Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth

TL;DR

This study explores how wild and cultivated rice species co-evolved with their microbiomes, showing that bacteria play a key role in supporting rice growth.

Contribution

The study reveals co-phylogenetic patterns between rice and bacteria, emphasizing the functional importance of co-evolved microbiomes in crop growth.

Findings

Host divergence time strongly influences root microbiota structure more than polyploidy or life cycle.

Bacteria show phylosymbiosis with rice hosts, while fungi do not.

A synthetic microbiome from wild rice improved rice growth, with key members being essential for this effect.

Abstract

Crop wild relatives and their microbiomes are essential for sustainable crop production. However, the co-evolution of wild rice species and their microbiomes remains poorly understood. Herein, we investigated microbiome assembly across 17 wild rice and one cultivated rice species under controlled conditions spanning ~15 million years of evolution.

Our data reveal distinct eco-evolutionary patterns for bacteria and fungi. Host divergence time was the predominant driver of root microbiota structure, outweighing polyploidy and life cycle, and exerted a stronger effect on bacteria than fungi. Bacterial community exhibited a significant phylosymbiosis with its host, but fungi did not. Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased. Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly. Potentially functional taxa, including nitrogen-fixing and methane-cycle bacteria, were differentially enriched across evolutionary time and polyploidization events. Notably, co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution. Using a synthetic community (SynCom) derived from the wild rice core microbiome and four nitrogen-fixing strains enriched in early- and medium-diverging Oryza species, we demonstrated that the SynCom strongly promoted rice growth, with the removal of key members markedly reducing its impact.

These results reveal co-phylogenetic patterns between Oryza and root-associated bacteria, highlighting the closer functional linkage between rice traits and bacteria than fungi, likely due to their co-evolution. Our findings provide new insights into crop–microbiome symbiosis from an eco-evolutionary perspective and underscore the importance of co-speciating microbiomes from wild relatives in supporting crop growth.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-026-02359-z.

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