Comparison of Methanotrophic Community and Methane Oxidation between Rhizospheric and Non-Rhizospheric Soils

REFERENCES

• Ait-Benichou , S , Jugnia , L B , Greer , C W and Cabral , A R . 2009 . Methanotrophs and methanotrophic activity in engineered landfill biocovers . Waste Manage , 29 : 2509 – 2517 .
   PubMed Web of Science ®Google Scholar
• Bais , H P , Park , S W , Weir , T L , Callaway , R M and Vivanco , J M . 2004 . How plants communicate using the underground information superhighway . Trends Plant Sci , 9 : 26 – 32 .
   PubMed Web of Science ®Google Scholar
• Bodelier , P LE , 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 .
   PubMed Web of Science ®Google Scholar
• Börjesson , G. 1997 . Methane oxidation in landfill cover soil , Uppsala Sweden : Sweedish University of Agricultural Sciences . Doctoral Thesis
   Google Scholar
• Calhoun , A and King , G M . 1997 . Regulation of root-associated methanotrophy by oxygen availability in the rhizosphere of two aquatic macroophytes . Appl Environ Microbiol , 63 : 3051 – 3058 .
   PubMed Web of Science ®Google Scholar
• Calhoun , A and King , G M . 1998 . Charaterization of root-associated methanotrophs from three freshwater macrophytes: Pontederia cordata, Sparganium eurycarpum, and Sagittaria latifolia . Appl Environ Microbiol , 64 : 1099 – 1105 .
   PubMed Web of Science ®Google Scholar
• Costello , A M and Lidstrom , M E . 1999 . Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments . Appl Environ Microbiol , 65 : 5066 – 5074 .
   PubMed Web of Science ®Google Scholar
• Crossman , Z M , Abraham , F and Evershed , R P . 2004 . 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 . Environ Sci Technol , 38 : 1359 – 1367 .
   PubMed Web of Science ®Google Scholar
• de Lipthay , J R , Johnsen , K , Albrechtsen , H J , Rosenberg , P and Aamand , J . 2004 . Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations . FEMS Microbiol Ecol , 49 : 59 – 69 .
   PubMed Web of Science ®Google Scholar
• DeJournett , T D , Arnold , W A and LaPara , T M . 2007 . The characterization and quantification of methanotrophic bacterial populations in constructed wetland sediments using PCR targeting 16S rRNA gene fragments . Appl Soil Ecol , 35 : 648 – 659 .
   Web of Science ®Google Scholar
• Eller , G , Krüger , M and Frenzel , P . 2005 . Comparing field and microcosm experiments: a case study on methano- and methylo-trophic bacteria in paddy soil . FEMS Microbiol Ecol , 51 : 279 – 291 .
   PubMed Web of Science ®Google Scholar
• Erkel , C , Kube , M , Reinhardt , R and Liesack , W . 2006 . Genome of Rice Cluster I archaea—the key methane producers in the rice rhizosphere . Science , 3 ( 13 ) : 370 – 372 .
   Web of Science ®Google Scholar
• Ferrando , L and Tarlera , S . 2009 . Activity and diversity of methanotrophs in the soil-water interface and rhizospheric soil from a flooded temperate rice field . J Appl Microbiol , 106 : 306 – 316 .
   PubMed Web of Science ®Google Scholar
• Fierer , N , Jackson , J A , Vilgalys , R and Jackson , R B . 2005 . Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays . Appl Environ Microbiol , 71 : 4117 – 4120 .
   PubMed Web of Science ®Google Scholar
• Gebert , J , Gröengröft , A , Schloter , M and Gattinger , A . 2004 . Community structure in a methanotroph biofilter as revealed by phospholipid fatty acid analysis . FEMS Microbiol Lett , 240 : 61 – 67 .
   PubMed Web of Science ®Google Scholar
• Gebert , J , Stralis-Pavese , N , Alawi , M and Bodrossy , L . 2008 . Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray . Environ Microbiol , 10 : 1175 – 1188 .
   PubMed Web of Science ®Google Scholar
• Gómez , K E , Gonzalez-Gil , G , Lazzaro , A and Schroth , M H . 2009 . Quantifying methane oxidation in landfill-cover soil by gas push-pull tests . Waste Manage , 29 : 2518 – 2526 .
