Chang Jingjing, Costa Ohana Y A, Sun Yu, Wang Jilin, Tian Lei, Shi Shaohua, Wang Enze, Ji Li, Wang Changji, Pang Yingnan, Yao Zongmu, Ye Libo, Zhang Jianfeng, Chen Hongping, Cai Yaohui, Chen Dazhou, Song Zhiping, Rong Jun, Raaijmakers Jos M, Tian Chunjie, Kuramae Eiko E
Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
Nat Commun. 2025 Feb 27;16(1):2038. doi: 10.1038/s41467-025-57213-x.
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 (NO) production. Measurements of NO 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 NO, highlighting the environmental trade-offs associated with crop domestication.
作物驯化彻底改变了粮食生产，但增加了农业对化肥和农药的依赖。我们研究了野生稻和驯化稻根际微生物群功能的差异，重点关注氮（N）循环基因。鸟枪法宏基因组学和实时聚合酶链反应揭示了野生稻根际微生物群中固氮基因的丰度更高。通过移植根际微生物群悬浮液进行验证表明，无论种植的水稻类型如何，含有野生稻悬浮液的土壤中固氮酶活性最高。然而，驯化稻中与一氧化二氮（N₂O）产生相关的基因数量有所增加。与野生稻相比，含有驯化稻的土壤中N₂O排放量的测量结果显著更高。野生稻和驯化稻之间的根系代谢组学比较进一步表明，野生稻根系分泌物分别与宏基因组学和定量聚合酶链反应所显示的微生物固氮基因的频率和丰度呈正相关。为了证实这一点，我们将野生稻和驯化稻的根系代谢产物添加到黑土中，定量聚合酶链反应表明野生稻分泌物使微生物固氮基因丰度和固氮酶活性最大化。总的来说，这些发现表明水稻驯化对固氮细菌产生负面影响，并使产生温室气体N₂O的细菌富集，凸显了与作物驯化相关的环境权衡。
