Archaea-An International Microbiological Journal最新文献

{"title":"Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences","authors":"S. Yadav, Sharbadeb Kundu, S. Ghosh, S. S. Maitra","doi":"10.1155/2015/563414","DOIUrl":"https://doi.org/10.1155/2015/563414","url":null,"abstract":"Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/563414","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65031390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnological Uses of Archaeal Proteins","authors":"F. Pecorari, V. Arcus, J. Wiegel","doi":"10.1155/2015/809758","DOIUrl":"https://doi.org/10.1155/2015/809758","url":null,"abstract":"Many industrial/biotechnological processes take place under extreme conditions of temperature, pH, salinity, or pressure which are not suitable for activities of proteins from model eukaryotic or common neutrophilic, mesophilic, and prokaryotic microorganisms. In contrast, Archaea offer a large panel of extremophile organisms that express proteins that are able to remain properly folded and functional under the harshest biophysical conditions. \u0000 \u0000The study of this group of organisms has uncovered archaeal enzymes and proteins with unusual properties compared to their traditional homologues. In addition, with their ease of production and better-behaved samples for X-ray crystallography, for example, archaeal proteins are often more convenient for structural biology studies than their eukaryotic equivalents. The knowledge thus gained can open routes to commercial biotechnological applications. These last years, with the emergence of next generation sequencing techniques to decode whole genomes and metagenomes and the pressure to develop “greener” industrial processes, the rate of new archaeal proteins reported has significantly increased, thereby widening again their potential of applications. In this special issue of Archaea, we present selected papers dealing with the uses of archaeal proteins as tools for various fields of biotechnologies and research. \u0000 \u0000DNA and RNA ligases are essential enzymes in living cells and have applications in molecular biology. A review by M. Tanabe et al. discusses the uses of DNA ligases and recent progress in deciphering their catalytic mechanisms via structural studies, and they describe how protein engineering can improve ligation efficiency of an archaeal DNA ligase over a broad temperature range. In another paper on ligases, C. R. Chambers and W. M. Patrick present the current state of knowledge on archaeal nucleic acid ligases including RNA ligases, highlighting their remarkable properties relevant to biotechnologists, and they discuss the modifications of the activities of archaeal RNA ligases by directed mutagenesis to develop more efficient molecular biology protocols. \u0000 \u0000J. A. Littlechild reviews research regarding the discovery and potential applications of a range of thermophilic archaeal proteins, illustrating the power of archaeal enzymes for various industrial biocatalysis. Then, an article by V. M. Gumerov et al. describes the characterization of a novel thermostable and multifunctional β-glycosidase from Acidilobus saccharovorans that displays a high tolerance to glucose, a desired property for such enzymes used to process lignocellulose biomass. C.-H. Wu et al. present a review summarizing the strategies used in engineering and characterizing three different forms of soluble hydrogenase I from the hyperthermophile Pyrococcus furiosus, an enzyme which has been used in vitro for hydrogen production. \u0000 \u0000Archaea are not only interesting for catalysis applications. J. C. Charlesworth and B. P. Burns giv","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/809758","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65160805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Production and Application of a Soluble Hydrogenase from Pyrococcus furiosus","authors":"Chang-Hao Wu, Patrick M McTernan, Mary E. Walter, M. Adams","doi":"10.1155/2015/912582","DOIUrl":"https://doi.org/10.1155/2015/912582","url":null,"abstract":"Hydrogen gas is a potential renewable alternative energy carrier that could be used in the future to help supplement humanity's growing energy needs. Unfortunately, current industrial methods for hydrogen production are expensive or environmentally unfriendly. In recent years research has focused on biological mechanisms for hydrogen production and specifically on hydrogenases, the enzyme responsible for catalyzing the reduction of protons to generate hydrogen. In particular, a better understanding of this enzyme might allow us to generate hydrogen that does not use expensive metals, such as platinum, as catalysts. The soluble hydrogenase I (SHI) from the hyperthermophile Pyrococcus furiosus, a member of the euryarchaeota, has been studied extensively and used in various biotechnological applications. This review summarizes the strategies used in engineering and characterizing three different forms of SHI and the properties of the recombinant enzymes. SHI has also been used in in vitro systems for hydrogen production and NADPH generation and these systems are also discussed.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"61 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/912582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64155804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Highly Thermostable Multifunctional Beta-Glycosidase from Crenarchaeon Acidilobus saccharovorans","authors":"V. Gumerov, A. Rakitin, A. Mardanov, N. Ravin","doi":"10.1155/2015/978632","DOIUrl":"https://doi.org/10.1155/2015/978632","url":null,"abstract":"We expressed a putative β-galactosidase Asac_1390 from hyperthermophilic crenarchaeon Acidilobus saccharovorans in Escherichia coli and purified the recombinant enzyme. Asac_1390 is composed of 490 amino acid residues and showed high sequence similarity to family 1 glycoside hydrolases from various thermophilic Crenarchaeota. The maximum activity was observed at pH 6.0 and 93°C. The half-life of the enzyme at 90°C was about 7 hours. Asac_1390 displayed high tolerance to glucose and exhibits hydrolytic activity towards cellobiose and various aryl glucosides. The hydrolytic activity with p-nitrophenyl (pNP) substrates followed the order pNP-β-D-galactopyranoside (328 U mg−1), pNP-β-D-glucopyranoside (246 U mg−1), pNP-β-D-xylopyranoside (72 U mg−1), and pNP-β-D-mannopyranoside (28 U mg−1). Thus the enzyme was actually a multifunctional β-glycosidase. Therefore, the utilization of Asac_1390 may contribute to facilitating the efficient degradation of lignocellulosic biomass and help enhance bioconversion processes.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/978632","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64192733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function","authors":"Justin M. Miller, E. J. Enemark","doi":"10.1155/2015/305497","DOIUrl":"https://doi.org/10.1155/2015/305497","url":null,"abstract":"In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/305497","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64895641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaeal Enzymes and Applications in Industrial Biocatalysts.","authors":"Jennifer A Littlechild","doi":"10.1155/2015/147671","DOIUrl":"https://doi.org/10.1155/2015/147671","url":null,"abstract":"<p><p>Archaeal enzymes are playing an important role in industrial biotechnology. Many representatives of organisms living in \"extreme\" conditions, the so-called Extremophiles, belong to the archaeal kingdom of life. This paper will review studies carried by the Exeter group and others regarding archaeal enzymes that have important applications in commercial biocatalysis. Some of these biocatalysts are already being used in large scale industrial processes for the production of optically pure drug intermediates and amino acids and their analogues. Other enzymes have been characterised at laboratory scale regarding their substrate specificity and properties for potential industrial application. The increasing availability of DNA sequences from new archaeal species and metagenomes will provide a continuing resource to identify new enzymes of commercial interest using both bioinformatics and screening approaches. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 ","pages":"147671"},"PeriodicalIF":2.4,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/147671","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9832298","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}

