Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
Microbiome. 2021 Jan 31;9(1):35. doi: 10.1186/s40168-020-00985-9.
The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.
We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others.
This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.
生物多样性与土壤微生物组稳定性之间的关系仍知之甚少。在这里，我们研究了细菌系统发育多样性对土壤微生物组功能特征和稳定性的影响。通过将系列稀释的土壤悬浮液接种到灭菌土壤中，产生系统发育多样性不同的群落，并通过检测不同 pH 值下群落的变化来评估微生物组的稳定性。通过 DNA 测序检测分类特征和潜在的功能特征。
我们发现，系统发育多样性较高的细菌群落往往更稳定，这意味着具有更高生物多样性的微生物组更能抵抗扰动。功能基因共现网络和机器学习分类分析确定了专门的代谢功能，特别是“氮代谢”和“膦酸盐和膦酸代谢”，作为关键功能。进一步的分类注释发现，关键功能是由特定的细菌类群执行的，包括硝化螺旋菌和Gemmatimonas 等。
本研究为我们理解土壤微生物组生物多样性与生态系统稳定性之间的关系提供了新的见解，并强调了关键类群中嵌入的专门代谢功能，这些功能可能对土壤微生物组的稳定性至关重要。视频摘要。
