Dry/wet cycles change the activity and population dynamics of methanotrophs in rice field soil

Applied and Environmental Microbiology

Volumn 79, Issue 16, 2013, Pages 4932-4939

  Ma, Ke ^a,b   Conrad, Ralf ^b   Lu, Yahul ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FLOODED CONDITIONS; METHANE EMISSIONS; METHANE MONOOXYGENASE; METHANE OXIDATION; METHANE OXIDATION RATES; METHANE PRODUCTION; SEASONAL DYNAMICS; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

DYNAMICS; IODINE; METHANE; OXIDATION; POLYMERASE CHAIN REACTION; TRANSCRIPTION;

SOILS;

BACTERIAL PROTEIN; METHANE; METHANE MONOOXYGENASE; OXYGENASE;

AGRICULTURAL SOIL; GENE; METHANOTROPHY; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PADDY FIELD; POLYMERASE CHAIN REACTION; POPULATION DYNAMICS; SEASONAL VARIATION;

AEROBIC BACTERIUM; AGRICULTURE; ARTICLE; BIOTA; CHINA; CLASSIFICATION; ECOSYSTEM; FLOODING; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PHYLOGENY; PHYSIOLOGY; PROTEOBACTERIA; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE; RICE; SEASON;

AGRICULTURE; BACTERIA, AEROBIC; BACTERIAL PROTEINS; BIOTA; CHINA; ECOSYSTEM; FLOODS; METHANE; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; OXIDATION-REDUCTION; OXYGENASES; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROTEOBACTERIA; REAL-TIME POLYMERASE CHAIN REACTION; RHIZOSPHERE; SEASONS; SOIL MICROBIOLOGY;

EID: 84881001386     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00850-13     Document Type: Article

References (50)

