BioSample Detail : SAMD00002574


Title16S rRNA gene study of rice-root associated bacteria in paddy fields dressed with low nitrogen.
Taxonomy ID939928
Organism Namerhizosphere metagenome
DescriptionField metadata., Country: Japan, Latitude: 38-27-39.37' N, Longitude: 141-5-33.33' E, Altitude: 4 m a.s.l., Classification: Gray lowland soil (classification of cultivated soils in Japan, 3rd approximation), Geomorphic Position: Alluvial plain, Slope Characteristics: Flat, Precipitation: Udic soil moisture regime, Water Table Depth: 97 cm, Drainage: Poorly drained, Land Use: Paddy rice field, Parent material: Unconsolidated alluvium, Vegetation: Paddy field after harvest

General Info

OrganizationLaboratory of Environmental Plant Microbiology, Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University


Sample typeGeneric


sample commentGeneral description. Rice plants (Oryza sativa L. cultivar gNipponbareh) were cultivated in paddy fields dressed with low N (LN; 0 kg ha-1). The roots (approximately 100 g) were sampled on August 26, 2009 and homogenized without surface sterilization to prepare the root-associated bacterial cells, and the bacterial cells were extracted and purified using a bacterial cell enrichment method. Total DNA was extracted from the cell fraction. We amplified 16S rRNA genes using a primer set 27F, 518R. These PCR primers target the V1 and V3 region.