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Journal of Integrative Agriculture
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Tobacco pathogen-microbiome dynamics reveal dual-functional microbial resources for disease control and growth promotion

Yinan Ma1, 2, 3*, Junzhou Li1*, Jing Liu4*, Sasa Zheng1, Peipei Wang5, Wen Zeng1, Jiaqi Zhang5, Kaiji Liao1, Hailei Wei1#

1 State Key Laboratory of Efficient Utilization of Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China

2 National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China

3 Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China

4 Zunyi Tobacco Company of Guizhou Provincial Tobacco Corporation, Zunyi 563000, China

5 Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs/IPM Innovation Center of Hebei Province/International Science and Technology Joint Research Center on IPM of Hebei Province, Baoding, 071000, China

 Highlights 

Mixed infections trigger rhizosphere microbiome disruption and diversity collapse.

New amplicon-qPCR method quantifies pathogens and microbiome shifts.

B. orbicola ZY288 combats pathogens and boosts tobacco growth.

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摘要  

烟草青枯病和黑胫病是全球烟草生产中面临的两种毁灭性土传病害,严重威胁烟草产量与品质。尽管根际微生物作物病害防治中发挥着重要作用,但目前对于多种病原混合侵染下根际微生物组动态变化还缺乏足够了解因此,解析烟草青枯病和黑胫病并发条件下烟草根际微生物群的多样性变化及功能潜力,将为有效防治这两种病害奠定理论和资源基础本研究从贵州遵义烟区汇川和绥阳两个典型产区,采集了健康植株、青枯病病发植株、黑胫病病发植株以及两种病害混发植株的根际土壤,基于高通量测序和多样性指数评价了物种丰富度和均匀度,明确了健康组根际微生物群落丰富度和多样性最高,而病害并发组的多样性最低且群落结构明显失衡,优势病原菌比例大幅提升。利用主坐标与物种组成分析解析群落差异,发现发病状态导致群落组成集中化并丧失部分功能性类群。同时,构建了两种病原菌的绝对定量PCRAbsolute Quantitative Real-time polymerase chain reactionqPCR)标准曲线,与田间病害症状调查比对,验证了测序数据一致,并弥补了传统16S方法对卵菌分辨率不足的缺陷利用培养组学从病害并发土样中分离到了与微生物组核心关键类群属一致的Burkholderia. orbicola ZY288,温室实验显示,该菌株能够有效防治烟草青枯病和黑胫病,防效分别达到53.16%57.28%,同时还可以显著促进植株生长,体现防病和促生长的双功能特性。本研究创新性主要体现在:1)解析了病害混发对微生物群落结构和多样性的影响;2)构建了高精度病原绝对定量与群落结构分析的联合分析方法;3)筛选并验证了兼具生防和促生长潜力的关键菌株资源。该研究为烟草病害的绿色防控提供了科学依据和技术方法,对微生物生态学应用于农业生产提高农作物产量具有重要意义。



Abstract  

Tobacco bacterial wilt and black shank, caused by Ralstonia solanacearum and Phytophthora nicotianae, respectively, severely threaten global tobacco production. Although the rhizosphere microbiome has emerged as a key factor in disease suppression, limited knowledge is available regarding how mixed infections by these pathogens reshapes microbial communities or affects soil health. Most existing studies focus on single-pathogen interactions, leaving a critical gap in understanding the complex microbiome responses to dual infections. Here, we investigated rhizosphere microbiome dynamics under single and mixed infections with these pathogens to identify microbial resources for disease suppression and growth enhancement. Using an amplicon-qPCR combined method, we demonstrated the restructuring of the microbiome. Healthy soils exhibited higher diversity and enrichment of beneficial taxa, including Sphingomonas and Rhizobium, whereas diseased soils were dominated by pathogens such as Ralstonia, with intensified diversity losses in mixed infected samples. Network analyses revealed collapsed microbial connectivity in diseased soils, indicating destabilized community resilience. Among the 2,048 rhizosphere isolates, Burkholderia orbicola ZY288 was identified as a potent biocontrol agent that suppressed pathogens and provided control effect by 53%–57% in greenhouse trials. Strain ZY288 also promoted plant growth via phosphate solubilization, protease activity, and ammonia synthesis, significantly increasing tobacco biomass and height. Phylogenetic and amplicon data linked strain ZY288 to disease-suppressive rhizosphere taxa, validating its ecological niche. Our findings highlight pathogen-driven microbiome shifts in tobacco soils and suggest that strain ZY288 is a sustainable biocontrol agent with plant-protective and growth-promoting capacities. This study advances microbiome-guided strategies for managing soil-borne diseases and promotes the integration of microbial ecology into agriculture.

Keywords:  rhizosphere microbiome        biological control        mixed infection        community structure        correlation network  
Online: 08 December 2025  
Fund: 

This work was funded by the Science and Technology Programs of the Zunyi Tobacco (2021XM03). Hai-Lei Wei was supported by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-CSCB-202401)

About author:  Yinan Ma, E-mail: mayinan@caas.cn; Junzhou Li, E-mail: lijunzhou@caas.cn; Jing Liu, E-mail: liujingcre@163.com; #Correspondence Hailei Wei, Tel: +86-10-82108636, E-mail: weihailei@caas.cn *These authors contributed equally to this work.

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Yinan Ma, Junzhou Li, Jing Liu, Sasa Zheng, Peipei Wang, Wen Zeng, Jiaqi Zhang, Kaiji Liao, Hailei Wei. 2025. Tobacco pathogen-microbiome dynamics reveal dual-functional microbial resources for disease control and growth promotion. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.12.014

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