# Adaptation of the Marine Bacterium _Shewanella baltica_ to Low Temperature Stress
## 4 Conclusions  
Here, we present evidence that _S. baltica_ undergoes global transcriptional changes in order to adapt to cold stress. The most pronounced response was massive downregulation of approximately 70% of differentially expressed genes, indicating a general shutting down of many energy-consuming pathways to increase survival. However, certain pathways were upregulated, and their roles generally correspond with stress adaptation and in some extent coincide with analogous responses observed in other _Shewanella_ genus representatives. In particular, cold induced proteins' gene expression was increased, and the fatty acids synthesis pathways were adjusted to alter membrane composition to higher content of unsaturated fatty acids to preserve membrane fluidity. Interestingly, global transcription reprogramming was observed in cold-stressed _S. baltica_: expression of the _rpoE_ gene, encoding the sigma E factor, was induced in response to the envelope and oxidative stress, while the housekeeping sigma factor, _rpoD_, expression decreased. We also observed an increase in the flagellar genes' expression indicating that _S. baltica_ intensifies its motility in response to cold stress. Modulation of amino acid metabolism and protein translation network is another evident response of _S. baltica_ to the temperature drop. Alterations in amino acid profiles during cold stress are apparently common in bacterial world, thus it may be assumed as a universal response mechanism ensuring adequate protein structural flexibility, stability and activity at low temperatures. Transcriptional downregulation of type II secretion system observed in our study will definitely affect the export of proteins outside the cell via this route. This phenomenon of complete transcriptional switch off of one specific secretion system needs further investigation to elucidate its role in bacterial survival and adaptation capacity at low temperatures. Our results also indicate that cold stress may stimulate _S. baltica_ to prepare for potentially upcoming anaerobic conditions, which are common at low temperatures in the complex marine environment. We detected a significant upregulation of expression of genes assigned to the assimilatory branch of the sulfate reduction pathway, but we did not observe a transcriptional switch to anaerobic respiration at the transcriptional level, perhaps due to a relatively short period of cold stress in our experimental design. However, as downregulation of genes encoding degradation of thiosulfate and tetrathionate was observed, we hypothesize that these two compounds might eventually serve as electron acceptors in alternative respiration pathways, which were previously described for the _Shewanella_ genus. _Shewanella_ species are considered as the main players in denitrification and bioremediation processes; they are also known for their spoilage and decomposition potential. Thus, revealing the mechanisms of _S. baltica_ response to low temperatures is important not only for the general knowledge of bacterial cold stress adaptability, but it is also of great importance for the marine environmental studies, as well as for biotechnology, with focus on e.g., bioremediation, and even for the fishery industry. Supplementary materials can be found at [[http://www.mdpi.com/1422-0067/21/12/4338/s1](http://www.mdpi.com/1422-0067/21/12/4338/s1)]([http://www.mdpi.com/1422-0067/21/12/4338/s1](http://www.mdpi.com/1422-0067/21/12/4338/s1)). Table S1. List of significantly altered genes upon cold stress. Filtering criteria: log2 FC] > 1 and \(q\) value < 0.01. Table S2. Summary statistics for sequencing and mapping. Table S3. KEGG pathway enrichment in genes up and downregulated upon cold stress. Table S4. Primers used in RT-qPCR assay. Figure S1. Gene enrichment of up- and downregulated metabolic pathways upon cold stress in _S. baltica_. Figure S2. Fatty acid biosynthesis metabolic pathways regulated upon cold stress in _S. baltica_. Figure S3. Fatty acid degradation metabolic pathway regulated upon cold stress in _S.