Comparative analysis of rhizosphere microbiomes of cultivated and wild rice under contrasting field water regimes

ABSTRACT Asian cultivated rice ( Oryza sativa L .) is domesticated from the common wild rice ( Oryza rufipogon Griff .). However, the increasing water stress caused by climate change in recent years has become a major threat to rice growth and yield. To explore the adaptive changes of rhizosphere microbiomes in annual cultivated and perennial wild rice under different water limitation conditions, we conducted metagenomic sequencing analysis on rice rhizosphere soil samples from natural environments with varying water conditions. In particular, the genus Pseudomonas plays a dominant role in the rhizosphere microbiome of wild rice under non-irrigated condition. For archaea, we found that, compared to non-irrigated condition, submergence condition enriched methanogenic Methanosarcina . In comparison to cultivated rice, wild rice showed significant enrichment of Nitrosarchaeum , as ammonia-oxidizing archaea play a key role in the nitrogen cycle, whereas cultivated rice tends to enrich methanogenic archaea ( Methanosarcina ), which may increase methane emissions and have adverse environmental impacts. The rhizosphere metabolites of wild rice also enriched DL-Norleucine, L-Phenylalanine, and Palmitic acid, which may enhance root water absorption and provide essential nutrients to help rice resist water-limiting stress. In terms of rhizosphere microbiome function, asnB and nirK were particularly enriched in wild rice under non-irrigated condition, suggesting that wild rice may exhibit higher ecological adaptability to water stress by enhancing nitrogen assimilation and denitrification processes. Excavating these microbiome communities and functional changes in rice rhizospheres is crucial for optimizing water-limiting resistance, protecting the environment, and improving rice yield. IMPORTANCE This study highlights the differences in rhizosphere microbiomes and metabolites between wild and cultivated rice, providing new insights into how water limitation impacts their interaction with the rhizosphere microbiome. These findings are crucial for advancing rice cultivation under submergence and non-irrigated conditions, offering strategies to optimize farming practices, manage water scarcity, and reduce methane emissions. In contrast to cultivated rice, wild rice may regulate its rhizosphere microbial community to enhance resistance to water stress. This discovery offers valuable theoretical support for improving rice growth and adaptation across diverse ecological environments.