Complete genome sequences of Geobacillus stearothermophilus strains EF60045 and SJEF4-2 from Korean hot springs.

We report the complete genomes of Geobacillus stearothermophilus strains EF60045 and SJEF4-2 from Korean hot springs, with 3,769 and 3,625 thermophilic genes, respectively. G. stearothermophilus EF60045 shows four methylation patterns. G. stearothermophilus SJEF4-2 harbors three plasmids. These findings enhance understanding of Geobacillus strains, aiding in their development as microbial platform hosts.

Complete genome sequences of Thermus thermophilus strains isolated from Shirahama Hot Spring in Japan.

We isolated six Thermus thermophilus strains from Shirahama Hot Spring in Japan. Complete genome sequences, determined by combining Oxford Nanopore long-read and Illumina short-read sequence data, revealed that they showed >99.9% average nucleotide identities with each other and approximately 97% to the genome of the type strain HB8T.

Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China.

Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.

Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities.

BACKGROUND: Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS: Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS: By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.

Could Life Have Started on Mars? Planetary Conditions That Assemble and Destroy Protocells.

Early Mars was likely habitable, but could life actually have started there? While cellular life emerged from prebiotic chemistry through a pre-Darwinian selection process relevant to both Earth and Mars, each planet posed unique selection 'hurdles' to this process. We focus on drivers of selection in prebiotic chemistry generic to Earth-like worlds and specific to Mars, such as an iron-rich surface. Iron, calcium, and magnesium cations are abundant in hydrothermal settings on Earth and Mars, a promising environment for an origin of life. We investigated the impact of cations on the stability and disruption of different primitive cell membranes under different pH conditions. The relative destabilizing effect of cations on membranes observed in this study is Ca2+ > Fe2+ > Mg2+. Cation concentrations in Earth systems today are too low to disrupt primitive membranes, but on Mars concentrations could have been elevated enough to disrupt membranes during surface dehydration. Membranes and RNA interact during dehydration-rehydration cycles to mutually stabilize each other in cation-rich solutions, and optimal membrane composition can be 'selected' by environmental factors such as pH and cation concentrations. We introduce an approach that considers how life may have evolved differently under the Martian planetary conditions and selective pressures.

Screening and characterization of thermostable enzyme-producing bacteria from selected hot springs of Ethiopia.

Hot springs are potential sources of diverse arrays of microbes and their thermostable hydrolytic enzymes. Water and sediment samples were collected from three hot springs of Ethiopia and enriched on nutrient and thermus agar media to isolate pure cultures of potential microbes. A total of 252 bacterial isolates were screened and evaluated for the production of amylase, protease, cellulase, and lipase. About 95.23%, 84.12%, 76.58%, and 65.07% of the isolates displayed promising amylase, proteases, cellulase, and lipase activities, respectively. Based on the diameter of the clear zone formed, 45 isolates were further screened and identified to species level using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. Five of the 45 isolates showed significantly high (P < 0.05) clear zone ratios as compared to others. The identified isolates were categorized under five bacterial species, namely, Bacillus licheniformis, Bacillus cereus, Paenibacillus thiaminolyticus, Paenibacillus dendritiformis, and Brevibacillus borstelensis. The most dominant species (66.7%) was B. licheniformis. It could be concluded that hot springs of Ethiopia are potential sources of thermostable extracellular hydrolytic enzymes for various industrial applications. Further optimization of the growth conditions and evaluation for better productivity of the desired products is recommended before attempting for large-scale production of the hydrolytic enzymes. IMPORTANCE: Thermostable microbial enzymes play an important role in industries due to their stability under harsh environmental conditions, including extreme temperatures. Despite their huge application in different industries, however, the thermostable enzymes of thermophilic microorganism origin have not yet been fully explored in Ethiopia. Here, we explored thermophilic bacteria and their enzymes from selected hot spring water and sediment samples. Accordingly, thermophilic bacteria were isolated and screened for the production of extracellular hydrolytic enzymes. Promising numbers of isolates were found as producers of the enzymes. The potent enzyme producers were further identified using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. The findings revealed the presence of potential hydrolytic enzyme-producing thermophilic bacteria in hot springs of Ethiopia and necessitate further comprehensive study involving other extreme environments. Our findings also revealed the potential of Ethiopian hot springs in the production of thermostable enzymes of significant application in different industries, including food industries.

From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More.

Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide-oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case.

