Characterization and expression analysis of three cold shock protein (CSP) genes under different stress conditions in the Antarctic bacterium Psychrobacter sp. G

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.

Antioxidant prodigiosin-producing cold-adapted Janthinobacterium sp. ERMR3:09 from a glacier moraine: Genomic elucidation of cold adaptation and pigment biosynthesis

Janthinobacterium from cold niches has been studied broadly for bioactive violacein production. However, reports on the atypical red-pigmented Janthinobacterium strains are shallow. The bioactive red prodigiosin pigment has immense pharmacological significance, including antioxidant, antimicrobial and anticancer potential. Here, we report the first complete genome of a prodigiosin-producing Janthinobacterium sp. ERMR3:09 from Sikkim Himalaya in an attempt to elucidate its cold adaptation and prodigiosin biosynthesis. Nanopore sequencing and Flye assembly of the ERMR3:09 genome resulted in a single contig of 6,262,330 bp size and 62.26% GC content. Phylogenomic analysis and genome indices indicate that ERMR3:09 is a potentially novel species of the genus Janthinobacterium. The multicopy cold-responsive genes and gene upregulation under cold stress denoted its cold adaptation mechanisms. Genome analysis identified the unique genes, gene cluster and pathway for prodigiosin biosynthesis in ERMR3:09. Considering the notable antioxidant activity, it can be the next powerhouse of bioactive prodigiosin production.

CspB and CspC are induced upon cold shock in Bacillus cereus strain D2

Bacillus cereus D2, a psychrotrophic strain, plays an essential role in the restoration of heavy metal-contaminated soils, especially at low temperatures. However, the cold shock response mechanisms of this strain are unclear. In this study, the cold shock response of B. cereus D2 was characterized; as per the Arrhenius curve, 10 °C was chosen as the cold shock temperature. Six cold shock-like proteins were found and temporarily named cold shock protein (Csp)1-6; the respective genes were cloned and identified. Quantitative real-time PCR results showed that csp1, csp2, csp3, and csp6 were overexpressed under cold shock conditions. Interestingly, after cloning the respective encoding genes into pET-28a (+) vector and their subsequent transformation into E. coli BL21 (DE3), the strains expressing Csp2 and Csp6 grew faster at 10 °C, showing a large number of bacteria. These results suggest that Csp2 and Csp6 are the major cold shock proteins in B. cereus D2. Of note, the comparison of amino acid sequences and structures showed that Csp2 and Csp6 belong to the CspB and CspC families, respectively. Additionally, we show that the number of hydrophobic residues is not a determining feature of major Csps, while, on the other hand, the formation of an α-helix in the context of a leucine residue is the most dominant difference between major, and other Bacillus and E. coli Csps.

Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.

Exploring the Brine Microbiota of a Traditional Norwegian Fermented Fish Product (Rakfisk) from Six Different Producers during Two Consecutive Seasonal Productions

The purpose of this study was to explore the microbiota of Norwegian fermented fish (rakfisk), a traditional product popular in the Norwegian market. Brine samples, collected from six producers during two subsequent years, were used. The producers applied different salt concentrations (between 3.8% and 7.2% NaCl), ripening temperatures (between 3.5 and 7.5 °C), fish species (trout or char), and fish upbringing (wild trout, on-shore farmed trout or char, and off-shore farmed char). The microbiota in the brine during the ripening process was mainly characterized by DNA-based, culture-independent methods. In total, 1710 samples were processed and of these 1342 were used for the final analysis. The microbiota was dominated by Gammaproteobacteria and Bacilli with the largest variance between samples associated with the genera Psychrobacter and Lactobacillus. The variance in the material was mainly determined by the origin of the samples, i.e., the different producers. The microbiota from the individual producers was to a large extent reproducible from one year to the next and appeared to be determined by the relatively small differences in the salinity and the ripening temperature. This is the first study exploring the microbiota in rakfisk brine and it provides insights into environmental factors affecting the rakfisk ecosystems.

