DOI: 10.5061/dryad.dfn2z350c
title: Data from: Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments

description: Understanding the role of horizontal gene transfer (HGT) in adaptation is
 a key challenge in evolutionary biology. In microbes, an important
 mechanism of HGT is prophage acquisition (phage genomes integrated into
 bacterial chromosomes). Prophages can influence bacterial fitness via
 transfer of beneficial genes (including antibiotic-resistance genes,
 ARGs), protection from superinfecting phages, or switching to a lytic
 lifecycle which releases free phages infectious to competitors. We expect
 these effects to depend on environmental conditions because of, for
 example, environment-dependent induction of the lytic lifecycle. However,
 it remains unclear how costs/benefits of prophages vary across
 environments. Here, studying prophages with/without ARGs
 in Escherichia coli, we disentangled effects of prophages alone
 and adaptive genes they carry. In competition with prophage-free strains,
 benefits from prophages and ARGs peaked in different environments.
 Prophages were most beneficial when induction of the lytic lifecycle was
 common, whereas ARGs were more beneficial upon antibiotic exposure and
 with reduced prophage induction. Acquisition of prophage-encoded ARGs by
 competing strains was most common when prophage induction, and therefore
 free phages, were common. Thus, selection on prophages and adaptive genes
 they carry varies independently across environments, which is important
 for predicting the spread of mobile/integrating genetic elements and their
 role in evolution
description: Sata have been collected from experimental work including
 competition assays, growth rate measurements, MIC assays, reduction in
 bacterial growth assays and spot assays
description: The folder contains files needed perform the analysis described
 in “FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND
 PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT
 ENVIRONMENT” by Carolin C Wendling, Dominik Refardt, Alex R Hall
 <br> A brief description of each file is given
 below.<br>
 ===========================================================
 Competition_Data.txt This file contains the
 raw data which was used to calculate the selection rate constant of
 lysogens relative to the YFP-labelled wild-types as well as to infer the
 absolute cel densities for each population per pair-wise competition. The
 column headings are:<br>     <br>     Strain-Which lysogen was
 used during pair-wise competition against the YFP-labelled WT. For a
 detailed description of each lysogen see Table 1 in the main
 manuscript.     Timepoint-Indicates if cell densities
 were measured at the beginning (T0) or after 24 hours of pair-wise
 competition (T24).     Environment-In which of the 8
 environmental conditions strains were competing (A1: IC20, A2: IC30, A3:
 IC50, M: MitomycinC, A1_M: IC20+MitomycinC, A2_M: IC30+MitomycinC, A3_M:
 IC50+MitomycinC, LB: LB-medium).     Replicate-Which
 replicate.     Antibiotic-Which antibiotic was used for
 the experiment (Amp: ampicillin, Kan: kanamycin, Cm:
 chloramphenicol).     Phage_Type-Which phage-type the
 lysogen contained (lambda, HK022, Phi80, mEp234, or no for competition
 between WT and YFP-lablled WT, which was later used to correct for the
 fitness effect of the YFP marker).     ARG-Indicates
 presence or absence of a resistance gene.<br>     <br>   
  WT_YFP-Measurment of absolute cell densities of the YFP-labelled
 WT.     Lysogen-Measurement of absolute cell densities
 of the lysogen. ____________________
 Free_phages.txt This file gives the absolute
 number of free phages in plaque forming units (PFU) per ml. The column
 headings are:     Strain-Which lysogen was used during
 pair-wise competition against the YFP-labelled WT. For a detailed
 description of each lysogen see Table 1 in the main manuscript.
     Antibiotic-Which antibiotic was used for the experiment (Amp:
 Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).   
  Replicate-Which replicate. <br>   
  ARG-Indicates presence or absence of a resistance gene.
     Phage_Type-Which phage-type the lysogen contained (lambda,
 HK022, Phi80, mEp234, or no for  YFP-labelled WT).   
  Environment-In which of the 8 environmental conditions strains were
 competing (A1: IC20, A2: IC30, A3: IC50, M: MitomycinC, A1_M:
 IC20+MitomycinC, A2_M: IC30+MitomycinC, A3_M: IC50+MitomycinC, LB:
 LB-medium).     PFU-Measurement of of free phages in
 (PFU/ml).      <br>
 ______________________________________________
 RBG.txt This file gives the OD readings used
 to calculate reduction in bacterial growth (RBG). The column headings
 are:     Strain-Which lysogen was used during pair-wise
 competition against the YFP-labelled WT. For a detailed description of
 each lysogen see Table 1 in the main manuscript.   
