Data from: Bacteria-phage coevolution drives variation in bacterial wilt disease incidence via resistance-virulence trade-offs
Data files
Apr 30, 2026 version files 4.75 MB
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README.md
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Source_data-0410.xlsx
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Abstract
Bacteria-phage coevolution often results in correlated fitness effects on partner species. Whether coevolutionary changes impact the ecology of the surrounding communities is unclear. Here, we link coevolution between the phytopathogenic bacterium, Ralstonia pseudosolanacearum, and its phage parasites to bacterial wilt disease patterns across four geographically disconnected tomato fields. We find that bacteria and phages are locally adapted between and within fields. Phage infectivity was highest on sympatric bacteria, and bacteria showed greater phage resistance when isolated from healthy than diseased plants. The modularity of phage-bacteria coevolution was associated with field-specific anti-phage defense system patterns and locally adapted phage populations. Moreover, phages selected for field-specific mutations in different phage receptor genes, which were negatively associated with virulence measured in planta, suggesting why phage-resistant but weakly virulent pathogen isolates are associated with healthy tomato plants within fields. Our findings demonstrate that bacteria-phage coevolution results in patchy plant disease distribution through phage resistance-virulence trade-offs.
Dataset DOI: 10.5061/dryad.3j9kd520g
Description of the data and file structure
Rhizosphere Microbiomes, Genomic Variation, and Experimental Evolution of Phage Resistance in Ralstonia pseudosolanacearum across Tomato Fields in China.
Field Microbiome & Physicochemical Analysis: Taxonomic profiling (16S rRNA) and metaviromic sequencing of 48 rhizosphere soil samples collected from healthy and diseased tomato plants across four Chinese provinces (Nanjing, Ningbo, Nanchang, and Nanning). This includes soil chemical properties (pH, C, N, P, K) and pathogen density quantified via qPCR.
Host-Phage Interaction Matrix: A large-scale infectivity screen consisting of 55,296 measurements testing the resistance of 1,152 field-isolated R. pseudosolanacearum strains against 48 local phage populations.
Genomic & Phenotypic Profiling: Comparative genomics of 80 representative isolates to identify anti-phage defense systems and mutations. Phenotypic data include in vitro growth traits, virulence assays (AUDPC), and metabolic profiles.
Experimental Evolution Data: Results from a 38-day in planta selection experiment tracking the evolution of phage resistance in R. pseudosolanacearum (strain QL-Rs1115) under pressure from four focal podoviruses. This includes genomic variant calling of evolved clones and fitness trade-off assessments.
Functional Validation: Characterization of engineered knockout mutants (targeting T2SS and T3SS genes) to validate the genetic basis of phage resistance and its associated virulence costs.
Phage Genomics: Genomic sequences and annotations for focal and supplementary phages (primarily Peduoviridae) used in the experiments.
Files and variables
File: Source_data-0410.xlsx
Description: This dataset integrates field surveys, metaviromics, and experimental evolution to investigate the role of bacteriophages in controlling the tomato bacterial wilt pathogen, Ralstonia pseudosolanacearum. The data comprises:
Variables
1. Plant status field
- D: disease (plants showing symptoms of bacterial wilt)
- H: health (plants without symptoms, healthy)
2. Strain and Phage Nomenclature
Throughout all figures and extended data, isolates are identified using the "A-B-C" coding convention:
- A: Sampling location.
- B: Plant identifier/number.
- C: Specific strain identifier.
- Example: "NJ-1-12" denotes strain number 12, isolated from plant 1 at the NJ location.
3. Trait Scoring and Values
- Resistance Levels: Values are binary, where 1 indicates high resistance and 0 indicates no resistance.
- Gene Presence/Absence: In Extended Data Fig. 7, 1 indicates the presence, and 0 indicates the absence of specific genes.
- Genomic Similarity: In Extended Data Fig. 10, values range from 100 (high genomic similarity) to 98.2587 (lower similarity/dissimilarity).
4. Figure-Specific Details
- Figure 2b (Heatmap): Values represent anti-phage system profile similarity; 0 indicates highly similar profiles, while 1 indicates highly dissimilar profiles.
- Figure 3: Displays in planta virulence and in vitro growth traits, including maximum growth rate, carrying capacity, siderophore production, extracellular polymeric substance (EPS) production, and swarming ability.
- Figure 4 (Disease Incidence): The disease_incidence_group is categorized as:
- Low: Disease incidence < 0.33.
- High: Disease incidence ≥ 0.33.
- NA: No variants identified at the target genomic position.
- Figure 5: Displays phage resistance, in planta virulence (tomato system), and in vitro growth traits (maximum growth rate, carrying capacity, carbon utilization, competitive ability, and swarming ability).
5. Extended Data Figure Details
- ED Fig. 1 (Soil Properties):
- AP: Available phosphorus (mg kg⁻¹)
- AK: Available potassium (mg kg⁻¹)
- TC: Total carbon (mg kg⁻¹)
- TN: Total nitrogen (mg kg⁻¹)
- swc: Soil water content (%)
- ED Fig. 5 & 9 (Phage Resistance):
- Focal: Resistance to the specific phage(s) used during the selection experiment (NJ-P3, NB-P21, NC-P34, and NN-P42).
- Other/Additional: Resistance to non-exposed or additional field phage isolates.
- ED Fig. 6: Compares in planta virulence in tomato (cyan) and Arabidopsis (red) systems. Fitness traits include growth rate, carrying capacity, carbon utilization, competitive ability, swarming motility, and antibiotic resistance against Bacillus amyloliquefaciens T-5. “ck” under group refers to control treatment (no phages added).