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.
Figure 1 Data
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).
Figure1Data.csv
Figure 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.csv
Figure 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.csv
Figure 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.csv
Figure 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.csv
Figure 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.csv
Plasmid Dynamics (parameter estimation)
R code used to analyse the data presented, and selected output.
PlasmidDynamics_Parameters.R
Plasmid Dynamics (analysis)
R code used to analyse the data presented, and selected output.
PlasmidDynamics_Stats.R
summarySE
summarySE R function used to analyse data. Reproduced from http://www.cookbookr.com/Manipulating_data/Summarizing_data/
Figure 3 Data
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).
Figure3Data.csv
Halletal.SInb1
Mathematica Worksheet 1
Halletal.SInb2
Mathematica Worksheet 2
mmc3.R
mmc3.R function used to analyse data. Reproduced from Bolker et al. Trends in Ecology & Evolution 24, 127–135 (2009).
modelCode9
MATLAB code for numeric model
twoSpecies9
MATLAB code for numeric model