Extremophiles : life under extreme conditions最新文献_第9页

Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers. 新设计的PCR引物揭示了深海热液区编码RubisCO形式II的cbbM基因的分布和系统发育多样性。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2012-03-01 Epub Date: 2012-01-03 DOI: 10.1007/s00792-011-0428-6

Shingo Kato, Michiyuki Nakawake, Moriya Ohkuma, Akihiko Yamagishi

{"title":"Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers.","authors":"Shingo Kato, Michiyuki Nakawake, Moriya Ohkuma, Akihiko Yamagishi","doi":"10.1007/s00792-011-0428-6","DOIUrl":"https://doi.org/10.1007/s00792-011-0428-6","url":null,"abstract":"To investigate the phylogenetic diversity of putative chemolithoautotrophs possessing the RubisCO form II gene (cbbM) in various environments, we designed a new PCR primer set targeting this gene. The primer set was designed to cover more diverse and longer sequences of cbbM genes than those reported previously. We analyzed various samples (i.e., benthic sands, basement rocks, sulfide chimneys, vent fluids and overlying bottom seawater) collected in a deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, by PCR-based analysis using the designed primer set. Most of the cbbM phylotypes recovered from the liquid samples were related to those of the SUP05 group that belongs to the Gammaproteobacteria and includes putative sulfide-oxidizing chemolithoautotrophs. In contrast, the cbbM phylotypes recovered from the solid samples were related to environmental clones with low similarity (74-90%) and not closely related to the SUP05 group (69-74%). The cbbM phylotypes recovered from the liquid samples were different from those of the solid samples. Furthermore, the cbbM phylotypes recovered from the solid samples were different from each other. Our results expand knowledge of the phylogenetic diversity and distribution of putative chemolithoautotrophs possessing RubisCO form II cbbM genes in deep-sea hydrothermal fields.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"277-83"},"PeriodicalIF":2.9,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-011-0428-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39966460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough. Thermotomaculum hydrothermale gen. nov., sp. nov.，一种来自冲绳海槽南部深海热液喷口烟囱的新型异养性嗜热菌。

Extremophiles : life under extreme conditions Pub Date : 2012-03-01 Epub Date: 2012-01-03 DOI: 10.1007/s00792-011-0425-9

Hiroshi Izumi, Takuro Nunoura, Masayuki Miyazaki, Sayaka Mino, Tomohiro Toki, Ken Takai, Yoshihiko Sako, Tomoo Sawabe, Satoshi Nakagawa

{"title":"Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough.","authors":"Hiroshi Izumi, Takuro Nunoura, Masayuki Miyazaki, Sayaka Mino, Tomohiro Toki, Ken Takai, Yoshihiko Sako, Tomoo Sawabe, Satoshi Nakagawa","doi":"10.1007/s00792-011-0425-9","DOIUrl":"10.1007/s00792-011-0425-9","url":null,"abstract":"A novel heterotrophic, thermophilic bacterium, designated strain AC55(T), was isolated from a deep-sea hydrothermal vent chimney at the Hatoma Knoll in the Okinawa Trough, Japan. Cells of strain AC55(T) were non-motile, long rods (2.0- to 6.8-μm long and 0.3- to 0.6-μm wide). The strain was an obligatory anaerobic heterotroph capable of fermentative growth on complex proteinaceous substances. Elemental sulfur was reduced to hydrogen sulfide but did not stimulate growth. Growth was observed between 37 and 60°C (optimum 55°C), pH 5.5 and 8.5 (optimum pH 6.6), and in the presence of 1.5-4.5% (w/v) NaCl (optimum 2.5%, w/v). Menaquinone-7 and -8 were the major respiratory quinones. The G + C content of the genomic DNA from strain AC55(T) was 51.6 mol%. The 16S rRNA gene sequence analysis revealed that strain AC55(T) was the first cultivated representative of Acidobacteria subdivision 10. Based on the physiological and phylogenetic features of the novel isolate, the genus name Thermotomaculum gen. nov. is proposed, with Thermotomaculum hydrothermale sp. nov. as the type species. The type strain is AC55(T) (=JCM 17643(T) = DSM 24660(T) = NBRC 107904(T)).","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"245-53"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39966666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil. 从南极沙漠土壤中提取的一种新型的极亲碱和冷活性酯酶。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2012-01-01 Epub Date: 2011-11-04 DOI: 10.1007/s00792-011-0407-y