Screening and Characterization of Bacillus Strains Producing Highly Thermostable Amylase from Various Hot Springs of Algeria

HIGHLIGHTS Screening extremophile Bacillus strains from various Hot Springs Characterization Of Bacillus Strains Producing Highly Thermostable Amylase Genetic identification of the best strains

Abstract Currently thermostable Amylase represents a broad biotechnological interest and desired by a various industries. In this study, forty-six bacterial strains belonging to the genus Bacillus were isolated from various hot springs in the North West of Algeria based on their ability to degrade starch and produce amylase in Starch Agar medium. The majority of isolates showed a positive amylolytic activity. In order to select the most thermostables amylase the effect of temperature on enzymes was estimated, therefore the study of amylase thermostability was culminated by the selection of Four Strains having an interesting optimum of activity and range of stability, reaching 75 °C for the strains HBH1-2, HBH1-3, HBH3-1and 85 °C for the strain HC-2, This indicates that the Enzyme produced by retained strains have optimum activity at high temperature. The identity of the selected strains was established on the basis of the morphological, biochemical characteristics and phylogenetic position as determined by 16S Ribosomal DNA gene sequencing. The whole strains belonged to the genus Bacillus and their phylogeny were also reported in this study.

Microbial mat ecosystems: structure types, functional diversity, and biotechnological application

Microbial mats are horizontally stratified microbial communities, exhibiting a structure defined by physiochemical gradients, which models microbial diversity, physiological activities, and their dynamics as a whole system. These ecosystems are commonly associated with aquatic habitats, including hot springs, hypersaline ponds, and intertidal coastal zones and oligotrophic environments, all of them harbour phototrophic mats and other environments such as acidic hot springs or acid mine drainage harbour non-photosynthetic mats. This review analyses the complex structure, diversity, and interactions between the microorganisms that form the framework of different types of microbial mats located around the globe. Furthermore, the many tools that allow studying microbial mats in depth and their potential biotechnological applications are discussed.

Consideration of the Physical and Environmental Factors and the Accident Sites in Case of Patients with Bathing Accidents, Requiring Ambulance Service in Noboribetsu City / 日本温泉気候物理医学会雑誌

  Japan has been speculated to have more than 10,000 bathing accidents per year, and the number increases annually. In particular, the number of bathing accidents in the elderly is increasing.   I investigated the bathing accidents that occurred in Noboribetsu City between April of 2014 and March of 2015 with the full cooperation of the Noboribetsu ambulance service. There were 52 accidents in total; 25 occurred in women with an average age of 64.4±20.5 years, and 27 occurred in men with an average age of 70.7±18.2 years.   In 11 cases, patients were transported via ambulance because of cardiopulmonary arrest (CPA). Eight of these patients were men, and three were women; 10 of the 11 CPA patients were brought to the hospital during the winter.   Although I was unable to clearly determine whether alcohol consumption influenced the increase in the number and seriousness of bathing accidents, I do not recommend heavy alcohol consumption because of the additional risk of consciousness disturbance and drowning.   The number of bathing accidents at the patient’s own home in Noboribetsu City increased significantly (P<0.05) in the winter, and I found no correlation between the season of the year and the number of accidents in public baths in Noboribetsu City and the number of accidents in hotels and inns in Noboribetsu hot springs.

Consideration of the Physical and Environmental Factors and the Accident Sites in Case of Patients with Bathing Accidents, Requiring Ambulance Service in Noboribetsu City / 日本温泉気候物理医学会雑誌

  Japan has been speculated to have more than 10,000 bathing accidents per year, and the number increases annually. In particular, the number of bathing accidents in the elderly is increasing.<BR>  I investigated the bathing accidents that occurred in Noboribetsu City between April of 2014 and March of 2015 with the full cooperation of the Noboribetsu ambulance service. There were 52 accidents in total; 25 occurred in women with an average age of 64.4±20.5 years, and 27 occurred in men with an average age of 70.7±18.2 years.<BR>  In 11 cases, patients were transported via ambulance because of cardiopulmonary arrest (CPA). Eight of these patients were men, and three were women; 10 of the 11 CPA patients were brought to the hospital during the winter.<BR>  Although I was unable to clearly determine whether alcohol consumption influenced the increase in the number and seriousness of bathing accidents, I do not recommend heavy alcohol consumption because of the additional risk of consciousness disturbance and drowning.<BR>  The number of bathing accidents at the patient’s own home in Noboribetsu City increased significantly (P<0.05) in the winter, and I found no correlation between the season of the year and the number of accidents in public baths in Noboribetsu City and the number of accidents in hotels and inns in Noboribetsu hot springs.

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively.

