Copper Biogeochemistry: A Cornerstone in Aerobic Methanotrophic Bacterial Ecology and Activity?

REFERENCES

• Amaral , J A and Knowles , R . 2006 . Growth of methanotrophs in methane and oxygen counter gradients . FEMS Microbiol Lett , 125 : 215 – 220 .
   Google Scholar
• Arnesano , F , Banci , L , Bertini , I and Bonvin , AMJJ . 2004 . A docking approach to the study of copper trafficking proteins: Interaction between metallochaperones and soluble domains of copper ATPases . Structure , 12 : 669 – 676 .
   PubMed Web of Science ®Google Scholar
• Auman , A J and Lidstrom , M E . 2002 . Analysis of sMMO-containing Type I methanotrophs in Lake Washington sediment . Environ Microbiol , 4 : 517 – 524 .
   PubMed Web of Science ®Google Scholar
• Baani , M and Liesack , W . 2008 . Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. Straon SC2 . Proc Nat Acad Sci USA , 105 : 10203 – 10208 .
   PubMed Web of Science ®Google Scholar
• Baker , P W , Futamata , H , Harayama , S and Watanabe , K . 2001 . Molecular diversity of pMMO and sMMO in a TCE contaminated aquifer during bioremediation . FEMS Microbiol Ecol , 38 : 161 – 167 .
   Web of Science ®Google Scholar
• Balasubramanian , R and Rosenzweig , A C . 2008 . Copper methanobactin: a molecule whose time has come . Curr Opin Chem Biol , 12 : 245 – 249 .
   PubMed Web of Science ®Google Scholar
• Balusubramanian , R , Smith , S M , Rawat , S , Yatsunyk , L A , Stemmler , T L and Rosenzweig , A C . 2010 . Oxidation of methane by a biological dicopper centre . Nature , 465 : 115 – 119 .
   PubMed Web of Science ®Google Scholar
• Behling , L A , Hartsel , S C , Lewis , D E , DiSpirito , A A , Choi , D W , Masterson , L R , Veglia , G and Gallagher , W H . 2008 . NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone . J Am Chem Soc , 130 : 12604 – 12605 .
   PubMed Web of Science ®Google Scholar
• Bengtson , P , Basiliko , N , Dumont , M G , Hills , M , Murrell , J C , Roy , R and Grayston , S J . 2009 . Links between methanotroph community composition and CH oxidation in a pine forest soil . FEMS Microbiol Ecol , 70 : 356 – 366 .
   PubMed Web of Science ®Google Scholar
• Benjamin , M M and Honey , B D . 1992 . “ Trace metals ” . In Global Biogeochemical Cycles , Edited by: Butcher , Samuel S. , Charlson , Robert J. , Orians , Gordon H. and Wolfe , Gordon V. 346 – 349 . 379 pp. San Diego: Academic Press .
   Google Scholar
• Berson , O and Lidstrom , M E . 1996 . Study of copper accumulation by the Type I Methanotroph Methylomicrobium albus BG8 . Environ Sci Technol , 30 : 802 – 809 .
   Web of Science ®Google Scholar
• Bertini , I , Gray , H B , Stiefel , E I and Valentine , H S , eds. 2007 . “ Biological inorganic chemistry: structure and reactivity ” . In University Science Books 739 Sausalito, CA:
   Google Scholar
• Bowman , J P and Sayler , G S . 1994 . “ Maximization of Methylococcus trichosporium OB3b soluble methane monooxygenase production in batch culture ” . In Hydrocarbon bioremediation , Edited by: Hinchee , R E , Alleman , B C , Hoeppel , R E and Miller , R N . 267 – 284 . Boca Raton, FL : CRC Press/Lewis Publishers .
   Google Scholar
• Bowman , J , Skerratt , J H , Nichols , P D and Sly , L I . 1991 . Phospholipid fatty acid and liposaccharide fatty acid signature lipids in methane utilizing bacteria . FEMS Microbiol Ecol , 85 : 15 – 22 .
   Web of Science ®Google Scholar
• Bowman , J P , Sly , L I , Nicholas , P D and Hayward , A C . 1993 . Revised taxonomy of methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs . Int J Syst Bacteriol , 43 : 735 – 753 .
   Google Scholar
• Brantner , C A , Buchholz , L A , McSwain , C L , Newcomb , L L , Remsen , C C and Collins , M LP . 1997 . Intracytoplasmic membrane formation in Methylomicrobium album BG8 is stimulated by copper in the growth medium . Can J Microbiol , 43 : 672 – 676 .
   Web of Science ®Google Scholar
• Bratina , B J , Brusseau , G A and Hanson , R S . 1992 . Use of 16S rRNA analysis to investigate phylogeny of the methylotrophic bacteria . Int J Syst Bacteriol , 42 : 645 – 648 .
   PubMedGoogle Scholar
• Brigmon , R L , Anderson , T A and Fliermans , C B . 1999 . Methanotrophic bacteria in the Rhizosphere of trichloroethylene degrading plants . Int J Phytoremed , 1 : 241 – 253 .
   Web of Science ®Google Scholar
• Brigmon , RL. 2001 . “ Methanotrophic Bacteria: Use in Bioremediation ” . In U.S. Department of Energy , Report No. WSRC-MS-2001-00058 37831 – 0062 . Oak Ridge, TN
   Google Scholar
• Bull , I D , Parekh , N R , Hall , G H , Ineson , P and Evershe , P R . 2000 . Detection and classification of atmospheric methane oxidizing bacteria in soils . Science Nat , 405 : 175 – 178 .
