title: Seasonal change in vertical distribution of ammonia-oxidizing archaea and bacteria and their nitrification in temperate forest soil.
abstract: Seasonal change in the vertical distribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in temperate forest soil was examined from March 2008 to January 2009 by quantitative PCR of the amoA genes. Abundances of AOA amoA genes (ranging from 2.0×10(8) to 1.2×10(9) copies per gram dry soil) were significantly higher than those of AOB amoA genes (1.9×10(5) to 1.7×10(7) copies). A significant increase in AOB was observed at a depth of 0-5 cm in July when net nitrification was also high in the top soil, while AOA increased significantly at depths of 5-10 cm, 10-15 cm, and over 15 cm in July. Sequencing of the crenarchaeotal amoA gene revealed shifts in major AOA components along the soil depth profile and among sampling dates. Betaproteobacterial amoA clone libraries at 0-5 cm in March, May, and July were dominated by Nitrosospira clusters 1 and 4. A microcosm experiment at 0-5 cm in July revealed a decrease in the ratio of AOA/AOB amoA genes in microcosms. These results suggest that AOB play an important role in net nitrification in the top layer in temperate forest soil.
authors.affiliation: Graduate School of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Onodera
authors.forename: Tatsunori
authors.initials: T
authors.lastname: Nakagawa
authors.forename: Reiji
authors.initials: R
authors.lastname: Takahashi
authors.forename: Tatsuaki
authors.initials: T
authors.lastname: Tokuyama
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D044822:Biodiversity; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D008969:Molecular Sequence Data; D058465:Nitrification; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012621:Seasons; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012988:Soil Microbiology; D014197:Trees
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D000641:Ammonia