   PubMed Web of Science ®Google Scholar
• Hall , TA. 1999 . BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT . Nucleic Acids Symposium Series , 41 : 95 – 98 .
   Google Scholar
• Hanson , R S and Hanson , T E . 1996 . Methanotrophic bacteria . Microbiol Rev , 60 : 439 – 471 .
   PubMedGoogle Scholar
• He , R , Ruan , A , Jiang , C and Shen , D S . 2008 . Responses of oxidation rate and microbial communities to methane in stimulated landfill cover soil microcosms . Bioresour Technol , 99 : 7192 – 7199 .
   PubMed Web of Science ®Google Scholar
• Hegde , U , Chang , T C and Yang , S S . 2003 . Methane and carbon dioxide emissions from Shan-Chu-Ku landfill site in northern Taiwan . Chemosphere , 52 : 1275 – 1285 .
   PubMed Web of Science ®Google Scholar
• Holmes , A J , Costello , A M , Lidstrom , M E and Murrell , J C . 1995 . Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related . FEMS Microbiol Lett , 132 : 203 – 208 .
   PubMed Web of Science ®Google Scholar
• Horz , H R , 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 Micro , 67 : 4177 – 4185 .
   PubMed Web of Science ®Google Scholar
• IPCC . 2007 . “ Climate change 2007: The scientific physical science basis ” . In Contribution of Working Group I to the Third Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) , Edited by: Solomon , S , Qin , D , Manning , M , Chen , Z , Marquis , M , Averyt , K B , Tignor , M and Miller , H L . UK : Cambridge University Press .
   Google Scholar
• Jugnia , L B , Benichou , S A , Fortin , N , Cabral , A R and Greer , C W . 2009 . Diversity and dynamics of methanotrophs within an experimental landfill cover soil . Soil Bio Biochem , 73 : 1479 – 1487 .
   Google Scholar
• Kallistova , A Y , Kevbrina , M V , Nekrasova , V K , Shnyrev , N A , Einola , J K , Kulomaa , M S , Rintala , J A and Nozhevnikova , A N . 2007 . Enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill . Microb Ecol , 54 : 637 – 645 .
   PubMed Web of Science ®Google Scholar
• King , GM. 1994 . Association of methanotrophs with the roots and rhizomes of aquatic vegetation . Appl Envion Microbiol , 60 : 3220 – 3227 .
   PubMed Web of Science ®Google Scholar
• Laanbroek , HJ. 2010 . Methane emission from natural wetlands: interplay between emergent machrophytes and soil microbial processes. A mini review . Ann Bot , 105 : 141 – 153 .
   PubMed Web of Science ®Google Scholar
• Lu , Y and Conrad , R . 2005 . In situ stable isotope probing of methanogenic archaea in the rice rhizosphere . Science , 309 : 1088 – 1090 .
   PubMed Web of Science ®Google Scholar
• Mohanty , S R , Bodelier , P LE and Conrad , R . 2007 . Effect of temperature on composition of the methanotrophic community in rice field and forest soil . FEMS microbial Ecol , 62 : 24 – 32 .
   PubMed Web of Science ®Google Scholar
• Murase , J and Frezel , P . 2007 . Amethane-driven microbial food web in a wetland rice soil . Environ Microbiol , 9 : 3025 – 3034 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Raghoebarsing , A A , Smolders , A J , Schmid , M C , Rijpstra , W I , Wolters-Arts , M , Derksen , J , Jetten , M S , Schouten , S , Sinninghe Damsté , J S , Lamers , L P , Roelofs , J G , Op den Camp , H J and Strous , M . 2005 . Methanotrophic symbionts provide carbon for photosynthesis in peat bogs . Nature , 436 : 1153 – 1156 .
   PubMed Web of Science ®Google Scholar
• Rahalkar , M , Deutzmann , J , Schink , B and Bussmann , I . 2009 . Abundance and activity of methanotrophic bacteria in Liioral and Profounddal sediments of Lake Constance (Germany) . Appl Environ Microbiol , 75 : 119 – 126 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Roslev , P and Iversen , N . 1999 . Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils . Appl Environ Microbiol , 65 : 4064 – 4070 .
   PubMed Web of Science ®Google Scholar
• Shannon , C E and Weaver , W . 1949 . The methmatical theory of communication , Urbana, IL : University of Illinois Press .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Spokas , K A and Bogner , J E . 2010 . Limits and dynamics of methane oxidation in landfill cover soils . Waste Manag , 31 : 823 – 832 .