   Google Scholar
• Campbell , C D , Hird , M , Lumsdon , D G and Meeussen , J CL . 2000 . The effect of EDTA and fulvic acid on Cd, Zn, and Cu toxicity to a bioluminescent construct (pUCD607) of Escherichia coli . Chemosphere , 40 : 319 – 325 .
   PubMed Web of Science ®Google Scholar
• Cao , M K , Gregson , K , Marshall , S , Dent , J B and Heal , O W . 196 . Global methane emissions from rice paddies Chemosphere , 33 879 – 897 .
   Google Scholar
• Chanton , J P , Powelson , D K and Green , R B . 2009 . Methane oxidation in landfill cover soils, is a 10% default value reasonable . J Environ Qual , 38 : 654 – 663 .
   PubMed Web of Science ®Google Scholar
• Chi Fru , E . 2008 . Constraints in the colonization of natural and engineered subterranean igneous rock aquifers by aerobic methane-oxidizing bacteria inferred by culture analysis . Geobiol J , 6 : 365 – 375 .
   PubMed Web of Science ®Google Scholar
• Chi Fru , E . 2009 . Iron oxides influence the distribution of bacterial community structure and the spatial distribution of the aerobic methanotrophs and sulphate reducers in granitic aquifers . Geomicrobiol J , 26 : 415 – 429 .
   Web of Science ®Google Scholar
• Chi Fru , E , Gray , N D , McCann , C , Baptista , J C , Christgen , B , Talbot , H M , El Ghazouani , A , Dennison , C and Graham , D W . 2011 . Effects of copper mineralogy and methanobactin on cell growth and sMMO activity in Methylosinus trichosporium OB3b . Biogeosci Discuss , 8 : 2851 – 2874 . doi:10.5194/bgd-8-2851–2011
   Web of Science ®Google Scholar
• Choi , D W , Kunz , R C , Boyd , E S , Semrau , J D , Antholine , W E , Han , J I , Zahn , J A , Boyd , J M , de la Mora , A M and DiSpirito , A A . 2003 . The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase complex from Methylococcus capsulatus Bath . J Bacteriol , 185 : 5755 – 5764 .
   PubMed Web of Science ®Google Scholar
• Choi , D W , Do , Y S , Zea , C J McEllistrem , M T . 2006 . Spectral and thermodynamic properties of Ag(I), Au(III), Cd(II), Co(II), Fe(III), Hg(II), Mn(II), Ni(II), Pb(II), U(IV), and Zn(II), binding by methanobactin from Methylosinus trichosporium OB3b . J Inorgan Biochem , 100 : 2150 – 2161 .
   PubMed Web of Science ®Google Scholar
• Choi , D , Bandow , W NL , McEllistrem , M T , Semrau , J D , Antholine , W E , Hartsel , S C , Gallagher , W , Zea , C J , Pohl , N L , Zahn , J A and DiSpirito , A A . 2010 . Spectral and thermodynamic properties of methanobactin from γ-proteobacterial methane oxidizing bacteria: A case for copper competition on a molecular level . J Inorg Biochem. , In Press doi: doi:10.1016/j.jinorgbio.2010.08.002
   PubMed Web of Science ®Google Scholar
• Collins , M LP , Buchholz , L A and Remsen , C C . 1991 . Effect of copper on Methylomonas albus BG8 . Appl Environ Microbiol , 57 : 1261 – 1264 .
   PubMed Web of Science ®Google Scholar
• Conrad , R and Rothfuss , F . 1991 . Methane oxidation in the soil surface layer of a flooded rice field and the effect of ammonium . Biol Fert Soils , 12 : 28 – 32 .
   Web of Science ®Google Scholar
• Crowe , S A , Katsev , S , Leslie , K , Sturm , A , Magen , C , Kessler , J D , Reeburgh , W S , Roberts , J A , González , A , Douglas , L , Haffner , G , Mucci , A , Sundby , B and Fowle , D . 2010 . The methane cycle in ferruginous Lake Matano . Geobiol J , 9 : 61 – 78 .
   PubMed Web of Science ®Google Scholar
• Davies , S L and Whittenbury , R . 1970 . Fine structure of methane and other hydrocarbon-utilizing bacteria . J Gen Microbiol , 61 : 227 – 232 .
   PubMedGoogle Scholar
• Davis , S L , Cornish , A and Higgins , I J . 1986 . Regulation of intracellular location of methane mono-oxygenase during growth of Methylosinus trichosporium OB3b on methanol . J Gen Microbiol , 133 : 191 – 197 .
   Google Scholar
• Dedysh , S N , Berestovskaya , Y Y , Vasylieva , L V , Belova , S E , Khmelenina , V N , Suzina , N E , Trotsenko , Y A , Liesack , W and Zavarzin , G A . 2004 . Methylocella tundrae sp. nov., a novel methanotrophic bacterium from acidic tundra peatlands . Int J Syst Evol Microbiol , 54 : 151 – 156 .
   PubMed Web of Science ®Google Scholar
• Dedysh , S N , Derakshani , M and Liesack , W . 2001a . Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris . Appl Environ Microbiol , 67 : 4850 – 4857 .
   PubMed Web of Science ®Google Scholar
• Dedysh , S N , Horz , H P , Dunfield , P F and Liesack , W . 2001b . A novel pmoA lineage represented by the acidophilic methanotrophic bacterium Methylocapsa acidophila B2 . Arch Microbiol , 177 : 117 – 121 .
