Effect of winter-flooding on methanogenic archaeal community structure in paddy field under organic farming

Soil Science and Plant Nutrition

Volumn 58, Issue 5, 2012, Pages 553-561

  Liu, Dongyan ^a   Suekuni, Chika ^a   Akita, Kazunori ^b   Ito, Toyoaki ^b   Saito, Masanori ^b   Watanabe, Takeshi ^a   Kimura, Makoto ^a   Asakawa, Susumu ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b TOHOKU UNIVERSITY   (Japan)

Author keywords

Denaturing gradient gel electrophoresis; methanogenic archaea; paddy field; quantitative polymerase chain reaction; winter flooding

Indexed keywords

ARCHAEA; METHANOMICROBIALES; METHANOSARCINALES;

EID: 84869790704     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1080/00380768.2012.726598     Document Type: Article

References (43)

1. Akita, K, Ito, T and Uno, T. 2010a. Effects of winter-flooding with organic farming on soil nutrients and methane emission from paddy field. Abst. Meet. Jpn. Soc. Soil Sci. Plant Nutr., 56: 103 (in Japanese)
2. Akita, K, Ito, T and Uno, T. 2010b. Effects of winter-flooding on soil nutrients and rice yield in paddy field with organic farming. J. Integ. Field Sci., 7: 113
3. Akita, K, Uno, T, Suzuki, K, Tajima, R, Saito, M and Ito, T. 2012: Aquatic biota in winter flooded paddy field with organic farming: Case study in Field Science Center, Tohoku University, Japan. J. Integ. Field Sci., 9, in press
4. Aoki, S. 1996: Black-box: Data analysis on the WWW. http://www.aoki2.si.gunma-u.ac.jp/BlackBox/BlackBox.html (January, 2012)
5. Asakawa, S, Akagawa-Mastushita, M, Morii, H, Koga, Y and Hayano, K. 1998. Communities of methanogenic bacteria in paddy field soils with long-term application of organic matter. Soil Biol. Biochem., 30: 299-303.
6. Asakawa, S and Hayano, K. 1995. Population of methanogenic bacteria in paddy field soil under double cropping conditions (rice-wheat). Biol. Fertil. Soils, 20: 113-117.
7. Cai, ZC, Tsuruta, H, Gao, M, Xu, H and Wei, C. 2003. Option for mitigation methane emission from a permanently flooded rice field. Global Change Biol., 9: 37-45.
8. Cai, ZC, Tsuruta, H and Minami, K. 2000. Methane emission from rice fields in China: Measurements and influencing factors. J. Geophys. Res., 105: 17231-17242.
9. Chen, Y-H and Prinn, RG. 2005. Atmospheric modeling of high- and low-frequency methane observations: Importance of interannually varying transport. J. Geophys. Res., 110: D10303 doi:10.1029/2004JD005542
10. Denman, KL, Brasseur, GChidthaisong, A. 2007. "Couplings between changes in the climate system and biogeochemistry". In Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, Edited by: Solomon, S, Qin, D, Manning, M, Chen, Z, Marquis, M, Avery, KB, Tignor, M and Miller, HL. 499-587. Cambridge, UK: Cambridge University Press.
11. Fey, A and Conrad, R. 2000. Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil. Appl. Environ. Microbiol., 66: 4790-4797.
12. Fitzgerald, GJ, Scow, KM and Hill, JE. 2000. Fallow season straw and water management effects on methane emissions in California rice. Global Biogeochem. Cycles, 14: 767-776.
13. Forster, P, Ramaswamy, VArtaxo, P. 2007. "Changes in atmospheric constituents and in radiative forcing". In Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, Edited by: Solomon, S, Qin, D, Manning, M, Chen, Z, Marquis, M, Avery, KB, Tignor, M and Miller, HL. 129-234. Cambridge, UK: Cambridge University Press.
14. Japan Meteorological Agency 2011: Weather Observations, Temperature. http://www.jma.go.jp/jp/amedas (September, 2011)
15. Krüger, M, Frenzel, P, Kemnitz, D and Conrad, R. 2005. Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol. Ecol., 51: 323-331.
16. Kumar, S, Dudley, J, Nei, M and Tamura, K. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform., 9: 299-306.
17. 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach. Soil Biol. Biochem., 43: 814-822.
18. Lopes, AR, Faria, C, Prieto-Fernández, Á, Trasar-Cepeda, C, Manaia, CM and Nunes, OC. 2011. Comparative study of the microbial diversity of bulk paddy soil of two rice fields subjected to organic and conventional farming. Soil Biol. Biochem., 43: 115-125.
19. Liu, Y and Whitman, WB. 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N.Y. Acad. Sci., 1125: 171-189.
