Extremophiles最新文献_第3页

Molecular diversity of green-colored microbial mats from hot springs of northern Japan. 日本北部温泉绿色微生物垫的分子多样性。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-31 DOI: 10.1007/s00792-024-01358-y

Yangtsho Gyaltshen, Yuu Ishii, Sophie Charvet, Eleanor Goetz, Shinichiro Maruyama, Eunsoo Kim

{"title":"Molecular diversity of green-colored microbial mats from hot springs of northern Japan.","authors":"Yangtsho Gyaltshen, Yuu Ishii, Sophie Charvet, Eleanor Goetz, Shinichiro Maruyama, Eunsoo Kim","doi":"10.1007/s00792-024-01358-y","DOIUrl":"10.1007/s00792-024-01358-y","url":null,"abstract":"We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"43"},"PeriodicalIF":2.6,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142105966","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

Molecular basis of hyper-thermostability in the thermophilic archaeal aldolase MfnB. 嗜热古细菌醛缩酶 MfnB 超耐热性的分子基础

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-31 DOI: 10.1007/s00792-024-01359-x

Rosie M A Maddock, Carl O Marsh, Samuel T Johns, Lynden D Rooms, Phillip W Duke, Marc W van der Kamp, James E M Stach, Paul R Race

{"title":"Molecular basis of hyper-thermostability in the thermophilic archaeal aldolase MfnB.","authors":"Rosie M A Maddock, Carl O Marsh, Samuel T Johns, Lynden D Rooms, Phillip W Duke, Marc W van der Kamp, James E M Stach, Paul R Race","doi":"10.1007/s00792-024-01359-x","DOIUrl":"10.1007/s00792-024-01359-x","url":null,"abstract":"Methanogenic archaea are chemolithotrophic prokaryotes that can reduce carbon dioxide with hydrogen gas to form methane. These microorganisms make a significant contribution to the global carbon cycle, with methanogenic archaea from anoxic environments estimated to contribute > 500 million tons of global methane annually. Archaeal methanogenesis is dependent on the methanofurans; aminomethylfuran containing coenzymes that act as the primary C1 acceptor molecule during carbon dioxide fixation. Although the biosynthetic pathway to the methanofurans has been elucidated, structural adaptations which confer thermotolerance to Mfn enzymes from extremophilic archaea are yet to be investigated. Here we focus on the methanofuran biosynthetic enzyme MfnB, which catalyses the condensation of two molecules of glyceralde-3-phosphate to form 4‑(hydroxymethyl)-2-furancarboxaldehyde-phosphate. In this study, MfnB enzymes from the hyperthermophile Methanocaldococcus jannaschii and the mesophile Methanococcus maripaludis have been recombinantly overexpressed and purified to homogeneity. Thermal unfolding studies, together with steady-state kinetic assays, demonstrate thermoadaptation in the M. jannaschii enzyme. Molecular dynamics simulations have been used to provide a structural explanation for the observed properties. These reveal a greater number of side chain interactions in the M. jannaschii enzyme, which may confer protection from heating effects by enforcing spatial residue constraints.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"42"},"PeriodicalIF":2.6,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11365854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142105965","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

Multifunctionality of a low-specificity L-threonine aldolase from the hyperthermophile Thermotoga maritima. 来自嗜热菌 Thermotoga maritima 的低特异性 L-苏氨酸醛缩酶的多功能性。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-27 DOI: 10.1007/s00792-024-01357-z

Tetsuya Miyamoto, Fugo Kobayashi, Konan Emori, Kumiko Sakai-Kato

引用次数: 0

Diversity of lichen mycobionts and photobionts and their relationships in the Ny-Ålesund region (Svalbard, High Arctic). Ny-Ålesund 地区（斯瓦尔巴群岛，高纬度北极地区）地衣霉菌和光菌的多样性及其关系。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-23 DOI: 10.1007/s00792-024-01355-1

Xiufei Chen, Jianju Feng, Liyan Yu, Tao Zhang

{"title":"Diversity of lichen mycobionts and photobionts and their relationships in the Ny-Ålesund region (Svalbard, High Arctic).","authors":"Xiufei Chen, Jianju Feng, Liyan Yu, Tao Zhang","doi":"10.1007/s00792-024-01355-1","DOIUrl":"10.1007/s00792-024-01355-1","url":null,"abstract":"Lichens are dual organisms, with one major mycobiont and one major photobiont in each lichen symbiosis, which can survive extreme environmental conditions in the Arctic. However, the diversity and distribution of lichen photobionts in the Arctic remain poorly understood compared to their mycobiont partners. This study explored the diversity of lichen mycobionts and photobionts in 197 lichen samples collected from the Ny-Ålesund region (Svalbard, High Arctic). The nuclear ribosomal internal transcribed spacer (ITS) regions were sequenced and phylogenetic analyses were performed. The relationships between mycobionts and photobionts, as well as the association patterns, were also investigated. A total of 48 species of lichen mycobionts (16 families, nine orders) and 31 species/lineages of photobionts were identified. These 31 photobiont species belonged to one class (Trebouxiophyceae) and five genera, including 22 species of Trebouxia, five species of Asterochloris, two species of Chloroidium, one species of Symbiochloris, and one species of Coccomyxa. The results indicated that most analyzed lichen mycobionts could associate with multiple photobiont species, and the photobionts also exhibited a similar pattern. The results provided an important reference dataset for characterizing the diversity of lichen mycobionts and photobionts in the High Arctic region.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"40"},"PeriodicalIF":2.6,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046551","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

