PRJNA379346
Rice paddy metagenome
Livestock compost amendment in agricultural systems aim at reducing the use of synthetic fertilizers and in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to different livestock compost amendment. In this Bio project we report on the structural response of the soil microbiome to composted cattle and swine manure application in a flooded rice paddy. DNA was extracted from 0.8 g of freshly collected rhizosphere soil using PowerSoil® DNA isolation kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s instructions. The variable region V4 of the 16S rDNA gene was amplified with the primer pair 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) and sequenced using Illumina MiSeq platform as paired-end reads (Caporaso et al., 2011). Raw sequences were processed using the FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) and the QIIME pipeline (Caporaso et al., 2010). The operational taxonomic units (OTUs) were identified based on 97% sequence similarity using UCLUST algorithm (Edgar, 2010) in QIIME. The Greengenes database was used to assign taxonomy to each OUT (DeSantis et al., 2006).