1. Thauer RK. 2010. Functionalization of methane in anaerobic microorganisms. Angew. Chem. Int. Ed. Engl. 49:6712-6713.
2. Chanton jp, whiting gj, blair ne, lindau cw, bollich pk. 1997.methane emission from rice: stable isotopes, diurnal variations, and co2 exchange. global biogeochem. cycles 11:15-27.
3. Holzapfel-Pschorn A, Conrad R, Seiler W. 1985. Production, oxidation and emission of methane in rice paddies. FEMS Microbiol. Ecol. 31:343-351.
4. Conrad R, Rothfuss F. 1991. Methane oxidation in the soil surfacelayer of a flooded rice field and the effect of ammonium. Biol. Fert. Soils 12:28-32.
5. Conrad R, Rothfuss F. 1991. Methane oxidation in the soil surfacelayer of a flooded rice field and the effect of ammonium. Biol. Fert. Soils 12:28-32.
6. Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A, Dunfield PF. 2009 Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ. Microbiol. Rep. 1:293-306.
7. Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM. 2000. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bags, representing a novel subtype of serine-pathway methanotrophs. Int. J. Syst. Evol. Microbiol. 50:955-969.
8. Vorobev AV, Baani M, Doronina NV, Brady AL, Liesack W, Dunfield PF, Dedysh SN. 2011. Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int. J. Syst. Evol. Microbiol. 61:2456-2463.
9. Holmes AJ, Roslev P, McDonald IR, Iversen N, Henriksen K, Murrell JC. 1999. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl. Environ. Microbiol.65:3312-3318.
10. Kolb S, Knief C, Stubner S, Conrad R. 2003. Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl. Environ. Microbiol. 69:2423-2429.
11. McDonald IR, Bodrossy L, Chen Y, Murrell JC. 2008. Molecular ecology techniques for the study of aerobic methanotrophs. Appl. Environ. Microbiol.74:1305-1315.
12. Conrad R. 2007. Microbial ecology of methanogens and methanotrophs. Adv. Agron. 96:1-63.
13. Horz HP, Yimga MT, 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. Microbiol. 67:4177-4185.
14. Ma K, Qiu QF, Lu YH. 2010. Microbial mechanism for rice variety control on methane emission from rice field soil. Glob. Change Biol. 16:3085-3095.
15. Hanson RS, Hanson TE. 1996. Methanotrophic bacteria. Microbiol. Rev.60:439-471.
16. Lüke C, Frenzel P. 2011. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl. Environ. Microbiol. 77:6305-6309.
17. Semrau jd, dispirito aa, yoon s. 2010. methanotrophs and copper.fems microbiol. rev. 34:496-531.
18. Amaral JA, Archambault C, Richards SR, Knowles R. 1995. Denitrification associated with groups I and II methanotrophs in a gradient enrichment system. FEMS Microbiol. Ecol. 18:289-298.
19. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. 2003. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5:566-582.
20. Henckel T, Roslev P, Conrad R. 2000. Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ. Microbiol. 2:666-679.
21. Baani M, Liesack W. 2008. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SCZ. Proc. Natl. Acad. Sci. U. S. A. 105:10203-10208.
22. Bodelier PLE. 2011. Interactions between nitrogenous fertilizers and methane cycling in wetland and upland soils. Curr. Opin. Environ. Sustain.3:379-388.
23. Liesack W, Schnell S, Revsbech NP. 2000. Microbiology of flooded rice paddies. FEMS Microbiol. Rev. 24:625-645.
24. Wu LQ, Ma K, Lu YH. 2009. Rice roots select for type I methanotrophs in rice field soil. Syst. Appl. Microbiol. 32:421-428.
25. Ma K, Lu YH. 2011. Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiol. Ecol.75:446-456.
26. Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. 2010.Biogeography of wetland rice methanotrophs. Environ. Microbiol. 12:862-872.
27. Eller G, Frenzel P. 2001. Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl. Environ. Microbiol. 67:2395-2403.
28. Qiu QF, Noll M, Abraham WR, Lu YH, 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.
29. Shrestha M, Shrestha PM, Frenzel P, Conrad R. 2010. Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere. ISME J.4:1545-1556.
30. Reim A, Lueke C, Krause S, Pratscher J, Frenzel P. 2012. One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME J. 6:2128-2139.
31. Eller G, Krüger M, 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.
32. Henckel T, Jackel U, Conrad R. 2001. Vertical distribution of the metha notrophic community after drainage of rice field soil. FEMS Microbiol. Ecol. 34:279-291.
33. Shrestha M, Abraham WR, Shrestha PM, Noll M, 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.
34. Krüger M, Eller G, Conrad R, Frenzel P. 2002. Seasonal variation in pathways of CH4 production and in CH4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors. Glob. Change Biol. 8:265-280.
35. Sass RL, Fisher FM, Wang YB, Turner FT, Jund MF. 1992. Methane emission from rice fields: the effect of floodwater management. Global Biogeochem. Cycles 6:249-262.
36. Yagi K, Tsuruta H, Kanda K, Minami K. 1996. Effect of water management on methane emission from a Japanese rice paddy field: automated methane monitoring. Global Biogeochem. Cycles 10:255-267.
37. Ma K, Conrad R, Lu YH. 2012. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Appl. Environ. Microbiol. 78:445-454.
38. Lu WF, Chen W, Duan BW, Guo WM, Lu YH, Lantin RS, Wassmann R, Neue HU. 2000. Methane emissions and mitigation options in irrigated rice fields in southeast China. Nutr. Cycl. Agroecosyst. 58:65-73.
39. Miller LG, Sasson C, Oremland RS. 1998. Difluoromethane, a new and improved inhibitor of methanotrophy. Appl. Environ. Microbiol. 64:4357-4362.
40. Krüger M, Frenzel P, Conrad R. 2001. Microbial processes influencing methane emission from rice fields. Glob. Change Biol. 7:49-63.
41. Bodelier PLE, Hahn AP, Arth IR, Frenzel P. 2000. Effects of ammoniumbased fertilisation on microbial processes involved in methane emission from soils planted with rice. Biogeochemistry 51:225-257.
42. Lu YH, Wassmann R, Neue HU, Huang CY. 2000. Dynamics of dissolved organic carbon and methane emissions in a flooded rice soil. Soil Sci. Soc. Am. J. 64:2011-2017.
43. Murase J, Noll M, Frenzel P. 2006. Impact of protists on the activity and structure of the bacterial community in a rice field soil. Appl. Environ. Microbiol. 72:5436-5444.
44. 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.
45. Dumont MG, Pommerenke B, Casper P, Conrad R. 2011. DNA-RRNA and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ. Microbiol. 13:1153-1167.
46. Gilbert B, Frenzel P. 1995. Methanotrophic bacteria in the rhizosphere of rice microcosms and their effect on porewater methane concentration and methane emission. Biol. Fertil. Soils 20:93-100.
47. Bodelier PLE, Roslev P, Henckel T, Frenzel P. 2000. Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403:421-424.
48. 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. Microbiol. 72:1346-1354.
49. Vicca S, Flessa H, Loftfield N, Janssens IA. 2009. The inhibitory effect of difluoromethane on CH4 oxidation in reconstructed peat columns and side-effects on CO2 and N2O emissions at two water levels. Soil Biol. Biochem. 41:1117-1123.
50. Krause S, Lüke C, Frenzel P. 2012. Methane source strength and energy flow shape methanotrophic communities in oxygen-methane countergradients. Environ. Microbiol. Rep. 4:203-208.