This dataset identified bacteria able to grow in the presence of several Antibiotics in a British agricultural soil, by DNA stable isotope probing (SIP). The dataset was created with samples of the 'heavy' and 'light' fractions of the treatments and also from control soils. The 16S rRNA genes from these samples were amplified and sequenced by barcoded Illumina sequencing. Polymerase chain reaction (PCR) primers 515FB (GTGYCAGCMGCCGCGGTAA) and 806RB (GGACTACNVGGGTWTCTAAT) from the Earth Microbiome project targeting the V4 region of the 16S rRNA gene (approximately 250 nucleotides) were used. Library preparation and sequencing was performed at the National Oceanographic Centre (NOC) of the University of Southampton, UK, following methodologies described by Caporaso et al. (2012). Samples were pooled in an equimolar concentration and sequenced on separate runs for MiSeq using a 2 bp x 300 bp paired end protocol.
Publication date: 2018-01-05
The first step was quality filtering of the sequences using the tool cutadapt (Martin, 2011). Forward and reverse reads were merged by using the usearch fastq_mergepairs command (Edgar, 2013). Downstream processing was performed by using UPARSE (Edgar, 2013) and UCHIME pipelines (Edgar et al., 2011). Briefly, sequences shorter than 250 bp were discarded, singletons were retained, and operational taxonomic units (OTUs) were defined at a sequence identity level of 97%.