Extremophiles最新文献

{"title":"Correction: 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/s00792-023-01307-1","DOIUrl":"10.1007/s00792-023-01307-1","url":null,"abstract":"","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"23"},"PeriodicalIF":2.9,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10113802","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}

{"title":"The genus Anoxybacillus: an emerging and versatile source of valuable biotechnological products.","authors":"Deisiane Fernanda da Rosa,&nbsp;Alexandre José Macedo","doi":"10.1007/s00792-023-01305-3","DOIUrl":"10.1007/s00792-023-01305-3","url":null,"abstract":"<p><p>Thermophilic and alkaliphilic microorganisms are unique organisms that possess remarkable survival strategies, enabling them to thrive on a diverse range of substrates. Anoxybacillus, a genus of thermophilic and alkaliphilic bacteria, encompasses 24 species and 2 subspecies. In recent years, extensive research has unveiled the diverse array of thermostable enzymes within this relatively new genus, holding significant potential for industrial and environmental applications. The biomass of Anoxybacillus has demonstrated promising results in bioremediation techniques, while the recently discovered metabolites have exhibited potential in medicinal experiments. This review aims to provide an overview of the key experimental findings related to the biotechnological applications utilizing bacteria from the Anoxybacillus genus.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"22"},"PeriodicalIF":2.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10010720","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}

{"title":"Functional expression of an antimicrobial peptide, belonging to halocin C8 family, from Natrinema sp. RNS21 in Escherichia coli.","authors":"Chang Ho Ri,&nbsp;Song Ryong Li,&nbsp;Chon Il Paek,&nbsp;Yu Sin Kim","doi":"10.1007/s00792-023-01308-0","DOIUrl":"10.1007/s00792-023-01308-0","url":null,"abstract":"<p><p>Halocins, the proteinaceous antimicrobial agents produced by haloarchaea, may be used for the preservation of salted foods and the treatment of diseases. For their application and function explanation, it is necessary to produce the active recombinants. In this work, a haloarchaeal strain producing halocin was isolated from the salt-fermented shrimp and identified as Natrinema sp. RNS21 by 16S rRNA gene sequence analysis. From 1 L of RNS21 culture, about 0.32 mg of halocin with 96% purity was obtained. Based on the molecular weight, stability and amino acid sequence alignment, the antimicrobial peptide belonged to the halocin C8 (HalC8) family. HalC8 was expressed by fusion with glutathione-S-transferase (GST) in E. coli, followed by affinity purification and enterokinase (EK) cleavage. About 6.2 mg of recombinant HalC8 with 95% purity was obtained from 1 L of E. coli culture. MALDI-TOF-MS and RP-HPLC analysis indicated that the molecular weight and folding pattern of purified recombinant HalC8 were the same as those of native HalC8. Recombinant HalC8 showed obvious inhibitory activity against Haloferax volcanii. Contrast to native HalC8, the active recombinant HalC8 could be easily produced in a short time with a high yield.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"21"},"PeriodicalIF":2.9,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9953592","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}

{"title":"Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis.","authors":"Michael T Madigan, Kelly S Bender, Sophia A Sanguedolce, Mary N Parenteau, Marisa H Mayer, Yukihiro Kimura, Zheng-Yu Wang-Otomo, W Matthew Sattley","doi":"10.1007/s00792-023-01304-4","DOIUrl":"10.1007/s00792-023-01304-4","url":null,"abstract":"<p><p>Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1^T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1^T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1^T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"19"},"PeriodicalIF":2.9,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9877045","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}

{"title":"Molecular evolution steered structural adaptations in the DNA polymerase III α subunit of halophilic bacterium Salinibacter ruber.","authors":"Aveepsa Sengupta,&nbsp;Kunwali Das,&nbsp;Nidhi Jha,&nbsp;Yusuf Akhter,&nbsp;Ashutosh Kumar","doi":"10.1007/s00792-023-01306-2","DOIUrl":"https://doi.org/10.1007/s00792-023-01306-2","url":null,"abstract":"<p><p>A significant portion of the earth has a salty environment, and the literature on bacterial survival mechanisms in salty environments is limited. During molecular evolution, halophiles increase acidic amino acid residues on their protein surfaces which leads to a negatively charged surface potential that helps them to maintain the protein integrity and protect them from denaturation by competing with salt ions. Through protein family analysis, we have investigated the molecular-level adaptive features of DNA polymerase III's catalytic subunit (alpha) and its structure-function relationship. This study throws light on the novel understanding of halophilic bacterial replication and the molecular basis of salt adaptation. Comparisons of the amino acid contents and electronegativity of halophilic and mesophilic bacterial proteins revealed adaptations that allow halophilic bacteria to thrive in high salt concentrations. A significantly lower isoelectric point of halophilic bacterial proteins indicates the acidic nature. Also, an abundance of disordered regions in halophiles suggests the requirement of the salt ions that play a crucial role in their stable protein folding. Despite having similar topology, mesophilic and halophilic proteins, a set of very prominent molecular modifications was observed in the alpha subunit of halophiles.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"20"},"PeriodicalIF":2.9,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9877046","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}

