Effect of temperature on the structure and activity of a methanogenic archaeal community during rice straw decomposition

Soil Biology and Biochemistry

Volumn 81, Issue , 2015, Pages 17-27

  Lu, Yue ^a,b   Fu, Li ^a   Lu, Yahai ^a   Hugenholtz, Floor ^b,c,d   Ma, Ke ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c Netherlands Consortium for Systems Biology   (Netherlands)

^d TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

Author keywords

CH4 production; McrA gene and transcript; Methanogenic archaeal community; Rice field soil; Straw degradation; Temperature effects

Indexed keywords

CARBON DIOXIDE; GENES; METHANE; RNA; SOILS; TEMPERATURE; THERMAL EFFECTS; VOLATILE FATTY ACIDS;

ARCHAEAL; CLONING AND SEQUENCING; HYDROGENOTROPHIC METHANOGENS; MCRA GENE AND TRANSCRIPT; METHANOGENIC COMMUNITY; RICE FIELD SOILS; STRUCTURE AND ACTIVITIES; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

METHANOGENS;

ANOXIC CONDITIONS; BIODEGRADATION; CROP PRODUCTION; DECOMPOSITION; ENZYME ACTIVITY; GENE EXPRESSION; HIGH TEMPERATURE; METHANOGENESIS; MICROBIAL COMMUNITY; POLYMORPHISM; STRAW; TEMPERATURE EFFECT;

CHINA; HEILONGJIANG; SANJIANG PLAIN;

ARCHAEA;

EID: 84911910231     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2014.10.031     Document Type: Article

References (38)

