Specialized metabolic functions of keystone taxa sustain soil microbiome stability

Weibing Xun,Yi Ren,Wu Xiong,Nan Zhang,Wei Li,Youzhi Miao,Qirong Shen,Zhihui Xu,Yunpeng Liu,Ruifu Zhang

doi:10.1186/s40168-020-00985-9

Abstract

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.71g_gU7sXqyRUXVnTuv-FBVideo abstract

Highlights

The relationship between biodiversity and soil microbiome stability remains poorly understood
The 16S rRNA gene copies in all microcosms did not increase after 8 weeks of incubation, and we found no significant changes among dilution levels and soil pH levels at the end of incubation period (Additional file: Figure S2)
Considering that manipulation of the soil pH was not performed to the undiluted initial soil sample along with the finding of no significant differences with the reassembled 10-1 diluted bacterial communities, we only analyzed the diluted and re-assembled communities in this study

Summary

Introduction

The relationship between biodiversity and soil microbiome stability remains poorly understood. We investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. The sustainability of both the functions and services rendered by the terrestrial ecosystem is dependent on a relatively stable microbiome [3], defined as the degree of variation or turnover rate of the microbial community [4]. These alterations in the microbiome in response to environmental changes fall into the two predominant categories of deterministic and stochastic processes [5]. It is important to understand the properties that underlie the stability of microbial assemblages as well as the possible downstream functional consequences that may have an impact on overall ecosystem function

Methods

Results

Discussion

Conclusion