  Replicate-Which replicate.     Phage_Type-Which
 phage-type the lysogen contained (lambda, HK022, Phi80, mEp234, or no for
 YFP-labelled WT).     Resistance-Which resistance gene
 is encoded in the respective prophage.   
  ARG-Indicates presence or absence of a resistance gene.
     Antibiotic-Which antibiotic was used for the experiment (Amp:
 Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).   
  Concentration-Which antibiotic concentration was used (no, low=IC20,
 middle=IC30, high=IC50).     OD_T0-OD reading at 660nm
 for time-point zero.     OD_T24-OD reading at 600nm for
 after 24 hours. <br>
 __________________________________
 GR_Monoculture.txt This file gives the OD
 readings from overnight growth assay used to calculate bacterial growth
 rates. The column headings are:     Strain-Which
 lysogen was used during pair-wise competition against the YFP-labelled WT.
 For a detailed description of each lysogen see Table 1 in the main
 manuscript.     Replicate-Which replicate.
     Antibiotic-Which antibiotic was used for the experiment (Amp:
 Ampicillin, Kan:kanamycin, Cm:Chloramphenicol).   
  ARG-Which resistance gene was encoded on the prophage (A: ampicillin, K:
 kanamycin, C: chloramphenicol, No: no resistance gene).
     Phage_Type-Which phage-type the lysogen contained (lambda,
 HK022, Phi80, mEp234, or no for WT_YFP).   
  Concentration-Which antibiotic concentration (µg/ml) was used in that
 assay     OD_0-reading of optical density (OD) at 660
 nm at timepoint 0.     OD_24-reading of optical density
 (OD) at 660 nm after 24 hours.
 __________________________________
 MitomycinC_Induction.txt This file gives the
 OD readings from the mitomycin C induction growth assay. The column
 headings are:     Strain-Which lysogen was used during
 pair-wise competition against the YFP-labelled WT. For a detailed
 description of each lysogen see Table 1 in the main manuscript.
     Replicate-Which replicate.     ARG-Which
 resistance gene was encoded on the prophage (Amp: ampicillin, Kan:
 kanamycin, Cm: chloramphenicol, No: no resistance gene).
     Phage_Type-Which phage-type the lysogen contained (lambda,
 HK022, Phi80, mEp234, or no for WT_YFP).   
  Timepoint-at which timepoint the measurement was taken.
     OD-reading of optical density (OD) at 660nm.
 ___________________________________
 MIC_Assay.txt This file gives the OD readings
 from the MIC assay. The column headings are:   
  Strain-Which lysogen was used during pair-wise competition against the
 YFP-labelled WT. For a detailed description of each lysogen see Table 1 in
 the main manuscript.     Replicate-Which
 replicate.     ARG-Which resistance gene was encoded on
 the prophage (Amp: ampicillin, Kan: kanamycin, Cm: chloramphenicol, No: no
 resistance gene).     Phage_Type-Which phage-type the
 lysogen contained (lambda, HK022, Phi80, mEp234, or no for
 WT_YFP).     Timepoint-at which timepoint the
 measurement was taken.     OD-reading of optical
 density (OD) at 660nm. <br>
 ___________________________________
 WT_Lysogen_Fitness.txt This file contains the
 raw data which was used to calculate the selection rate constant of
 WT-lysogens relative to the one of three ancestral strains.The column
 headings are:<br>          Strain-Which
 WT-lysogen was used during pair-wise competition against one of the three
 ancestors.     Antibiotic-Which antibiotic was used for
 the experiment (Amp: ampicillin, Kan: kanamycin, Cm:
 chloramphenicol).      Phage_Type-Which phage-type the
 lysogen contained (lambda, HK022, Phi80, mEp234, or no for competition
 between WT and YFP-lablled WT, which was later used to correct for the
 fitness effect of the YFP marker).     ARG-Which
 resistance gene was present in the WT-lysogen (Amp: ampicillin, Kan:
 Kanamycin, Cm: Chloramphenicol).     Competitor-Which
 competitor the WT-lysogen was competing with (WT: phage-free,
 antibiotic-susceptible WT, P: Lysogen, witouht ARG, P_ARG: lysogen with
 ARG)     Replicate-Which replicate.
     Environment-In which of the 2 environmental conditions
 strains were competing (A3: IC20, LB: LB-medium).   
  Timepoint-Indicates if cell densities were measured at the beginning (T0)
 or after 24 hours of pair-wise competition (T24).<br>     <br>
     WT_lysogen-Measurment of absolute cell densities of the
 WT-lysogen.     Competitor-Measurement of absolute cell
 densities of one of the three different competitors.
 <br>
 =================================================<br>