Extremophiles最新文献_第9页

Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine. 溶干酪藻Natrinema caseinicum sp.nov.，溶胶藻Natrinima glugelicum sp.nov.，海洋藻Natrineman marinum sp.nov..，从海洋环境和盐矿中分离的极嗜盐古菌。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-03-31 DOI: 10.1007/s00792-023-01294-3

Yao Hu, Xue Ma, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui

{"title":"Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine.","authors":"Yao Hu, Xue Ma, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui","doi":"10.1007/s00792-023-01294-3","DOIUrl":"https://doi.org/10.1007/s00792-023-01294-3","url":null,"abstract":"Four extremely halophilic archaeal strains (ZJ2T, BND6T, DT87T, and YPL30T) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2T, BND6T, DT87T, YPL30T and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2T, BND6T, DT87T, and YPL30T cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2T, BND6T, DT87T, and YPL30T could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2T (= CGMCC 1.18786 T = JCM 34918 T), BND6T (= CGMCC 1.18777 T = JCM 34909 T), DT87T (= CGMCC 1.18921 T = JCM 35420 T), and YPL30T (= CGMCC 1.15337 T = JCM 31113 T) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"9"},"PeriodicalIF":2.9,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9593841","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

Quantitative evaluation of endogenous reference genes for ddPCR under salt stress using a moderate halophile. 利用中等嗜盐菌对盐胁迫下ddPCR内源内参基因进行定量评价。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-03-28 DOI: 10.1007/s00792-023-01295-2

Qinghua Xing, Noha M Mesbah, Haisheng Wang, Jun Li, Baisuo Zhao

{"title":"Quantitative evaluation of endogenous reference genes for ddPCR under salt stress using a moderate halophile.","authors":"Qinghua Xing, Noha M Mesbah, Haisheng Wang, Jun Li, Baisuo Zhao","doi":"10.1007/s00792-023-01295-2","DOIUrl":"https://doi.org/10.1007/s00792-023-01295-2","url":null,"abstract":"Droplet digital PCR (ddPCR) is being increasingly adopted for gene detection and quantification because of its higher sensitivity and specificity. According to previous observations and our laboratory data, it is essential to use endogenous reference genes (RGs) when investigating gene expression at the mRNA level under salt stress. This study aimed to select and validate suitable RGs for gene expression under salt stress using ddPCR. Six candidate RGs were selected based on the tandem mass tag (TMT)-labeled quantitative proteomics of Alkalicoccus halolimnae at four salinities. The expression stability of these candidate genes was evaluated using statistical algorithms (geNorm, NormFinder, BestKeeper and RefFinder). There was a small fluctuation in the cycle threshold (Ct) value and copy number of the pdp gene. Its expression stability was ranked in the vanguard of all algorithms and was the most suitable RG for quantification of expression by both qPCR and ddPCR of A. halolimnae under salt stress. Single RG pdp and RG combinations were used to normalize the expression of ectA, ectB, ectC and ectD under four salinities. The present study constitutes the first systematic analysis of endogenous RG selection for halophiles responding to salt stress. This work provides a valuable theory and an approach reference of internal control identification for ddPCR-based stress response models.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"8"},"PeriodicalIF":2.9,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10099454","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

Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena. 从海洋潮滩中分离出的一种新型丝状嗜盐古菌&对盐藻属的修正描述。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-03-12 DOI: 10.1007/s00792-023-01292-5

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

{"title":"Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena.","authors":"Zhang-Ping Wu, Xi-Wen Zheng, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui","doi":"10.1007/s00792-023-01292-5","DOIUrl":"https://doi.org/10.1007/s00792-023-01292-5","url":null,"abstract":"Three novel filamentous halophilic archaea, strains DFN5T, RDMS1, and QDMS1, were isolated from the coastal saline soil samples of the intertidal zones located in different regions of Jiangsu Province, China. The colonies of these strains were pinkish-white due to the presence of white spores. These three strains are extremely halophilic and grew optimally at 35-37 °C and pH 7.0-7.5. Based on 16S rRNA and rpoB' gene analysis, strains DFN5T, RDMS1, and QDMS1 gathered together in phylogenetic trees and then clustered with the current species of the genus Halocatena showing 96.9-97.4% and 82.2-82.5% similarities, respectively. Both the 16S rRNA gene-based and rpoB' gene-based phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes indicated that strains DFN5T, RDMS1, and QDMS1 should be a novel species of the genus Halocatena. Genome mining revealed that there are considerable differences in the genes related to β-carotene synthesis among these three strains and the current species of Halocatena. The major polar lipids of strains DFN5T, RDMS1, and QDMS1 are PA, PG, PGP-Me, S-TGD-1, TGD-1, and TGD-2. The minor polar lipids, S-DGD-1, DGD-1, S2-DGD, and S-TeGD may be detected. According to the phenotypic characteristics, phylogenetic analysis, genomic and chemotaxonomic features, strains DFN5T (= CGMCC 1.19401 T = JCM 35422 T), RDMS1 (= CGMCC 1.19411) and QDMS1 (= CGMCC 1.19410) were classified as a novel species of the genus Halocatena with the proposed name, Halocatena marina sp. nov. This is the first report of the description of a novel filamentous haloarchaeon isolated from marine intertidal zones.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"7"},"PeriodicalIF":2.9,"publicationDate":"2023-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9155189","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

