Soil pH and bacterial diversity synergistically regulate trace element transfer and accumulation in soil-rice systems

Abstract

Rice, feeding billions, accumulates both toxic trace elements (Cd, As, Al) and essential micronutrients (Se, Cu, Zn, Mn, Fe), posing food safety challenges. This study explores the interactions among soil properties, bacterial communities, and trace element dynamics across Chinaʼs major paddy soil types. Our analysis showed that strongly acidic soils (pH ≤ 5.5) had higher total As, Al, and Se, while neutral soils (6.5 < pH ≤ 7.5) exhibited greater Cd and Mn bioavailability. Bacterial diversity (alpha and beta) significantly influenced trace element accumulation in rice. Bacterial diversity, soil nutrients, and pH explained a large part of the variance in trace element content in soil (total: 35.24%, 21.69%, and 13.02%; bioavailable: 23.68%, 29.63%, and 11.81%) and rice grains (23.09%, 10.25%, and 17.42%). Co-occurrence networks identified keystone bacterial ASVs, predominantly uncultured lineages (64%), strongly correlated with specific ASVs (R² = 0.53−0.80, P < 0.001). Structural Equation Modeling revealed soil type, pH, and nutrients collectively explained 32% of bacterial alpha diversity and 75% of community composition variation, driving subsequent trace element distribution in soil and rice. Our findings underscore complex soil-microbe-element interactions, emphasizing managing soil pH and bacterial diversity to optimize rice nutrition of essential elements and mitigate risks from toxic elements.

Graphical abstract

Keywords

trace elements / soil-rice system / soil physicochemical properties / bacterial communities / co-occurrence network

Highlight

	● Soil pH drives trace element mobility and bioavailability.
	● Bacterial β-diversity enhances trace element accumulation via functional diversity.
	● Uncultured bacterial ASVs are key in trace element cycling and plant interactions.
	● Networks analysis shows Pseudonocardia -Fe/As and Blastopirellula -Al regulatory nodes.

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