20. Luton, PE, Wayne, JM, Sharp, RJ and Riley, PW. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogentic analysis of methanogen populations in landfill. Microbiol., 148: 3521-3530.
21. Ma, K, Conrad, R and 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.
22. Mäder, P, Fließbach, A, Dubois, D, Gunst, L, Fried, P and Niggli, U. 2002. Soil fertility and biodiversity in organic farming. Science, 296: 1694-1697.
23. Manley, SW, Kaminski, RM, Reinecke, KJ and Gerard, PD. 2005. Agronomic implications of waterfowl management in Mississippi ricefields. Wildlife Soc. Bull., 33: 981-992.
24. Masco, L, Vanhoutte, T, Temmerman, R, Swings, J and Huys, G. 2007. Evaluation of real-time PCR targeting the 16S rRNA and recA genes for the enumeration of bifidobacteria in probiotic products. Int. J. Food Microbiol., 113: 315-357.
25. Matsumoto, J, Minamiyama, Y, Akahori, S and Takahashi, K. 2002. Suppression of methane emission from paddy field supplemented with organic matter. Jpn. J. Soil Sci. Plant Nutr., 73: 315-318 (in Japanese).
26. Minami, K. 1994. Methane from rice production. Fertil. Res., 37: 167-179.
27. Mineta, T, Koizumi, N and Ishida, K. 2009. Contribution of winter flooding in multifunctionality of paddy fields: Some notes in a case of biota conservation function in Tajiri-Shinpo, Miyagi prefetture. J. Rural Plan. Assoc., 27: 335-340. (in Japanese with English summary)
28. Nanzyo, M. 2002. Unique properties of volcanic ash soils. Glob. Environ. Res., 6: 99-112.
29. Peng, J, Lu, Z, Rui, J and Lu, Y. 2008. Dynamics of methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl. Environ. Microbiol., 74: 2894-2901.
30. Ramakrishnan, B, Lueders, T, Dunfield, PF, Conrad, R and Friedrich, MW. 2001. Archaeal community in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiol. Ecol., 37: 175-186.
31. Sakai, S, Imachi, H, Sekiguchi, Y, Tseng, I-C, Ohashi, A, Harada, H and Kamagata, Y. 2009. Cultivation of methanogens under low-hydrogen conditions by using the coculture method. Appl. Environ. Microbiol., 75: 4892-4896.
32. Shoji, S, Nanzyo, M and Dahlgren, RA. 1993. Volcanic ash soils: Genesis, properties and utilization. Dev. Soil Sci., 21: 1-288.
33. 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.
34. Wang, G, Watanabe, T, Jin, J, Liu, X, Kimura, M and Asakawa, S. 2010. Methanogenic archaeal communities in paddy field soils in northeast China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses. Soil Sci. Plant Nutr., 56: 831-838.
35. Watanabe, T, Kimura, M and Asakawa, S. 2006. Community structure of methanogenic archaea in paddy field soil under double cropping (rice-wheat). Soil Biol. Biochem., 38: 1264-1274.
36. Watanabe, T, Kimura, M and Asakawa, S. 2007. Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils. Soil Biol. Biochem., 39: 2877-2887.
37. Watanabe, T, Kimura, M and Asakawa, S. 2009. Distinct members of a stable methanogenic archaeal community transcribe mcrA genes under flooded and drained conditions in Japanese paddy field soil. Soil Biol. Biochem., 41: 276-285.
38. Watanabe, T, Kimura, M and Asakawa, S. 2010a. Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis. Biol. Fertil. Soils, 46: 343-353.
39. Watanabe, T, Wang, G, Taki, K, Ohashi, Y, Kimura, M and Asakawa, S. 2010b. Vertical changes in bacterial and archaeal communities with soil depth in Japanese paddy fields. Soil Sci. Plant Nutr., 56: 705-715.
40. Yoshida, O, Fujiwara, S, Ushiyama, K, Imai, S and Kubota, C. 2010a. Methane emission from early pooled and organic paddy rice field around the lake Miyajimanuma in Bibai city, Hokkaido. J. Rakuno Gakuen Univ., 34: 211-221. (in Japanese with English summary)
41. Yoshida, O, Sawamoto, T, Fujiwara, S, Kobayashi, K, Imai, S, Kubota, C, Okazaki, Y, Ogimoto, H and Ushiyama, K. 2010b. Methane emission of early pooled and organic paddy rice field around the lake Miyajimanuma in Bibai city, Hokkaido during 2008-2009. J. Rakuno Gakuen Univ., 35: 93-102. (in Japanese with English summary)
42. Yuan, YL, Conrad, R and Lu, YH. 2009. Response of methanogenic archaeal community to oxygen exposure in rice field soil. Environ. Microbiol. Rep., 1: 347-354.
43. Zhang, G, Tian, J, Jiang, N, Guo, X, Wang, Y and Dong, X. 2008. Methanogen community in Zoige wetland of Tibetan Plateau and phyentype characterization of a dominant uncultured methanogen cluster ZC-I. Environ. Microbiol., 10: 1850-1860.