Extremophiles最新文献

{"title":"Assessment of pathogenic traits in selected bacteria isolated from snowy environments in France and Greenland.","authors":"Masoumeh Kashiri, Athanasios Zervas, Florian H H Brill, Jörg Steinmann, Bernd Neumann, Diana C Mogrovejo, Alexandre M Anesio","doi":"10.1007/s00792-026-01444-3","DOIUrl":"10.1007/s00792-026-01444-3","url":null,"abstract":"<p><p>Microorganisms inhabiting cold environments have gained increasing attention in recent decades due to their unique adaptation mechanisms that enable survival under extreme conditions. Growing evidence indicates that some cold-adapted bacteria possess phenotypic and genomic traits linked to pathogenicity, raising concerns about their potential environmental and public health relevance. Here, we characterized three culturable bacteria isolated from human-impacted snow in the French Alps (Chamrousse) and coastal Greenland (Nuuk). Snow samples were cultured on R2A medium, and isolates were identified by Sanger sequencing as Peribacillus, Sphingomonas, and Subtercola. Temperature tolerance, haemolytic activity, and antibiotic susceptibility were assessed by culture-based assays, while whole-genome sequencing was used to screen for antibiotic resistance and virulence-associated genes using reference databases. Only the Peribacillus isolate tolerated 37 °C and showed α-haemolysis. Antibiotic susceptibility testing indicated full susceptibility in Peribacillus, while Sphingomonas and Subtercola showed reduced susceptibility to a limited number of antibiotics, mainly to cefotaxime, chloramphenicol, and colistin. Genomes encoded genes associated with efflux, target modification, motility/adhesion, and stress adaptation, indicating environmental resilience rather than clinical pathogenicity. Overall, these isolates displayed limited pathogenic phenotypes with genomic traits primarily supporting environmental adaptation and survival.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147422","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}

{"title":"Comparative genomic analysis of Rahnella sp. PAMC25617 isolated from cryoconite reveals a glutathione-dependent formaldehyde detoxification pathway.","authors":"Srijana Tiwari, Prasansah Shrestha, Bashu Dev Pardhe, So-Ra Han, Tae-Jin Oh","doi":"10.1007/s00792-026-01443-4","DOIUrl":"10.1007/s00792-026-01443-4","url":null,"abstract":"<p><p>Rahnella species are environmentally versatile bacteria widely distributed in terrestrial and aquatic ecosystems; however, the genomic basis of formaldehyde detoxification and stress adaptation in cryoconite-associated Rahnella remains poorly understood. In this study, we performed phylogenomic, comparative genomic, pan-genomic, stress-response, and functional analyses of Rahnella sp. PAMC25617 isolated from polar cryoconite to investigate glutathione (GSH)-dependent formaldehyde detoxification and its evolutionary conservation. Genome-based phylogeny, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) analyses demonstrated that PAMC25617 represents a distinct genomic lineage within the genus Rahnella. The draft genome comprised 5.33 Mb with a GC content of 52% and encoded multiple genes associated with formaldehyde detoxification and one-carbon metabolism, including frmA, yeiG, yeiP, yeiR, and a putative formate dehydrogenase gene cluster. Comparative genomic analyses further showed that these detoxification genes were consistently associated with GSH transport (gsiA-D), redox-associated (frdA-D), and regulatory (fnr) genes, suggesting coordinated roles in detoxification and redox homeostasis. Comparative stress-response gene profiling across 121 Rahnella genomes further revealed widespread conservation of oxidative stress defense systems, including oxidoreductases, aldehyde dehydrogenases, GSH-associated enzymes, thioredoxin, catalase, and molecular chaperones. Notably, PAMC25617 possessed an enriched repertoire of oxidative stress and detoxification-related genes, indicating enhanced stress adaptation potential in cold and chemically challenging environments. Pan-genome analysis indicated a highly diverse and open pan-genome structure with a low Heap's law exponent (γ = 0.336), reflecting ongoing genome diversification and ecological adaptation. Multiple sequence alignment (MSA) further demonstrated strong conservation of catalytic motifs and active-site residues in FrmA and YeiG among phylogenetically diverse bacteria. Physiological assays showed that PAMC25617 exhibited tolerance to formaldehyde stress under liquid culture conditions. These findings suggest that R. sp. PAMC25617 employs an integrated GSH-dependent detoxification and oxidative stress response system that may facilitate survival and adaptation in extreme polar environments.