title: Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil.
abstract: Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.
authors.affiliation: Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan, liu.dongyan@f.mbox.nagoya-u.ac.jp.
authors.forename: Dongyan
authors.initials: D
authors.lastname: Liu
authors.forename: Hiroki
authors.initials: H
authors.lastname: Ishikawa
authors.forename: Mizuhiko
authors.initials: M
authors.lastname: Nishida
authors.forename: Kazunari
authors.initials: K
authors.lastname: Tsuchiya
authors.forename: Tomoki
authors.initials: T
authors.lastname: Takahashi
authors.forename: Makoto
authors.initials: M
authors.lastname: Kimura
authors.forename: Susumu
authors.initials: S
authors.lastname: Asakawa
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
references.citation: PLoS One. 2011;6(5):e20453
references.pmid: 21655270
references.citation: Arch Microbiol. 2000 Sep;174(3):213-6
references.pmid: 11041352
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: FEMS Microbiol Ecol. 2009 Jun;68(3):312-9
references.pmid: 19453494
references.citation: Environ Microbiol. 2013 Sep;15(9):2588-602
references.pmid: 23763330
references.citation: ISME J. 2012 Apr;6(4):847-62
references.pmid: 22071343
references.citation: FEMS Microbiol Ecol. 2011 Mar;75(3):446-56
references.pmid: 21198683
references.citation: Curr Microbiol. 2008 Mar;56(3):214-8
references.pmid: 17990030
references.citation: Microbiology (Reading). 2002 Nov;148(Pt 11):3521-3530
references.pmid: 12427943
references.citation: Appl Environ Microbiol. 2001 Jul;67(7):3041-5
references.pmid: 11425719
references.citation: Syst Appl Microbiol. 2003 Jun;26(2):312-8
references.pmid: 12866859
references.citation: J Microbiol Methods. 2007 Apr;69(1):161-73
references.pmid: 17289189
references.citation: FEMS Microbiol Ecol. 2014 Apr;88(1):195-212
references.pmid: 24410836