Influence of nitrogen fertilization and the indigenous soil microbiome on rice (Oryza sativa L.) seedling stage

Abstract

Soil microbial communities are important to nutrient cycling and rice plant growth. Increasingly frequent extreme climate events pose a severe threat to the stability of soil microbial communities, yet the consequences of a catastrophic microbial disturbance on rice seedling stage remain poorly understood. Therefore, we used a gamma-sterilization experiment to eliminate the native microbiome and investigate its functional importance for rice seedlings under four N input levels (0, 50, 100, and 200 mg N kg⁻¹). Amplicon sequencing showed that sterilization showed more significant impacts than N input on microbial diversity and composition. Sterilization reduced alpha diversity, enriched copiotrophs, and suppressed oligotrophs, while increasing unclassified fungal taxa. Microbial communities in non-sterilized soils were resilient to N addition, likely due to fertilization legacy. Rice biomass declined significantly in sterilized soils under low N, indicating the critical role of indigenous microbes in nutrient acquisition. Correlation analyses revealed distinct rice biomass associated taxa among treatments, suggesting disrupted plant–microbe interactions. Although the relative abundance of plant growth-promoting taxa increased in sterilized soils, their enrichment did not compensate for the loss of indigenous microbial community functions. These findings highlighted the ecological importance of native soil microbiota in supporting rice growth under variable N inputs and provided insights for nutrient management.

Graphical abstract

Keywords

rice paddy soil / PGPR / soil sterilization / rice seedling stage / nitrogen input level, soil microbial community

Highlight

	● Rice cultivars exhibited distinct rice seedling stage growth responses to severe microbial community disturbance.
	● Gamma irradiation sterilization reshaped bacterial and fungal community structure more than N input.
	● Sterilized soils showed increased relative abundance of PGPR genera (e.g., Azospirillum , Ralstonia ) but failed to restore seedling biomass.
	● Recolonized microbial communities were strongly governed by urea-N input levels, altering diversity and composition.

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