   PubMed Web of Science ®Google Scholar
• Dedysh , S N , Liesack , W , Khmelenina , V N , Suzina , N E , Trotsenko , YA, , Semrau , J D , Abing , A M , Panikov , N S and Tiedje , J M . 2000 . Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs . Int J Syst Evol Microbiol , 50 : 955 – 969 .
   PubMed Web of Science ®Google Scholar
• Dedysh , S N , Panikov , N S , Liesack , W , Grosskopf , R , Zhou , J and Tiedje , J M . 1998 . Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands . Science , 282 : 281 – 284 .
   PubMed Web of Science ®Google Scholar
• Dilly , O , Franke , G , Nii-Annang , S , Weber , K , Freese , D and Hüttl , R-F . 2008 . Soil respiratory indicators including carbon isotope characteristics in response to copper . Geomicrobiol J , 25 : 390 – 395 .
   Web of Science ®Google Scholar
• DiSpirito , A A , Zahn , J A , Graham , D W , Kim , H J , Larive , C K , Derrick , T S , Cox , C D and Taylor , A . 1998 . Copper-Binding Compounds from Methylosinus trichosporium OB3b . J Bacteriol , 180 : 3606 – 3613 .
   PubMed Web of Science ®Google Scholar
• Dunfield , P F , Khelenina , V N , Suzina , N E , Trotsenko , Y and Dedysh , S N . 2003 . Methylocella silvestris sp. Nov., a novel methanotroph isolated from an acidic forest cambisol . Int J Syst Evol Microbiol , 53 : 1231 – 1239 .
   PubMed Web of Science ®Google Scholar
• Dunfield , P F , Liesack , W , Henckel , T , Knowles , R and Conrad , R . 1999 . High-affinity methane oxidation by soil enrichment culture containing a Type II methanotroph . Appl Environ Microbiol , 65 : 1009 – 1014 .
   PubMed Web of Science ®Google Scholar
• Dunfield , P F , Yuryev , A Senin , P . 2007 . Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia . Nature , 450 : 879 – 883 .
   PubMed Web of Science ®Google Scholar
• Edwards , K J , Bach , W and McCollom , T M . 2005 . Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor . Trends Microbiol , 13 : 449 – 456 .
   PubMed Web of Science ®Google Scholar
• Eggers , K W , Rees , A A , Siegal , J and Hobbs , R L . 2008 . Pilot-scale evaluation of in situ cometabolic bioremediation of TCE in groundwater using PHOSter® technology . Remediation , 18 : 49 – 66 .
   Google Scholar
• Eisentraeger , A , Klag , P , Vansbotter , B , Heymann , E and Dott , W . 2001 . Denitrification of groundwater with methane as sole hydrogen donor . Water Res , 35 : 2261 – 2267 .
   PubMed Web of Science ®Google Scholar
• Eller , G , Känel , L and Krüger , M . 2005 . Co-occurrence of aerobic and anaerobic methane oxidation in the water column of Lake Plußsee . Appl Environ Microbiol , 71 : 8925 – 8928 .
   PubMed Web of Science ®Google Scholar
• Ellis , M J , Dodd , F E , Sawers , G , Eady , R R and Hasnain , S S . 2003 . Atomic resolution structures of native copper nitrite reductase from Alcaligenes xylosoxidans and the active site mutant Asp92Glu . J Mol Biol , 328 : 429 – 438 .
   PubMed Web of Science ®Google Scholar
• Elsaied , H E , Hayashi , T and Naganuma , T . 2004 . Molecular analysis of deep-sea hydrothermal vent aerobic methanotrophs by targeting genes of 16S rRNA and particulate methane monooxygenase . Mar Biotechnol , 6 : 503 – 509 .
   PubMed Web of Science ®Google Scholar
• Ensign , S A , Hyman , M R and Arp , D J . 1993 . In vitro activation of ammonia monooxygenase from Nitrosomonas europaea by copper . J Bacteriol , 1993 : 1971 – 1980 .
   Web of Science ®Google Scholar
• Ettwig , K F , Butler , M K Le Paslier , D . 2010 . Nitrite-driven anaerobic methane oxidation by oxygenic bacteria . Nature , 464 : 543 – 548 .
   PubMed Web of Science ®Google Scholar
• Ferris , FG. 2005 . Biogeochemical properties of bacteriogenic iron oxides . Geomicrobiol J , 22 : 79 – 85 .
   Web of Science ®Google Scholar
• Fitch , M W , Graham , D W , Arnold , R G , Agarwal , S K , Phelps , P , Speitel , G E Jr and Georgiou , G . 1993 . Phenotypic characterization of copper-resistant mutants of Methylosinus trichosporium OB3b . Appl Environ Microbiol , 59 : 2771 – 2776 .
   PubMed Web of Science ®Google Scholar
• Flemming , C A and Trevors , J T . 1989 . Copper toxicity and chemistry in the environment: a review . Water Air Soil Poll , 44 : 143 – 158 .
   Web of Science ®Google Scholar
• Forget , N L , Murdock , S A and Juniper , S K . 2010 . Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes . Geobiol , 8 : 417 – 432 .
   PubMed Web of Science ®Google Scholar
• Frenzel , P , Rothfuss , F and Conrad , R . 1992 . Oxygen profiles and methane turnover in a flooded rice microcosm . Biol Fert Soils , 4 : 84 – 89 .
   Web of Science ®Google Scholar
• Graham , D W , Chaudhary , J A , Hanson , R S and Arnold , R G . 1993 . Factors affecting competition between type I and type II methanotrophs in two-organism, continuous-flow reactors . Microb Ecol , 25 : 1 – 17 .
