# Soil microbial composition and abundance influence the growth of Lotus japonicus

## TL;DR

The growth of Lotus japonicus is influenced by the abundance of specific soil bacteria, particularly Mesorhizobium, which helps the plant through nitrogen fixation.

## Contribution

This study identifies Mesorhizobium as the key bacterial group influencing Lotus japonicus growth in natural soil environments.

## Key findings

- Plant growth varied significantly based on soil microbiota composition.
- Mesorhizobium abundance was most strongly linked to improved plant growth.
- Local presence of Lotus japonicus correlates with higher Mesorhizobium abundance.

## Abstract

In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume–rhizobia interactions could trigger a positive plant–soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.

The online version contains supplementary material available at 10.1007/s10265-025-01689-7.