# Lateral root enriched Massilia associated with plant flowering in maize

## TL;DR

The study shows that a specific soil bacterium, Massilia, supports maize flowering and growth by interacting with genes related to plant reproduction.

## Contribution

The novel finding is that the bacterium Massilia influences maize flowering time and biomass through interactions with lateral root development genes.

## Key findings

- Mutations in lateral root development genes most strongly affect host gene expression and microbiome assembly.
- Massilia is a keystone bacterium associated with genes controlling flowering time and plant biomass in maize.
- Microbial inoculation experiments confirmed that Massilia promotes maize growth via flowering time mediation.

## Abstract

Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and to what extent such recruited microbiomes determine crop performance. Here, we surveyed the root transcriptome and the root and rhizosphere microbiome via RNA sequencing and full-length (V1–V9) 16S rRNA gene sequencing from genetically distinct monogenic root mutants of maize (Zea mays L.) under different nutrient-limiting conditions.

Overall transcriptome and microbiome display a clear assembly pattern across the compartments, i.e., from the soil through the rhizosphere to the root tissues. Co-variation analysis identified that genotype dominated the effect on the microbial community and gene expression over the nutrient stress conditions. Integrated transcriptomic and microbial analyses demonstrated that mutations affecting lateral root development had the largest effect on host gene expression and microbiome assembly, as compared to mutations affecting other root types. Cooccurrence and trans-kingdom network association analysis demonstrated that the keystone bacterial taxon Massilia (Oxalobacteraceae) is associated with root functional genes involved in flowering time and overall plant biomass. We further observed that the developmental stage drives the differentiation of the rhizosphere microbial assembly, especially the associations of the keystone bacteria Massilia with functional genes in reproduction. Taking advantage of microbial inoculation experiments using a maize early flowering mutant, we confirmed that Massilia-driven maize growth promotion indeed depends on flowering time.

We conclude that specific microbiota supporting lateral root formation could enhance crop performance by mediating functional gene expression underlying plant flowering time in maize.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-024-01839-4.