Specialized metabolic functions of keystone taxa sustain soil microbiome stability

TLDR

The link between biodiversity and soil microbiome stability is poorly understood. The study examined how bacterial phylogenetic diversity affects functional traits and microbiome stability. Researchers generated communities with varying phylogenetic diversity by serially diluting soil suspensions into sterilized soil, assessed stability through community variation under different pH levels, and used DNA sequencing to profile taxonomic features and functional traits. Higher phylogenetic diversity correlated with greater microbiome stability, and network and machine‑learning analyses revealed that specialized metabolic functions—particularly nitrogen metabolism and phosphonate/phosphinate metabolism—serve as keystone functions carried by taxa such as Nitrospira and Gemmatimonas. A video abstract is available.

Abstract

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.