Data from: Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

Hall J, Wood AJ, Harrison E, Brockhurst M

Date Published: July 7, 2016

DOI: http://dx.doi.org/10.5061/dryad.488dk

 

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Title Figure 1 Data
Downloaded 11 times
Description Comma-separated values formatted file containing data presented in Figure 1 of the manuscript. rep = replicate, tra = transfer number, spc = species (‘pf’ = Pseudomonas fluorescens SBW25, ‘pp’ = Pseudomonas putida KT2440), mrk = species markers, mer = mercury concentration (µg/g), cul = culture type (‘ss’ = single-species, ‘co’ = co-culture), type = PCR genotype (‘p+ t+’ = plasmid and transposon, ‘p- t+’ = transposon without plasmid, ‘p- t-‘ = neither plasmid nor transposon), num.cols = number of positive colonies, tot.cols = total number of colonies tested, type.dens = calculated density (cfu/g), tot.dens = calculated total density (cfu/g).
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Title Figure 1 Data (endpoint)
Downloaded 11 times
Description Comma separated values formatted file containing data presented in Figure 1 of the manuscript. This table includes data obtained from spreading samples on KB agar containing mercury. spc = species (as above), cul = culture type (as above), mer = mercury concentration (as above), plasmid_survived = number of populations with plasmid-positive clones at transfer 65, plasmid_extinct = number of populations without plasmid-positive clones at transfer 65.
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Title Figure 2 Data (alpha and K estimation)
Downloaded 6 times
Description Comma separated values formatted file containing data used to estimate alpha1, alpha2, K1 and K2 (used to produce Figure 3 and SI Figures 1, 2 and 3). Columns as Figure1Data.csv, except time = time of sampling (h).
Download Figure2DataAlphaK.csv (1.289 Kb)
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Title Figure 2 Data (beta estimation)
Downloaded 4 times
Description Comma separated values formatted file containing data used to estimate beta1 and beta2 (used to produce Figure 3 and SI Figures 1, 2 and 3). Columns as Figure1Data.csv, except mrk = marker of plasmid-bearing strain, start.gm.dens = starting density of Gm-labelled strain (cfu/g), start.sm.dens = starting density of Sm-labelled strain (cfu/g), end.gm.dens = final density of Gm-labelled strain (cfu/g), end.sm.dens = final density of Sm-labelled strain (cfu/g), fitness.w.gm = relative fitness W of Gm-labelled strain (calculated as described in SI Text).
Download Figure2DataBeta.csv (2.772 Kb)
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Title Figure 2 Data (gamma estimation)
Downloaded 5 times
Description Comma separated values formatted file containing data used to estimate gamma11, gamma12, gamma21 and gamma22. Columns as Figure1Data.csv, except donor = donor species ('pf' or 'pp', codes as Figure1Data.csv), recipient = recipient species, type = description of conjugation experiment ('donor - recipient'), donor_marker = marker of plasmid donor, rate = log10 transformation of calculated conjugation rate gamma (Simonsen et al. (1990), J. Gen Microbiol 136:2319-2325).
Download Figure2DataGamma.csv (781 bytes)
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Title Figure 3 Data (endpoint)
Downloaded 4 times
Description Comma separated values formatted file containing data presented in Figure 3 of the manuscript. This table includes data obtained from spreading samples on KB agar containing mercury. As Figure3Data.csv except selection = selective agents in KB agar, spread = volume spread on plate (µl), dilution = log[10] dilution of sample spread on plate, count = number of colonies, total = calculated density.
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Title Plasmid Dynamics (parameter estimation)
Downloaded 8 times
Description R code used to analyse the data presented, and selected output.
Download PlasmidDynamics_Parameters.R (18.05 Kb)
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Title Plasmid Dynamics (analysis)
Downloaded 32 times
Description R code used to analyse the data presented, and selected output.
Download PlasmidDynamics_Stats.R (42.00 Kb)
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Title summarySE
Downloaded 13 times
Description summarySE R function used to analyse data. Reproduced from http://www.cookbookr.com/Manipulating_data/Summarizing_data/
Download summarySE.r (830 bytes)
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Title Figure 3 Data
Downloaded 4 times
Description Comma separated values formatted file containing data presented in Figure 3 of the manuscript. Columns as Figure1Data.csv, except src.mrk = marker of source species, trt = treatment (source.sink), hgr = calculated density of mercury resistant cfu/g from replica plating colonies onto 100 µM Hg(II), tot = total density (cfu/g), src.snk = source or sink (src = source, snk = sink).
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Title Halletal.SInb1
Downloaded 4 times
Description Mathematica Worksheet 1
Download Halletal.SInb1.nb (95.02 Kb)
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Title Halletal.SInb2
Downloaded 5 times
Description Mathematica Worksheet 2
Download Halletal.SInb2.nb (19.30 Kb)
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Title mmc3.R
Downloaded 4 times
Description mmc3.R function used to analyse data. Reproduced from Bolker et al. Trends in Ecology & Evolution 24, 127–135 (2009).
Download mmc3.R (3.435 Kb)
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Title modelCode9
Downloaded 4 times
Description MATLAB code for numeric model
Download modelCode9.m (3.174 Kb)
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Title twoSpecies9
Downloaded 11 times
Description MATLAB code for numeric model
Download twoSpecies9.m (889 bytes)
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When using this data, please cite the original publication:

Hall JPJ, Wood AJ, Harrison E, Brockhurst MA (2016) Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 113(29): 8260–8265. http://dx.doi.org/10.1073/pnas.1600974113

Additionally, please cite the Dryad data package:

Hall J, Wood AJ, Harrison E, Brockhurst M (2016) Data from: Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.488dk
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