Abstract
Introduction Synchytrium endobioticum , the biotrophic pathogen causing potato wart, poses persistent challenges due to its long-term soil survival and quarantine status. Biological control agents (BCAs) offer a promising avenue for sustainable management, yet the ecological context of wart-associated microbiomes remains unexplored. Methods We present the first comprehensive microbiome characterization of the potato wart disease system using full-length 16S rRNA gene Nanopore sequencing across bioassay-grown warts, field-collected wart tissues, diseased tare soils, and long-term descheduled (wart-free) soils. Whole genome amplification (WGA) enabled profiling of low-biomass samples, albeit with compositional shifts towards dominant taxa. Results and discussion Microbiome compositional structure differed significantly across sieving fractions, host genotypes, and compartments (wart vs. tare soil). Wart microbiomes were enriched in Pseudomonas trivialis and Bacillus atrophaeus , taxa potentially involved in pathogen-specific suppression. Tare soils harbored transitional microbiomes shaped by host proximity, enriched with Bacillus species that may offer both generalist and targeted BCA activity. Descheduled soils under long-term nonhost crop rotations harbored broad-spectrum BCAs contributing to environmental sensing and nutrient requisition. Functional prediction suggested enrichment of xenobiotic degradation and chitin metabolism pathways in diseased soils, primarily associated with Bacillus, Pseudomonas , and Paenibacillus . Network analysis indicated fragile yet densely connected communities in diseased soils versus modular and stable structures in descheduled systems. Altogether, this study represents a first critical step toward developing biocontrol strategies for S. endobioticum by revealing a gradient of biocontrol reservoirs associated with disease pressure and management history. The use of functional prediction and correlation network tools provides essential starting points for hypothesis-driven research into disease suppression and biocontrol in a system with no prior microbiome data, and these findings warrant targeted isolation and in vitro / in planta validation for BCA development.
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Claims 7
Claim · model-written summary
Microbiome compositional structure differed significantly across sieving fractions, host genotypes and compartments (wart versus tare soil).
- Taxon
- potato
Solanum tuberosumt0 - Outcome
- Microbiome compositional structuree0
- Direction
- differede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Microbiome compositional structure differed significantly across sieving fractions, host genotypes, and compartments (wart vs. tare soil)”
Claim · model-written summary
Wart microbiomes were enriched in Pseudomonas trivialis, a taxon potentially involved in pathogen-specific suppression.
- Taxon
- potatoSolanum tuberosumt0
- Interactor
- Pseudomonas trivialisPseudomonas trivialise0other
- Outcome
- Wart microbiomes were enrichede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Wart microbiomes were enriched in Pseudomonas trivialis”
Claim · model-written summary
Wart microbiomes were enriched in Bacillus atrophaeus, a taxon potentially involved in pathogen-specific suppression.
- Taxon
- potatoSolanum tuberosumt0
- Interactor
- Bacillus atrophaeusBacillus atrophaeuse0other
- Outcome
- Wart microbiomes were enrichede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Wart microbiomes were enriched in Pseudomonas trivialis and Bacillus atrophaeus”
Claim · model-written summary
Tare soils harbored transitional microbiomes shaped by host proximity and enriched with Bacillus species.
- Taxon
- potatoSolanum tuberosumt0
- Interactor
- Bacillus speciese0other
- Outcome
- transitional microbiomese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Tare soils harbored transitional microbiomes shaped by host proximity, enriched with Bacillus species”
Claim · model-written summary
Descheduled soils under long-term nonhost crop rotations harbored broad-spectrum biocontrol agents.
- Taxon
- potatoSolanum tuberosumt0
- Outcome
- broad-spectrum BCAse0
- Setting
- Descheduled soilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Descheduled soils under long-term nonhost crop rotations harbored broad-spectrum BCAs”
Claim · model-written summary
Functional prediction suggested enrichment of xenobiotic degradation and chitin metabolism pathways in diseased soils.
- Taxon
- potatoSolanum tuberosumt0
- Outcome
- xenobiotic degradation and chitin metabolism pathwayse0
- Direction
- enrichmente0
- Setting
- diseased soilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Functional prediction suggested enrichment of xenobiotic degradation and chitin metabolism pathways in diseased soils”
Claim · model-written summary
Network analysis indicated fragile yet densely connected communities in diseased soils versus modular and stable structures in descheduled systems.
- Taxon
- potatoSolanum tuberosumt0
- Outcome
- fragile yet densely connected communitiese0
- Comparator
- descheduled systemse0
- Setting
- diseased soilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“potato wart disease”
e0“Network analysis indicated fragile yet densely connected communities in diseased soils versus modular and stable structures in descheduled systems”