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

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.

Short-Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups

“…Therefore, our research was fully focused on 2-day exposure to salt stress. In pure-culture transcriptome studies, this exposure time is considered long-term incubation given that microorganisms that are able to cope with moderate and high salt stress exhibit an adaptive transcriptome response within 2 days (Zaprasis et al, 2015; Nagler et al, 2016). …”

“…Depending on the ability of the particular microorganism to cope with salt stress, this early period is followed by an adaptive transcriptome response that is governed by up-regulation of gene expression. This adaptive response occurs within a few hours or days (Zaprasis et al, 2015; Nagler et al, 2016). The key taxonomic groups involved in the methanogenic breakdown of plant polymers significantly differed in their ability to cope with salt stress.…”

Towards the minimal proteome of life: Proteome profiles ofBacillus subtilisvegetative cells and spores

“…These proteins belong to the ABC transporters family, including the protein and amino acid transporters, as well as families of ion transporters. Interestingly, in a recent transcriptome study, almost 80 transcripts encoding different transporters have been identified from spore mRNA isolates 23 .…”

Investigating germination and outgrowth of bacterial spores at several scales

“…2G). RNA is extracted from germinated spores or outgrowing cells over time and analyzed using different methods such as microarrays (Keijser et al, 2007), RNA-seq (Nagler et al, 2016) or RT qPCR (Bassi et al, 2016). Gene expression can be analyzed by specific pipelines such as T-Rex or JBrowse (Skinner, Uzilov, Stein, Mungall, & Holmes, 2009;de Jong, van der Meulen, Kuipers, & Kok, 2015).…”