   PubMed Web of Science ®Google Scholar
• Guckert , J B , Ringelberg , D B , White , D C , Hanson , R S and Bratina , B J . 1991 . Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria . J Gen Microbiol , 137 : 2631 – 2640 .
   PubMedGoogle Scholar
• Hakemian , A S and Rosenzweig , A C . 2007 . The biochemistry of methane oxidation . Annu Rev Biochem , 76 : 223 – 241 .
   PubMed Web of Science ®Google Scholar
• Han , J-I , Lontoh , S and Semrau , J D . 1997 . Degradation of chlorinated and brominated hydrocarbons by Methylomicrobium album BG8 . Arch Microbiol , 172 : 393 – 400 .
   Web of Science ®Google Scholar
• Hansen , S K , Rainey , P B , Haagensen , J AJ and Molin , S . 2007 . Evolution of species interactions in a biofilms community . Nature , 445 : 533 – 536 .
   PubMed Web of Science ®Google Scholar
• Hanson , R S and Hanson , T E . 1996 . Methanotropic bacteria . Microbiol Rev , 60 : 439 – 471 .
   PubMedGoogle Scholar
• Henry , S M and Grbic-Galic , D . 1990 . Effect of mineral media on trichloroethylene oxidation by aquifer methanotrophs . Microbial Ecol , 20 : 51 – 169 .
   Web of Science ®Google Scholar
• Hoostal , M J , Bidart-Bouzat , Bouzat , J L and Local adaptation of microbial communities to heavy metal stress in polluted sediments of Lake Erie . 2008 . Local adaptation of microbial communities to heavy metal stress in polluted sediments of Lake Erie . Microbial Ecol , 65 : 156 – 168 .
   Web of Science ®Google Scholar
• Houbron , E , Torrijos , M and Capdeville , B . 1999 . An alternative use of biogas applied at the water denitrification . Water Sci Tech , 40 : 115 – 122 .
   Web of Science ®Google Scholar
• Hsiao , M C , Wang , H P , Huang , C-H , Chang , J-E and Wei , Y-L . Tracking of copper in contaminated soils . J Elec Spec Rel Phen , 156–158 208 – 210 .
   Web of Science ®Google Scholar
• Inaba , S and Takenaka , C . 2005 . Effects of dissolved organic matter on toxicity and bioavailability of copper for lettuce sprouts . Environ Int , 31 : 603 – 608 .
   PubMed Web of Science ®Google Scholar
• IPCC. IPCC fourth assessment report . 2007 . “ Climate change 2007: Working Group I: The Physical Science Basis ” . www.ipcc.ch
   Google Scholar
• Jaatinen , K , Tuittila , E-S , Laine , J , Yrjälä , K and Fritze , H . 2005 . Methane-oxidizing bacteria in a Finnish raised mire complex: Effects of site fertility and drainage . Microbial Ecol , 50 : 429 – 439 .
   PubMed Web of Science ®Google Scholar
• Kato , S , Kobayashi , C , Kakegawa , T and Yamagishi , A . 2009 . Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough . Environ Microbiol , 11 : 2094 – 2111 .
   PubMed Web of Science ®Google Scholar
• Kiehl , J T and Trenberth , K E . 1997 . Earth's Annual Global Mean Energy Budget . Bull Am Meteorol Soc , 78 : 197 – 208 .
   Web of Science ®Google Scholar
• Kightley , D , Nedwell , D B and Cooper , M . 1995 . Capacity for methane oxidation in landfill cover soils measured in laboratory-scale soil microcosms . Appl Environ Microbiol , 61 : 592 – 601 .
   PubMed Web of Science ®Google Scholar
• Kim , H J , Graham , D W , DiSpirito , A A , Alterman , M A , Galeva , N , Larive , C K , Asunskis , D and Sherwood , P MA . 2004 . Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria . Science , 305 : 1612 – 1615 .
   PubMed Web of Science ®Google Scholar
• Knapp , C W , Fowle , D A , Kulczycki , J , Roberts , E A and Graham , D W . 2007 . Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources . Proc Nat Acad Sci USA , 104 : 12040 – 12045 .
   PubMed Web of Science ®Google Scholar
• Knief , C , Lipski , A and Dunfield , P F . 2003 . Diversity and activity of methanotrophic bacteria in different upland soils . Appl Environ Microbiol , 69 : 6703 – 6714 .
   PubMed Web of Science ®Google Scholar
• 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 Reports , 1 : 393 – 397 .
   PubMed Web of Science ®Google Scholar
• Krause , S , Lüke , C and Frenzel , P . 2010 . Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies . ISME J , 4 : 1603 – 1607 .
   PubMed Web of Science ®Google Scholar
• Kulczycki , E , Fowle , D A , Graham , D W and Roberts , J A . 2007 . Methanobactin-promoted dissolution of Cu-substituted borosilicate glass . Geobiol J , 5 : 251 – 263 .
   Web of Science ®Google Scholar
• Kulczycki , E , Fowle , D A , Kenward , P A , Leslie , K , Graham , D W and Roberts , J A . 2010 . Stimulation of methanotroph activity by Cu-substituted borosilicate glass . Geomicrobiol J , 28 : 1 – 10 .
   Web of Science ®Google Scholar
• Kulczycki , E , Fowle , D A , Knapp , C , Graham , D W and Roberts , J A . 2007 . Methanobactin-promoted dissolution of Cu-substituted borosilicate glass . Geobiol. , 5 : 251 – 263 .
