title: Effect of soil type and fertilizer management on archaeal community in upland field soils.
abstract: The effects of soil and fertilizer types on archaeal communities were evaluated by real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S rRNA gene of total DNA directly extracted from upland field soils. Twelve experimental upland field plots containing four different soil types, i.e., Cumulic Andosol, Low-humic Andosol, Yellow Soil and Gray Lowland Soil, were maintained under three different fertilizer management systems for 8 years (chemical fertilizer, rice husks and cow manure, and pig manure, respectively). Two-way ANOVA and RDA analyses showed that the copy number and PCR-DGGE profile of archaeal 16S rRNA gene were affected mainly by soil type, especially between Andosol and non-Andosol, but were also influenced by fertilizer type. Among several soil chemical properties, total N content showed a significant correlation to archaeal community. Sequence analyses showed that most of the major DGGE bands corresponded to uncultured Crenarchaeota of Group I.1b that contained ammonia-oxidizing archaea (AOA). These sequences were separated into two clusters in the phylogenetic tree and each lineage showed a different response to total N content.
authors.affiliation: National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki, Japan. yuko422@affrc.go.jp
authors.forename: Yuko Takada
authors.initials: YT
authors.lastname: Hoshino
authors.forename: Sho
authors.initials: S
authors.lastname: Morimoto
authors.forename: Masahito
authors.initials: M
authors.lastname: Hayatsu
authors.forename: Kazunari
authors.initials: K
authors.lastname: Nagaoka
authors.forename: Chika
authors.initials: C
authors.lastname: Suzuki
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Karasawa
authors.forename: Makoto
authors.initials: M
authors.lastname: Takenaka
authors.forename: Hiroko
authors.initials: H
authors.lastname: Akiyama
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D058448:Biota; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D005308:Fertilizers / Q000706:statistics & numerical data*; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000032:analysis; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012418:Ruminants; D017422:Sequence Analysis, DNA; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D013552:Swine
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D005308:Fertilizers; D012336:RNA, Ribosomal, 16S; D012987:Soil; D009584:Nitrogen