   PubMed Web of Science ®Google Scholar
• Steer , J and Harris , J A . 2000 . Shifts in the microbial community in rhizosphere and non-rhizsphere soils during the growth of Agrostis stolonifera . Soil Biol Biochem , 32 : 869 – 878 .
   Web of Science ®Google Scholar
• Stolyar , S , Costello , A M , Peeples , T L and Lidstrøm , M E . 1999 . Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath . Micobiol , 145 : 1235 – 1244 .
   PubMed Web of Science ®Google Scholar
• Stolyar , S , Franke , M and Lidstrøm , M E . 2001 . Expression of individual copies of Methylococcus capsulatus Bath particulate methane monooxygenase genes . J Bacteriol , 183 : 1810 – 1812 .
   PubMed Web of Science ®Google Scholar
• Su , Y H and Yang , X Y . 2009 . Interactions between selected PAHs and the microbial community in rhizosphere of paddy soil . Sci Total Environ , 407 : 1027 – 1034 .
   PubMed Web of Science ®Google Scholar
• Tamura , K , Dudley , J , Nei , M and Kumar , S . 2007 . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 . Mol Biol Evol , 24 : 1596 – 1599 .
   PubMed Web of Science ®Google Scholar
• Tong , C L , Zhang , W J , Wang , H Q , Tang , G Y , Yang , G R and Wu , J S . 2005 . Relationship between organic carbon and water content in four type wetland sediments in Sanjiang Plain . Huan Jing Ke Xue , 26 : 38 – 42 .
   PubMedGoogle Scholar
• Uz , I , Rasche , M E , Townsend , T , Ogram , A V and Lindner , A S . 2003 . Characterization of methanogenic and methanotrophic assemblages in landfill samples . Proc Biol Sci , 270 ( Suppl 2 ) : S202 – S205 .
   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 der Nat , F , Middelburg , J J , Meteren , D and Wielemakers , A . 1998 . Diel methane emission patterns from Scirpus lacustris and Phragmites australis . Biogeochem. , 41 : 1 – 22 .
   Web of Science ®Google Scholar
• Vishwakarma , P and Dubey , S K . 2007 . The effect of soil type and plant age on the population size of rhizospheric methanotrophs and their activities in tropical rice soils . J Basic Micobiol , 47 : 351 – 357 .
   PubMed Web of Science ®Google Scholar
• Wang , Y , Wu , W , Ding , Y , Liu , W , Perera , A , Chen , Y and Devare , M . 2008 . Methane oxidation activity and bacterial community composition in a simulated landfill cover soil is influenced by the growth of Chenopodium album L . Soil Biol Biochem , 40 : 2452 – 2459 .
   Web of Science ®Google Scholar
• Wartiainen , I , Hestnes , A G and Svenning , M M . 2003 . Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway)-denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures . Can J Microbiol , 49 : 602 – 612 .
   PubMed Web of Science ®Google Scholar
• Wise , M G , McArthur , J V and Shimkets , L J . 1999 . Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis . Appl Environ Microbiol , 65 : 4887 – 4897 .
   PubMed Web of Science ®Google Scholar
• Wu , L , Ma , K and Lu , Y . 2009 . Rice roots selected for type I methanotrphs in rice field soil . Sys Appl Microbiol , 32 : 421 – 428 .
   PubMed Web of Science ®Google Scholar
• Xu , H , Cai , Z C and Tsuruta , H . 2003 . Soil moisture between rice-growing seasons affects methane emission, production, and oxidation . Soil Sci Soc Am J , 67 : 1147 – 1157 .
   Web of Science ®Google Scholar
• Yang , S S and Chang , H L . 1998 . Effect of environmental conditions on methane production and emission from paddy soil . Agr Ecosys Environ , 69 : 69 – 80 .
   Web of Science ®Google Scholar
• Zhu , N , An , P , Krishnakumar , B , Zhao , L , Sun , L , Mizuochi , M and Inamori , Y . 2007 . Effect of plant harvest on methane emission from two constructed wetlands designed for the treatment of wastewater . J Environ Manage , 85 : 936 – 943 .
   PubMed Web of Science ®Google Scholar