   Web of Science ®Google Scholar
• Kumaresan , D , Abell , G CJ , Bodrossy , L , Stralis-Pavese , N and Murrell , J C . 2009 . Spatial and temporal diversity of methanotrophs in a landfill cover soil are differentially related to soil abiotic factors . Environ Microbiol Repts , 1 : 398 – 407 .
   PubMed Web of Science ®Google Scholar
• Lantzy , R J and Mackenzie , F T . 1979 . Atmospheruc trace metals: Global cycles and assessment of man's impact . Geochem Cosmochim Acta , 43 : 511 – 525 .
   Web of Science ®Google Scholar
• Larmola , T , Tuittila , E-S , Tiirola , M , Nykänen , H , Martikainen , P J , Yrjälä , K , Tuomivirta , T and Fritze , H . The role of Sphagnum mosses in the methane cycling of boreal mire . Ecology , In Press
   Web of Science ®Google Scholar
• Leak , D J and Dalton , H . 1986 . Growth yields of methanotrophs 1. Effect of copper on the energetics of methane oxidation . Appl Microbiol Biotech , 23 : 470 – 476 .
   Web of Science ®Google Scholar
• Lees , V N , Owens , J P and Murrell , J C . 1991 . Nitrogen metabolism in marine methanotrophs . Arch Microbiol , 157 : 60 – 65 .
   Web of Science ®Google Scholar
• Lieberman , R L and Rosenzweig , A C . 2004 . Biological methane oxidation: Regulation, biochemistry, and active site structure of particulate methane monooxygenase . Crit Rev Biochem Mol Biol , 39 : 147 – 164 .
   PubMed Web of Science ®Google Scholar
• Lieberman , R L , Shrestha , D B , Doan , P E , Hoffman , B M , Stemmler , T L and Rosenzweig , A C . 2003 . Bioinorganic chemistry special feature: Purified particulate methane monooxygenase from Methylococcus capsulatus (Bath) is a dimer with both mononuclear copper and a copper-containing cluster . Proc Nat Acad Sci USA , 100 : 3820 – 3825 .
   PubMed Web of Science ®Google Scholar
• Liebner , S , Rublack , K , Stuehrmann , T and Wagner , D . 2009 . Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia . Microb Ecol , 57 : 25 – 35 .
   PubMed Web of Science ®Google Scholar
• Liebner , S and Wagner , D . 2007 . Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia . Environ Microbiol , 9 : 107 – 117 .
   PubMed Web of Science ®Google Scholar
• Lindner , A S , Pacheco , A , Aldrich , H C , Staniec , A C , Uz , I and Hodson , D J . 2007 . Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer . Int J Syst Evol Microbiol , 57 : 1891 – 1900 .
   PubMed Web of Science ®Google Scholar
• Lindner , A S , Semrau , J D and Adriaens , P . 2005 . Substituent effects on the oxidation of substituted biphenyl congeners by type II methanotroph strain CSC1 . Arch Microbiol , 183 : 266 – 276 .
   PubMed Web of Science ®Google Scholar
• Lontoh , S , DiSpirito , A A , Krema , C L , Whittaker , M R , Hooper , A B and Semrau , J D . 2000 . Differential inhibition of in vivo ammonia monooxygenase, soluble methane monooxygenase and membrane-associated methane monooxygenase by phenylacetylene . Environ Microbiol , 2 : 485 – 494 .
   PubMed Web of Science ®Google Scholar
• Louis-B , J , Roy , R , Pacheco-Oliver , M , Planas , D , Miguez , C B and Greer , C W . 2006 . Potential activity and diversity of methanotrophic bacteria in forest soil, peat, and sediments from a hydroelectric reservoir (Robert-Bourassa) and lakes in the Canadian Taiga . Soil Sci , 171 : 127 – 137 .
   Web of Science ®Google Scholar
• Lüke , C , Krause , S , Cavigiolo , S , Greppi , D , Lupotto , E and Frenzel , P . 2010 . Biogeography of wetland rice methanotrophs . Environ Microbiol , 12 : 862 – 872 .
   PubMed Web of Science ®Google Scholar
• Lysnes , K , Thorseth , I H , Steinsbu , B O , Øvreas , L , Torsvik , T and Pedersen , R O . 2004 . Microbial community diversity in seafloor basalt from the Arctic spreading ridges . FEMS Microbiol Ecol , 50 : 213 – 230 .
   PubMed Web of Science ®Google Scholar
• Ma , Y B , Lombi , E , Oliver , I W , Nolan , A L and McLaughlin , M J . 2006 . Long-term aging of copper added to soils . Environ Sci Technol , 40 : 6310 – 6317 .
   PubMed Web of Science ®Google Scholar
• Maxfield , P J , Hornibrook , E RC and Evershed , R P . 2009 . Substantial high-affinity methanotroph populations in Andisols effect high rates of atmospheric methane oxidation . Environ Microbiol Repts , 1 : 450 – 456 .
   PubMed Web of Science ®Google Scholar
• McBride , M B and Blasiak , J J . 1979 . Zinc and copper solubility as a function of pH in an acid soil . Soil Sci Soc Am J , 43 : 866 – 870 .
   Web of Science ®Google Scholar
• Modin , O , Fukushi , K , Nakajima , F and Yamamoto , K . 2010 . Nitrate removal and biofilm characteristics in methanotrophic membrane reactors with various gas supply regimes . Water Res , 44 : 85 – 96 .
   PubMed Web of Science ®Google Scholar
• Moussard , H , Stralis-Pavese , N , Bodrossy , L , Neufeld , J D and Murrell , J C . 2009 . Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary . Environ Microbiol Rep , 1 : 424 – 433 .
