Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions

Jingjing Chang, Ohana Y. A. Costa, Yu Sun, Jilin Wang, Lei Tian, Shaohua Shi, Enze Wang, Li Ji, Changji Wang, Yingnan Pang, Zongmu Yao, Libo Ye, Jianfeng Zhang, Hongping Chen, Yaohui Cai, Dazhou Chen, Zhiping Song, Jun Rong, Jos M. Raaijmakers, Chunjie Tian (tiancj@iga.ac.cn) and Eiko E. Kuramae (e.kuramae@nioo.knaw.nl)
Additional contact information
Jingjing Chang: Chinese Academy of Sciences
Ohana Y. A. Costa: Netherlands Institute of Ecology (NIOO-KNAW)
Yu Sun: Chinese Academy of Sciences
Jilin Wang: National Engineering Laboratory for Rice
Lei Tian: Chinese Academy of Sciences
Shaohua Shi: Chinese Academy of Sciences
Enze Wang: Chinese Academy of Sciences
Li Ji: Chinese Academy of Sciences
Changji Wang: Chinese Academy of Sciences
Yingnan Pang: Chinese Academy of Sciences
Zongmu Yao: Chinese Academy of Sciences
Libo Ye: Chinese Academy of Sciences
Jianfeng Zhang: Changchun
Hongping Chen: National Engineering Laboratory for Rice
Yaohui Cai: National Engineering Laboratory for Rice
Dazhou Chen: National Engineering Laboratory for Rice
Zhiping Song: Fudan University
Jun Rong: Nanchang University
Jos M. Raaijmakers: Netherlands Institute of Ecology (NIOO-KNAW)
Chunjie Tian: Chinese Academy of Sciences
Eiko E. Kuramae: Netherlands Institute of Ecology (NIOO-KNAW)

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.

Date: 2025
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DOI: 10.1038/s41467-025-57213-x

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