What question did this study set out to answer?

This study aims to understand how the soil microbiome adapts over time to continuous pressure from the pathogen Phytophthora nicotianae.

May 17, 2026BMC Microbiology0 citationsOpen Access

Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease

Q: What does this research mean for the field?

Sustained pressure from the soil-borne pathogen Phytophthora nicotianae triggers a coordinated adaptive succession that reshapes the genetic, functional, and taxonomic structure of the soil microbiome into a more defended, specialized, and taxonomically homogenized state. Novelty: ClaimNovelty.NOVEL_FINDING. Consensus alignment: ConsensusAlignment.NEUTRAL.

UBUmer BasuMinistry of Agriculture SAShafat Ahmad AhangerMinistry of Agriculture TSTianyu SongMinistry of Agriculture

Key Points

This study aims to understand how the soil microbiome adapts over time to continuous pressure from the pathogen Phytophthora nicotianae.
Conducted a six-year longitudinal metagenomic study in a tobacco field
Performed shotgun sequencing, gene catalog construction, and functional annotation
Analyzed differences in rhizosphere microbiome from Year_1 to Year_6.
45.88% of antibiotic resistance genes were differentially abundant (p<0.001).
53.2% of carbohydrate-active enzymes showed differential abundance, indicating functional metabolic shifts.
Shannon index for species diversity decreased from 5.52 to 5.31, despite a 14.8% increase in overall species abundance.

Abstract

BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year₁ and Year₆ was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases. RESULTS: FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45. 88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53. 2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52. 9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5. 52 to 5. 31) that coexisted with a 14. 8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa. CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.

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