{"title":"Recombinant expression and characterization of a new laccase, bioinformatically identified, from the Antarctic thermophilic bacterium Geobacillus sp. ID17.","authors":"Rodrigo Cortés-Antiquera,&nbsp;Sebastián L Márquez,&nbsp;Giannina Espina,&nbsp;Jorge Sánchez-SanMartín,&nbsp;Jenny M Blamey","doi":"10.1007/s00792-023-01299-y","DOIUrl":"https://doi.org/10.1007/s00792-023-01299-y","url":null,"abstract":"<p><p>Geobacillus sp. ID17 is a gram-positive thermophilic bacterium isolated from Deception Island, Antarctica, which has shown to exhibit remarkable laccase activity in crude extract at high temperatures. A bioinformatic search using local databases led to the identification of three putative multicopper oxidase sequences in the genome of this microorganism. Sequence analysis revealed that one of those sequences contains the four-essential copper-binding sites present in other well characterized laccases. The gene encoding this sequence was cloned and overexpressed in Escherichia coli, partially purified and preliminary biochemically characterized. The resulting recombinant enzyme was recovered in active and soluble form, exhibiting optimum copper-dependent laccase activity at 55 °C, pH 6.5 with syringaldazine substrate, retaining over 60% of its activity after 1 h at 55 and 60 °C. In addition, this thermophilic enzyme is not affected by common inhibitors SDS, NaCl and L-cysteine. Furthermore, biodecolorization assays revealed that this laccase is capable of degrading 60% of malachite green, 54% of Congo red, and 52% of Remazol Brilliant Blue R, after 6 h at 55 °C with aid of ABTS as redox mediator. The observed properties of this enzyme and the relatively straightforward overexpression and partial purification of it could be of great interest for future biotechnology applications.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"18"},"PeriodicalIF":2.9,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9866583","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}

{"title":"Survival of Icelandic airborne microbes towards simulated atmospheric stress factors.","authors":"Aurélien Daussin,&nbsp;Pauline Vannier,&nbsp;Émilien Mater,&nbsp;Tina Šantl-Temkiv,&nbsp;Charles Cockell,&nbsp;Viggó Þór Marteinsson","doi":"10.1007/s00792-023-01302-6","DOIUrl":"https://doi.org/10.1007/s00792-023-01302-6","url":null,"abstract":"<p><p>Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms, wildland fires, and volcano eruptions. Only microbial cells that survive the various atmospheric stressors during their transportation will deposit and colonize new environments. These stressors include desiccation, oxidative stress, solar radiation, osmotic shock, and freeze-thaw cycles. In this paper, we specifically studied the survival of representative microbial model strains isolated from the atmosphere over pristine volcanic landscapes to understand their potential to successfully disperse to novel terrestrial environments. In line with previous studies, we found that the most stringent selection factors were the freeze-thaw and osmotic shock cycles and that the strains affiliated with Proteobacteria and Ascomycota were the best to survive simulated atmospheric stresses. Specifically, isolates belonging to Paracoccus marinus, Janthinobacterium rivuli, and Sarocladium kiliense exhibited the highest levels of resistance to atmospheric stress. However, the number of strains tested in our study was limited and caution should be taken when generalizing these findings.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"17"},"PeriodicalIF":2.9,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9923122","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}

