Abstract
Introduction Plant root-associated microbiomes play an important role in plant health, yet their responses to bacterial wilt remain unclear poorly understood. Methods This study investigated spatial variations in microbiome and metabolome composition across three root-associated niches—root-surrounding soil, rhizosphere, and endosphere—of healthy and Ralstonia solanacearum -infected potato plants. A total of 36 samples were analyzed, with microbial diversity assessed by full-length 16S rRNA and ITS sequencing, and metabolic profiles characterized using LC-QTOF-MS. Results Alpha diversity analysis revealed that bacterial diversity in healthy plants was consistently higher than in diseased plants, progressively increasing from the root-surrounding soil to the rhizosphere, and most notably in the endosphere, where the Shannon index declined from 5.3 (healthy) to 1.2 (diseased). In contrast, fungal diversity was lower in diseased plants in the root-surrounding soil and rhizosphere, but significantly elevated in the endosphere, suggesting niche-specific microbial responses to pathogen stress. Beta diversity confirmed significant microbiome restructuring under pathogen stress ( R² > 0.5, p = 0.001). Taxonomic analysis showed over 98% dominance of Proteobacteria in the diseased endosphere, where Burkholderia , Pseudomonas , and Massilia enriched in healthy plants were significantly reduced. R. solanacearum infection promotes the enrichment of Fusarium species in both the rhizosphere and endosphere. Metabolomic analysis revealed extensive pathogen-induced metabolic reprogramming, with 299 upregulated and 483 downregulated metabolites in the diseased endosphere, including antimicrobial metabolites such as verruculogen and aurachin A. Network analysis identified XTP as a central metabolite regulating microbial interactions, whereas antimicrobial metabolites exhibited targeted pathogen suppression. O2PLS analysis revealed that pathogen-induced antimicrobial metabolites (e.g., Gentamicin X2, Glutathionylspermine) were associated with Clostridia and Ketobacter in diseased plants, while nucleotide-related compounds (e.g., XTP) correlated with Rhodomicrobium and others, indicating infection-driven microbial adaptation and metabolic restructuring. Discussion These findings provide insights into pathogen-driven disruptions in root microbiomes and suggest potential microbiome engineering strategies for bacterial wilt management.
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Claims 13
Claim · model-written summary
Bacterial diversity was higher in healthy than diseased potato plants, especially in the endosphere, where Shannon index fell from 5.3 to 1.2.
- Taxon
- potatoes
Solanum tuberosumt0 - Organ / stage
- endospheree0
- Outcome
- bacterial diversitye0
- Direction
- highere0
- Value
- 5.3 (healthy) to 1.2 (diseased)e0
- Comparator
- diseased plantse0
Not reportedInteractor
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“bacterial diversity in healthy plants was consistently higher than in diseased plants, progressively increasing from the root-surrounding soil to the rhizosphere, and most notably in the endosphere, where the Shannon index declined from 5.3 (healthy) to 1.2 (diseased)”
Claim · model-written summary
Fungal diversity was lower in diseased potato root-surrounding soil and rhizosphere.
- Taxon
- potatoesSolanum tuberosumt0
- Outcome
- fungal diversitye0
- Direction
- lowere0
- Comparator
- diseased plantse0
- Setting
- root-surrounding soil and rhizospheree0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“fungal diversity was lower in diseased plants in the root-surrounding soil and rhizosphere”
Claim · model-written summary
Fungal diversity was significantly elevated in the endosphere of diseased potato plants.
- Taxon
- potatoesSolanum tuberosumt0
- Organ / stage
- endospheree0
- Outcome
- fungal diversitye0
- Direction
- elevatede0
- Comparator
- diseased plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“fungal diversity was lower in diseased plants in the root-surrounding soil and rhizosphere, but significantly elevated in the endosphere”
Claim · model-written summary
Pathogen stress significantly restructured the potato root-associated microbiome.
- Taxon
- potatoesSolanum tuberosumt0
- Treatment
- pathogen stresse0
- Outcome
- microbiome restructuringe0
- Value
- R² > 0.5e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“significant microbiome restructuring under pathogen stress ( R² > 0.5, p = 0.001)”
Claim · model-written summary
Proteobacteria dominated more than 98% of the diseased potato endosphere.
- Taxon
- potatoesSolanum tuberosumt0
- Organ / stage
- diseased endospheree0
- Outcome
- dominance of Proteobacteriae0
- Value
- over 98%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“over 98% dominance of Proteobacteria in the diseased endosphere”
Claim · model-written summary
Burkholderia, Pseudomonas and Massilia enriched in healthy potato plants were significantly reduced in diseased endosphere.
- Taxon
- potatoesSolanum tuberosumt0
- Outcome
- Burkholderia , Pseudomonas , and Massiliae0
- Direction
- reducede0
- Comparator
- healthy plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“Burkholderia , Pseudomonas , and Massilia enriched in healthy plants were significantly reduced”
Claim · model-written summary
R. solanacearum infection enriched Fusarium species in the potato rhizosphere and endosphere.
- Taxon
- potatoesSolanum tuberosumt0
- Organ / stage
- rhizosphere and endospheree0
- Interactor
- R. solanacearum
Ralstonia solanacearume0pathogen - Outcome
- enrichment of Fusarium speciese0
- Direction
- enrichmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“R. solanacearum infection promotes the enrichment of Fusarium species in both the rhizosphere and endosphere”
Claim · model-written summary
In the diseased potato endosphere, 299 metabolites were upregulated.
- Taxon
- potatoesSolanum tuberosumt0
- Organ / stage
- diseased endospheree0
- Outcome
- metabolitese0
- Direction
- upregulatede0
- Value
- 299e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“299 upregulated and 483 downregulated metabolites in the diseased endosphere”
Claim · model-written summary
In the diseased potato endosphere, 483 metabolites were downregulated.
- Taxon
- potatoesSolanum tuberosumt0
- Organ / stage
- diseased endospheree0
- Outcome
- metabolitese0
- Direction
- downregulatede0
- Value
- 483e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“299 upregulated and 483 downregulated metabolites in the diseased endosphere”
Claim · model-written summary
Network analysis identified XTP as a central metabolite regulating microbial interactions in potatoes.
- Taxon
- potatoesSolanum tuberosumt0
- Compound
- XTPe0
- Outcome
- microbial interactionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“Network analysis identified XTP as a central metabolite regulating microbial interactions”
Claim · model-written summary
Antimicrobial metabolites exhibited targeted pathogen suppression in potatoes.
- Taxon
- potatoesSolanum tuberosumt0
- Compound
- antimicrobial metabolitese0
- Outcome
- pathogen suppressione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“antimicrobial metabolites exhibited targeted pathogen suppression”
Claim · model-written summary
Gentamicin X2 and Glutathionylspermine were associated with Clostridia and Ketobacter in diseased potato plants.
- Taxon
- potatoesSolanum tuberosumt0
- Compound
- Gentamicin X2, Glutathionylsperminee0
- Outcome
- Clostridia and Ketobactere0
- Qualifier
- diseased plantse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“Gentamicin X2, Glutathionylspermine) were associated with Clostridia and Ketobacter in diseased plants”
Claim · model-written summary
XTP correlated with Rhodomicrobium and other microbes in diseased potato plants.
- Taxon
- potatoesSolanum tuberosumt0
- Compound
- XTPe0
- Outcome
- Rhodomicrobium and otherse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potatoes”
e0“XTP) correlated with Rhodomicrobium and others”