Archaea-An International Microbiological Journal最新文献_第10页

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans. 孙德尔本斯红树林沉积物中古细菌的多样性和分布。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-08-06 eCollection Date: 2015-01-01 DOI: 10.1155/2015/968582

Anish Bhattacharyya, Niladri Shekhar Majumder, Pijush Basak, Shayantan Mukherji, Debojyoti Roy, Sudip Nag, Anwesha Haldar, Dhrubajyoti Chattopadhyay, Suparna Mitra, Maitree Bhattacharyya, Abhrajyoti Ghosh

{"title":"Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans.","authors":"Anish Bhattacharyya, Niladri Shekhar Majumder, Pijush Basak, Shayantan Mukherji, Debojyoti Roy, Sudip Nag, Anwesha Haldar, Dhrubajyoti Chattopadhyay, Suparna Mitra, Maitree Bhattacharyya, Abhrajyoti Ghosh","doi":"10.1155/2015/968582","DOIUrl":"https://doi.org/10.1155/2015/968582","url":null,"abstract":"Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/968582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34152497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 47

Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses. 利用比较转录组分析评价超嗜热硫酸盐还原古菌富氏古舌菌VC-16的一氧化碳代谢。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-08-06 eCollection Date: 2015-01-01 DOI: 10.1155/2015/235384

William P Hocking, Irene Roalkvam, Carina Magnussen, Runar Stokke, Ida H Steen

{"title":"Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses.","authors":"William P Hocking, Irene Roalkvam, Carina Magnussen, Runar Stokke, Ida H Steen","doi":"10.1155/2015/235384","DOIUrl":"https://doi.org/10.1155/2015/235384","url":null,"abstract":"The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by \"Mitchell-type\" loops facilitated by Fqo catalyzing a Fd(red):menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase-associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fd(red) and APS reduction is discussed. Multiple membrane-bound heterodisulfide reductase (DsrMK) could promote both energy-conserving and non-energy-conserving menaquinol oxidation. Finally, the FqoF subunit may catalyze a Fd(red):F420 oxidoreductase reaction. In the absence of electron acceptor, downregulation of F420H2 dependent steps of the acetyl-CoA pathway is linked to transient formate generation. Overall, carboxidotrophic growth seems as an intrinsic capacity of A. fulgidus with little need for novel resistance or respiratory complexes.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/235384","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33983927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 16

Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork. 了解超嗜热古细菌的DNA修复:持续的间隙和其他关注叉的原因。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-06-04 eCollection Date: 2015-01-01 DOI: 10.1155/2015/942605

Dennis W Grogan

{"title":"Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork.","authors":"Dennis W Grogan","doi":"10.1155/2015/942605","DOIUrl":"https://doi.org/10.1155/2015/942605","url":null,"abstract":"Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/942605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34263742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 44

Isolation and Molecular Identification of Auxotrophic Mutants to Develop a Genetic Manipulation System for the Haloarchaeon Natrinema sp. J7-2. 钠盐古菌J7-2基因操作系统的建立及其营养突变体的分离与分子鉴定

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-05-21 eCollection Date: 2015-01-01 DOI: 10.1155/2015/483194

Jie Lv, Shuai Wang, Yuchen Wang, Yuping Huang, Xiangdong Chen

{"title":"Isolation and Molecular Identification of Auxotrophic Mutants to Develop a Genetic Manipulation System for the Haloarchaeon Natrinema sp. J7-2.","authors":"Jie Lv, Shuai Wang, Yuchen Wang, Yuping Huang, Xiangdong Chen","doi":"10.1155/2015/483194","DOIUrl":"https://doi.org/10.1155/2015/483194","url":null,"abstract":"Our understanding of the genus Natrinema is presently limited due to the lack of available genetic tools. Auxotrophic markers have been widely used to construct genetic systems in bacteria and eukaryotes and in some archaeal species. Here, we isolated four auxotrophic mutants of Natrinema sp. J7-2, via 1-methyl-3-nitro-1-nitroso-guanidin mutagenesis, and designated them as J7-2-1, J7-2-22, J7-2-26, and J7-2-52, respectively. The mutant phenotypes were determined to be auxotrophic for leucine (J7-2-1), arginine (J7-2-22 and J7-2-52), and lysine (J7-2-26). The complete genome and the biosynthetic pathways of amino acids in J7-2 identified that the auxotrophic phenotype of three mutants was due to gene mutations in leuB (J7-2-1), dapD (J7-2-26), and argC (J7-2-52). These auxotrophic phenotypes were employed as selectable makers to establish a transformation method. The transformation efficiencies were determined to be approximately 10(3) transformants per µg DNA. And strains J7-2-1 and J7-2-26 were transformed into prototrophic strains with the wild type genomic DNA, amplified fragments of the corresponding genes, or the integrative plasmids carrying the corresponding genes. Additionally, exogenous genes, bgaH or amyH gene, were expressed successfully in J7-2-1. Thus, we have developed a genetic manipulation system for the Natrinema genus based on the isolated auxotrophic mutants of Natrinema sp. J7-2. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/483194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33276243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 8