   PubMed Web of Science ®Google Scholar
• Murrell , J C , McDonald , I R and Gilbert , B . 2000 . Regulation of expression of methane monooxygenases by copper ions . Trends Microbiol , 8 : 221 – 225 .
   PubMed Web of Science ®Google Scholar
• Mokhele , K , Tang , Y J , Clark , M A and Ingraham , J L . 1987 . A Pseudomonas stutzeri outer membrane protein inserts copper into N2O reductase . J Bacteriol , 169 : 5721 – 5726 .
   PubMed Web of Science ®Google Scholar
• Morton , J D , Hayes , K F and Semrau , J D . 2000 . Bioavailability of chelated and soil-adsorbed copper to Methylosinus trichosporium OB3b . Environ Sci Technol , 34 : 4917 – 4922 .
   Web of Science ®Google Scholar
• Nguyen , H H , Shiemke , A K , Jacobs , S J , Hales , B J , Lidstrom , M E and Chan , S I . 1994 . The nature of the copper ions in the membranes containing the particulate methane monooxygenase from Methylococcus capsulatus (Bath) . J Biol Chem , 269 : 14995 – 15005 .
   PubMed Web of Science ®Google Scholar
• Nguyen , H-HT , Elliott , S J , Yip , JH-K and Chan , S I . 1998 . The Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath) Is a Novel copper-containing three-subunit enzyme. Isolation and characterization . J Biol Chem , 273 : 7957 – 7966 .
   PubMed Web of Science ®Google Scholar
• Nielsen , A K , Gerdes , K , Degn , H and Murrell , J C . 1996 . Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions . Microbiol , 142 : 1289 – 96 .
   PubMed Web of Science ®Google Scholar
• 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 . Mol Microbiol , 25 : 399 – 409 .
   PubMed Web of Science ®Google Scholar
• Nriagu , JO. 1979 . “ Copper in the environment. Part 1. Ecological cycling. Inc ” . Environmental Science and Technology Series, (15D NRI) 534 New York : John Wiley & Sons .
   Google Scholar
• Omoregie , E O , Mastalerz , V , de Lange , G , Straub , K L , Kappler , A , Røy , H , Stadnitskaia , A , Foucher , J-P and Boetius , A . 2008 . Biogeochemistry and community composition of iron- and sulfur-precipitating microbial mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean) . Appl Environ Microbiol , 74 : 3198 – 3215 .
   PubMed Web of Science ®Google Scholar
• Ogram , A , Castro , H , Stanley , E , Chen , W and Prenger , J . 2006 . Distribution of methanotrophs in managed and highly disturbed watersheds . Ecological Indicators , 6 : 631 – 643 .
   Web of Science ®Google Scholar
• Peltola , P , Priha , P and Laak , S . 1993 . Effect of copper on membrane lipids and on methane monooxygenase activity of Methylococcus capsulatus (Bath) . Arch Microbiol , 159 : 521 – 525 .
   Web of Science ®Google Scholar
• Pol , A , Heijmans , K , Harhangi , H R , Tedesco , D , Jetten , M SM and Op den Camp Huub , J M . 2007 . Methanotrophy below pH 1 by a new Verrucomicrobia species . Nature , 450 : 874 – 878 .
   PubMed Web of Science ®Google Scholar
• Prior , S D and Dalton , H . 1984 . The Effect of Copper Ions on Membrane Content and Methane Monooxygenase Activity in Methanol-grown Cells of Methylococcus capsulatus (Bath) . J Gen Microhiol , 131 : 155 – 163 .
   Google Scholar
• Prior , S D and Dalton , H . 1985 . The effect of copper ions on membrane content and methane monooxygenase activity in methanol-grown cells of Methylococcus capsulatus (Bath) . J Gen Microbiol , 131 : 155 – 163 .
   Google Scholar
• Ramette , A and Tiedje , J . 2005 . Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution . Microbial Ecol , 53 : 197 – 207 .
   Web of Science ®Google Scholar
• Raghoebarsing , A A , Smolders , A JP , Schmid , M C , Rijpstra , W IC , Wolters-Arts , M , Derksen , J , Jetten , M SM , Schouten , S , Damsté , J SS , Lamers , L PM , Roelofs , J GM , Op den Camp , H JM and Strous , M . 2005 . Methanotrophic symbionts provide carbon for photosynthesis in peat bogs . Nat , 436 : 1153 – 1156 .
   Web of Science ®Google Scholar
• Richter , O-MH and Ludwig , B . 2003 . Cytochrome c oxidase—structure, function, and physiology of a redox-driven molecular machine . Rev Physiol Biochem Pharmacol , 147 : 47 – 74 .
   PubMed Web of Science ®Google Scholar
• Rosenzweig , A C and Sazinsky , M H . 2006 . Structural insights into dioxygen-activating copper enzymes . Curr Opin Struct Biol , 16 : 729 – 735 .
   PubMed Web of Science ®Google Scholar
• Rudd , JWM. 1980 . Methane oxidation in Lake Tanganyika (East Africa) . Limnol Oceangr , 25 : 958 – 963 .
   Web of Science ®Google Scholar
• Sangwan , P , Kovac , S , Davis , K ER , Sait , M and Janssen , P H . 2005 . Detection and cultivation of soil Verrucomicrobia . Appl Environ Microbiol , 71 : 8402 – 8410 .
   PubMed Web of Science ®Google Scholar
• Santelli , C M , Orcutt , B N , Banning , E , Bach , W , Moyer , C L , Sogin , M L , Staudigel , H and Edwards , K J . 2008 . Abundance and diversity of microbial life in ocean crust . Science , 453 : 653 – 656 .
