Is the accumulation of osmoprotectant the unique mechanism involved in bacterial osmoprotection?

Tune in to the terrific applications of turanose

Turanose, a rare sugar with low calorific value and glycemic index, used as an alternative to sucrose and other artificial sweeteners. The occurrence of turanose is in limited quantities, especially found in honey. Thus, it should be produced by either chemical or biological means. Turanose is released as a by-product during synthesis of the linear α-(1,4)-glucan from sucrose by the action of amylosucrase. In recent times, turanose attracted interest in several industries such as agricultural, food, and pharmaceuticals due to its feasible production. Hence, this review outlines about the history of turanose, its physiochemical properties, production along with inhibition and inducing effects. It is high time to tune in the terrific applications of turanose, as it retains the potential for more than a century of discovery, since 1889. These applications include detection of pathogens, facilitation of cellular respiration, regulation of inflammation, authentication of honey, phagodeterrency effects, osmoprotection, stabilization of therapeutical proteins, and edibility enhancement of foods.

Simultaneous Quantification of Trehalose and Trehalose 6-Phosphate by Hydrophilic Interaction Chromatography/Electrospray Accurate Mass Spectrometry with Application in Non-Targeted Metabolomics

High-resolution mass spectrometry (HRMS) was coupled with ultra-high-performance liquid chromatography (UHPLC) to simultaneously quantify trehalose and trehalose 6-phosphate without derivatization or sample preparation. The use of full scan mode and exact mass analysis also makes it possible to carry out metabolomic analyses as well as semi-quantification. In addition, the use of different clusters in negative mode makes it possible to compensate for deficiencies in linearity and inerrant saturation at time-of-flight detectors. The method has been approved and validated for different matrices, yeasts, and bacteria, and has shown differentiation between bacteria as a function of growth temperatures.

A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome

Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress

Background

For microorganisms on a paper surface, the lack of water is one of the most important stress factors. A strain of Bacillus megaterium FDU301 was isolated from plaques on a paper surface using culture medium with polyethylene glycol 200 (PEG200) to simulate an arid condition. Global transcriptomic analysis of B. megaterium FDU301 grown under normal and simulated arid conditions was performed via RNA-seq technology to identify genes involved in arid stress adaptation.

Results

The transcriptome of B. megaterium FDU301 grown in LB medium under arid (15% PEG200 (w/w)) and normal conditions were compared. A total of 2941 genes were differentially expressed, including 1422 genes upregulated and 1519 genes downregulated under arid conditions. Oxidative stress-responsive regulatory genes perR, fur, and tipA were significantly upregulated, along with DNA protecting protein (dps), and catalase (katE). Genes related to Fe²⁺ uptake (feoB), sporulation stage II (spoIIB, spoIIE, spoIIGA), small acid-soluble spore protein (sspD), and biosynthesis of compatible solute ectoine (ectB, ectA) were also highly expressed to various degrees. Oxidative phosphorylation-related genes (atpB, atpE, atpF, atpH, atpA, atpG, atpD, atpC) and glycolysis-related genes (pgk, tpiA, frmA) were significantly downregulated.

Conclusion

This is the first report about transcriptomic analysis of a B. megaterium to explore the mechanism of arid resistance. Major changes in transcription were seen in the arid condition simulated by PEG200 (15%), with the most important one being genes related to oxidative stress. The results showed a complex mechanism for the bacteria to adapt to arid stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02039-4.

Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

Whole genome sequences of four bacterial strains Dietzia maris SST1, Pseudomonas zhaodongensis SST2, Pseudomonas sp. SST3 and Halomonas sulfidaeris SST4, recovered from the South Shetland Trench sediment in Antarctica were analyzed using Ion Torrent sequencing technology. The respective sizes of their genomes (3.88, 4.99, 5.60 and 4.25 Mb) and GC contents (70.0, 60.3, 59.9 and 53.8%) are in agreement with these values of other strains of the species. The bacterial strains displayed promising antimicrobial activity against a number of pathogenic bacterial and fungal species. Whole genomes have been assembled and biosynthetic gene clusters (BGCs) have been identified using the antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) web platform. Comparative analysis of the genome sequences revealed that the strains host abundant BGCs encoding for terpenes, siderophores, arylpolyene, bacteriocins, and lassopeptides. Furthermore, the key stress-related genes were identified and their distribution provided an insight into how these isolates adapt to key marine environmental conditions. This comprehensive study is a contribution to understanding the nature of life on the deep-sea environments.