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149106253","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 insights into the response of Acidithiobacillus caldus to leached metal toxicity during bioleaching of spent FCC catalyst.","authors":"Lu Zheng, Yue-Jie Wang, Ling-Ling Li, Sheng Zhao, Chang-Yun Zhang, An-Feng Yu","doi":"10.1007/s00792-026-01441-6","DOIUrl":"10.1007/s00792-026-01441-6","url":null,"abstract":"<p><p>Acidithiobacillus caldus, a thermoacidophilic sulfur-oxidizing bacterium, is utilized in bioleaching owing to its robust metabolic capabilities. This study explored the roles of A. caldus in metal bioleaching, the mechanisms of metal toxicity resistance, and the concentration-dependent strategies, aiming to provide insights for process optimization. In this study, an integrated approach was employed, encompassing dynamic monitoring of metal release, enzymatic activity assays, and de novo transcriptome sequencing. The integrated mechanism of \"bioleaching promotion-toxicity response-resistance regulation\" in A. caldus under SFCCC-induced stress was systematically revealed. The bacterium demonstrated high bioleaching efficiency of heavy metals from SFCCC. Under metal-induced stress, it employed defense mechanisms primarily through a glutathione peroxidase (GSH-Px) mediated antioxidant system. This response was sustained by the continuous activation of H⁺-ATPase and NADPH-generating metabolic pathways to maintain energy supply and reducing power. The bacterial response exhibited concentration dependence. Under low-concentration stress, A. caldus prioritized basal metabolic maintenance alongside initiation of defensive measures. However, under high-concentration stress, it employed a comprehensive survival strategy involving metabolic reprogramming to sacrifice non-essential functions in favor of critical survival processes. The transition reflects a strategic shift from a growth-oriented to a survival-oriented mode. These findings enhance the theoretical framework for understanding concentration-dependent strategic transitions in microbe-metal interactions and offer a molecular biology basis for improving the practical application of bioleaching technologies.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149024321","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":"Hydrochemical associations with microbial community structure in the Reshuigou hot springs, northeastern Qinghai-Tibet Plateau.","authors":"Wenqiang Zhao, Qingda Feng, Huaisheng Zhang, Runsheng Ma, Shengchao Shi, Caixiong Fan, Fuzhi Qi, Jun Zhou","doi":"10.1007/s00792-026-01442-5","DOIUrl":"10.1007/s00792-026-01442-5","url":null,"abstract":"<p><p>Geothermal hot springs provide important windows into the links among deep hydrothermal circulation, water-rock interaction, and microbial ecology in extreme environments. This study investigated six hot-spring water samples from Reshuigou, Guide County, Qinghai Province, by integrating hydrochemical analysis, PHREEQC mineral saturation calculations, microbial community profiling, RDA, PCoA environmental fitting, and Spearman correlation analysis. The Reshuigou waters were characterized by medium to high temperature, weak alkalinity, reducing conditions, and moderate to relatively high mineralization. Their hydrochemical facies were consistently of the Na+K/Cl-SO₄ type, reflecting deep-circulation water-rock interaction, sulfate and chloride inputs, silicate dissolution, and ion exchange. The microbial communities were dominated by Proteobacteria, Aquificota, Deinococcota, Chloroflexi, and Bacteroidota, with Hydrogenobacter, Thermus, Herbaspirillum, and Delftia as important genera. Phylum- and genus-level RDA accounted for 71.9 and 77.4% of the constrained community variation, respectively. Spearman analysis further showed an inverse relationship between Chloroflexi and ORP, a positive relationship between Chloroflexi and HCO₃⁻, and positive covariation of Proteobacteria with several major ions and mineralization indicators. Taken together, the results show that a shared deep-geothermal background establishes the regional community baseline, whereas temperature, redox state, mineralization, major-ion composition, and local discharge conditions jointly structure microbial differentiation among spring sites.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149024306","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":"Screening of hyperthermostable proteins from hyperthermophilic archaeon Palaeococcus pacificus DY20341^T.","authors":"Junxi Hu, Jing Zhang, Jiaju Xu, Xiang Zeng","doi":"10.1007/s00792-026-01440-7","DOIUrl":"10.1007/s00792-026-01440-7","url":null,"abstract":"<p><p>Palaeococcus pacificus DY20341^T, a hyperthermophilic archaeon from deep sea hydrothermal sediments, grows at temperature range from 50 to 90 ℃ (Topt = 80℃). To explore the molecular basis of its thermal adaptation, we identified six representative hyperthermostable proteins from its cytosolic fraction that remained soluble after a stringent in vitro heat treatment at 100 °C. MALDI-TOF mass spectrometry identified these as an inorganic pyrophosphatase (PPase), a 5'-methylthioadenosine phosphorylase (MTAP), and four putative transporter components (one TRAP