   Google Scholar
• Scheffer , F , Schachtschabel , P , Blume , H P , Brümmer , G , Schwertmann , U , Horn , R , Kögel-Knabner , I , Stahr , K and Wilke , B M . 2002 . “ Lehrbuch der Bodenkunde, 15. Auflage, Spektrum ” . Berlin : Akademischer Verlag Heidelberg .
   Google Scholar
• Scheutz , C and Kjeldsen , P . 2005 . Biodegradation of trace gases in simulated landfill soil cover systems . J Air Waste Manag Assoc , 55 : 878 – 885 .
   PubMedGoogle Scholar
• Scheutz , C , Mosbæk , H and Kjeldsen , P . 2004 . Attenuation of methane and volatile organic compounds in landfill soil covers . J Environ Qual , 33 : 61 – 71 .
   PubMed Web of Science ®Google Scholar
• Scheutz , C , Pedersen , G B , Costa , G and Kjeldsen , P . 2009 . Biodegradation of methane and halocarbons in simulated landfill biocover systems containing compost materials . J Environ Qual , 38 : 1363 – 1371 .
   PubMed Web of Science ®Google Scholar
• Scranton , M I and McShane , K . 1991 . Methane fluxes in the Southern North Sea: the role of European rivers . Continental Shelf Res , 11 : 37 – 52 .
   Web of Science ®Google Scholar
• Seiburth , J M , Johnson , P W , Eberhardt , M A , Sieracki , ME, , Listrom , M and Laux , D . 1987 . The first methane-oxidizing bacterium from the upper mixed layer of the deep ocean. Methylomonas pelagica sp. nov . Curr Microbiol , 14 : 285 – 293 .
   Web of Science ®Google Scholar
• Shigematsu , T , Hanada , S , Eguchi , M , Kamagata , Y , Kanagawa , T and Kurane , R . 1999 . Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation . Appl Environ Microbiol , 65 : 5198 – 5206 .
   PubMed Web of Science ®Google Scholar
• Shukla , A K , Vishwakarma , P , Upadhyay , S N , Tripathi , A K , Prasana , S H and Dubey , S K . 2009 . Biodegradation of trichloroethylene (TCE) by methanotrophic community . Biores Tech , 100 : 2469 – 2474 .
   PubMed Web of Science ®Google Scholar
• Smith , K S , Costello , A M and Lidstrom , M E . 1997 . Methane and trichloroethylene oxidation by an estuarine methanotroph, Methylobacter sp, strain BB5.1 . Appl Environ Microbiol , 63 : 4617 – 4620 .
   PubMed Web of Science ®Google Scholar
• Stahl , S S and Lippard , S J . 1999 . “ Dioxygen and alkane activation by iron-containing enzymes ” . In Iron metabolism , Edited by: Ferreira , G C , Moura , J JG and Franco , R . 303 – 320 . Weinheim : WILEY-VCH Verlag GmbH .
   Google Scholar
• Stanley , S H , Prior , S D , Leak , D J and Dalton , H . 1983 . Copper stress underlies the fundamental change in intracellular location of methane mono-oxygenase in methane-oxidizing organisms: Studies in batch and continuous cultures . Biotech Lett , 5 : 487 – 492 .
   Web of Science ®Google Scholar
• Stoecker , K , Bendinger , B , Schöning , B , Nielsen , P H , Nielsen , J L , Baranyi , C , Toenshoff , E R , Daims , H and Wagner , M . 2006 . Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase . Proc Natl Acad Sci USA , 103 : 2363 – 2367 .
   PubMed Web of Science ®Google Scholar
• Sudek , L A , Templeton , A S , Tebo , B M and Staudigel , H . 2009 . Microbial ecology of Fe (hydr)oxide mats and basaltic rock from Vailulu’u Seamount, American Samoa . Geomicrobiol , 26 : 581 – 596 .
   Web of Science ®Google Scholar
• Sundh , I , Bastviken , D and Tranvik , L J . 2005 . Abundance, Activity, and Community Structure of Pelagic Methane- Oxidizing Bacteria in Temperate Lakes . Appl Environ Microbiol , 71 : 6746 – 6752 .
   PubMed Web of Science ®Google Scholar
• Takeda , K , Tezuka , C , Fukuoka , S and Takahara , Y . 1976 . Role of copper ions in methane oxidation by Methanomonas margaritae . J Ferment Technol , 54 : 557 – 562 .
   Google Scholar
• Takeda , K and Tanaka , K . 1980 . Ultrastructure of intracytoplasmic membranes of Methanomonas margaritae cells grown under different conditions . Antoine van Leeuwenhoek J Microbiol. Serol , 46 : 15 – 25 .
   PubMed Web of Science ®Google Scholar
• Téllez , C M , Kristen , P G , Graham , D W , Arnold , R G and Guzman , R Z . 1998 . Isolation of copper chelates from methylosinus trichosporium OB3b and soluble methane monooxygenase mutants . Appl Environ Microbiol , 64 : 1115 – 1122 .
   PubMed Web of Science ®Google Scholar
• Tovanabootr , A and Semprin , L . 1998 . Comparison of TCE transforming abilities of methane- and propane-utilizing microorganisms . Bioremediation J , 2 : 105 – 124 .
   Google Scholar
• Trotsenko , YA, and Khmelenina , V N . 2006 . Aerobic methanotrophic bacteria of cold ecosystems . FEMS Microbiol Ecol , 53 : 15 – 26 .
