Sample Detail

TitleShoot associated microbial community in rice cultivar ‘Nipponbare’ (Oryza sativa L. japonica-type)
Description1. Raising seedling Seeds (Oryza sativa L. japonica-type 'Nipponbare') were placed on two layers of filter paper (Toyo Roshi Kaisha, Ltd, Tokyo, Japan) in a Petri dish (6-cm diameter) containing 4 mL tap water. The Petri dishes were placed in an incubator at 30 °C. After two days (30 April 2008), the germinated seeds were sown in a commercial soil (Mitsui-Toatsu No. 3, Tokyo, Japan) in a 60 × 30 cm cell tray (cell diameter, 1.5 cm; depth, 3 cm) and grown in a greenhouse under natural light conditions for four weeks. Total seedlings of each cultivar were planted in an experimental field on 29 May 2008. Hills were spaced 30 cm apart. 2. Fertilization Basal fertilizer (P2O5, K2O, and N) was applied to the paddy fields four days before transplanting. N, P2O5 and K2O (Temairazu 666, Co-op Chemical Co.,Ltd., Tokyo, Japan) were fertilized at 30, 30 and 30 kg ha-1, respectively in the paddy field. 3. Agricultural chemical application 5 L ha-1 of chemical herbicide (KusatoryⓇ DX Flowable L, Mitsui Chemicals Agro, Inc., Tokyo, Japan) with emulsion formulation was used at late May, 2008. 5 Kg ha-1 of bactericide (OryzemateⓇ, Meiji Seika Kaisha, Ltd., Tokyo, Japan) with granular formulation was used to tolerant to rice blast at Mid-June, 2008. 3 L ha-1 of insecticide (Nagekomi Trebon, Kumiai Chemical Industry Co., Ltd., Tokyo, Japan) with emulsion formulation was used at late June, 2008. 1 L ha-1 of insecticide (Starkle mate™, Mitsui Chemicals Agro, Inc., Tokyo, Japan) with liquid formulation was used at Mid-August, 2008. 4. Sampling The cut into soil around a rice plant was put in all sides 30cm with depth about 30 cm from soil surface on 4 August 2008. The plant was turned up and washed with irrigation. The plant was washed with tap water until the dust disappears from root in laboratory. 5. Soil metadata The paddy field has been continuously managed for wetland rice production since 1940 as an experimental field in Tohoku University. Soil type is classified as Gray Lowland Soil (Classification of cultivated soils in Japan, 3ed approximation) with water table depth 97 cm, which is located on alluvial plain (Sendai plain) as geomorphic position. The characteristics of the field soils used in the present study are shown in Table. On December 5, 2003, Soil pedon have been sampled from this field and described in details as follows: Location: 134-2, Uchinoura, Hironaga, Kashimadai, Osaki, Miyagi, 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 Water Table Depth: 97 cm Drainage: Poorly drained Land Use: Paddy rice field Parent material: Unconsolidated alluvium Vegetation: Paddy field after harvest Described by : M. Nanzyo Date: December 5, 2003 Apg 0 to 10 cm: grayish yellow brown (10YR4/2) moist, clay loam; few faint medium brown (10YR4/6) Fe masses, massive; friable, sticky, plastic; many very fine and common fine roots; clear smooth boundary; positive dipyridyl reaction (++). Bg 10 to 18 cm: 70% dark olive gray (2.5GY4/1) and 30 % brown (7.5YR4/6) moist, clay; many fine distinct Fe masses; massive; friable, sticky, plastic; many very fine and common fine roots; common very fine tubular pores; abrupt smooth boundary; dipyridyl reaction (). Cg 18 to 26 cm: 90% gray yellowish brown (10YR5/2) and 10% brown (7.5YR4/6) moist, clay; common fine to medium Fe masses, massive; friable, sticky, very plastic; common very fine roots; common very fine tubular pores; abrupt smooth boundary; negative dipyridyl reaction. Ag 26 to 41 cm: 50% gray yellowish brown (10YR4/1) and 30% brownish black (10YR3/1) and 20% brown (7.5YR4/6) moist, clay; massive; friable, sticky, very plastic; few very fine roots; common very fine tubular pores; clear smooth boundary; negative dipyridyl reaction. Cg2 41 to 65 cm: 90% grayish yellow brown (7.5YR6/2) and 10% yellowish brown (10YR5/6) moist, clay; common medium to coarse prominent Fe masses, massive; friable, sticky, very plastic; few very fine roots; common very fine tubular pores and few medium tubular pores; abrupt; abrupt smooth boundary; negative dipyridyl reaction. Cg3 65 to 78 cm: greenish gray (7.5GY5/1) moist, sandy loam; few medium prominent dark reddish brown (5YR3/6) Fe masses, massive; friable, slightly sticky, non plastic; no roots; few fine tubular pores; clear smooth boundary; positive dipyridyl reaction (+++). Cg4 78 to 86 cm: dark olive gray (5GYR4/1) moist, fine loamy sand; massive; friable, slightly sticky, non plastic; no roots; few fine tubular pores; clear smooth boundary; positive dipyridyl reaction (+++). Cg5 86 to 100+ cm: greenish gray (7.5GR5/1) wet, sandy loamy; massive; friable, slightly sticky, non plastic; no roots; few fine tubular pores; positive dipyridyl reaction (+++).

Organism Info

Taxon ID1006967
Common Name
Scientific Nameshoot metagenome
Anonymized Name
Individual Name