and three ABC transporter solute-binding proteins). RT-qPCR analysis revealed that the transcription of all six corresponding genes was significantly upregulated when the growth temperature was elevated from 80 °C to 90 °C, suggesting a potential role in the cellular response to heat stress. Biochemical characterization of the recombinant PPase demonstrated remarkable thermostability and an optimal temperature of 90 °C. Kinetic analysis revealed high catalytic efficiency, with a maximal specific activity of 590 ± 30 U/mg and a strong substrate affinity ([Formula: see text] = 6.24 µM). Phylogenetic analysis of the identified thermostable MTAP (PAP_00250) revealed its evolutionary origin from hyperthermophilic archaea, distinguishing it clearly from a second MTAP homolog (PAP_07050) in the genome, which aligns with mesophilic bacteria. The structural stability of the identified ABC and TRAP transporter components hypothesizes that efficient nutrient scavenging remains critical at extreme temperatures. Together, these findings provide valuable insights into the stable molecular machinery and potential physiological strategies enabling P. pacificus to thrive in hydrothermal environments.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148789944","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":"Salinity and ionic composition drive prokaryotic community assembly in Tuolekule Lake, China.","authors":"Liping Xu, Longteng Fang, Rehan Shayibas, Yiman Li, Reziyamu Wufuer, Shiyang Lu, Nan Wei, Dong Wang, Zhiwei Zhang","doi":"10.1007/s00792-026-01439-0","DOIUrl":"10.1007/s00792-026-01439-0","url":null,"abstract":"<p><p>Saline lakes in arid and semi-arid regions are home to unique ecosystems characterized by high salinity and alkalinity, as well as extreme environmental stresses. Despite these harsh conditions, they support diverse extremophilic microbial communities with distinct structures, offering substantial biomedical and biotechnological potential. Tuolekule Lake is a hypersaline, alkaline lake situated in a closed basin in the northern foothills of the East Tianshan Mountains in Xinjiang, China. This high-altitude extreme environment constitutes a distinct ecosystem. However, the structure of its microbial communities, their environmental drivers and their biotechnological potential remain largely unexplored. This study systematically analyzed the physicochemical properties of sediment samples from Tuolekule Lake. Subsequently, high-throughput sequencing identified a strong association between environmental factors and microbial community structure, paving the way for the targeted cultivation of microorganisms based on these insights. Results revealed that the sediments are dominated by Cl⁻, SO₄²⁻, Na⁺, and Mg²⁺ ions, confirming the lake's classification as a sulfate-chloride type. Salinity, SO₄²⁻ concentration, and pH emerged as the key environmental factors structuring the microbial community, predominantly composed of Pseudomonadota, Halanaerobiaeota, and Bacteroidota. Co-occurrence network analysis revealed distinct modular associations among taxa. Functional prediction based on 16S rRNA gene sequences for these communities indicated that chemoheterotrophy and fermentation served as putative core metabolic processes, alongside a significant enrichment of sulfur cycling pathways. These inferred metabolic capabilities collectively suggest potential adaptive strategies employed by the microbial community under extreme conditions. Building on these community insights, a targeted cultivation strategy was implemented, successfully isolating 54 halotolerant microbial strains and revealing the environment's rich reservoir of extremophilic microorganisms.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148758005","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":"Correction: Cultivation and characterization of haloarchaea from Moroccan Atlantic solar salterns: insights into diversity and bioactive potential.","authors":"Imane Charroud, Naima Boum'handi, Mohamed Alouani, Altaf El Blidi, Yannick Fleury, Mohamed Jebbar","doi":"10.1007/s00792-026-01438-1","DOIUrl":"10.1007/s00792-026-01438-1","url":null,"abstract":"","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148724158","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":"L-asparaginase by filamentous fungi and yeasts from lichens and soils across maritime Antarctic islands.","authors":"Averlane Vieira da Silva, Bárbara Emanuelle Fernandes Ferro, Vanessa Daiany Vieira Medeiros, Valdilene Canazart Dos Santos, Maria Nicolle Pereira da Silva, Cledna Kaline Dos Santos Duarte, Aline Cavalcanti de Queiroz, Magna Suzana Alexandre Moreira, Luiz Henrique Rosa, Alysson Wagner Fernandes Duarte","doi":"10.1007/s00792-026-01437-2","DOIUrl":"10.1007/s00792-026-01437-2","url":null,"abstract":"<p><p>This study aimed to evaluate L-asparaginase (L-ASNase) production by fungi isolated from soils across different Antarctic islands. Out of 138 isolates, 33 filamentous fungi and 5 