Abstract

ABSTRACTBacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments. In-depth understanding of these mechanisms can allow for better developing and utilizing of bacteria with various biological functions. In this study, we found that water-soluble humic materials (WSHM), a well-known environment-friendly plant growth biostimulant, significantly promoted the free-living growth and survival of Sinorhizobium fredii CCBAU45436 in a bell-shaped, dose-dependent manner, along with more-efficient carbon source consumption and relief of medium acidification. By using RNA-Seq analysis, a total of 1,136 genes significantly up-/downregulated by external addition of WSHM were identified under test conditions. These differentially expressed genes (DEGs) were enriched in functional categories related to carbon/nitrogen metabolism, cellular stress response, and genetic information processing. Further protein-protein interaction (PPI) network analysis and reverse genetic engineering indicated that WSHM might reprogram the transcriptome through inhibiting the expression of key hub gene rsh, which encodes a bifunctional enzyme catalyzing synthesis and hydrolysis of the “magic spot” (p)ppGpp. In addition, the root colonization and viability in soil of S. fredii CCBAU45436 were increased by WSHM. These findings provide us with new insights into how WSHM benefit bacterial adaptations and demonstrate great application value to be a unique inoculant additive.IMPORTANCE Sinorhizobium fredii CCBAU45436 is a highly effective, fast-growing rhizobium that can establish symbiosis with multiple soybean cultivars. However, it is difficult to maintain the high-density effective viable cells in the rhizobial inoculant for the stressful conditions during production, storage, transport, and application. Here, we showed that WSHM greatly increased the viable cells of S. fredii CCBAU45436 in culture, modulating metabolism and triggering stress defense. The root colonization and viability in soil of S. fredii CCBAU45436 were also increased by WSHM. Our results shed new insights into the effects of WSHM on bacteria and the importance of metabolism and stress defense during the bacteria’s whole life. In addition, the functional mechanism of WSHM may provide candidate genes for improving environmental adaptability and application potential of bacteria through genetic engineering.

Highlights

  • Bacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments

  • S. fredii CCBAU45436 in yeast mannitol (YM) broth was promoted by water-soluble humic materials (WSHM), but the efficiency varied according to the concentration

  • The results showed that supplying WSHM in YM broth significantly promoted the growth and survival of S. fredii CCBAU45436 (Fig. 1B)

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Summary

Introduction

Bacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments. By using RNA-Seq analysis, a total of 1,136 genes significantly up-/downregulated by external addition of WSHM were identified under test conditions These differentially expressed genes (DEGs) were enriched in functional categories related to carbon/nitrogen metabolism, cellular stress response, and genetic information processing. In the past few decades, the complex stress response network has been gradually elucidated by integrating the “stressomics” approaches and different induced conditions or genetic mutants These responses include protecting the cell envelope, regulating cellular metabolism, and defending macromolecules, etc. The cell envelope is the first barrier of bacteria; when cells are confronted with environmental perturbations, the envelope stress responses (ESRs), including Cpx and s E system, are trigged to maintain cellular homeostasis [6, 7]. Any stress leads to protein denaturation and influences the growth of bacteria, and a set of chaperones and proteases are induced to maintain protein homeostasis and help bacteria overcome stresses [9, 10]

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