Chi Yaowei, Ma Xianzhong, Chu Shaohua, You Yimin, Chen Xunfeng, Wang Juncai, Wang Renyuan, Zhang Xia, Zhang Dongwei, Zhao Ting, Zhang Dan, Zhou Pei
School of Agriculture and Biology, Shanghai Jiaotong University; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education; Bor S. Luh Food Safety Research Center; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China.
Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland, Jilin Agricultural University, Changchun, 130118, China.
Microbiome. 2025 May 6;13(1):113. doi: 10.1186/s40168-025-02113-x.
Using plant growth-promoting rhizobacteria (PGPR) combined with hyperaccumulator is an ecologically viable way to remediate cadmium (Cd) pollution in agricultural soil. Despite recent advances in elucidating PGPR-enhanced phytoremediation, the response of plant-associated microbiota to PGPR remains unclear.
Here, we found that the effective colonization of PGPR reshaped the rhizosphere nutrient microenvironment, especially driving the nitrogen cycle, primarily mediated by soil nitrate reductase (S-NR). Elevated S-NR activity mobilized amino acid metabolism and synthesis pathways in the rhizosphere, subsequently driving a shift in life history strategies of the rhizosphere microbiota, and enriching specific rare taxa. The reconstructed synthetic community (SynCom3) confirmed that the inclusion of two crucial collaborators (Lysobacter and Microbacterium) could efficiently foster the colonization of PGPR and aid PGPR in executing phytoremediation enhancement. Finally, the multi-omics analysis highlighted the critical roles of phenylpropanoid biosynthesis and tryptophan metabolism pathways in inducing SynCom3 reorganization and PGPR-enhanced phytoremediation.
Our results underscore the significance of the rhizosphere microenvironment modification by PGPR for its colonization and efficacy, and highlight the collaborative role of rare microbiota in the context of PGPR-enhanced phytoremediation. Video Abstract.
利用促生根际细菌（PGPR）与超富集植物相结合是修复农业土壤中镉（Cd）污染的一种生态可行方法。尽管在阐明PGPR增强植物修复方面取得了最新进展，但植物相关微生物群对PGPR的反应仍不清楚。
在这里，我们发现PGPR的有效定殖重塑了根际养分微环境，特别是驱动了氮循环，主要由土壤硝酸还原酶（S-NR）介导。S-NR活性的升高调动了根际的氨基酸代谢和合成途径，随后驱动了根际微生物群生活史策略的转变，并丰富了特定的稀有类群。重建的合成群落（SynCom3）证实，加入两个关键的协同菌（溶杆菌属和微杆菌属）可以有效地促进PGPR的定殖，并帮助PGPR增强植物修复效果。最后，多组学分析突出了苯丙烷生物合成和色氨酸代谢途径在诱导SynCom3重组和PGPR增强植物修复中的关键作用。
我们的结果强调了PGPR对根际微环境的修饰对其定殖和功效的重要性，并突出了稀有微生物群在PGPR增强植物修复中的协同作用。视频摘要。
