# Biogeography influences plant–microbe interactions and natural soil suppressiveness to black root rot disease of tobacco

## TL;DR

This study shows how the geography and geology of soils influence plant-microbe interactions and the natural ability of soils to suppress black root rot disease in tobacco.

## Contribution

The study reveals distinct biogeographic patterns in soil suppressiveness mechanisms between Swiss and Savoie soils.

## Key findings

- Soil suppressiveness is shaped by both geological origin and geographic positioning.
- Swiss soils show suppressiveness through differences in rhizosphere microbiota composition and function.
- Savoie soils show suppressiveness through plant physiological responses rather than microbial shifts.

## Abstract

In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant–microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant–microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.

Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.

Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.

The online version contains supplementary material available at 10.1186/s13059-025-03911-0.