Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing.

Katja Nagler,Antonina O Krawczyk,Kazimierz Madela,Oscar P Kuipers,Michael Laue,Ralf Moeller,Erhard Bremer,Tamara Hoffmann,Anne De Jong

doi:10.3389/fmicb.2016.01564

Abstract

In its natural habitat, the soil bacterium Bacillus subtilis often has to cope with fluctuating osmolality and nutrient availability. Upon nutrient depletion it can form dormant spores, which can revive to form vegetative cells when nutrients become available again. While the effects of salt stress on spore germination have been analyzed previously, detailed knowledge on the salt stress response during the subsequent outgrowth phase is lacking. In this study, we investigated the changes in gene expression during B. subtilis outgrowth in the presence of 1.2 M NaCl using RNA sequencing. In total, 402 different genes were upregulated and 632 genes were downregulated during 90 min of outgrowth in the presence of salt. The salt stress response of outgrowing spores largely resembled the osmospecific response of vegetative cells exposed to sustained high salinity and included strong upregulation of genes involved in osmoprotectant uptake and compatible solute synthesis. The σB-dependent general stress response typically triggered by salt shocks was not induced, whereas the σW regulon appears to play an important role for osmoadaptation of outgrowing spores. Furthermore, high salinity induced many changes in the membrane protein and transporter transcriptome. Overall, salt stress seemed to slow down the complex molecular reorganization processes (“ripening”) of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.

Highlights

In its natural habitat, the soil bacterium Bacillus subtilis is frequently confronted with fluctuating environmental conditions and has evolved a broad range of elaborate stress responses (Marles-Wright and Lewis, 2007, 2010; Lopez et al, 2009; Schultz et al, 2009)
B. subtilis spore germination at high salinity has previously been investigated (Nagler et al, 2014, 2015; Nagler and Moeller, 2015), but only little is known about the effects of salt stress on the transcriptional profile of outgrowing spores
This salt concentration was chosen in accordance with former studies on the salt stress response in vegetative B. subtilis cells and studies on B. subtilis spore germination at high salinity (Boch et al, 1994; Steil et al, 2003; Nagler et al, 2014, 2015, 2016)

Summary

Introduction

The soil bacterium Bacillus subtilis is frequently confronted with fluctuating environmental conditions and has evolved a broad range of elaborate stress responses (Marles-Wright and Lewis, 2007, 2010; Lopez et al, 2009; Schultz et al, 2009). When soil desiccation creates hyperosmotic conditions, cells have to adjust their internal osmolality to avoid water efflux and plasmolysis (Wood et al, 2001; Hoffmann and Bremer, 2016). B. subtilis cells quickly take up large amounts of K+ via the KtrAB and KtrCD transport systems to restore internal osmotic pressure (Whatmore et al, 1990; Holtmann et al, 2003). B. subtilis subsequently replaces K+ by compatible solutes, highly soluble organic compounds that do not disturb cell physiology, to adjust its intracellular osmotic potential (Whatmore et al, 1990; Kempf and Bremer, 1998). The most important compatible solutes for B. subtilis are glycine betaine (GB) and proline (Hoffmann and Bremer, 2016)

Methods

Results

Conclusion