# Host genome and bacterial taxa shape the Arabidopsis seed microbiome

## TL;DR

This study shows that the Arabidopsis seed microbiome is shaped by geography, soil, and the plant's genes, with a key role for the RPB47B protein.

## Contribution

The study identifies host genetic loci, including RPB47B, that influence seed microbiome composition and function.

## Key findings

- Seed microbiome composition varies with geography and soil features.
- GWAS links key bacterial taxa and shared functional traits to host genetic loci.
- RPB47B mutants show altered plant physiology related to soil and microbial diversity.

## Abstract

Plant-microbiome interactions are crucial in shaping plant growth, stress resilience, and disease resistance. Among these, the seed microbiome plays a pivotal role in early plant development and ecological adaptation. However, little is known about the factors that determine the abundance and functions of the seed microbiome, as well as the role of the host genome in shaping the microbial diversity across different ecotypes. In this study, we investigated the diversity of the Arabidopsis seed microbiomes that originate from multiple geographical locations. High-throughput sequencing identified key bacterial taxa that govern Arabidopsis seed microbiota diversity. Distinct compositions of bacterial taxa were identified in Arabidopsis accessions sharing geographical location and similar soil features. Genome-wide association studies (GWAS) revealed that both the abundance of key taxa and common functional traits are associated with specific host genetic loci such as the RNA-binding protein RPB47B, mutants of which showed altered physiological properties related to soil properties and microbial diversity. Overall, our study establishes that geographical, soil and genetic host factors shape the Arabidopsis seed microbiome.

Geographical origin, soil properties and host genetics jointly shape the Arabidopsis seed microbiome. Across accessions from multiple locations, high throughput sequencing revealed key bacterial taxa that structure seed associated diversity. Genome-wide association mapped taxon abundance and shared functional traits to host loci, including the RNA-binding protein RPB47B. Mutants of RPB47B altered plant physiology in ways consistent with soil linked microbial differences, indicating that environmental and genetic drivers converge to pattern seed microbiota and early adaptation.

Seed microbiome composition varies with geography and soil features.GWAS links key taxa and shared functional traits to host loci.The RNA-binding protein RPB47B is implicated in shaping seed microbial diversity.Environmental and host genetic factors shape plant microbe assembly.

Seed microbiome composition varies with geography and soil features.

GWAS links key taxa and shared functional traits to host loci.

The RNA-binding protein RPB47B is implicated in shaping seed microbial diversity.

Environmental and host genetic factors shape plant microbe assembly.

Geographical origin, soil properties and host genetics jointly shape the Arabidopsis seed microbiome. Across accessions from multiple locations, high throughput sequencing revealed key bacterial taxa that structure seed associated diversity. Genome-wide association mapped taxon abundance and shared functional traits to host loci, including the RNA-binding protein RPB47B. Mutants of RPB47B altered plant physiology in ways consistent with soil linked microbial differences, indicating that environmental and genetic drivers converge to pattern seed microbiota and early adaptation.