Transcriptomic and cortisol analysis reveals differences in stress alleviation by different methods of anesthesia in Crucian carp (Carassius auratus)

Stress response has negative effect on fish in aquaculture and research, which can be alleviated with anesthetic. To determine the optimal anesthetic, we investigated the physiological response of crucian carp (Carassius auratus) treated with three different anti-stress treatments: MS-222, eugenol and percussive stunning. Stress responses were evaluated by analyzing serum cortisol level and gene expression in blood. We determined the optimal concentrations of MS-222 (100 mg L^-1) and eugenol (20 mg L^-1) by dose selection. We found that the control group had significantly higher cortisol levels (172.78 ± 19.95 ng mL^-1) compared to the MS-222 treated group (46.85 ± 3.22 ng mL^-1), the eugenol treated group (72.78 ± 9.07 ng mL^-1), and the stunning treatment group (82.78 ± 8.16 ng mL^-1). Transcriptome analysis revealed 1572 differentially expressed genes (DEGs), including 155 DEGs related to the stress response, mainly involved in oxidative-stress response, heat shock proteins, and cold shock domain-containing protein. The heat shock protein genes were the primary DEGs in response to stress. RT-qPCR analysis confirmed differential expression of Hsps. We analyzed the function of the DEGs, which were enriched in genes involved in cellular response to stress and antigen processing and presentation. Combining the results from biochemical, transcriptome, and gene expression analysis, our data suggest that eugenol is more effective than MS-222 and percussive stunning in alleviating stress in crucian carp.

Exploring the genome of Arctic Psychrobacter sp. DAB_AL32B and construction of novel Psychrobacter-specific cloning vectors of an increased carrying capacity

Cold-active bacteria are currently of great interest in biotechnology, and their genomic and physiological features have been extensively studied. One of the model psychrotolerant bacteria are Psychrobacter spp. Analysis of Arctic psychrophilic Psychrobacter sp. DAB_AL32B genome content provided an insight into its overall stress response, and genes conferring protection against various life-limiting factors (i.e., low temperature, increased ultraviolet radiation, oxidative stress and osmotic pressure) were recognized and described. Moreover, it was revealed that the strain carries a large plasmid pP32BP2. Its replication system was used for the construction of two novel shuttle vectors (pPS-NR-Psychrobacter-Escherichia coli-specific plasmid and pPS-BR-Psychrobacter-various Proteobacteria-specific plasmid) of an increased carrying capacity, which may be used for genetic engineering of Psychrobacter spp.

CspE is Overproduced by Temperature Downshift in the Acinetobacter johnsonii DBP-3

The denitrifying bacterium Acinetobacter johnsonii strain DBP-3 which was capable of removing phosphate, nitrate, and ammoniacal salt is psychrotolerant, whereas, the cold shock response mechanisms or the cold shock proteins (Csps) was unclear. In this article, the optimal growth temperature (25 °C) and cold shock temperature (7.5 °C) were determined firstly by an Arrhenius plot of the growth of the strain DBP-3. Then, among the seven cold shock-like protein genes which were cloned and identified referenced by A. johnsonii SH046 genome, qRT-PCR and shotgun-LTQ mass spectrometry showed that Csp3 and Csp4 were overexpressed under cold shock condition. Furthermore, Western blotting confirmed the result with the antibodies against Csp3 and Csp4 prepared by ourselves. Finally, the phylogenetic analysis showed that the similarity percent between Csp3 and Csp4 was 76.85 %, and Csp3 and Csp4 belonged to CspE family. The results indicated that CspE is overproduced by temperature downshift and may play an important role in the psychrotolerant process of strain DBP-3.

Response of heat-shock protein (HSP) genes to temperature and salinity stress in the antarctic psychrotrophic bacterium Psychrobacter sp. G

Temperature and salinity fluctuations are two of the most important factors affecting the growth of polar bacteria. In an attempt to better understand the function of heat-shock proteins (HSPs) in the adaptive mechanisms of the Antarctic psychrotrophic bacterium Psychrobacter sp. G to such conditions, genes Hsp845, Hsp2538, Hsp2666, and Hsp2667 were cloned on the basis of the draft genome. The expression characteristics of these HSP genes under different stress conditions were analyzed by the qRT-PCR method. Expression of Hsp845 and Hsp2667 was inhibited significantly by low temperature (0 and 10 °C, respectively). There was no difference of expression when Hsp2538 and Hsp2666 were exposed to 0 °C but the expression of Hsp2666 was inhibited when exposed to 10 °C. Expression of Hsp2538 and Hsp2667 was not sensitive but expression of Hsp845 and Hsp2666 was increased at low salinity (0 and 15, respectively). Expression of the four HSP genes was enhanced at high salinity (90 and 120) and at high temperature independent of salinity. By contrast, low temperature had no significant effect independent of salinity.