Soil microbial activities are an important factor driving material and nutrient cycling in the terrestrial ecosystem. The sustainability of both the functions and services rendered by the terrestrial ecosystem depends on a relatively stable microbiome. In recent years, the threat of loss in soil microbial diversity to the ecosystem has attracted worldwide attention, and research on microbial diversity and ecosystem stability has accelerated.

The top journal in the field of microbiology, Microbiome (IF 12.16), recently published online the latest research results of the Innovation Team of Agricultural Microbial Resources of the Institute of Agricultural Resources and Regional Planning (IARRP) of the Chinese Academy of Agricultural Sciences (CAAS), under the title Specialized Metabolic Functions of Keystone Taxa Sustain Soil Microbiome Stability.

Microbiome stability can be measured by the resilience or resistance of a community. Based on the high-throughput sequencing data which is currently widely used in soil microbial community research, this work proposed and verified the reliability and application of the Average Variation Degree (AVD) values as an indicator of microbiome stability. This strategy is not limited by the number of samples.

The study found that with the decline in soil microbial diversity, the AVD values increased and the community stability decreased. To elucidate the relationship between functional genes and microbiome stability, evaluation of the importance of gene categories associated with AVD values was conducted by the “random forest” method, which identified key specialized metabolic functions, especially “nitrogen metabolism” and “phosphonate and phosphinate metabolism”.

In this work, the key functional genes were detected as critical members in the functional gene co-occurrence network. These functional genes decreased with the decline of microbial diversity, simplified the modularity of functional gene co-occurrence networks, and decreased soil microbiome stability.

Further taxonomic annotation found that the relative abundance of all bacterial taxa decreased with the decline in microbial diversity, and that key functions are carried out by various specific bacterial taxa, including Nitrospira and Gemmatimonas.

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.

Associate Professor Xun Weibing from Nanjing Agricultural University and associate research fellow Liu Yunpeng from the Innovation Team of Agricultural Microbial Resources of IARRP, CAAS, are the co-first authors. Research fellow Zhang Ruifu from the Innovation Team of Agricultural Microbial Resources of IARRP, CAAS, is the corresponding author. The research was funded by the National Natural Science Foundation of China, the Innovation Project of CASS, and the Young Talent Support Project of the China Association for Science and Technology.

Zhang Ruifu has carried out research on farmland soil microbial diversity and rhizosphere microbial community assembly over recent years. The research results illustrate the major driving factors of soil microbiome structure and functions (Soil Biology and Biochemistry, 2015&2016; Environmental Microbiology, 2016; and Microbiome, 2018); reveal the specialized functions in microbiome community assembly processes (Nature Communications, 2019), and propose the functional compensation mechanism that dominates the assembly of the plant rhizospheric bacterial community (Soil Biology and Biochemistry, 2020).

https://doi.org/10.1186/s40168-020-00985-9