Isolation, partial purification and characterization of thermophilic uricase from Pseudomonas otitidis strain SN4

Aims: The present study aimed at isolating new source of uricase producers from Malaysian hot springs together with partial purification and characterization of thermophilic uricase from novel strain. Methodology and results: A bacteria strain, designated as SN4, was found to have the ability to degrade uric acid. 16S rRNA analysis identified SN4 as Pseudomonas otitidis. Uricase was then extracted from SN4 and purification was performed via ammonium sulphate precipitation. The effects of temperature, pH and metal ions on partially purified uricase were evaluated. Results showed that 70% ammonium sulphate concentration gave the highest uricase activity at 4.18 U/mL compared to other concentrations. The molecular weight of the partially purified uricase was 33 kilodalton (kDa). The optimum temperature for uricase was 45 °C and its activity was highest at pH 8.0. Calcium ions and copper ions enhanced uricase activity while cobalt ions reduced uricase activity. Conclusion, significance and impact of study: Isolation and investigation of uricase producers from new sources such as thermophiles would increase availability and thermal stability of the uricase that could be used for significant purposes such as in biochemical and clinical applications.

Expression of miRNAs in peripheral blood plasma of the residents surrounding hot springs with radon / 中华放射医学与防护杂志

Objective To investigate the expressions of miR-16,miR-106b,miR-449a,miR-34a and let-7g in peripheral blood plasma of the residents surrounding hot springs with radon in Hebei province.Methods A total of 41 randomly selected residents surrounding hot springs with radon were considered as the radon group,and 46 residents with same living habit but without contact with hot springs were considered as control.The miRNAs in the peripheral blood plasma of these two groups were detected with qRT-PCR.Results The levels of miR-16,miR-106b,miR-449a and let-7g in the radon group were significantly higher than those in control group (Z=-2.278,-3.835,-2.719,-2.721,P＜0.05).Alterations of these miRNAs were associated with radon exposure (t =2.154,3.711,2.319,2.015,P ＜ 0.05) but had no relationship with age,sex,smoking and drinking factors.No significant difference was observed in the plasma levels of miR-34a between the two groups.Conclusions miR-16,miR-106b,miR-449a and let-7g could be applied as potential biomarkers for radon exposure.

Expressions of lung cancer related genes and miRNA in peripheral blood of the residents surrounding hot springs with extremely high radon / 中华放射医学与防护杂志

Objective To investigate the expressions of lung cancer related genes and miRNA in peripheral blood of the residents surrounding the extremely high radon hot springs in Ruoergai County,Sichuan Province. Methods Peripheral blood samples were collected from the local residents.Expressions of lung cancer related genes (p53,k-ras) and miRNA (let-7a,miR-34a/b) were detected by real-time PCR and the protein expressions of p53 and k-ras were detected by Western blot.Results The expressions of p53 and k-ras mRNA of the residents in high radon area were 0.97 and 1.33 times of the control respectively (t =0.13,-1.12,P ＞0.05),and the p53 and k-ras protein levels were 0.70 and 1.23 times of the control respectively (t =0.72,0.46,P ＞ 0.05).The let-7a of the residents in high radon area was lower (t =1.63,P ＞ 0.05 ) while the miR-34a and miR-34b were significantly higher than those of the controls (t =- 3.20,- 3.32,P ＜ 0.05).Conclusions Based on the expressions of p53 and k-ras gene and miRNA,it can be concluded that the residents surrounding the high radon hot springs received radiation damage.

Use of Hot Springs by Ambulatory Orthopaedic Patients / 日本温泉気候物理医学会雑誌

 The effects of hot springs have been described in many studies. However, few studies have reported the use of hot springs by patients. This study aimed to elucidate the use of hot springs by ambulatory orthopaedic patients. We prepared paper questionnaires on the use of hot springs by patients; these questionnaires were administered to ambulatory orthopaedic patients in our general hospital. The questions were as follows: (Q1) Is (Are) there any hot spring(s) near your residence? (Q2) Do you think hot springs are effective for improving your health? (Q3) Have you ever visited a hot spring in the past 1 year? If yes, what was the reason for visiting the hot spring? (Q4) If you did not visit any hot spring, what was the reason for not going? When you are unable to visit hot springs, do you use any alternative methods? (Q5) Do you want hot springs near your residence? The results were as follows: (Q1) Yes, 33 (61%); No, 20 (37%); and No answer, 1 (2%) (Q2) Yes, 15 (28%); Yes (a little), 29 (54%); Neutral, 7 (13%); and No, 3 (6%) (Q3) 1-2 times per year, 18 (33%); 3-4 times per year, 6 (11%); More than 5 times per year, 13 (24%); and No, 17 (31%) (Q4) Bear, 13 (24 %); Alternative, 23 (43%); Use spa, 8 (15%); and Others, 10 (19%) (Q5) Yes, 30 (56%); Yes (a little), 14 (26%); Neutral, 7 (13%); No, 1 (2%); and No answer, 2 (4%). The results of this study suggest that ambulatory orthopaedic patients have a good opinion about the effects of hot springs. Further, these patients visited hot springs. Orthopaedic surgeons must be well informed about the therapeutic use of hot springs.

