BioSample Detail : SAMD00002566

Description

Title16S rRNA gene study of rice-root associated bacteria in paddy fields dressed with standard nitrogen.
Taxonomy ID939928
Organism Namerhizosphere metagenome
DescriptionSoil metagenome., Soil was also sampled on August 26, 2009 from each fields. We extracted soil DNA and amplified 16S rRNA genes using a primer set 27F, 518R. These PCR primers target the V1 and V3 region. Field 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

Model

Sample typeGeneric

Attributes

sample_nameDRS000529
sample commentGeneral description. Rice plants (Oryza sativa L. cultivar "Nipponbare") were cultivated in paddy fields dressed with standard N (SN; 30 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.