# Acetoin and 2,3-Butanediol Differentially Restructure Fungal and Bacterial Communities and Their Links to Host Transcription in the Rhizosphere of a Medicinal Plant

## TL;DR

This study shows how two microbial compounds, acetoin and 2,3-butanediol, affect the root microbiome and gene activity in a medicinal plant, offering insights for sustainable cultivation.

## Contribution

The study reveals how microbial VOCs differentially reshape fungal and bacterial communities and their links to plant gene expression in the rhizosphere.

## Key findings

- 2,3-butanediol caused greater restructuring of fungal communities and triggered widespread changes in root gene expression.
- Fungal taxa showed stronger associations with host gene expression than bacterial taxa.
- Both compounds reduced plant growth, challenging the common belief that microbial VOCs promote plant growth.

## Abstract

This study explored how two common microbial volatile organic compounds—acetoin and 2,3-butanediol—affect the medicinal plant Pseudostellaria heterophylla and its rhizosphere microbial communities. Using a specialized pot system that allowed only volatile exchange, we found that both compounds reduced root growth and altered the composition of bacteria and fungi living around the roots. Fungal communities were particularly sensitive to 2,3-butanediol, which also triggered widespread changes in root gene expression, especially in pathways related to stress and secondary metabolism. By linking specific microbes to host gene activity, our findings reveal that volatile compounds can reshape both the root microbiome and plant molecular responses. These insights may inform sustainable strategies for improving medicinal plant cultivation.

Microbial volatile organic compounds (VOCs) mediate rhizosphere plant-microbe interactions, yet their integrated effects on plant microbiome assembly and host transcriptional regulation remain unresolved. Here we address this gap by investigating how two common VOCs, acetoin (AC) and 2,3-butanediol (BD), influence growth, rhizosphere communities, and root gene expression in the medicinal plant Pseudostellaria heterophylla using a split-pot system. Bacterial and fungal communities were monitored across three developmental stages via amplicon sequencing, alongside root transcriptome profiling during tuber enlargement. Contrasting with widely reported growth-promoting effects of microbial VOCs, both compounds significantly reduced tuber number and biomass. Bacterial communities remained taxonomically stable, shaped primarily by species replacement, with modest VOC responses but clear shifts across developmental stages. Fungal communities exhibited marked compositional restructuring and greater treatment sensitivity, particularly under BD. Neutral community modeling indicated predominantly stochastic bacterial assembly, while fungal assembly—especially under BD—showed stronger influence of deterministic processes. BD associated with broader transcriptional reprogramming than AC, including downregulation of photosynthesis, specialized metabolism, and defense pathways. Cross-omics network analysis revealed discriminant genera (e.g., Granulicella, Harposporium) that correlated strongly with host genes involved in stress response, development, and epigenetic regulation, with fungal taxa showing tighter associations with host expression than bacteria. Together, these findings establish a mechanistic framework for how microbial VOCs shape rhizosphere communities and host responses, with implications for microbiome-based strategies in medicinal plant cultivation.