yeasts exhibited enzymatic activity in solid culture media. Filamentous fungi were identified by sequencing the Internal Transcribed Spacer (ITS) region, while yeasts were identified using the D1/D2 domains of the 26 S rDNA gene. The blue filamentous fungus Antarctomyces F13.CR.LASP exhibited a maximum L-ASNase productivity of 0.76 U/L. Regarding the yeasts, the isolate Vishniacozyma victoriae G.L11 reached a productivity of 0.17 U/L, while corresponding values for glutaminase and urease were 0.11 and 0.06 U/L, respectively. Furthermore, V. victoriae G.L11 was capable of producing the enzyme using different low-cost substrates, particularly pineapple peel waste, which yielded 5.17 U/L. In this scenario, future optimization could further enhance L-asparaginase production levels by these fungi, providing valuable insights into the biotechnological potential of Antarctic fungi.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13428764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148653280","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}

{"title":"Rising from the fragments: a multi-factorial regulatory framework of DNA damage response in Deinococcus radiodurans.","authors":"Narasimha Anaganti, Aman Kumar Ujaoney, Mahesh Kumar Padwal, Bhakti Basu","doi":"10.1007/s00792-026-01436-3","DOIUrl":"10.1007/s00792-026-01436-3","url":null,"abstract":"<p><p>Understanding the coordinated regulation of gene expression in response to environmental challenges is critical for unravelling the resistance strategies of the extremophiles that endure extreme habitats. Deinococcus radiodurans is a notable extremophile for rebuilding entire genome from the fragmented DNA, a property that enables it to withstand acute exposure to high levels of DNA-damaging agents, including gamma radiation, ultraviolet (UV) rays, desiccation, and chemical mutagens. In the context of DNA damage, a variety of DNA lesions from base damages to double strand breaks are acted upon by appropriate DNA repair pathways which operate either in tandem or in a sequential manner to efficiently restore the entire genome and restart normal growth. To achieve a high-regulatory specificity, a multi-factorial regulatory mechanism is required to activate or repress target pathway genes in vivo, in a dose and time dependent manner. Several studies have explored a role of cis-acting elements including genomic sequences like promoters, enhancers, or operators, structural elements, or trans-acting factors such as transcriptional regulators or non-coding RNAs (ncRNAs) in the regulation of DNA damage response. This review explores the intricate regulatory networks employed by D. radiodurans, offering a comprehensive overview of its DNA damage response mechanisms. These insights help shed light on the molecular strategies that enable this organism to thrive in extreme environments. The knowledge gaps which need the focus of future research are discussed.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148430402","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":"Elucidation of D-amino acid metabolic activity of ornithine decarboxylase from the hyperthermophile Thermotoga maritima.","authors":"Kanon Nogawa, Tetsuya Miyamoto","doi":"10.1007/s00792-026-01435-4","DOIUrl":"10.1007/s00792-026-01435-4","url":null,"abstract":"<p><p>The hyperthermophilic bacterium Thermotoga maritima possesses a unique peptidoglycan characterized by the presence of an unusual D-lysine. We have previously identified and characterized a lysine racemase involved in the D-lysine biosynthetic pathway in T. maritima. The lysine racemase possesses high racemase activity toward ornithine as well as lysine. However, the physiological significance of D-ornithine is unknown in T. maritima. In the present study, we characterized ornithine decarboxylase (TM1873), which catalyzes the first step of polyamine biosynthesis, to determine its substrate specificity for D-amino acids including D-ornithine. TM1873 displayed the highest decarboxylase activity toward L-ornithine, followed by L-lysine, and lowest activity toward L-arginine. Based on our kinetic analysis, the k_cat/K_m value for L-ornithine was higher than that for L-lysine. These results suggest that TM1873 has a dual specificity for L-ornithine and L-lysine. Decarboxylase activity of TM1873 was maintained under the physiological pH and growth temperature in T. maritima. Intriguingly, TM1873 also acted on D-ornithine and D-lysine, whereas these activities were lower than those toward corresponding L-amino acids. Additionally, diaminopimelate decarboxylase (TM1517) exhibited nominal activity toward D-ornithine and D-lysine. These results suggest that these two decarboxylases have the ability to metabolize basic D-amino acids, although their substrate preferences were oriented toward basic L-amino acids and meso- diaminopimelate, respectively.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148351419","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}