DOI: 10.5061/dryad.488dk
title: Data from: Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

description: Horizontal gene transfer is a fundamental process in bacterial evolution
 that can accelerate adaptation via the sharing of genes between lineages.
 Conjugative plasmids are the principal genetic elements mediating the
 horizontal transfer of genes, both within and between bacterial species.
 In some species, plasmids are unstable and likely to be lost through
 purifying selection, but when alternative hosts are available,
 interspecific plasmid transfer could counteract this and maintain access
 to plasmid-borne genes. To investigate the evolutionary importance of
 alternative hosts to plasmid population dynamics in an ecologically
 relevant environment, we established simple soil microcosm communities
 comprising two species of common soil bacteria, Pseudomonas fluorescens
 and Pseudomonas putida, and a mercury resistance (HgR) plasmid, pQBR57,
 both with and without positive selection [i.e., addition of Hg(II)]. In
 single-species populations, plasmid stability varied between species:
 although pQBR57 survived both with and without positive selection in P.
 fluorescens, it was lost or replaced by nontransferable HgR captured to
 the chromosome in P. putida. A simple mathematical model suggests these
 differences were likely due to pQBR57’s lower intraspecific conjugation
 rate in P. putida. By contrast, in two-species communities, both models
 and experiments show that interspecific conjugation from P. fluorescens
 allowed pQBR57 to persist in P. putida via source–sink transfer dynamics.
 Moreover, the replacement of pQBR57 by nontransferable chromosomal HgR in
 P. putida was slowed in coculture. Interspecific transfer allows plasmid
 survival in host species unable to sustain the plasmid in monoculture,
 promoting community-wide access to the plasmid-borne accessory gene pool
 and thus potentiating future evolvability.
description: Figure 1
 DataComma-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).Figure1Data.csvFigure 1 Data (endpoint)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.Figure1DataEndpoint.csvFigure 2 Data (alpha and K estimation)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).Figure2DataAlphaK.csvFigure 2 Data (beta estimation)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).Figure2DataBeta.csvFigure 2 Data (gamma estimation)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).Figure2DataGamma.csvFigure 3 Data (endpoint)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.Figure3DataEndpoint.csvPlasmid Dynamics (parameter estimation)R code used to analyse the data presented, and selected output.PlasmidDynamics_Parameters.RPlasmid Dynamics (analysis)R code used to analyse the data presented, and selected output.PlasmidDynamics_Stats.RsummarySEsummarySE R function used to analyse data. Reproduced from http://www.cookbookr.com/Manipulating_data/Summarizing_data/Figure 3 DataComma 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).Figure3Data.csvHalletal.SInb1Mathematica Worksheet 1Halletal.SInb2Mathematica Worksheet 2mmc3.Rmmc3.R function used to analyse data. Reproduced from Bolker et al. Trends in Ecology & Evolution 24, 127–135 (2009).modelCode9MATLAB code for numeric modeltwoSpecies9MATLAB code for numeric model