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil. 非均质高盐碱土壤中的古细菌群落。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-05-13 eCollection Date: 2015-01-01 DOI: 10.1155/2015/646820

Yendi E Navarro-Noya, César Valenzuela-Encinas, Alonso Sandoval-Yuriar, Norma G Jiménez-Bueno, Rodolfo Marsch, Luc Dendooven

{"title":"Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil.","authors":"Yendi E Navarro-Noya, César Valenzuela-Encinas, Alonso Sandoval-Yuriar, Norma G Jiménez-Bueno, Rodolfo Marsch, Luc Dendooven","doi":"10.1155/2015/646820","DOIUrl":"https://doi.org/10.1155/2015/646820","url":null,"abstract":"In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/646820","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33263350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 23

Corrigendum to "unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette". “产甲烷菌7阶热解赖氨酸系统的独特特征:对遗传密码扩展盒进化的影响”的勘误。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-02-02 eCollection Date: 2015-01-01 DOI: 10.1155/2015/941836

Guillaume Borrel, Nadia Gaci, Pierre Peyret, Paul W O'Toole, Simonetta Gribaldo, Jean-François Brugère

引用次数: 0

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. 来自澳大利亚Tyrrell湖的Haloquadratum walsbyi的从头序列揭示了一个可变的基因组景观。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-02-01 eCollection Date: 2015-01-01 DOI: 10.1155/2015/875784

Benjamin J Tully, Joanne B Emerson, Karen Andrade, Jochen J Brocks, Eric E Allen, Jillian F Banfield, Karla B Heidelberg

{"title":"De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.","authors":"Benjamin J Tully, Joanne B Emerson, Karen Andrade, Jochen J Brocks, Eric E Allen, Jillian F Banfield, Karla B Heidelberg","doi":"10.1155/2015/875784","DOIUrl":"https://doi.org/10.1155/2015/875784","url":null,"abstract":"Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/875784","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33077731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 10

Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses. 通过基因组分析推断嗜盐叠层石古盐球菌的适应、生态和进化。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-01-29 eCollection Date: 2015-01-01 DOI: 10.1155/2015/241608

Reema K Gudhka, Brett A Neilan, Brendan P Burns

{"title":"Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.","authors":"Reema K Gudhka, Brett A Neilan, Brendan P Burns","doi":"10.1155/2015/241608","DOIUrl":"https://doi.org/10.1155/2015/241608","url":null,"abstract":"Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/241608","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33077728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 22

Recombinant cyclodextrinase from Thermococcus kodakarensis KOD1: expression, purification, and enzymatic characterization. 柯达热球菌KOD1重组环糊精酶:表达、纯化和酶学表征。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-01-26 eCollection Date: 2015-01-01 DOI: 10.1155/2015/397924

Ying Sun, Xiaomin Lv, Zhengqun Li, Jiaqiang Wang, Baolei Jia, Jinliang Liu

{"title":"Recombinant cyclodextrinase from Thermococcus kodakarensis KOD1: expression, purification, and enzymatic characterization.","authors":"Ying Sun, Xiaomin Lv, Zhengqun Li, Jiaqiang Wang, Baolei Jia, Jinliang Liu","doi":"10.1155/2015/397924","DOIUrl":"https://doi.org/10.1155/2015/397924","url":null,"abstract":"A gene encoding a cyclodextrinase from Thermococcus kodakarensis KOD1 (CDase-Tk) was identified and characterized. The gene encodes a protein of 656 amino acid residues with a molecular mass of 76.4 kDa harboring four conserved regions found in all members of the α-amylase family. A recombinant form of the enzyme was purified by ion-exchange chromatography, and its catalytic properties were examined. The enzyme was active in a broad range of pH conditions (pHs 4.0-10.0), with an optimal pH of 7.5 and a temperature optimum of 65°C. The purified enzyme preferred to hydrolyze β-cyclodextrin (CD) but not α- or γ-CD, soluble starch, or pullulan. The final product from β-CD was glucose. The V max and K m values were 3.13 ± 0.47 U mg(-1) and 2.94 ± 0.16 mg mL(-1) for β-CD. The unique characteristics of CDase-Tk with a low catalytic temperature and substrate specificity are discussed, and the starch utilization pathway in a broad range of temperatures is also proposed. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2015-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/397924","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33061487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 15

Archaeal Enzymes and Applications in Industrial Biocatalysts. 古细菌酶及其在工业生物催化剂中的应用。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-01-01 DOI: 10.1155/2015/147671

Jennifer A Littlechild

引用次数: 47