Specialized metabolic functions of keystone taxa sustain soil microbiome stability

BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.

Automated summary

The study revealed that bacterial communities with higher phylogenetic diversity tend to be more stable, indicating that microbiomes with higher biodiversity are more resilient to disturbances. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially nitrogen metabolism and phosphonate and phosphinate metabolism, as key functions. Further taxonomic annotation revealed that these key functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas.