Extremophiles最新文献_第9页

Hyper-stimulation of Pyrococcus furiosus CRISPR DNA uptake by a self-transmissible plasmid. 自传播质粒对暴怒火球菌 CRISPR DNA 摄取的过度刺激。

IF 2.6 3区生物学

Extremophiles Pub Date : 2022-11-16 DOI: 10.1007/s00792-022-01281-0

Elizabeth A Watts, Sandra C Garrett, Ryan J Catchpole, Landon M Clark, Brenton R Graveley, Michael P Terns

{"title":"Hyper-stimulation of Pyrococcus furiosus CRISPR DNA uptake by a self-transmissible plasmid.","authors":"Elizabeth A Watts, Sandra C Garrett, Ryan J Catchpole, Landon M Clark, Brenton R Graveley, Michael P Terns","doi":"10.1007/s00792-022-01281-0","DOIUrl":"10.1007/s00792-022-01281-0","url":null,"abstract":"Pyrococcus furiosus is a hyperthermophilic archaeon with three effector CRISPR complexes (types I-A, I-B, and III-B) that each employ crRNAs derived from seven CRISPR arrays. Here, we investigate the CRISPR adaptation response to a newly discovered and self-transmissible plasmid, pT33.3. Transconjugant strains of Pyrococcus furiosus exhibited dramatically elevated levels of new spacer integration at CRISPR loci relative to the strain harboring a commonly employed, laboratory-constructed plasmid. High-throughput sequence analysis demonstrated that the vast majority of the newly acquired spacers were preferentially selected from DNA surrounding a particular region of the pT33.3 plasmid and exhibited a bi-directional pattern of strand bias that is a hallmark of primed adaptation by type I systems. We observed that one of the CRISPR arrays of our Pyrococcus furiosus laboratory strain encodes a spacer that closely matches the region of the conjugative plasmid that is targeted for adaptation. The hyper-adaptation phenotype was found to strictly depend both on the presence of this single matching spacer as well as the I-B effector complex, known to mediate primed adaptation. Our results indicate that Pyrococcus furiosus naturally encountered this conjugative plasmid or a related mobile genetic element in the past and responds to reinfection with robust primed adaptation.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9838737/pdf/nihms-1859798.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10583449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rahnella sikkimica sp. nov., a novel cold-tolerant bacterium isolated from the glacier of Sikkim Himalaya with plant growth-promoting properties. 锡金拉氏菌(Rahnella sikkimica sp. nov.):一种从锡金喜马拉雅冰川中分离出来的具有促进植物生长特性的新型耐寒细菌。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-11-15 DOI: 10.1007/s00792-022-01283-y

Anil Kumar, Anne Le Flèche-Matéos, Rakshak Kumar, Fabienne Lomprez, Frédéric Fichenick, Dharam Singh, Patrick A D Grimont, Sanjay Kumar

{"title":"Rahnella sikkimica sp. nov., a novel cold-tolerant bacterium isolated from the glacier of Sikkim Himalaya with plant growth-promoting properties.","authors":"Anil Kumar, Anne Le Flèche-Matéos, Rakshak Kumar, Fabienne Lomprez, Frédéric Fichenick, Dharam Singh, Patrick A D Grimont, Sanjay Kumar","doi":"10.1007/s00792-022-01283-y","DOIUrl":"https://doi.org/10.1007/s00792-022-01283-y","url":null,"abstract":"The current study describes a novel species with the strain name ERMR1:05T isolated from the forefield soil of East Rathong Glacier in West Sikkim Himalaya (India). The isolate was facultatively anaerobic, gram-stain negative, non-spore-forming, rod-shaped, and oxidase negative. Whole-genome-based bacterial core gene phylogenetic analysis placed the strain in the genus Rahnella, well separated from Rouxiella spp. The digital DNA-DNA hybridisation and average nucleotide identity values between strain ERMR1:05T and other members of genus Rahnella were below the proposed thresholds for the species delineation. Based on these results, a new species, Rahnella sikkimica sp. nov., is proposed with strain ERMR1:05T (CIP 111636T, MTCC 12598T) as the type strain. The bacterium showed upregulation of cold-stress genes in cold conditions. Additionally, the genome analysis of the bacterium showed the presence of plant growth-promotion factors suggesting its role in crop improvement in cold hilly regions.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40686234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Self-assembly of Aeropyrum pernix bacilliform virus 1 (APBV1) major capsid protein and its application as building blocks for nanomaterials. 沼草杆菌状病毒1 (APBV1)主要衣壳蛋白的自组装及其在纳米材料构建中的应用

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-11-13 DOI: 10.1007/s00792-022-01284-x

Yuka Sumikama, Atsushi Takashima, Tomohiro Mochizuki, Haruhiko Sakuraba, Toshihisa Ohshima, Shinji Sugihara, Shin-Ichiro Suye, Takenori Satomura

引用次数: 0

Moorella sulfitireducens sp. nov., a thermophilic anaerobic bacterium isolated from a terrestrial thermal spring. 硫酸还原摩尔氏菌，一种从陆地温泉中分离出来的嗜热厌氧细菌。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-11-09 DOI: 10.1007/s00792-022-01285-w

Galina B Slobodkina, A Y Merkel, A A Kuchierskaya, A I Slobodkin

{"title":"Moorella sulfitireducens sp. nov., a thermophilic anaerobic bacterium isolated from a terrestrial thermal spring.","authors":"Galina B Slobodkina, A Y Merkel, A A Kuchierskaya, A I Slobodkin","doi":"10.1007/s00792-022-01285-w","DOIUrl":"https://doi.org/10.1007/s00792-022-01285-w","url":null,"abstract":"In hydrothermal ecosystems, the dissolution of sulfur dioxide in water results in the formation of sulfite, which can be used in microbial metabolism. A limited number of thermophiles have been isolated using sulfite as an electron acceptor. From a terrestrial thermal spring, Sakhalin Island, Russia, we isolated a thermophilic anaerobic bacterium (strain SLA38T). Cells of strain SLA38T were spore-forming straight rods. Growth was observed at temperatures 45-65 °C (optimum at 60 °C) and pH 5.5-9.0 (optimum at pH 6.5-7.0). The novel isolate was capable of anaerobic respiration with sulfite, thiosulfate, fumarate and perchlorate or fermentative growth. Strain SLA38T utilized glycerol, lactate, pyruvate and yeast extract. It grew lithoautotrophically on carbon monoxide with thiosulfate as electron acceptor, producing acetate. The genome size of the isolate was 2.9 Mbp and genomic DNA G + C content was 53.6 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SLA38T belongs to the genus Moorella. Based on the physiological features and phylogenetic analysis, we propose to assign strain SLA38T to a new species of the genus Moorella, as Moorella sulfitireducens sp. nov. The type strain is SLA38T (= DSM 111068T = VKM B-3584T).","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40453686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil. vallussus sp. nov.、Halorussus aquaticus sp. nov.、Halorussus gelatinilyticus sp. nov.、Halorussus salilacus sp. nov.、Halorussus salinisoli sp. nov.:六种从太阳盐湖、盐湖和盐碱地中分离出来的极端嗜盐古细菌。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-10-14 DOI: 10.1007/s00792-022-01280-1

Xi-Wen Zheng, Zhang-Ping Wu, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui

{"title":"Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.","authors":"Xi-Wen Zheng, Zhang-Ping Wu, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui","doi":"10.1007/s00792-022-01280-1","DOIUrl":"https://doi.org/10.1007/s00792-022-01280-1","url":null,"abstract":"Six novel halophilic archaeal strains of XZYJT10T, XZYJ18T, XZYJT40T, XZYJT49T, YCN54T and LT46T were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10T, XZYJ18T, XZYJT40T, XZYJT49T, YCN54T, LT46T and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33511058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Electron transfer of extremophiles in bioelectrochemical systems. 生物电化学系统中极端微生物的电子转移。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-10-12 DOI: 10.1007/s00792-022-01279-8

Miriam Edel, Laura-Alina Philipp, Jonas Lapp, Johannes Reiner, Johannes Gescher

引用次数: 2

Isotherm and kinetics modeling of biosorption and bioreduction of the Cr(VI) by Brachybacterium paraconglomeratum ER41. Brachybacterium paraconglomeratum ER41 对六价铬的生物吸附和生物还原的等温线和动力学模型。

IF 2.6 3区生物学

Extremophiles Pub Date : 2022-09-23 DOI: 10.1007/s00792-022-01278-9

Kaoutar Harboul, Imad Alouiz, Khalil Hammani, Abdenbi El-Karkouri

{"title":"Isotherm and kinetics modeling of biosorption and bioreduction of the Cr(VI) by Brachybacterium paraconglomeratum ER41.","authors":"Kaoutar Harboul, Imad Alouiz, Khalil Hammani, Abdenbi El-Karkouri","doi":"10.1007/s00792-022-01278-9","DOIUrl":"10.1007/s00792-022-01278-9","url":null,"abstract":"Chromium is one of the most widely used metals in industry. Hexavalent form [Cr(VI)], which is found in industrial discharges, is very toxic and very soluble in water. From soil taken from an abandoned lead and iron mine, a bacterial strain capable of reducing Cr(VI) was isolated and identified as Brachybacterium paraconglomeratum ER41. Objective of this work was to evaluate the power of this bacterium to reduce Cr(VI). Results obtained showed that this bacterium is capable of eliminating 100 mg/L of Cr(VI) after 48 h (pH 8 and temperature 30 °C). For modeling biosorption kinetics, pseudo-first-order and intraparticle diffusion models gave a better fit. Furthermore, the adsorption mechanism conformed well to Langmuir's isothermal model indicating monolayer type sorption. Biomass analysis of this bacterium before and after contact with chromium by scanning electron microscopy-energy-dispersive X-ray and by Fourier transform infrared spectroscopy showed that the surface ligands of bacterial wall are probably responsible for biosorption and bioreduction process. These results suggest a potential application of B. paraconglomeratum ER41 in bioremediation of polluted discharges.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33479359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. 古细菌甘油磷脂生物合成的催化和结构基础。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-08-17 DOI: 10.1007/s00792-022-01277-w

