Soil bacteria show different tolerance ranges to an unprecedented disturbance

Abstract

Soil microbial communities have remarkable capacities to cope with ceaseless environmental changes, but little is known about their adaptation potential when facing an unprecedented disturbance. We tested the effect of incremental dose of microwaving on soil bacteria as a model of unprecedented stress. 16S rRNA gene qPCR at both the DNA and cDNA levels was used to characterize the total (DNA) and transcriptionally active (cDNA) fractions of the bacterial community. Amplicon sequencing of 16S rRNA gene transcripts was performed to decipher tolerance ranges within the community using the concept of functional response groups (FRGs). Increasing microwaving doses resulted in 90% loss in total and transcriptionally active bacterial communities after 6.8 and 4.7 min, respectively. Four distinct FRGs with peculiar phylogenetic signatures were identified, revealing a link between taxonomy and increasing stress doses. FRG1, the most sensitive group, was dominated by Actinobacteria. FRG2 and FRG3, with intermediate tolerance, displayed prevalence of Proteobacteria, while FRG4, the most resistant group, was driven by Firmicutes. While the most sensitive FRGs showed predictable responses linked to changes in temperature and soil water content associated with microwaving, more tolerant FRG4 members exhibited a stochastic response nested within the Firmicutes phylum, potentially revealing bet-hedging strategists. The concept of FRGs based on 16S rRNA gene transcripts stood as an efficient tool for unraveling bacterial survival strategies and tolerance ranges triggered by incremental doses of an unprecedented stress, with regard to phylogeny linkages.