Specialized metabolic functions of keystone taxa sustain soil microbiome stability

Microbiome

Youzhi Miao¹  Wei Li¹  Ruifu Zhang¹  Wu Xiong¹  Zhihui Xu¹  Yi Ren¹  Qirong Shen¹  Weibing Xun¹  Nan Zhang¹  Yunpeng Liu² 

[1]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

[2]Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences

关键词: Soil incubation;    Microbial diversity and stability;    Co-occurrence network;    Machine learning;    Keystone function;   

DOI  :  10.1186/s40168-020-00985-9

来源: DOAJ

【 摘 要 】

Abstract Background 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. Results 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. Conclusions 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

【 授权许可】

Unknown