Role of cell-substrate association during plant biomass solubilization by the extreme thermophile Caldicellulosiruptor bescii. 细胞-底物结合在极端嗜热Caldicelllosiruptor bescii溶解植物生物质过程中的作用。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-02-21 DOI: 10.1007/s00792-023-01290-7

Tunyaboon Laemthong, Ryan G Bing, James R Crosby, Mohamad J H Manesh, Michael W W Adams, Robert M Kelly

{"title":"Role of cell-substrate association during plant biomass solubilization by the extreme thermophile Caldicellulosiruptor bescii.","authors":"Tunyaboon Laemthong, Ryan G Bing, James R Crosby, Mohamad J H Manesh, Michael W W Adams, Robert M Kelly","doi":"10.1007/s00792-023-01290-7","DOIUrl":"10.1007/s00792-023-01290-7","url":null,"abstract":"Caldicellulosiruptor species are proficient at solubilizing carbohydrates in lignocellulosic biomass through surface (S)-layer bound and secretomic glycoside hydrolases. Tāpirins, surface-associated, non-catalytic binding proteins in Caldicellulosiruptor species, bind tightly to microcrystalline cellulose, and likely play a key role in natural environments for scavenging scarce carbohydrates in hot springs. However, the question arises: If tāpirin concentration on Caldicellulosiruptor cell walls increased above native levels, would this offer any benefit to lignocellulose carbohydrate hydrolysis and, hence, biomass solubilization? This question was addressed by engineering the genes for tight-binding, non-native tāpirins into C. bescii. The engineered C. bescii strains bound more tightly to microcrystalline cellulose (Avicel) and biomass compared to the parent. However, tāpirin overexpression did not significantly improve solubilization or conversion for wheat straw or sugarcane bagasse. When incubated with poplar, the tāpirin-engineered strains increased solubilization by 10% compared to the parent, and corresponding acetate production, a measure of carbohydrate fermentation intensity, was 28% higher for the Calkr_0826 expression strain and 18.5% higher for the Calhy_0908 expression strain. These results show that enhanced binding to the substrate, beyond the native capability, did not improve C. bescii solubilization of plant biomass, but in some cases may improve conversion of released lignocellulose carbohydrates to fermentation products.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"6"},"PeriodicalIF":2.9,"publicationDate":"2023-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514702/pdf/nihms-1931674.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10604733","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

Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches. 通过培养依赖型和非培养依赖型方法研究Xichú河(墨西哥)旁酸性矿井排水的细菌多样性。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-02-17 DOI: 10.1007/s00792-023-01291-6

Elcia Margareth Souza Brito, Rémy Guyoneaud, César Augusto Caretta, Manon Joseph, Marisol Goñi-Urriza, Bernard Ollivier, Agnès Hirschler-Réa

{"title":"Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches.","authors":"Elcia Margareth Souza Brito, Rémy Guyoneaud, César Augusto Caretta, Manon Joseph, Marisol Goñi-Urriza, Bernard Ollivier, Agnès Hirschler-Réa","doi":"10.1007/s00792-023-01291-6","DOIUrl":"https://doi.org/10.1007/s00792-023-01291-6","url":null,"abstract":"Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, \"Desulfobacterota\" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio (\"Desulfobacterota\"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"5"},"PeriodicalIF":2.9,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9258613","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

Structural characterization and physicochemical properties of the exopolysaccharide produced by the moderately halophilic bacterium Chromohalobacter salexigens, strain 3EQS1. 中等嗜盐细菌salexigens嗜盐杆菌3EQS1产胞外多糖的结构表征和理化性质。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-01-30 DOI: 10.1007/s00792-023-01289-0

Ibrahim M Ibrahim, Yuliya P Fedonenko, Elena N Sigida, Maxim S Kokoulin, Vyacheslav S Grinev, Ivan G Mokrushin, Gennady L Burygin, Andrey M Zakharevich, Alexander A Shirokov, Svetlana A Konnova

