Soil-dwelling Naegleria enhances plant performance by stimulating beneficial bacterial functions in the rhizosphere

Yang Yue, Zhihui Xu, Yijin Wang, Chen Liu, Shuo Sun, Xiangyu Ren, Qihui Lv, Jingchi Liu, Francisco Dini-Andreote, Wu Xiong () and Qirong Shen
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Yang Yue: Nanjing Agricultural University
Zhihui Xu: Nanjing Agricultural University
Yijin Wang: Nanjing Agricultural University
Chen Liu: Nanjing Agricultural University
Shuo Sun: Nanjing Agricultural University
Xiangyu Ren: Nanjing Agricultural University
Qihui Lv: Nanjing Agricultural University
Jingchi Liu: Nanjing Agricultural University
Francisco Dini-Andreote: The Pennsylvania State University
Wu Xiong: Nanjing Agricultural University
Qirong Shen: Nanjing Agricultural University

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

Abstract: Abstract Soil protists play vital roles in influencing plant performance, yet their interactions with plant-beneficial bacteria are still poorly understood. Here, we examine how two soil protists (Naegleria sp. and Cercomonas sp.) affect the pathogen Ralstonia solanacearum, both on individual beneficial bacteria and within a synthetic microbial community (SynCom). Combining in vitro and pot experiments, we find that the SynCom together with Naegleria provided significantly greater suppression of the pathogen (enhanced suppressiveness by 74.29% compared to SynCom alone). Additionally, Naegleria increases SynCom biofilm biomass by 2.44 times. Population dynamics tracking revealed that Naegleria enriched Bacillus populations, leading to a positive correlation between Bacillus and Pseudomonas. Metatranscriptomics analysis shows upregulation of genes related to biofilm formation (such as epsA-O and tapA-sipW-tasA operon) and secondary metabolite biosynthesis (e.g., macrolactin H, bacillaene, and difficidin) in the presence of Naegleria. Our study demonstrates that Naegleria enhances plant health by predating on pathogens, promoting beneficial bacteria, and stimulating protective microbial functions in the rhizosphere.

Date: 2025
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DOI: 10.1038/s41467-025-64139-x

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