Identification

Title

Multi-drug resistant bacteria in agricultural soil

Abstract

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.

Resource type

dataset

Resource locator

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA428598

name: Access the data

description: Dataset is held by NCBI-SRA.

function: information

Unique resource identifier

code

https://catalogue.ceh.ac.uk/id/595bca1f-9299-45d0-a224-a28ed136ea91

codeSpace

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

1-H: gradient 1 - DNA-fresh soil-1H, 18H2O, Antibiotics, day-2, heavy fraction

2-H: gradient 2 - DNA-fresh soil-2H, 18H2O, Antibiotics, day-2, heavy fraction

3-H: gradient 3 - DNA-fresh soil-3H, 18H2O, Antibiotics, day-2, heavy fraction

1-L: gradient 1 - DNA-fresh soil-1L, 18H2O, Antibiotics, day-2, light fraction

2-L: gradient 2 - DNA-fresh soil-2L, 18H2O, Antibiotics, day-2, light 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

5-H: gradient 5 - DNA-fresh soil-5H, H2O, Antibiotics, day-4, heavy fraction

6-H: gradient 6 - DNA-fresh soil-6H, H2O, Antibiotics, day-4, heavy fraction

4-L: gradient 4 - DNA-fresh soil-4L, H2O, Antibiotics, day-4, light fraction

5-L: gradient 5 - DNA-fresh soil-5L, H2O, Antibiotics, day-4, light 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

8-H: gradient 8 - DNA-fresh soil-8H, H2O, Control, day-4, heavy fraction

9-H: gradient 9 - DNA-fresh soil-9H, H2O, Control, day-4, heavy fraction

7-L: gradient 7 - DNA-fresh soil-7L, H2O, Control, day-4, light fraction

8-L: gradient 8 - DNA-fresh soil-8L, H2O, Control, day-4, light fraction

9-L: gradient 9 - DNA-fresh soil-9L, H2O, Control, day-4, light fraction

10-H: gradient 10 - DNA-fresh soil-10H, 18H2O, Antibiotics, day-4, heavy fraction

11-H: gradient 11 - DNA-fresh soil-11H, 18H2O, Antibiotics, day-4, heavy fraction

12-H: gradient 12 - DNA-fresh soil-12H, 18H2O, Antibiotics, day-4, heavy fraction

10-L: gradient 10 - DNA-fresh soil-10L, 18H2O, Antibiotics, day-4, light fraction

11-L: gradient 11 - DNA-fresh soil-11L, 18H2O, Antibiotics, day-4, light 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

14-H: gradient 14 - DNA-fresh soil-14H, 18H2O, Control, day-4, heavy fraction

15-H: gradient 15 - DNA-fresh soil-15H, 18H2O, Control, day-4, heavy fraction

13-L: gradient 13 - DNA-fresh soil-13L, 18H2O, Control, day-4, light fraction

14-L: gradient 14 - DNA-fresh soil-14L, 18H2O, Control, day-4, light fraction

15-L: gradient 15 - DNA-fresh soil-15L, 18H2O, 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

Geographic location

West bounding longitude

-1.43

East bounding longitude

-1.42

North bounding latitude

50.97

South bounding latitude

50.96

Temporal reference

Temporal extent

Begin position

2016-10-01

End position

2016-10-31

Dataset reference date

date type

publication

effective date

2018-01-05

Frequency of update

notPlanned

Quality and validity

Lineage

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%.

Conformity

Data format

name of format

fastq

version of format

unknown

Constraints related to access and use

Constraint set

Use constraints

No restrictions

Constraint set

Limitations on public access

Responsible organisations

Responsible party

organisation name

University of Southampton

email address

m.t.hernandez-garcia@soton.ac.uk

responsible party role

pointOfContact

Responsible party

organisation name

EIDC

email address

eidc@ceh.ac.uk

responsible party role

mediator

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

email address

eidc@ceh.ac.uk

responsible party role

pointOfContact

Metadata date

2018-09-11T15:06:02

Metadata language

eng