Niels A W de Kok, Arnold J M Driessen

{"title":"The catalytic and structural basis of archaeal glycerophospholipid biosynthesis.","authors":"Niels A W de Kok, Arnold J M Driessen","doi":"10.1007/s00792-022-01277-w","DOIUrl":"https://doi.org/10.1007/s00792-022-01277-w","url":null,"abstract":"Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the \"lipid-divide\". The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9385802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40618200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Role of carnitine in adaptation of Chromohalobacter salexigens DSM 3043 and its mutants to osmotic and temperature stress in defined medium. 肉碱在salexigens色盐杆菌DSM 3043及其突变体适应特定介质渗透和温度胁迫中的作用

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-08-14 DOI: 10.1007/s00792-022-01276-x

Xiang-Lin Meng, Xia Gao, Yuan-Ming Si, Li-Li Xu, Li-Zhong Guo, Wei-Dong Lu

{"title":"Role of carnitine in adaptation of Chromohalobacter salexigens DSM 3043 and its mutants to osmotic and temperature stress in defined medium.","authors":"Xiang-Lin Meng, Xia Gao, Yuan-Ming Si, Li-Li Xu, Li-Zhong Guo, Wei-Dong Lu","doi":"10.1007/s00792-022-01276-x","DOIUrl":"https://doi.org/10.1007/s00792-022-01276-x","url":null,"abstract":"L-Carnitine is widespread in nature, but little information is available on its metabolism and physiological functions in moderate halophiles. In this study, we found that Chromohalobacter salexigens DSM 3043 could utilize carnitine not only as a nutrient, but also as an osmolyte. When grown at 37 °C under salt-stress conditions, the strain utilized carnitine as an osmoprotectant by enzymatically converting it into GB. When grown at low and high temperature, both carnitine and its metabolic intermediate GB were simultaneously accumulated intracellularly, serving as cryoprotectants and thermoprotectants. The genes (csal_3172, csal_3173, and csal_3174) which were predicted to participate in L-carnitine degradation to GB were deleted to construct the corresponding mutants. The effects of salinity and temperature on the growth rates and cytoplasmic solute pools of the C. salexigens wild-type and mutant strains were investigated. 13C-NMR analysis revealed that GB was still detected in the Δcsal_3172Δcsal_3173Δcsal_3174 mutant grown in a defined medium with added DL-carnitine, but not with L-carnitine, indicating that an unidentified D-carnitine degradation pathway exists in C. salexigens. Taken together, the data presented in this study expand our knowledge on carnitine metabolism and its physiological functions in C. salexigens exposed to single or multiple environmental abiotic stress.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40611225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Organic layer characteristics and microbial utilization of the biosulfur globules produced by haloalkaliphilic Thioalkalivibrio versutus D301 during biological desulfurization. 嗜卤硫酸弧菌D301在生物脱硫过程中产生的生物硫球的有机层特征及微生物利用

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-08-13 DOI: 10.1007/s00792-022-01274-z

Zhixia Liu, Maohua Yang, Tingzhen Mu, Jinlong Liu, Linxu Chen, Delu Miao, Jianmin Xing

{"title":"Organic layer characteristics and microbial utilization of the biosulfur globules produced by haloalkaliphilic Thioalkalivibrio versutus D301 during biological desulfurization.","authors":"Zhixia Liu, Maohua Yang, Tingzhen Mu, Jinlong Liu, Linxu Chen, Delu Miao, Jianmin Xing","doi":"10.1007/s00792-022-01274-z","DOIUrl":"https://doi.org/10.1007/s00792-022-01274-z","url":null,"abstract":"The haloalkaliphilic genus Thioalkalivibrio, widely used in bio-desulfurization, can oxidize H2S to So, which is excreted outside cells in the form of biosulfur globules. As by-product of bio-desulfurization, information on biosulfur globules is still very scant, which limits its high-value utilization. In this paper, the characteristics of biosulfur globules produced by Thioalkalivibrio versutus D301 and the possibility of cultivating sulfur-oxidizing bacteria as a high biological-activity sulfur source were studied. The sulfur element in the biosulfur globules existed in the form α-S8, which was similar to chemical sulfur. The biosulfur globule was wrapped with an organic layer composed of polysaccharides and proteins. The composition of this organic layer could change. In the formation stage of biosulfur globules, the organic layer was dominated by polysaccharides, and in later stage, proteins became the main component. We speculated that the organic layer was mainly formed by the passive adsorption of organic matter secreted by cells. The existence of organic layer endowed biosulfur with better bioavailability. Compared with those found using chemical sulfur, the growth rates of Acidithiobacillus thiooxidans ATCC 19377T, Thiomicrospira microaerophila BDL05 and Thioalkalibacter halophilus BDH06 using biosulfur increased several folds to an order of magnitude, indicating that biosulfur was a good sulfur source for cultivating sulfur-oxidizing bacteria.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40625661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0