{"title":"Structural characterization and physicochemical properties of the exopolysaccharide produced by the moderately halophilic bacterium Chromohalobacter salexigens, strain 3EQS1.","authors":"Ibrahim M Ibrahim, Yuliya P Fedonenko, Elena N Sigida, Maxim S Kokoulin, Vyacheslav S Grinev, Ivan G Mokrushin, Gennady L Burygin, Andrey M Zakharevich, Alexander A Shirokov, Svetlana A Konnova","doi":"10.1007/s00792-023-01289-0","DOIUrl":"https://doi.org/10.1007/s00792-023-01289-0","url":null,"abstract":"A strain, 3EQS1, was isolated from a salt sample taken from Lake Qarun (Fayoum Province, Egypt). On the basis of physiological, biochemical, and phylogenetic analyses, the strain was classified as Chromohalobacter salexigens. By 72 h of growth at 25 °C, strain 3EQS1 produced large amounts (15.1 g L-1) of exopolysaccharide (EPS) in a liquid mineral medium (initial pH 8.0) containing 10% sucrose and 10% NaCl. The EPS was precipitated from the cell-free culture medium with chilled ethanol and was purified by gel-permeation and anion-exchange chromatography. The molecular mass of the EPS was 0.9 × 106 Da. Chemical analyses, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the EPS was a linear β-D-(2 → 6)-linked fructan (levan). In aqueous solution, the EPS tended to form supramolecular aggregates with a critical aggregation concentration of 240 µg mL-1. The EPS had high emulsifying activity (E24, %) against kerosene (31.2 ± 0.4%), sunflower oil (76.9 ± 1.3%), and crude oil (98.9 ± 0.8%), and it also had surfactant properties. A 0.1% (w/v) aqueous EPS solution reduced the surface tension of water by 11.9%. The levan of C. salexigens 3EQS1 may be useful in various biotechnological processes.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"4"},"PeriodicalIF":2.9,"publicationDate":"2023-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9312981","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

Post-dispersal astrobiological events: modelling macroevolutionary dynamics for lithopanspermia. 分散后的天体生物学事件:模拟岩石生源论的宏观进化动力学。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-01-14 DOI: 10.1007/s00792-023-01288-1

Maico Stochero Fiedler, Milton de Souza Mendonça

{"title":"Post-dispersal astrobiological events: modelling macroevolutionary dynamics for lithopanspermia.","authors":"Maico Stochero Fiedler, Milton de Souza Mendonça","doi":"10.1007/s00792-023-01288-1","DOIUrl":"https://doi.org/10.1007/s00792-023-01288-1","url":null,"abstract":"Lithopanspermia is defined as dispersal of living extremophiles from one planetary body to another, through life-bearing rocks ejected by meteor impacts. If lithopanspermia proves concrete, it should be viewed as an eco-evolutionary phenomenon. Biogeographic/microevolutionary models have been proposed as analogues for lithopanspermia dynamics; however, extremophile arrival on a planetary body is not the end of story. Here, we suggest that eco-evolutionary (environment + organismal microevolution) dynamics can lead to distinct macroevolutionary scenarios after extremophile arrival on a planetary body. Speciation would be the most important factor in interplanetary dynamics due to the possibly long time and distance between dispersive events, similar to long-distance dispersal dynamics on Earth. In previously uninhabited planets, persistence of extremophiles and descendants depends almost only on evolvability of extremophiles against abiotic filters. Considering a previously inhabited planet, ecological interactions at local or global scales could drive persistence (speciation/extinction) of extremophiles in the new habitat. Thus, we might expect high extinction rates if negative interactions are dominant, or, high speciation, if positive interactions occur, with extremophile lineages overpower (or not) the native biota. If interplanetary dispersal is possible, theories about the evolution of life may be universal, leading to a general eco-evolutionary model for life in the Universe.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"3"},"PeriodicalIF":2.9,"publicationDate":"2023-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9251985","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

Assessment of diversity of archaeal communities in Algerian chott. 阿尔及利亚肖特古菌群落多样性评价。

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-12-05 DOI: 10.1007/s00792-022-01287-8

Imene Ikram Hassani, Inès Quadri, Archana Yadav, Sonia Bouchard, Didier Raoult, Hocine Hacène, Christelle Desnues

{"title":"Assessment of diversity of archaeal communities in Algerian chott.","authors":"Imene Ikram Hassani, Inès Quadri, Archana Yadav, Sonia Bouchard, Didier Raoult, Hocine Hacène, Christelle Desnues","doi":"10.1007/s00792-022-01287-8","DOIUrl":"https://doi.org/10.1007/s00792-022-01287-8","url":null,"abstract":"Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 103 CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 1","pages":"2"},"PeriodicalIF":2.9,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9264748","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

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":"26 3","pages":"36"},"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

Evansella halocellulosilytica sp. nov., an alkali-halotolerant and cellulose-dissolving bacterium isolated from bauxite residue 从铝土矿残渣中分离的耐碱、溶纤维素细菌Evansella halocellulosillica sp.nov

IF 2.9 3区生物学

Extremophiles Pub Date : 2022-06-04 DOI: 10.1007/s00792-022-01267-y

Guo-Hong Liu, Manik Prabhu Narsing Rao, Qianqian Chen, Jian-mei Che, Huai Shi, Bo Liu, Wenjun Li

引用次数: 2