1. Bao Q.L., Xiao K.Q., Chen Z., Yao H.Y., Zhu Y.G. Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw. FEMS Microbiology Ecology 2014, 88:372-385.
2. Conrad R. Control of microbial methane production in wetland rice fields. Nutrient Cycling in Agroecosystems 2002, 64:59-69.
3. Conrad R. Microbial ecology of methanogens and methanotrophs. Advances in Agronomy 2007, 96:1-63.
4. Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. Environmental Microbiology Reports 2009, 1:285-292.
5. Conrad R., Klose M. Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw. European Journal of Soil Science 2006, 57:476-484.
6. Conrad R., Klose M., Lu Y., Chidthaisong A. Methanogenic pathway and archaeal communities in three different anoxic soils amended with rice straw and maize straw. Frontiers in Microbiology 2012, 3. Article 4.
7. Conrad R., Klose M., Noll M. Functional and structural response of the methanogenic microbial community in rice field soil to temperature change. Environmental Microbiology 2009, 11:1844-1853.
8. Conrad R., Klose M., Noll M., Kemnitz D., Bodelier P.L.E. Soil type links microbial colonization of rice roots to methane emission. Global Change Biology 2008, 14:657-669.
9. Fey A., Chin K.J., Conrad R. Thermophilic methanogens in rice field soil. Environmental Microbiology 2001, 3:295-303.
10. Fey A., Conrad R. Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil. Applied and Environmental Microbiology 2000, 66:4790-4797.
11. Huang Y., Sun W.J., Zhang W., Yu Y.Q., Su Y.H., Song C.C. Marshland conversion to cropland in northeast China from 1950 to 2000 reduced the greenhouse effect. Global Change Biology 2010, 16:680-695.
12. IPCC Summary for policymakers. Climate Change 2007: the Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change 2007, Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. S. Solomon, D. Qin, M. Manning (Eds.).
13. Jetten M.S.M., Stams A.J.M., Zehnder A.J.B. Methanogenesis from acetate - a comparison of the acetate metabolism in Methanothrix-Soehngenii and Methanosarcina spp. FEMS Microbiology Reviews 1992, 88:181-197.
14. Kemnitz D., Chin K.J., Bodelier P., Conrad R. Community analysis of methanogenic archaea within a riparian flooding gradient. Environmental Microbiology 2004, 6:449-461.
15. Li T., Huang Y., Zhang W., Yu Y.Q. Methane emissions associated with the conversion of marshland to cropland and climate change on the Sanjiang Plain of northeast China from 1950 to 2100. Biogeosciences 2012, 9:5199-5215.
16. Liesack W., Schnell S., Revsbech N.P. Microbiology of flooded rice paddies. FEMS Microbiology Reviews 2000, 24:625-645.
17. Lu Y.H., Conrad R. In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 2005, 309:1088-1090.
18. Lu Y.H., Lueders T., Friedrich M.W., Conrad R. Detecting active methanogenic populations on rice roots using stable isotope probing. Environmental Microbiology 2005, 7:326-336.
19. Lueders T., Chin K.J., Conrad R., Friedrich M. Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environmental Microbiology 2001, 3:194-204.
20. Lueders T., Friedrich M.W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied and Environmental Microbiology 2003, 69:320-326.
21. Ma K., Conrad R., Lu Y.H. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Applied and Environmental Microbiology 2012, 78:445-454.
22. Ma K., Lu Y.H. Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiology Ecology 2011, 75:446-456.
23. Ma K., Qiu Q.F., Lu Y.H. Microbial mechanism for rice variety control on methane emission from rice field soil. Global Change Biology 2010, 16:3085-3095.
24. Page A., Miller R., Keeney D. Methods of Soil Analysis; Chemical and Microbiological Properties, Part 2 1982, Soil Science Society of America, Madison, WI.
25. Peng J.J., Lu Z., Rui J., Lu Y.H. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Applied and Environmental Microbiology 2008, 74:2894-2901.
26. Rui J.P., Peng J.J., Lu Y.H. Succession of bacterial populations during plant residue decomposition in Rice field soil. Applied and Environmental Microbiology 2009, 75:4879-4886.
27. Schütz H., Seiler W., Conrad R. Influence of soil temperature on methane emission from rice paddy fields. Biogeochemistry 1990, 11:77-95.
28. ter Braak C.J.F., Smilauer P. Canoco Reference Manual and User's Guide: Software for Ordination (Version 5.0) 2012, 151-230. Microcomputer Power, Ithaca, NY, USA.
29. Van den Brink P.J., Ter Braak C.J. Principal response curves: analysis of time-dependent multivariate responses of biological community to stress. Environmental Toxicology and Chemistry 1999, 18:138-148.
30. Wang G.H., Watanabe T., Jin J.A., Liu X.B., Kimura M., Asakawa S. Methanogenic archaeal communities in paddy field soils in north-east China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses. Soil Science and Plant Nutrition 2010, 56:831-838.
31. Weber S., Lueders T., Friedrich M.W., Conrad R. Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiology Ecology 2001, 38:11-20.
32. Wu X.L., Friedrich M.W., Conrad R. Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils. Environmental Microbiology 2006, 8:394-404.
33. Yagi K., Minami K. Effect of organic matter application on methane emission from some Japanese paddy fields. Soil Science and Plant Nutrition 1990, 36:599-610.
34. Yao H., Conrad R. Effect of temperature on reduction of iron and production of carbon dioxide and methane in anoxic wetland rice soils. Biology and Fertility of Soils 2000, 32:135-141.
35. Yuan Q., Lu Y.H. Response of methanogenic archaeal community to nitrate addition in rice field soil. Environmental Microbiology Reports 2009, 1:362-369.
36. Zhang W., Yu Y., Huang Y., Li T., Wang P. Modeling methane emissions from irrigated rice cultivation in China from 1960 to 2050. Global Change Biology 2011, 17:3511-3523.
37. Zhang Y., Su S., Zhang F., Shi R., Gao W. Characterizing spatiotemporal dynamics of methane emissions from rice paddies in Northeast China from 1990 to 2010. Plos One 2012, 7.
38. Zou J.W., Huang Y., Jiang J.Y., Zheng X.H., Sass R.L. A3-year field measurement of methane and nitrous oxide emissions from rice paddies in China: effects of water regime, crop residue, and fertilizer application. Global Biogeochemical Cycles 2005, 19.