Xiao Ping Hu, Caroline Heath, Mark Paul Taylor, Marla Tuffin, Don Cowan

{"title":"A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil.","authors":"Xiao Ping Hu, Caroline Heath, Mark Paul Taylor, Marla Tuffin, Don Cowan","doi":"10.1007/s00792-011-0407-y","DOIUrl":"https://doi.org/10.1007/s00792-011-0407-y","url":null,"abstract":"A novel, cold-active and highly alkaliphilic esterase was isolated from an Antarctic desert soil metagenomic library by functional screening. The 1,044 bp gene sequence contained several conserved regions common to lipases/esterases, but lacked clear classification based on sequence analysis alone. Moderate (<40%) amino acid sequence similarity to known esterases was apparent (the closest neighbour being a hypothetical protein from Chitinophaga pinensis), despite phylogenetic distance to many of the lipolytic \"families\". The enzyme functionally demonstrated activity towards shorter chain p-nitrophenyl esters with the optimal activity recorded towards p-nitrophenyl propionate (C3). The enzyme possessed an apparent T(opt) at 20°C and a pH optimum at pH 11. Esterases possessing such extreme alkaliphily are rare and so this enzyme represents an intriguing novel locus in protein sequence space. A metagenomic approach has been shown, in this case, to yield an enzyme with quite different sequential/structural properties to known lipases. It serves as an excellent candidate for analysis of the molecular mechanisms responsible for both cold and alkaline activity and novel structure-function relationships of esterase activity.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"79-86"},"PeriodicalIF":2.9,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-011-0407-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40127360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

Cultivable bacteria from ancient algal mats from the McMurdo Dry Valleys, Antarctica. 来自南极洲麦克默多干谷的古藻垫中的可培养细菌。

Extremophiles : life under extreme conditions Pub Date : 2012-01-01 Epub Date: 2011-11-08 DOI: 10.1007/s00792-011-0410-3

Doug E Antibus, Laura G Leff, Brenda L Hall, Jenny L Baeseman, Christopher B Blackwood

{"title":"Cultivable bacteria from ancient algal mats from the McMurdo Dry Valleys, Antarctica.","authors":"Doug E Antibus, Laura G Leff, Brenda L Hall, Jenny L Baeseman, Christopher B Blackwood","doi":"10.1007/s00792-011-0410-3","DOIUrl":"10.1007/s00792-011-0410-3","url":null,"abstract":"The McMurdo Dry Valleys in Antarctica are a favorable location for preservation of dormant microbes due to their persistent cold and dry climate. In this study, we examined cultivable bacteria in a series of algal mat samples ranging from 8 to 26539 years old. Cultivable bacteria were found in all samples except one (12303 years old), but abundance and diversity of cultivable bacteria decreased with increasing sample age. Only members of the Actinobacteria, Bacteroidetes, and Firmicutes were found in the ancient samples, whereas bacteria in the 8-year-old sample also included Cyanobacteria, Proteobacteria, and Deinococcus-Thermus. Isolates of the Gram-positive spore-forming bacterium Sporosarcina were found in 5 of 8 samples. The growth of these isolates at different temperatures was related to the phylogenetic distance among genotypes measured by BOX-PCR. These findings suggest that adaptation to growth at different temperatures had occurred among Sporosarcina genotypes in the Dry Valleys, causing the existence of physiologically distinct but closely related genotypes. Additionally, fully psychrophilic isolates (that grew at 15°C, but not 25°C) were found in ancient samples, but not in the modern sample. The preservation of viable bacteria in the Dry Valleys could potentially represent a legacy of bacteria that impacts on current microbial communities of this environment.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"105-14"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40137196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects. 冰岛五个地热水中的细菌多样性:温度和烧结矿生长速率的影响。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2011-07-01 Epub Date: 2011-05-24 DOI: 10.1007/s00792-011-0378-z

Dominique J Tobler, Liane G Benning

{"title":"Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects.","authors":"Dominique J Tobler, Liane G Benning","doi":"10.1007/s00792-011-0378-z","DOIUrl":"https://doi.org/10.1007/s00792-011-0378-z","url":null,"abstract":"The microbial ecology associated with siliceous sinters was studied in five geochemically diverse Icelandic geothermal systems. Bacterial 16S rRNA clone libraries were constructed from water-saturated precipitates from each site resulting in a total of 342 bacterial clone sequences and 43 species level phylotypes. In near-neutral, saline (2.6-4.7% salinity) geothermal waters where sinter growth varied between 10 and ~300 kg year(-1) m(-2), 16S rRNA gene analyses revealed very low (no OTUs could be detected) to medium (9 OTUs) microbial activity. The most dominant phylotypes found in these waters belong to marine genera of the Proteobacteria. In contrast, in alkaline (pH = 9-10), meteoric geothermal waters with temperature = 66-96°C and <1-20 kg year(-1)m(-2) sinter growth, extensive biofilms (a total of 34 OTUs) were observed within the waters and these were dominated by members of the class Aquificae (mostly related to Thermocrinis), Deinococci (Thermus species) as well as Proteobacteria. The observed phylogenetic diversity (i.e., number and composition of detected OTUs) is argued to be related to the physico-chemical regime prevalent in the studied geothermal waters; alkaliphilic thermophilic microbial communities with phylotypes related to heterotrophic and autotrophic microorganisms developed in alkaline high temperature waters, whereas halophilic mesophilic communities dominated coastal geothermal waters.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"473-85"},"PeriodicalIF":2.9,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-011-0378-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40104794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 68

Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. 为研究古细菌病毒和质粒生命周期而对医院酸杆菌W1宿主的基因组分析。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2011-07-01 Epub Date: 2011-05-24 DOI: 10.1007/s00792-011-0379-y

