Abstract
BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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Claims 11
Claim · model-written summary
Host divergence time was the main driver of root microbiota structure in Oryza, stronger for bacteria than fungi
- Outcome
- root microbiota structuree1
- Direction
- predominant drivere1
- Comparator
- polyploidy and life cyclee1
OryzaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e1“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”
Claim · model-written summary
Bacterial root communities in Oryza showed significant phylosymbiosis with their host, unlike fungi
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e2“Bacterial community exhibited a significant phylosymbiosis with its host, but fungi did not”
Claim · model-written summary
Bacterial diversity in Oryza root microbiota decreased over evolutionary time
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e3“Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased”
Claim · model-written summary
Phylogenetic clustering of Oryza root bacteria increased over evolutionary time
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e3“Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased”
Claim · model-written summary
Deterministic and stochastic processes co-drove bacteria assembly in the Oryza root microbiome
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e4“Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly”
Claim · model-written summary
Stochastic processes strongly drove fungi assembly in the Oryza root microbiome
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e4“Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly”
Claim · model-written summary
Potentially functional root bacteria of Oryza were differentially enriched across polyploidization events
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e5“Potentially functional taxa, including nitrogen-fixing and methane-cycle bacteria, were differentially enriched across evolutionary time and polyploidization events”
Claim · model-written summary
Co-speciating bacteria better predicted grain weight in Oryza than fungi
- Interactor
- co-speciating bacteriae6symbiont
- Outcome
- grain weighte6
- Direction
- better predictede6
- Comparator
- fungie6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e6“co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution”
Claim · model-written summary
Core species made a major contribution to the prediction of grain weight in Oryza
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“across the genus Oryza”
e6“co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution”
Claim · model-written summary
A synthetic community derived from the wild rice core microbiome strongly promoted rice growth
- Taxon
- rice
Oryza sativae7 - Treatment
- synthetic community (SynCom)e7
- Interactor
- four nitrogen-fixing strainse7symbiont
- Outcome
- rice growthe7
- Direction
- strongly promotede7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“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”
Claim · model-written summary
Removal of key members markedly reduced the rice growth promotion by the SynCom
- Taxon
- riceOryza sativae7
- Treatment
- removal of key memberse0
- Outcome
- impacte0
- Direction
- markedly reducinge0
- Comparator
- SynCome7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“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”
e0“with the removal of key members markedly reducing its impact”