{"title":"Diversity and distribution of archaea community along a stratigraphic permafrost profile from Qinghai-Tibetan Plateau, China.","authors":"Shiping Wei,&nbsp;Hongpeng Cui,&nbsp;Hao He,&nbsp;Fei Hu,&nbsp;Xin Su,&nbsp;Youhai Zhu","doi":"10.1155/2014/240817","DOIUrl":"https://doi.org/10.1155/2014/240817","url":null,"abstract":"<p><p>Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"240817"},"PeriodicalIF":2.4,"publicationDate":"2014-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/240817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32921123","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}

{"title":"Children living near a sanitary landfill have increased breath methane and Methanobrevibacter smithii in their intestinal microbiota.","authors":"Humberto Bezerra de Araujo Filho,&nbsp;Mirian Silva Carmo-Rodrigues,&nbsp;Carolina Santos Mello,&nbsp;Lígia Cristina Fonseca Lahoz Melli,&nbsp;Soraia Tahan,&nbsp;Antonio Carlos Campos Pignatari,&nbsp;Mauro Batista de Morais","doi":"10.1155/2014/576249","DOIUrl":"https://doi.org/10.1155/2014/576249","url":null,"abstract":"<p><p>This study evaluated the breath CH4 excretion and concentration of M. smithii in intestinal microbiota of schoolchildren from 2 slums. One hundred and eleven children from a slum near a sanitary landfill, 35 children of a slum located away from the sanitary landfill, and 32 children from a high socioeconomic level school were included in the study. Real-time PCR was performed to quantify the M. smithii nifH gene and it was present in the microbiota of all the participating children, with higher (P < 0.05) concentrations in those who lived in the slum near the landfill (3.16 × 10(7) CFU/g of feces), comparing with the children from the slum away from the landfill (2.05 × 10(6) CFU/g of feces) and those from the high socioeconomic level group (3.93 × 10(5) CFU/g of feces). The prevalence of children who present breath methane was 53% in the slum near the landfill, 31% in the slum further away from the landfill and, 22% in the high socioeconomic level group. To live near a landfill is associated with higher concentrations of M. smithii in intestinal microbiota, comparing with those who live away from the landfill, regardless of their socioeconomics conditions. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"576249"},"PeriodicalIF":2.4,"publicationDate":"2014-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/576249","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32795373","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}

{"title":"A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life.","authors":"Arshan Nasir,&nbsp;Kyung Mo Kim,&nbsp;Gustavo Caetano-Anollés","doi":"10.1155/2014/706468","DOIUrl":"https://doi.org/10.1155/2014/706468","url":null,"abstract":"<p><p>The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"706468"},"PeriodicalIF":2.4,"publicationDate":"2014-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/706468","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32691334","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}

{"title":"Seasonal effects in a lake sediment archaeal community of the Brazilian Savanna.","authors":"Thiago Rodrigues,&nbsp;Elisa Catão,&nbsp;Mercedes M C Bustamante,&nbsp;Betania F Quirino,&nbsp;Ricardo H Kruger,&nbsp;Cynthia M Kyaw","doi":"10.1155/2014/957145","DOIUrl":"https://doi.org/10.1155/2014/957145","url":null,"abstract":"<p><p>The Cerrado is a biome that corresponds to 24% of Brazil's territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra's amoA gene. The principal coordinate analysis (PCoA) test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"957145"},"PeriodicalIF":2.4,"publicationDate":"2014-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/957145","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32605739","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}