2000. Molecular biology and regulation of methane monooxygenase [ J ]. Arch. Microbiol., 173: 325 ～332.
[69] Murrell JC, Dalton H. 1983. Nitrogen fixation in obligate methanotrophs[J] .J. Gen. Microbiol., 129:3481～3486.
[70] Nguyen HT, Sheimke AK. 1994. The nature of the copper ions in the membranes containing the particulate methane monoxygenase from Methylococcus capsulatus (bath) [ J ]. J . Biol. Chem.,69:14995～15005.
[71] Nguyen HT, Elliot SJ. 1998. The particulate methane monooxygenase from Methylococcus capsulatus (Bath) is a novel coppercontaining three-subunit enzyme[J]. J. Biol. Chem., 273: 7957～7966.
[72] Nicbola PD, Smith GA, Wallace JB, et al. 1985. Phospholipid and lipopolysaccharide normal and hydroxy fatty acids as potential signatures for methane-oxidizing bacteria[J]. FEMS Microbiol. Ecol., 31:327～335.
[73] Nicolaidis AA, Sargent AW. 1987 Isolation of methane monooxygenase-deficient mutants from Methylosinus trichosporium OB3b[J ]. FEMS Microbiol. Lett., 41: 47～52.
[74] O'Neill JG, Wilkinson JF. 1977. Oxidation of ammonia by methaneoxidizing bacteria and the effects of ammonia on methane oxidation [J] . J . Gen. Microbiol . , 100:407～412.
[75] Oldenhuis R, Vink RL. 1989. Degradation of chlorinated aliphatic hydrocarbons by Methylosinus trichosporium OB3b expressing soluble methane monooxygenase [ J ]. Appl. Environ. Microbiol., 55: 2819～2826.
[76] Prior SD, Dalton H. 1985. Acetylene as a suicide substrate and active site probe for methane monooxygenase from Methylococcus capsulatus (Bath) [J]. FEMS Microbiol . Lett . , 29:105 ～109.
[77] Roslev P, Iversen N. 1997. Oxidation and assimilation of atmospheric methane by soil methane oxidizers[J]. Appl. Environ.Microbiol., 63: 874～880.
[78] Schnell S, King GM. 1995. Stability of methane oxidation capacity to variations in methane and nutrient concentrations [ J ].FEMS Microbiol. Ecol., 17: 285～294.
[79] Shen RN, Yu CL. 1997. Direct evidence for a soluble methane monooxygenase from type I methanotrophic bacteria: purification and properties of a soluble methane monooxygenase from Methylomonus sp. GYJ3 [ J ]. Arch. Biochem. Biophys., 345:223～229.
[80] Sohngen NL. 1906. Uber bakterien, welche methan ab kohlenstoffnahrung and energiequelle gebranchen[J ]. Parasitenkd Infectionskr Abt., 15: 513～517.
[81] Stirling DI, Dalton H. 1977. Effect of metal binding agents and other compounds on methane oxidation by two strains of Methylococcus capsulatus [ J ]. Arch. Microbiol . , 114: 71～76.
[82] Trotsenko YA, Khmelenina VN. 2001. Biology of extremophilic and extremotolerant methanotrophs [ J ]. Arch. Microbiol., 38:674～683.
[83] Van Bodegom P. 1988. Methane emissions from rice paddies;experiments and modeling [J ]. Sci. New-Guinea., 16 (2): 87 ～96.
[84] Vorholt JA, Chistoserdova L. 1999. Distribution of tetrahydromethanopterin -dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cydohydrolases[ J ].J. Bacteriol., 181: 5750～5757.
[85] Whalen SC, Reeburgh WS. 1990. Rapid methane oxidation in a landfill cover soil [ J ]. Appl. Environ. Microbiol., 56: 3405 ～3411.
[86] Whittenbury R, Phillips KC. 1970. Enrichment, isolation and some properties of methane u tilizing bacteria[J]. J. Gen. Microbial., 61:205～218.
[87] Whittenbury R, Krieg NR, Archibod OW. 1984. Methylococcacea fam .nov[ A]. In: Krieg NR, eds. Bergey's Mannul of Systematic Bacteriology(Vol. 1) [ C]. Baltimore: The Williams Co., 256～262.
[88] Whittenbury R. 1981. The interrelationship of autotrophy and methylotrophy as seen in Methylococcus capsulatus (Bath) [ A]. In:Dalton H, ed. Microbial Growth on C1 Compounds[ C]. London: Heyden,181～190.
[89] Wise MG, McArthur JV. 2001. Methylosarcina fibrata gen. nov.,sp. nov. and Methylosarcina quisquiliarum sp. nov., novel type I methanotrophs[ J ]. Int. J. Syst. Evol. Microbiol., 51: 611～621.