Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria
Data files
Dec 22, 2023 version files 919.67 KB
-
Fitness_assay_dataset_for_orfamide_exposure_(Figure_5B-C).csv
5.10 KB
-
Fitness_assay_dataset_of_pyoluteorin_exposure_(Figure_5D).csv
4.35 KB
-
Fitness_assay_reduction_dataset_for_DAPG_exposure_(Figure_5A_analysis).csv
223.09 KB
-
Fitness_assay_reduction_dataset_of_orfamides_(Figure_5B-C_analysis).csv
3.66 KB
-
Fitness_assay_reduction_dataset_of_pyoluteorin_(Figure_5D_analysis).csv
4.21 KB
-
Fitness_assays_dataset_(Figure_2).csv
87.67 KB
-
Fitness_assays_reduction_dataset_by_Pseudomonas_strain_(Figure_4_analysis).csv
116.93 KB
-
Fitness_assays_reduction_dataset_by_Ralstonia_strain_(Figure_2_and_3_analysis).csv
107.45 KB
-
README.md
6.96 KB
-
Selection_experiment_dataset_(Figure_1).csv
125.67 KB
-
Selection_experiment_dataset_as_reductions_(Figure1_analysis).csv
234.57 KB
Abstract
Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strain and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.
README: Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria
https://doi.org/10.5061/dryad.1g1jwsv3g
All the data produced by the experiments.
Description of the data and file structure
README file
Author names: S.E. Clough (1,2), J.G. Elphinstone (3) and V-P. Friman (1,4)
(1) University of York (Dept. of Biology, Wentworth Way, University of York, York, YO10 5DD, U.K)
(2) Durham University (Dept. of Chemistry and Dept. of Biosciences, South Road, Durham University, Durham, DH1 3LE, U.K)
(3) Fera Science Ltd (National Agri-Food Innovation Campus, Sand Hutton, York, U.K)
(4) University of Helsinki (Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland)
Title of study: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria
Summary of study: Here, we used an in vitro experimental evolution approach to investigate the capability of phytopathogenic bacterium Ralstonia solanacearum, which is the causative agent of bacterial wilt, to evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We first conducted a selection experiment followed by fitness assays in bacterial supernatant as well as in synthetic Pseudomonas metabolites. Most of the data is based on changes in bacterial densities, which was measured as optical density (OD) using spectrophotometer (600 nm wavelength).
S.E. Clough is responsible for collecting data.
Overview of files:
1) Selection experiment dataset (Figure 1).csv
Dataset used to produce Figure 1 with OD values – each row represents which Ralstonia culture (7 strains) was inoculated into which Pseudomonas supernatant (8 strains) and at which supernatant concentration (50% or 80%). What date that OD value was recorded (0-21 days), growth is displayed as the raw OD value and normalised OD value (these were normalised by subtracted the OD of LB broth alone).
2) Selection experiment dataset as reductions (Figure1 analysis.csv
Dataset used for Figure 1 analysis with OD data converted into growth reduction shown as a percentage - each row represents which Ralstonia culture (7 strains) was inoculated into which Pseudomonas supernatant (8 strains) and at which supernatant concentration (50% or 80%). What date that OD value was recorded (24-504 hours), the raw OD value and normalised OD value (these were normalised by subtracting the OD of LB broth alone). The additional column ‘OD of control’ is the average OD for the control sample at that timepoint. ‘OD reduction’ is the ‘OD of control’ column subtracted from the ‘Normalised OD’ column which is then converted to ‘Reduction %’.
3) Fitness assays dataset (Figure 2).csv
Dataset for initial analysis of Figure 2 of the growth data (OD values) - each row represents which Ralstonia culture (7 strains) was inoculated into which Pseudomonas supernatant (8 strains), the evolutionary origin of the Ralstonia sample (Ancestral, Evolved, Control) and which condition they were grown in during the fitness assay (LB broth ‘LB’ or Pseudomonas supernatant ‘SN’). What date that OD value was recorded (24 or 72h), the raw OD value and normalised OD value (these were normalised by subtracted the OD of LB broth alone).
4) Fitness assays reduction dataset by Ralstonia strain (Figure 2 and 3 analysis).csv
Dataset used to produce Figure 2 and 3 as well as the analysis with OD data converted into growth reduction shown as a percentage – each row represents the growth reduction of each Ralstonia culture (7 strains), the evolutionary origin of the Ralstonia sample (Ancestral, Evolved, Control), what date that OD value was recorded (24 or 72h), ‘Reduction OD’ was calculated like previously described and converted to ‘Reduction %’. The column ‘Supernatant concentration in comparisons’ identifies the different high and low supernatant environment comparisons (e.g. 50LB = 50% LB broth and 100LB = 100% LB broth, 50SN = 50% supernatant, 80SN = 80% supernatant).
5) Fitness assays reduction dataset by Pseudomonas strain (Figure 4 analysis).csv
Dataset used to produce Figure 4 as well as the analysis with OD data converted into growth reduction shown as a percentage – this is the same as the ‘fitness assays reduction dataset by Ralstonia strain (Figure 2 and 3 analysis).csv’ above except it is averaged over the Ralstonia strains to focus on Pseudomonas identity effects.
6) Fitness assay reduction dataset for DAPG exposure (Figure 5A analysis).csv
Dataset used to produce Figure 5A with normalised OD data and OD data converted into growth reduction shown as a percentage - each row represents the growth reduction of each Ralstonia culture (7 strains), the evolutionary origin of the Ralstonia sample (Ancestral, Evolved, Control), what date that OD value was recorded (24 or 72h), ‘OD Reduction’ was calculated like previously described and converted to ‘Reduction %’ and at what concetration of DAPG (50-1000uM).
7) Fitness assay dataset for orfamide exposure (Figure 5B-C).csv
Dataset used to analyse Figure 5B-C with OD values- Dataset for initial analysis of Figure 2 of the growth data (OD values) - each row represents which Ralstonia culture (strain #1) was inoculated into which Pseudomonas supernatant during the selection experiment (2 strains), the evolutionary origin of the Ralstonia sample (Ancestral, Evolved, Control) and which metabolite they were exposed to during the fitness assay (orfamide A ‘OrfA’ or orfamide B ‘OrfB’).
8) Fitness assay reduction dataset of orfamides (Figure 5B-C analysis).csv
Dataset used to produce Figure 5B-C with OD values converted into growth reduction shown as a percentage.
9) Fitness assay dataset of pyoluteorin exposure (Figure 5D).csv
Dataset used to analyse Figure 5D with OD values - Dataset used to analyse Figure 5B-C with OD values- Dataset for initial analysis of Figure 2 of the growth data (OD values) - each row represents which Ralstonia culture (strain #1 or strain #7) was inoculated into which Pseudomonas supernatant during the selection experiment (2 strains), the evolutionary origin of the Ralstonia sample (Ancestral, Evolved, Control) grown in one concentration of pyoluteorin.
10) Fitness assay reduction dataset of pyoluteorin (Figure 5D analysis).csv
Dataset used to produce Figure 5D with OD values converted into growth reduction shown as a percentage.
All statistical analyses and graphs were produced using R (R Foundation for Statistical Computing, R Studio Version.3.4.4. Packages included: ggplot (v3.4.3), dplyr (v1.1.2), magrittr (v2.0.3), multcomp (1.4-25), plyr (v1.8.8), RColorBrewer (v1.1-3), readr (v2.1.2), reshape2 (v1.4.4) and tidyr (v1.3.0). Colour blind friendly palettes were used in all figures (viridis, magma, plasma and inferno).