   Web of Science ®Google Scholar
• Tsiridis , V , Petala , M , Samaras , P , Hadjispyrou , S , Sakellaropoulos , G and Kungolos , A . 2006 . Interactive toxic effects of heavy metals and humic acids on Vibrio fischeri . Ecotox Environ Saf , 63 : 158 – 167 .
   PubMed Web of Science ®Google Scholar
• van Bodegom , P , Stams , F , Mollema , L , Boeke , S and Leffelaar , P . 2001 . Methane oxidation and the competition for oxygen in the rice rhizosphere . Appl Environ Microbiol , 67 : 3586 – 3597 .
   PubMed Web of Science ®Google Scholar
• van Hylckama , V J , de Koning , W and Janssen , D B . 1996 . Transformation kinetics of chlorinated ethenes by Methylosinus trichosporium OB3b and detection of unstable epoxides by on-line gas chromatography . Appl Environ Microbiol , 62 : 3304 – 3312 .
   PubMed Web of Science ®Google Scholar
• Vigliotta , G , Nutricati , E , Carata , E , Tredici , S M , De Stefano , M , Pontieri , P , Massardo , D R , Prati , M V , De Bellis , L and Alifano , P . 2007 . Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium . Appl Environ Microbiol , 73 : 3556 – 3565 .
   PubMed Web of Science ®Google Scholar
• Visscher , A D , Thomas , D , Boeckx , P and Cleemput , O V . 1990 . Methane oxidation in simulated landfill cover environments . Environ Sci Technol , 33 : 1854 – 1859 .
   Web of Science ®Google Scholar
• Visvanathan , C , Pokhrel , D , Cheimchaisri , W , Hettiaratchi , J PA and Wu , J S . 1999 . Methanotrophic activities in tropical landfill cover soils: effects of temperature, moisture content and methane concentration . Waste Manag Res , 4 : 313 – 323 .
   Web of Science ®Google Scholar
• Völker , H , Schweisfurth , R and Hirsch , P . 1977 . Morphology and ultrastructure of Crenothrix polyspora Cohn . J Bacteriol , 131 : 306 – 313 .
   PubMed Web of Science ®Google Scholar
• Vorholt , J. 2002 . Cofactor dependent pathways of formaldehyde oxidation in methylotrophic bacteria . Arch Microbiol , 178 : 239 – 249 .
   PubMed Web of Science ®Google Scholar
• Vulkan , R , Zhao , F-J , Barbosa-Jefferson , V , Preston , S , Paton , G I , Tipping , E and McGrath , S P . 2000 . Copper speciation and impacts on bacterial biosensors in the pore water of copper-contaminated soils . Environ Sci Technol , 34 : 5115 – 5121 .
   Web of Science ®Google Scholar
• Wagner , M and Horn , M . 2006 . The Planctomycetes, Verrucomicrobia, Chlamydiae, and sister phyla comprise a superphylum with biotechnological and medical reference . Curr Opin Biotech , 17 : 241 – 249 .
   PubMed Web of Science ®Google Scholar
• Wankel , S D , Joye , S B , Samarkin , V A , Shah , S R , Friederich , F , Melas-Kyriazi , J and Girguis , P R . 2010 . New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry . Deep-Sea Res II , 57 : 2022 – 2029 .
   Web of Science ®Google Scholar
• Wartiainen , I , Hestnes , A G , McDonald , I R and Svenning , 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 .
   PubMed Web of Science ®Google Scholar
• Watzinger , A , Stemmer , M , Pfeffer , M , Rasche , F and Reichenauer , T G . 2008 . Methanotrophic communities in a landfill cover soil as revealed by [13C] PLFAs and respiratory quinones: Impact of high methane addition and landfill leachate irrigation . Soil Biol Biochem , 40 : 751 – 762 .
   Web of Science ®Google Scholar
• Whalen , S C , Reeburgh , W S and Sandbeck , K A . 1990 . Rapid methane oxidation in a landfill cover soil . Appl Environ Microbiol , 56 : 3405 – 3411 .
   PubMed Web of Science ®Google Scholar
• Whittenbury , R and Dalton , H . 1981 . “ The methylotrophic bacteria ” . In The Prokaryotes , Edited by: Starr , M P , Stolph , H G , Tüper , Balows , A and Schlegel , H G . 894 – 902 . Berlin : Springer-Verlag .
   Google Scholar
• Whittenbury , R , Phillips , K C and Wilkinson , J F . 1970 . Enrichment, isolation and some properties of methane-utilizing bacteria . J Gen Microbiol , 61 : 205 – 218 .
   PubMedGoogle Scholar
• Yoon , S , Kraemer , SM, , DiSpirito , A A and Semrau , J D . 2010 . An assay for screening microbial cultures for chalkophore production . Environ Microbiol Rep , 10.1111/j.1758-2229.2009.00125.x
   Web of Science ®Google Scholar
• Yrjälä, Tero , T , Heli , J , Putkinen , A , Lappi , K , Tuittila , E-S , Penttila , T , Minkkenen , K , Laine , J , Peltoniemi , K and Fritze , H . 2011 . CH4 production and oxidation processes in a boreal fen ecosystem after long-term water table drawdown . Global Change Biol , 17 : 1311 – 1320 .
   Web of Science ®Google Scholar
• Zahn , J A , Bergmann , D B , Boyd , J , Kunz , R C and DiSpirito , A A . 2001 . Membrane-associated quinoprotein formaldehyde dehydrogenase from Methylococcus capsulatus . J Bacteriol , 183 : 6832 – 6840 .
   PubMed Web of Science ®Google Scholar