Genomic signatures of cold adaptation in the family Colwelliaceae. 高良姜科植物适应寒冷的基因组特征。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-23 DOI: 10.1007/s00792-024-01356-0

Anais Gentilhomme, Charles Sweet, Gwenn M M Hennon, R Eric Collins

{"title":"Genomic signatures of cold adaptation in the family Colwelliaceae.","authors":"Anais Gentilhomme, Charles Sweet, Gwenn M M Hennon, R Eric Collins","doi":"10.1007/s00792-024-01356-0","DOIUrl":"10.1007/s00792-024-01356-0","url":null,"abstract":"Psychrophily is a phenotype describing microbial growth at low temperatures; elucidating the biomolecular and genomic adaptations necessary for survival in the cold is important for understanding life in extreme environments on Earth and in outer space. We used comparative genomics and temperature growth experiments of bacteria from the family Colwelliaceae to identify genomic factors correlated with optimal growth temperature (OGT). A phylogenomic analysis of 67 public and 39 newly sequenced strains revealed three main clades of Colwelliaceae. Temperature growth experiments revealed significant differences in mean OGT by clade, wherein strains of Colwelliaceae had similar growth rates at -1 °C but varied in their ability to tolerate 17 °C. Using amino acid compositional indices, a multiple linear regression model was constructed to predict the OGT of these organisms (RMSE 5.2 °C). Investigation of Colwelliaceae functional genes revealed a putative cold-adaptive gene cassette that was present in psychrophilic strains but absent in a closely related strain with a significantly higher OGT. This study also presents genomic evidence suggesting that the clade of Colwelliaceae containing Colwellia hornerae should be investigated as a new genus. These contributions offer key insights into the psychrophily phenotype and its underlying genomic foundation in the family Colwelliaceae.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"39"},"PeriodicalIF":2.6,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035610","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 Tet-on system for controllable gene expression in the rock-inhabiting black fungus Knufia petricola. 岩石栖息黑真菌 Knufia petricola 中可控基因表达的 Tet-on 系统。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-08-06 DOI: 10.1007/s00792-024-01354-2

Eileen A Erdmann, Antonia K M Brandhorst, Anna A Gorbushina, Julia Schumacher

{"title":"The Tet-on system for controllable gene expression in the rock-inhabiting black fungus Knufia petricola.","authors":"Eileen A Erdmann, Antonia K M Brandhorst, Anna A Gorbushina, Julia Schumacher","doi":"10.1007/s00792-024-01354-2","DOIUrl":"10.1007/s00792-024-01354-2","url":null,"abstract":"Knufia petricola is a black fungus that colonizes sun-exposed surfaces as extreme and oligotrophic environments. As ecologically important heterotrophs and biofilm-formers on human-made surfaces, black fungi form one of the most resistant groups of biodeteriorating organisms. Due to its moderate growth rate in axenic culture and available protocols for its transformation and CRISPR/Cas9-mediated genome editing, K. petricola is used for studying the morpho-physiological adaptations shared by extremophilic and extremotolerant black fungi. In this study, the bacteria-derived tetracycline (TET)-dependent promoter (Tet-on) system was implemented to enable controllable gene expression in K. petricola. The functionality i.e., the dose-dependent inducibility of TET-regulated constructs was investigated by using GFP fluorescence, pigment synthesis (melanin and carotenoids) and restored uracil prototrophy as reporters. The newly generated cloning vectors containing the Tet-on construct, and the validated sites in the K. petricola genome for color-selectable or neutral insertion of expression constructs complete the reverse genetics toolbox. One or multiple genes can be expressed on demand from different genomic loci or from a single construct by using 2A self-cleaving peptides, e.g., for localizing proteins and protein complexes in the K. petricola cell or for using K. petricola as host for the expression of heterologous genes.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"38"},"PeriodicalIF":2.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893232","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

Comparative analysis of cyanobacterial communities in gypsum outcrops: insights from sites in Israel and Poland. 石膏露头蓝藻群落的比较分析：以色列和波兰遗址的启示。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-07-30 DOI: 10.1007/s00792-024-01352-4

