Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation

2025/03/26 by Daniel Garrido‐Sanz, Christoph Keel · 1 voice · 70 citations
Agricultural and Biological Sciences · Environmental Science · #Bacteria #Biology #Ecology #Gene #Genetics #Metagenomics #Microbial Community Ecology and Physiology #Microbial ecology #Microbial population biology #Microbiome #Nematode management and characterization studies #Niche #Niche differentiation #Plant-Microbe Interactions and Immunity #Rhizosphere

paper · pdf · doi:10.1038/s41564-025-01973-1

published in Nature Microbiology 10(5), 1130-1144 (Nature Portfolio)

openalex publication_date 2025/03/26 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Abstract

Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.

Citations

• TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA
• Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes
• Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria

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Discussions

• Wow! Our paper in @natmicrobiol.nature.com has just surpassed 10,000 views in less than a month!! a rare feat for a #plant #microbiome study! We argue that seed-borne bacteria are the architects of th [bsky, 26 points, 0 comments]

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