Expected Balneological Effects of Hot Springs in Tokyo 23 Wards / 日本温泉気候物理医学会雑誌

 Hot sprigs elements and balneological effects of Tokyo 23 wards, which is not recognized as hot spring region were considered. The density of the hot spring’s source in this region is high compared to other parts of the country. Moreover, a useful element and temperature for the balneological treatment was confirmed by the hot springs with deep digging in a lot of places.<br> The hot springs in Tokyo can be classified into the NaCl strong salt hot springs, NaHCO<SUB>3</SUB>, and the sodium metasilicates. The strong Na-Cl (salt) springs are recognized in hot springs found by deep digging, and exists everywhere in Tokyo. The hot springs of the NaHCO<SUB>3</SUB> are localized in Ohta ward by moderate depth digging. The hot springs including with the rich sodium metasilicates in Ohta ward by shallow digging.<br>If the hot springs in Tokyo are to be used the balneologically, the following effects are expected.<br> Thermal and warm keeping effects can be expected from the strong Na-Cl (salt) springs. Cleanness and smoothing effects of the skin can be expected of NaHCO<SUB>3</SUB>. Hyperkeratosis of the skin can be expected from rich sodium metasilicates.

Use of Hot Springs by Ambulatory Orthopaedic Patients / 日本温泉気候物理医学会雑誌

 The effects of hot springs have been described in many studies. However, few studies have reported the use of hot springs by patients. This study aimed to elucidate the use of hot springs by ambulatory orthopaedic patients. We prepared paper questionnaires on the use of hot springs by patients; these questionnaires were administered to ambulatory orthopaedic patients in our general hospital. The questions were as follows: (Q1) Is (Are) there any hot spring(s) near your residence? (Q2) Do you think hot springs are effective for improving your health? (Q3) Have you ever visited a hot spring in the past 1 year? If yes, what was the reason for visiting the hot spring? (Q4) If you did not visit any hot spring, what was the reason for not going? When you are unable to visit hot springs, do you use any alternative methods? (Q5) Do you want hot springs near your residence? The results were as follows: (Q1) Yes, 33 (61%); No, 20 (37%); and No answer, 1 (2%) (Q2) Yes, 15 (28%); Yes (a little), 29 (54%); Neutral, 7 (13%); and No, 3 (6%) (Q3) 1-2 times per year, 18 (33%); 3-4 times per year, 6 (11%); More than 5 times per year, 13 (24%); and No, 17 (31%) (Q4) Bear, 13 (24 %); Alternative, 23 (43%); Use spa, 8 (15%); and Others, 10 (19%) (Q5) Yes, 30 (56%); Yes (a little), 14 (26%); Neutral, 7 (13%); No, 1 (2%); and No answer, 2 (4%). The results of this study suggest that ambulatory orthopaedic patients have a good opinion about the effects of hot springs. Further, these patients visited hot springs. Orthopaedic surgeons must be well informed about the therapeutic use of hot springs.

Expected Balneological Effects of Hot Springs in Tokyo 23 Wards / 日本温泉気候物理医学会雑誌

 Hot sprigs elements and balneological effects of Tokyo 23 wards, which is not recognized as hot spring region were considered. The density of the hot spring’s source in this region is high compared to other parts of the country. Moreover, a useful element and temperature for the balneological treatment was confirmed by the hot springs with deep digging in a lot of places.  The hot springs in Tokyo can be classified into the NaCl strong salt hot springs, NaHCO3, and the sodium metasilicates. The strong Na-Cl (salt) springs are recognized in hot springs found by deep digging, and exists everywhere in Tokyo. The hot springs of the NaHCO3 are localized in Ohta ward by moderate depth digging. The hot springs including with the rich sodium metasilicates in Ohta ward by shallow digging. If the hot springs in Tokyo are to be used the balneologically, the following effects are expected.  Thermal and warm keeping effects can be expected from the strong Na-Cl (salt) springs. Cleanness and smoothing effects of the skin can be expected of NaHCO3. Hyperkeratosis of the skin can be expected from rich sodium metasilicates.