The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the ...mechanisms governing the environmental adaptability and antimicrobial activity of desert
remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a
strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H
O
). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against
. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m
(D10 = 80 J/m
) and tolerate stress up to 70 mM H
O
. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that
D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain
D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of
D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.
Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine ...have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, ...designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
Glaciers, which constitute the world's largest global freshwater reservoir, are also natural microbial repositories. The frequent pandemic in recent years underscored the potential biosafety risks ...associated with the release of microorganisms from the accelerated melting of glaciers due to global warming. However, the characteristics of pathogenic microorganisms in glaciers are not well understood. The glacier surface is the primary area where glacier melting occurs that is often the main subject of research on the dynamics of pathogenic microbial communities in efforts to assess glacier biosafety risks and devise preventive measures. In this study, high-throughput sequencing and quantitative polymerase chain reaction methods were employed in analyses of the composition and quantities of potential pathogenic bacteria on the surfaces of glaciers in the southeastern Tibetan Plateau. The study identified 441 potential pathogenic species ranging from 215 to 4.39 × 1011 copies/g, with notable seasonal and environmental variations being found in the composition and quantity of potential pathogens. The highest level of diversity was observed in April and snow, while the highest quantities were observed in October and cryoconite. Host analysis revealed that >70 % of the species were pathogens affecting animals, with the highest proportion of zoonotic pathogens being observed in April. Analysis of aerosols and glacial meltwater dispersion suggested that these microbes originated from West Asia, primarily affecting the central and southern regions of China. Null model analysis indicated that the assembly of potential pathogenic microbial communities on glacier surfaces was largely governed by deterministic processes. In conclusion, potential pathogenic bacteria on glacier surfaces mainly originated from the snow and exhibited significant temporal and spatial variation patterns. These findings can be used to enhance researchers' ability to predict potential biosafety risks associated with pathogenic bacteria in glaciers and to prevent their negative impact on populations and ecological systems.
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•Annually, approximately 1.7 × 1020 cells of potential pathogenic bacteria are released downstream.•Snow is the main carrier of potential pathogenic bacteria on glaciers.•Animals are the potential primary hosts for pathogenic bacteria on glaciers.•Pathogens found on glacier surfaces shows notable seasonal and environmental variations.•Deterministic processes dominated the potential pathogenic bacteria community assembly.
A bacterial strain, designated S9-5
, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the ...affiliation of the strain with the genus
. Strain S9-5
was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10-40 °C, pH 5-8 and with 0-9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5
. Its major fatty acids were summed feature 8 (C
7
and/or C
6
) and C
. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5
was phylogenetically closely related to
DCY91
(98.17 %),
K-1-16
(98.11 %) and
DSM 17494
(97.39 %). The average nucleotide identity values among strain S9-5
and
DCY91
,
K-1-16
and
DSM 17494
were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5
(=JCM 34750
=GDMCC 1.2714
) should represent a novel species of the genus
, for which we propose the name
sp. nov.
•For the first time, habitat suitability and metabolic mechanism of Planococcus halotolerans Y50 were analyzed at the genetic level.•P. halotolerans Y50 could degrade n-alkanes from C11-C23 and about ...30% of the total petroleum. Meanwhile, the strain still has survival under 5 × 103 J/m2 UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH.•Genomic analysis of P. halotolerans Y50 indicated that presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment.•The analyses on pan-genome and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically.•Genomic analysis and experimental verification provided more clues for the study of this bacterium on stress adaptability, bioremediation, antioxidation and antiradiation, and effectively expanded its application potential for dealing with petroleum pollution in alpine regions.
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C11-C23, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 103 J/m2 UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the ...mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (Hsub.2Osub.2). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/msup.2 (D10 = 80 J/msup.2) and tolerate stress up to 70 mM Hsub.2Osub.2. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, ...designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59sup.T and S8-45sup.T . (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59sup.T and S8-45sup.T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59sup.T and S8-45sup.T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59sup.T and S8-45sup.T strains. Additionally, strain S5-59sup.T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59sup.T (=JCM 35564T =GDMCC 1.3193T) and S8-45sup.T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59sup.T and S8-45sup.T , were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
Although the interferon-γ release assay (IGRA) has become a common diagnostic method for tuberculosis, its value in the diagnosis of tuberculosis in human immunodeficiency virus (HIV) seropositive ...patients remains controversial. Therefore, this systematically reviews the data for exploring the diagnostic value of IGRA in HIV-infected individuals complicated with active tuberculosis, aiming to provide a clinical basis for future clinical diagnosis of the disease.
Relevant studies on IGRA for diagnosing tuberculosis in HIV-infected patients were comprehensively collected from Excerpta Medica Database (EMBASE), Medline, Cochrane Library, Chinese Sci-tech Periodical Full-text Database, Chinese Periodical Full-text Database, China National Knowledge Infrastructure (CNKI) and China Wanfang Data up to July 2020. Subsequently, Stata 15.0, an integrated statistical software, was used to analyse the sensitivity, specificity, diagnostic odds ratio (DOR), positive likelihood ratio (PLR) and negative likelihood ratio (NLR) to create receiver operator characteristic (ROC) curves.
A total of 18 high-quality articles were selected, including 20 studies, 11 of which were related to QuantiFERON-TB Gold In-Tube (QFT-GIT) and nine to T-SPOT.TB. The meta-analysis indicated that the pooled sensitivity = 0.75 (95% CI 0.63-0.85), the pooled specificity = 0.82 (95% CI 0.66-0.92), PLR = 4.25 (95% CI 1.97-9.18), NLR = 0.30 (95% CI 0.18-0.50), DOR = 14.21 (95% CI 4.38-46.09) and the area under summary ROC curve was 0.85 (95% CI 0.81-0.88).
IGRA has a good diagnostic value and therefore can aid in the preliminary screening of active tuberculosis in HIV-infected individuals. Its diagnostic effectiveness can be improved by modifying and optimizing the assay design.
Polynitrogen energetic materials have become an important branch of high-energy-density materials. In this work, a theoretical exploration of structures and thermal stability in polynitrogen ...compounds N6, N8, and N10 was conducted based on synthesized azide and pentazolate compounds. By employing wave function analyses and kinetic simulations, the equilibrium geometries, properties of bonds, and indices to represent aromaticity were explored and represented. In addition, their crystal structures were predicted, and the decomposition processes and products of ab initio molecular dynamics (AIMD) simulations and transition-state calculations were carried out. Moreover, their decomposition barrier can be significantly increased by forming complexes with HMX and CL-20. Compounds HMX–1, HMX–4, CL-20–1, and CL-20–4 showed satisfactory thermal stability compared with pentazolate salts. These research results provide theoretical support and possibilities for the synthesis of polynitrogen compounds.
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