Deciphering the Symbiotic Plant Microbiome: Translating the Most Recent Discoveries on Rhizobia for the Improvement of Agricultural Practices in Metal-Contaminated and High Saline Lands

Rhizosphere and plant-associated microorganisms have been intensely studied for their beneficial effects on plant growth and health. These mainly include nitrogen-fixing bacteria (NFB) and plant-growth promoting rhizobacteria (PGPR). This beneficial fraction is involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses, which include water deficiency and heavy-metal contamination. Consequently, crop yield emerges as the net result of the interactions between the plant genome and its associated microbiome. Here, we provide a review covering recent studies on PGP rhizobia as effective inoculants for agricultural practices in harsh soil, and we propose models for inoculant combinations and genomic manipulation strategies to improve crop yield.

Glycine betaine enhances biodegradation of phenol in high saline environments by the halophilic strainOceanobacillussp. PT-20

Glycine betaine enhanced the biodegradation of phenol by halophilic strain PT-20 in high salinity conditions.

Adaptations of Bacillus shacheensis HNA-14 required for long-term survival under osmotic challenge: a multi-omics perspective

Genomic sequence, transcriptomic, metabolomic and fatty acid analyses of strain HNA-14 were performed to understand the mechanism of salt tolerance for long-term survival. The results indicated that strain HNA-14 has different osmotic resistance mechanisms for long-term survival and short-term salt stress. The cells mainly synthesized compatible solutes to resist osmotic pressure when cultured under nutrient deficient conditions, while they can slow down the synthesis rate and uptake from the environment when cultured under a nutritionally rich environment. Also, the amounts of branched and unsaturated fatty acids in the cell membrane are maintained to a high degree (>50%) to maintain the fluidity of the cell membrane; when the cells are cultured in a high osmotic environment for long-term survival, they may increase the content of branched fatty acids and phosphoric fatty acids to increase the fluidity of the cell membrane to resist the high osmotic pressure.

DEOP: a database on osmoprotectants and associated pathways

Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, 'Dragon Explorer of Osmoprotection associated Pathways' (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/

Osmotic stress adaptations in rhizobacteria

Rhizobacteria have been reported to be beneficial to the plants in many different ways. Increasing salinity in the coastal agricultural zones has been shown to be a threat to the plant and microbial life in the area. Exposure of microorganisms to high-osmolality environments triggers rapid fluxes of cell water along the osmotic gradient out of the cell, thus causing a reduction in turgor and dehydration of the cytoplasm. The microorganisms have developed various adaptations to counteract the outflow of water. The first response to osmotic up shifts and the resulting efflux of cellular water is uptake of K⁺ and cells start to accumulate compatible solutes. Yet another mechanism is by altering the cell envelope composition resulting in changes in proteins, periplasmic glucans, and capsular, exo and lipopolysaccharides. Bacteria also initiate a program of gene expression in response to osmotic stress by high NaCl concentrations, which are manifested as a set of proteins produced in increased amounts in response to the stress. Genomics, transcriptomics and proteomics approaches have revealed the key components in molecular basis of bacteria salt adaptation. Understanding the mechanisms of osmo-adaptation in rhizobacteria would also be relevant from an ecological and an applicative point of view.