{"title":"Selection of Antarctic yeasts as gray mold biocontrol agents in strawberry.","authors":"Eskálath Morganna Silva Ferreira,&nbsp;Gabriela Garmendia,&nbsp;Vívian Nicolau Gonçalves,&nbsp;Juliana Fonseca Moreira da Silva,&nbsp;Luiz Henrique Rosa,&nbsp;Silvana Vero,&nbsp;Raphael Sanzio Pimenta","doi":"10.1007/s00792-023-01298-z","DOIUrl":"https://doi.org/10.1007/s00792-023-01298-z","url":null,"abstract":"<p><p>The postharvest disease popularly known as gray mold is considered one of the most limiting factors strawberry fruit production. The most effective way to control this disease is still the use of chemical fungicides. However, other alternative sources of control are being explored. Among these, psychrophilic yeasts adapted to extreme conditions, such as those found in the Antarctic region, may have great potential for use as biocontrol agents. Thus, the present study aimed to select psychrotolerant yeasts obtained from Antarctic region and to evaluate their potential for biocontrol under gray mold, caused by Botrytis cinerea in strawberries stored at low temperature. For this, 20 potential antagonist yeasts were evaluated in vitro (thermotolerance and enzymatic) assays. Debaryomyces hansenii, Rhodotorula mucilaginosa and Dioszegia hungarica were selected for growing in strawberry juice. However, only D. hansenii was selected for in vivo studies and showed a reduction in the incidence of gray mold by 82% for the tests performed on injury and 86% for the tests on non-injured fruits treated by immersion bath. Thus, demonstrating that the selection of this cold-adapted Antarctic yeast can be a promising strategy as a biocontrol agent used to curb the development of gray mold in strawberry fruits.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"16"},"PeriodicalIF":2.9,"publicationDate":"2023-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9871793","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}

{"title":"Salinilacihabitans rarus gen. nov., sp. nov., Natrononativus amylolyticus gen. nov., sp. nov., Natronobeatus ordinarius gen. nov., sp. nov., and Halovivax gelatinilyticus sp. nov., halophilic archaea, isolated from a salt lake and soda lakes.","authors":"Xin-Xin Li,&nbsp;Shun Tan,&nbsp;Mu Cheng,&nbsp;Yao Hu,&nbsp;Xue Ma,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1007/s00792-023-01303-5","DOIUrl":"https://doi.org/10.1007/s00792-023-01303-5","url":null,"abstract":"<p><p>Four halophilic archaea strains, AD-4^T, CGA30^T, CGA73^T, and WLHSJ27^T, were isolated from a salt lake and two soda lakes located in different regions of China. The 16S rRNA and rpoB' gene sequence similarities among strains AD-4^T, CGA30^T, CGA73^T, WLHSJ27^T, and the current species of the family Natrialbaceae were 90.9-97.5% and 83.1-91.8%, respectively. The phylogenetic and phylogenomic analyses revealed that these four strains separated from existing genera in the family Natrialbaceae and formed distant branches. The ANI, isDDH, and AAI values among these four strains and the current members of the family Natrialbaceae were 72-79%, 20-25%, and 63-73%, respectively, much lower than the threshold values for species demarcation. Strains AD-4^T, CGA73^T, and WLHSJ27^T may represent three novel genera of the family Natrialbaceae according to the cutoff value of AAI (≤ 76%) proposed to differentiate genera within the family Natrialbaceae. These four strains could be distinguished from the related genera according to differential phenotypic characteristics. The major phospholipids of these four strains were identical while their glycolipid profiles were diverse. DGD-1 is a major glycolipid found in strain AD-4^T, trace glycolipids, DGD-1, and S-DGD-1, and (or) S-TGD-1 was found in the other three strains. The major respiratory quinones detected in the four strains were menaquinone MK-8 and MK-8(H₂). This polyphasic classification indicated that strains AD-4^T, CGA73^T, and WLHSJ27^T represent three novel species of three new genera with the family Natrialbaceae, and strain CGA30^T represents a novel species of Halovivax.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"15"},"PeriodicalIF":2.9,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9753691","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}

{"title":"Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain.","authors":"Hajra Kayani,&nbsp;Muhammad Asif Rasheed,&nbsp;Wadi B Alonazi,&nbsp;Farrukh Jamil,&nbsp;Annam Hussain,&nbsp;ChangHui Yan,&nbsp;Raza Ahmed,&nbsp;Muhammad Ibrahim","doi":"10.1007/s00792-023-01301-7","DOIUrl":"https://doi.org/10.1007/s00792-023-01301-7","url":null,"abstract":"<p><p>Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 2","pages":"14"},"PeriodicalIF":2.9,"publicationDate":"2023-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9686132","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}