Liu Sijia, Wu Jiadong, Cheng Zhen, Wang Haofei, Jin Zhelun, Zhang Xiang, Zhang Deqiang, Xie Jianbo
State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
Microbiome. 2025 May 4;13(1):111. doi: 10.1186/s40168-025-02103-z.
Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.
This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.
Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.
自然环境中的植物经常面临各种形式的胁迫，已知微生物在帮助植物抵御这些挑战中发挥着关键作用。然而，从复杂的微生物群落中挖掘和利用与植物相关的抗逆微生物亚群落仍然知之甚少。
本研究基于四种处理（对照、干旱、盐和病害）下13周的微生物群落，以定义共享的核心微生物群和胁迫特异性微生物群。通过共现网络分析，构建了四种处理下微生物群落的动态变化网络，揭示了对应不同处理的独特变化轨迹。此外，通过模拟物种灭绝，定量评估了选择性去除微生物对网络稳健性的影响。研究发现，在不同环境条件下，核心微生物群对维持网络稳定性具有重要潜在贡献。我们利用零模型和中性模型的评估表明，胁迫特异性微生物群的组装主要由确定性过程驱动，而核心微生物群的组装则受随机过程支配。我们还从功能角度确定了微生物组特征：共享微生物群倾向于增强生物体抵御多种环境胁迫的能力，而胁迫特异性微生物群落与缓解特定胁迫的多种机制相关。采用 culturomic 方法分离出781株细菌菌株，并选择9株构建不同的合成群落（SynComs）。这些实验证实，含有胁迫特异性微生物的群落能有效帮助植物应对环境胁迫。
总的来说，我们不仅系统地揭示了根际微生物群在各种胁迫下的动态变化模式，还从变化中寻求不变，确定了核心微生物群和胁迫特异性微生物群对植物胁迫耐受性的潜在贡献，最终旨在为植物制定有益的微生物接种策略。我们的研究为理解植物中微生物介导的抗逆过程提供了新的见解。视频摘要。
