Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
College of Ecology, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China.
Microbiome. 2024 Nov 14;12(1):236. doi: 10.1186/s40168-024-01959-x.
Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome.
Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation.
In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract.
虽然已经从镉（Cd）超积累植物中分离和鉴定了许多内生细菌，但核心内生微生物组在促进植物修复方面的贡献和潜在应用仍缺乏深入认识。因此，我们首先在不同地点进行了为期两年的现场采样，以确定 Cd 超积累植物中的独特核心微生物组，然后从中选择不同属的有代表性的可培养细菌来构建合成群落（SynComs）。最后，研究了优化的 SynCom 对不同生态型的垂盆草 Cd 积累的影响和机制，以基于核心微生物组来证明细菌制剂的潜在应用。
通过创新的网络分析工作流程，我们基于两年的 16S rRNA 测序数据，确定了 97 个特属于超积累植物垂盆草的核心细菌分类群。然后构建了一个包含 13 株属于 6 个不同属的选定菌株的 SynCom。在植物和 Cd 污染的联合选择压力下，产碱杆菌属的 Alcaligenes sp. 与其他属和植物 Cd 浓度表现出拮抗关系。其他五个属的五个代表性菌株进一步进行了基因组重测序，并开发了六个 SynComs，通过水培实验比较了它们对 Cd 植物修复的影响与单菌株的影响。结果表明，包含 4 株菌（包括浅野黄单胞菌、解淀粉芽孢杆菌、恶臭假单胞菌和藤黄微球菌）的 SynCom-NS 具有最大的增强 Cd 植物修复的潜力。接种 SynCom-NS 后，两种生态型的垂盆草中与 Cd 转运、抗氧化防御和植物激素信号通路相关的基因均显著上调，从而促进了植物生长、Cd 吸收和转运。
在本研究中，我们设计了一种创新的网络分析工作流程来鉴定超积累植物中的核心内生微生物组。基于可培养的核心细菌，构建并验证了优化的 SynCom-NS，具有增强植物修复的巨大潜力。这项工作不仅为识别与特定特征相关的核心微生物组提供了框架，也为从核心微生物组构建功能合成群落以开发高效农业制剂铺平了道路。
