Multi-drug resistant bacteria in agricultural soil

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

Get the data

This record describes NERC-funded data managed by NCBI To access the data visit https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA428598

Where/When

Study area
Temporal extent
2016-10-01    to    2016-10-31

Supplemental information

Other useful information regarding this dataset:

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., … Knight, R. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal, 6(8), 1621–1624.
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10), 996–998.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194–2200.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10.

Provenance & quality

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%.

Correspondence/contact details

Marcela Hernandez
University of Southampton
m.t.hernandez-garcia@soton.ac.uk

Tags

Topic categories
Biota
Keywords
10-H: gradient 10 - DNA-fresh soil-10H, 18H2O, Antibiotics, day-4, heavy fraction,  10-L: gradient 10 - DNA-fresh soil-10L, 18H2O, Antibiotics, day-4, light fraction,  11-H: gradient 11 - DNA-fresh soil-11H, 18H2O, Antibiotics, day-4, heavy fraction,  11-L: gradient 11 - DNA-fresh soil-11L, 18H2O, Antibiotics, day-4, light fraction,  12-H: gradient 12 - DNA-fresh soil-12H, 18H2O, Antibiotics, day-4, heavy fraction,  12-L: gradient 12 - DNA-fresh soil-12L, 18H2O, Antibiotics, day-4, light fraction,  13-H: gradient 13 - DNA-fresh soil-13H, 18H2O, Control, day-4, heavy fraction,  13-L: gradient 13 - DNA-fresh soil-13L, 18H2O, Control, day-4, light fraction,  14-H: gradient 14 - DNA-fresh soil-14H, 18H2O, Control, day-4, heavy fraction,  14-L: gradient 14 - DNA-fresh soil-14L, 18H2O, Control, day-4, light fraction,  15-H: gradient 15 - DNA-fresh soil-15H, 18H2O, Control, day-4, heavy fraction,  15-L: gradient 15 - DNA-fresh soil-15L, 18H2O, Control, day-4, light fraction,  1-H: gradient 1 - DNA-fresh soil-1H, 18H2O, Antibiotics, day-2, heavy fraction,  1-L: gradient 1 - DNA-fresh soil-1L, 18H2O, Antibiotics, day-2, light fraction,  2-H: gradient 2 - DNA-fresh soil-2H, 18H2O, Antibiotics, day-2, heavy fraction,  2-L: gradient 2 - DNA-fresh soil-2L, 18H2O, Antibiotics, day-2, light fraction,  3-H: gradient 3 - DNA-fresh soil-3H, 18H2O, Antibiotics, day-2, heavy fraction,  3-L: gradient 3 - DNA-fresh soil-3L, 18H2O, Antibiotics, day-2, light fraction,  4-H: gradient 4 - DNA-fresh soil-4H, H2O, Antibiotics, day-4, heavy fraction,  4-L: gradient 4 - DNA-fresh soil-4L, H2O, Antibiotics, day-4, light fraction,  5-H: gradient 5 - DNA-fresh soil-5H, H2O, Antibiotics, day-4, heavy fraction,  5-L: gradient 5 - DNA-fresh soil-5L, H2O, Antibiotics, day-4, light fraction,  6-H: gradient 6 - DNA-fresh soil-6H, H2O, Antibiotics, day-4, heavy fraction,  6-L: gradient 6 - DNA-fresh soil-6L, H2O, Antibiotics, day-4, light fraction,  7-H: gradient 7 - DNA-fresh soil-7H, H2O, Control, day-4, heavy fraction,  7-L: gradient 7 - DNA-fresh soil-7L, H2O, Control, day-4, light fraction,  8-H: gradient 8 - DNA-fresh soil-8H, H2O, Control, day-4, heavy fraction,  8-L: gradient 8 - DNA-fresh soil-8L, H2O, Control, day-4, light fraction,  9-H: gradient 9 - DNA-fresh soil-9H, H2O, Control, day-4, heavy fraction,  9-L: gradient 9 - DNA-fresh soil-9L, H2O, Control, day-4, light fraction,  O-1: DNA-fresh soil-O1 - Original soil,  O-2: DNA-fresh soil-O2 - Original soil,  O-3: DNA-fresh soil-O3 - Original soil