Kateřina Němečková, Jan Mareš, Filip Košek, Adam Culka, Jan Dudák, Veronika Tymlová, Jan Žemlička, Jan Jehlička

{"title":"Comparative analysis of cyanobacterial communities in gypsum outcrops: insights from sites in Israel and Poland.","authors":"Kateřina Němečková, Jan Mareš, Filip Košek, Adam Culka, Jan Dudák, Veronika Tymlová, Jan Žemlička, Jan Jehlička","doi":"10.1007/s00792-024-01352-4","DOIUrl":"10.1007/s00792-024-01352-4","url":null,"abstract":"Today, the biodiversity of endolithic microbial colonisations are only partly understood. In this study, we used a combination of molecular community metabarcoding using the 16S rRNA gene, light microscopy, CT-scan analysis, and Raman spectroscopy to describe gypsum endolithic communities in 2 sites-southern Poland and northern Israel. The obtained results have shown that despite different geographical areas, climatic conditions, and also physical features of colonized gypsum outcrops, both of these sites have remarkably similar microbial and pigment compositions. Cyanobacteria dominate both of the gypsum habitats, followed by Chloroflexi and Pseudomonadota. Among cyanobacteria, Thermosynechococcaceae were more abundant in Israel while Chroococcidiopsidaceae in Poland. Interestingly, no Gloeobacteraceae sequences have been found in Poland, only in Israel. Some of the obtained 16S rRNA gene sequences of cyanobacteria matched previously detected sequences from endolithic communities in various substrates and geographical regions, supporting the hypothesis of global metacommunity, but more data are still needed. Using Raman spectroscopy, cyanobacterial UV-screening pigments-scytonemin and gloeocapsin have been detected alongside carotenoids, chlorophyll a and melanin. These pigments can serve as potential biomarkers for basic taxonomic identification of cyanobacteria. Overall, this study provides more insight into the diversity of cyanobacterial endolithic colonisations in gypsum across different areas.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"37"},"PeriodicalIF":2.6,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855266","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

Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula. 为沉积金属藻的异养培养开发限定培养基。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-07-26 DOI: 10.1007/s00792-024-01348-0

Viktor Laurin Sedlmayr, Maximilian Luger, Ernst Pittenauer, Martina Marchetti-Deschmann, Laura Kronlachner, Andreas Limbeck, Philipp Raunjak, Julian Quehenberger, Oliver Spadiut

{"title":"Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula.","authors":"Viktor Laurin Sedlmayr, Maximilian Luger, Ernst Pittenauer, Martina Marchetti-Deschmann, Laura Kronlachner, Andreas Limbeck, Philipp Raunjak, Julian Quehenberger, Oliver Spadiut","doi":"10.1007/s00792-024-01348-0","DOIUrl":"10.1007/s00792-024-01348-0","url":null,"abstract":"The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"36"},"PeriodicalIF":2.6,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141765897","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

RNase R vs. PNPase: selecting the best-suited exoribonuclease for environmental adaptation. RNase R 与 PNPase：选择最适合环境适应的外切核酸酶。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-07-25 DOI: 10.1007/s00792-024-01350-6

Theetha L Pavankumar

引用次数: 0

Effects of temperature, chloride and perchlorate salt concentration on the metabolic activity of Deinococcus radiodurans. 温度、氯化物和高氯酸盐浓度对放射球菌代谢活动的影响。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-07-24 DOI: 10.1007/s00792-024-01351-5

Eftychia Symeonidou, Uffe Gråe Jørgensen, Morten Bo Madsen, Anders Priemé

{"title":"Effects of temperature, chloride and perchlorate salt concentration on the metabolic activity of Deinococcus radiodurans.","authors":"Eftychia Symeonidou, Uffe Gråe Jørgensen, Morten Bo Madsen, Anders Priemé","doi":"10.1007/s00792-024-01351-5","DOIUrl":"10.1007/s00792-024-01351-5","url":null,"abstract":"The extremophile bacterium Deinococcus radiodurans is characterized by its ability to survive and sustain its activity at high levels of radiation and is considered an organism that might survive in extraterrestrial environments. In the present work, we studied the combined effects of temperature and chlorine-containing salts, with focus on perchlorate salts which have been detected at high concentrations in Martian regolith, on D. radiodurans activity (CO2 production rates) and viability after incubation in liquid cultures for up to 30 days. Reduced CO2 production capacity and viability was observed at high perchlorate concentrations (up to 10% w/v) during incubation at 0 or 25 °C. Both the metabolic activity and viability were reduced as the perchlorate and chloride salt concentration increased and temperature decreased, and an interactive effect of temperature and salt concentration on the metabolic activity was found. These results indicate the ability of D. radiodurans to remain metabolically active and survive in low temperature environments rich in perchlorate.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"34"},"PeriodicalIF":2.6,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751442","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