State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China.
Appl Environ Microbiol. 2019 Mar 6;85(6). doi: 10.1128/AEM.02523-18. Print 2019 Mar 15.
A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion. Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.
缺乏对物种和功能水平上微生物对环境变化反应的了解，阻碍了我们理解微生物生态系统维持内在机制的能力。在这里，我们展示了在 90 天内将无机和有机污染物引入农业土壤中，同时种植三种常见豆科植物的时间微宇宙的结果。通过对 16S rRNA 扩增子的测序和 shotgun 宏基因组学，探索了在不同植物生长影响下，土壤微生物群落的时间动态和组合以及对污染的反应。土壤微生物在分类和功能水平上的α多样性和结构表现出弹性模式。功能谱比分类谱更具弹性。不同的豆科植物对分类谱的选择比对功能谱的选择更强。网络和随机森林分析表明，土壤微生物群落的功能潜力是由各种分类群促进的。关键功能特征（如氨基酸代谢、核酸代谢和碳氢化合物降解）的重要预测因子。我们的研究揭示了土壤微生物组对化学污染的强大弹性，以及对不同豆科植物选择过程的敏感反应，而不是功能谱。这对于开发方法和政策以保护具有不同响应策略的农业生态系统中的土壤微生物多样性和功能至关重要，这些策略来自全球环境驱动因素，如土壤污染和植物入侵。探索微生物对环境干扰的反应是微生物生态学的一个核心问题。了解土壤微生物群落对化学污染的动态响应以及微生物-土壤-植物相互作用对于预测土壤生态系统的长期变化至关重要。然而，很少有研究应用多组学方法来评估土壤微生物对化学污染的响应以及分类和功能水平上的微生物-土壤-植物相互作用。我们的研究揭示了土壤微生物多样性和结构对化学污染响应的清晰演替和弹性模式。在污染土壤中，不同的豆科植物对分类谱的选择比对功能谱的选择要强，这有利于植物的生长和适应性，以及促进烃类降解和金属耐受性的潜在能力。这些结果为在物种和功能水平上研究农业生态系统中土壤微生物组对环境干扰的弹性和组合提供了新的见解。