Xiao-Yan You, Chao Liu, Sheng-Yue Wang, Cheng-Ying Jiang, Shiraz A Shah, David Prangishvili, Qunxin She, Shuang-Jiang Liu, Roger A Garrett

{"title":"Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles.","authors":"Xiao-Yan You, Chao Liu, Sheng-Yue Wang, Cheng-Ying Jiang, Shiraz A Shah, David Prangishvili, Qunxin She, Shuang-Jiang Liu, Roger A Garrett","doi":"10.1007/s00792-011-0379-y","DOIUrl":"https://doi.org/10.1007/s00792-011-0379-y","url":null,"abstract":"The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. Within these variable regions, a few orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class of MITE-like repeat elements. There are also 26 highly diverse vapBC antitoxin-toxin gene pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for sulphur metabolism show some significant differences from those proposed for other Acidianus and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it a promising candidate for developing the first Acidianus genetic systems.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"487-97"},"PeriodicalIF":2.9,"publicationDate":"2011-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-011-0379-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40104793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches. 微生物多样性在突尼斯地热泉作为检测分子和培养为基础的方法。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2010-11-01 Epub Date: 2010-09-11 DOI: 10.1007/s00792-010-0327-2

Raja Sayeh, Jean Louis Birrien, Karine Alain, Georges Barbier, Mokhtar Hamdi, Daniel Prieur

{"title":"Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches.","authors":"Raja Sayeh, Jean Louis Birrien, Karine Alain, Georges Barbier, Mokhtar Hamdi, Daniel Prieur","doi":"10.1007/s00792-010-0327-2","DOIUrl":"https://doi.org/10.1007/s00792-010-0327-2","url":null,"abstract":"Prokaryotic diversities of 12 geothermal hot springs located in Northern, Central and Southern Tunisia were investigated by culture-based and molecular approaches. Enrichment cultures for both aerobic and anaerobic microorganisms were successfully obtained at temperatures ranging from 50 to 75°C. Fourteen strains including four novel species were cultivated and assigned to the phyla Firmicutes (9), Thermotogae (2), Betaproteobacteria (1), Synergistetes (1) and Bacteroidetes (1). Archaeal or universal oligonucleotide primer sets were used to generate 16S rRNA gene libraries. Representative groups included Proteobacteria, Firmicutes, Deinococcus-Thermus, Thermotogae, Synergistetes, Bacteroidetes, Aquificae, Chloroflexi, candidate division OP9 in addition to other yet unclassified strains. The archaeal library showed a low diversity of clone sequences belonging to the phyla Euryarchaeota and Crenarchaeota. Furthermore, we confirmed the occurrence of sulfate reducers and methanogens by amplification and sequencing of dissimilatory sulfite reductase (dsrAB) and methyl coenzyme M reductase α-subunit (mcrA) genes. Altogether, we discuss the diverse prokaryotic communities arising from the 12 geothermal hot springs studied and relate these findings to the physico-chemical features of the hot springs.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"501-14"},"PeriodicalIF":2.9,"publicationDate":"2010-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-010-0327-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40063160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 68

Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1. 极端嗜酸古菌“酸铁原体”Fer1的生物膜发育。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2010-11-01 Epub Date: 2010-09-12 DOI: 10.1007/s00792-010-0328-1

Craig Baker-Austin, Joanna Potrykus, Margaret Wexler, Philip L Bond, Mark Dopson

{"title":"Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.","authors":"Craig Baker-Austin, Joanna Potrykus, Margaret Wexler, Philip L Bond, Mark Dopson","doi":"10.1007/s00792-010-0328-1","DOIUrl":"https://doi.org/10.1007/s00792-010-0328-1","url":null,"abstract":"'Ferroplasma acidarmanus' Fer1 is an iron-oxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA. This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies. Bioinformatic analysis of the 'F. acidarmanus' Fer1 genome identified genes annotated as involved in attachment and biofilm formation. No putative quorum sensing signaling genes were identified and no N-acyl homoserine lactone-like compounds were found in 'F. acidarmanus' Fer1 biofilm supernatant. Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth. Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations. Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth. This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"485-91"},"PeriodicalIF":2.9,"publicationDate":"2010-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-010-0328-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40063942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. 长链烷烃降解热变形地杆菌B23醛脱氢酶基因的克隆及特性研究

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2010-01-01 Epub Date: 2009-09-29 DOI: 10.1007/s00792-009-0285-8

Tomohisa Kato, Asuka Miyanaga, Shigenori Kanaya, Masaaki Morikawa

引用次数: 21

Overexpression and characterization of a thermostable trehalose synthase from Meiothermus ruber. 一种耐热海藻糖合成酶的过表达及特性研究。

IF 2.9

Extremophiles : life under extreme conditions Pub Date : 2010-01-01 Epub Date: 2009-09-25 DOI: 10.1007/s00792-009-0281-z

Yueming Zhu, Dongsheng Wei, Jun Zhang, Yufan Wang, Hengyi Xu, Laijun Xing, Mingchun Li

引用次数: 38