Mg2+ as an indicator of nutritional status in marine bacteria

Cells maintain an osmotic pressure essential for growth and division, using organic compatible solutes and inorganic ions. Mg(2+), which is the most abundant divalent cation in living cells, has not been considered an osmotically important solute. Here we show that under carbon limitation or dormancy native marine bacterial communities have a high cellular concentration of Mg(2+) (370-940 mM) and a low cellular concentration of Na(+) (50-170 mM). With input of organic carbon, the average cellular concentration of Mg(2+) decreased 6-12-fold, whereas that of Na(+) increased ca 3-4-fold. The concentration of chlorine, which was in the range of 330-1200 mM, and was the only inorganic counterion of quantitative significance, balanced and followed changes in the concentration of Mg(2+)+Na(+). In an osmotically stable environment, like seawater, any major shift in bacterial osmolyte composition should be related to shifts in growth conditions, and replacing organic compatible solutes with inorganic solutes is presumably a favorable strategy when growing in carbon-limited condition. A high concentration of Mg(2+) in cells may also serve to protect and stabilize macromolecules during periods of non-growth and dormancy. Our results suggest that Mg(2+) has a major role as osmolyte in marine bacteria, and that the [Mg(2+)]/[Na(+)] ratio is related to its physiological condition and nutritional status. Bacterial degradation is a main sink for dissolved organic carbon in the ocean, and understanding the mechanisms limiting bacterial activity is therefore essential for understanding the oceanic C-cycle. The [Mg(2+)]/[Na(+)]-ratio in cells may provide a physiological proxy for the transitions between C-limited and mineral nutrient-limited bacterial growth in the ocean's surface layer.

Identification and characterization of metagenomic fragments from tidal flat sediment

Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shotgun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.

Osmoadaptative responses in the rhizobia nodulating Acacia isolated from south-eastern Moroccan Sahara

Four strains of rhizobia nodulating Acacia were isolated from the Moroccan desert soil by trapping with seedlings of Acacia gummifera and Acacia raddiana, and were studied for their ability to tolerate high salinity and dryness conditions. The strains MDSMC 2, MDSMC 18 and MDSMC 50 were halotolerant (they tolerated up to 1 M NaCl) and they accumulated glutamate and mannosucrose. The synthesis of the latter solute, which is the major endogenous osmolyte, is partially repressed in the presence of glycine betaine. The strain MDSMC 34 was less halotolerant (growth inhibited by a concentration greater than 0.5 M NaCl), and accumulated trehalose (as the main endogenous osmolyte) and glutamate. Rhizobia from the Moroccan desert soil were highly resistant to desiccation and their tolerance to dryness was stimulated by osmotic pretreatment. Thus, the accumulation of mannosucrose or trehalose by desert rhizobia represents both an osmoadaptative response and a part of a desiccation tolerance mechanism.

Ectoine-induced proteins in Sinorhizobium meliloti include an Ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism

To understand the mechanisms of ectoine-induced osmoprotection in Sinorhizobium meliloti, a proteomic examination of S. meliloti cells grown in minimal medium supplemented with ectoine was undertaken. This revealed the induction of 10 proteins. The protein products of eight genes were identified by using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Five of these genes, with four other genes whose products were not detected on two-dimensional gels, belong to the same gene cluster, which is localized on the pSymB megaplasmid. Four of the nine genes encode the characteristic components of an ATP-binding cassette transporter that was named ehu, for ectoine/hydroxyectoine uptake. This transporter was encoded by four genes (ehuA, ehuB, ehuC, and ehuD) that formed an operon with another gene cluster that contains five genes, named eutABCDE for ectoine utilization. On the basis of sequence homologies, eutABCDE encode enzymes with putative and hypothetical functions in ectoine catabolism. Analysis of the properties of ehuA and eutA mutants suggests that S. meliloti possesses at least one additional ectoine catabolic pathway as well as a lower-affinity transport system for ectoine and hydroxyectoine. The expression of ehuB, as determined by measurements of UidA activity, was shown to be induced by ectoine and hydroxyectoine but not by glycine betaine or by high osmolality.

Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence

Two general strategies exist for the growth and survival of prokaryotes in environments of elevated osmolarity. The 'salt in cytoplasm' approach, which requires extensive structural modifications, is restricted mainly to members of the Halobacteriaceae. All other species have convergently evolved to cope with environments of elevated osmolarity by the accumulation of a restricted range of low molecular mass molecules, termed compatible solutes owing to their compatibility with cellular processes at high internal concentrations. Herein we review the molecular mechanisms governing the accumulation of these compounds, both in Gram-positive and Gram-negative bacteria, focusing specifically on the regulation of their transport/synthesis systems and the ability of these systems to sense and respond to changes in the osmolarity of the extracellular environment. Finally, we examine the current knowledge on the role of these osmostress responsive systems in contributing to the virulence potential of a number of pathogenic bacteria.