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A Web Tool for Hydrogenase Classification and Analysis Dan Søndergaard1, Christian N
www.nature.com/scientificreports OPEN HydDB: A web tool for hydrogenase classification and analysis Dan Søndergaard1, Christian N. S. Pedersen1 & Chris Greening2,3 H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The Received: 24 June 2016 metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla Accepted: 09 September 2016 and are present in all major ecosystems. We developed a classification system and web tool, HydDB, Published: 27 September 2016 for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/ Microorganisms conserve energy by metabolizing H2. Oxidation of this high-energy fuel yields electrons that can be used for respiration and carbon-fixation. This diffusible gas is also produced in diverse fermentation and 1 anaerobic respiratory processes . H2 metabolism contributes to the growth and survival of microorganisms across the three domains of life, including chemotrophs and phototrophs, lithotrophs and heterotrophs, aerobes and 1,2 anaerobes, mesophiles and extremophiles alike . -
Archaeoglobus Profundus Type Strain (AV18T)
Standards in Genomic Sciences (2010) 2:327-346 DOI:10.4056/sigs.942153 Complete genome sequence of Archaeoglobus profundus type strain (AV18T) Mathias von Jan1, Alla Lapidus2, Tijana Glavina Del Rio2, Alex Copeland2, Hope Tice2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, Lynne Goodwin2,3, Cliff Han2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinnikova2, Olga Chertkov2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Elizabeth Saunders2, Thomas Brettin2,3, John C. Detter2,3, Patrick Chain2,4, Konrad Eichinger6, Harald Huber6, Ste- fan Spring1, Manfred Rohde7, Markus Göker1, Reinhard Wirth6, Tanja Woyke2, Jim Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophilic, marine, strictly anaerobic, sulfate respiration, hydrogen utili- zation, hydrothermal systems, Archaeoglobaceae, GEBA Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the eu- ryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeog- lobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no va- lidly published name. -
Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus Fulgidus VC-16 by Comparative Transcriptome Analyses
Hindawi Publishing Corporation Archaea Volume 2015, Article ID 235384, 12 pages http://dx.doi.org/10.1155/2015/235384 Research Article Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses William P. Hocking, Irene Roalkvam, Carina Magnussen, Runar Stokke, and Ida H. Steen Department of Biology, Centre for Geobiology, University of Bergen, 5020 Bergen, Norway Correspondence should be addressed to Ida H. Steen; [email protected] Received 10 April 2015; Revised 9 June 2015; Accepted 14 June 2015 Academic Editor: Uwe Deppenmeier Copyright © 2015 William P. Hocking et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 catalyzingred aFd :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 Fdred and APS reduction is discussed. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
MIAMI UNIVERSITY the Graduate School Certificate for Approving The
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota -
Microbial and Geochemical Investigation Down to 2000 M Deep Triassic Rock (Meuse/Haute Marne, France)
geosciences Article Microbial and Geochemical Investigation down to 2000 m Deep Triassic Rock (Meuse/Haute Marne, France) Vanessa Leblanc 1,2,3, Jennifer Hellal 1 , Marie-Laure Fardeau 4,5, Saber Khelaifia 4,5, Claire Sergeant 2,3, Francis Garrido 1, Bernard Ollivier 4,5 and Catherine Joulian 1,* 1 BRGM, Geomicrobiology and Environmental Monitoring Unit, F-45060 Orléans CEDEX 02, France; [email protected] (V.L.); [email protected] (J.H.); [email protected] (F.G.) 2 Bordeaux University, Centre d’Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33170 Gradignan, France; [email protected] 3 CNRS-IN2P3, Centre d’Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33170 Gradignan, France 4 Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France; [email protected] (M.-L.F.); Saber.Khelaifi[email protected] (S.K.); [email protected] (B.O.) 5 Université de Toulon, CNRS/INSU, 83957 La Garde, France * Correspondence: [email protected]; Tel.: +33-2-3864-3089 Received: 31 August 2018; Accepted: 13 December 2018; Published: 20 December 2018 Abstract: In 2008, as part of a feasibility study for radioactive waste disposal in deep geological formations, the French National Radioactive Waste Management Agency (ANDRA) drilled several boreholes in the transposition zone in order to define the potential variations in the properties of the Callovo–Oxfordian claystone formation. This consisted of a rare opportunity to investigate the deep continental biosphere that is still poorly known. Four rock cores, from 1709, 1804, 1865, and 1935 m below land surface, were collected from Lower and Middle Triassic formations in the Paris Basin (France) to investigate their microbial and geochemical composition. -
Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus Fulgidus VC-16 by Comparative Transcriptome Analyses
Hindawi Publishing Corporation Archaea Volume 2015, Article ID 235384, 12 pages http://dx.doi.org/10.1155/2015/235384 Research Article Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses William P. Hocking, Irene Roalkvam, Carina Magnussen, Runar Stokke, and Ida H. Steen Department of Biology, Centre for Geobiology, University of Bergen, 5020 Bergen, Norway Correspondence should be addressed to Ida H. Steen; [email protected] Received 10 April 2015; Revised 9 June 2015; Accepted 14 June 2015 Academic Editor: Uwe Deppenmeier Copyright © 2015 William P. Hocking et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 catalyzingred aFd :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 Fdred and APS reduction is discussed. -
Extremophiles 90C
Limits of Life on Earth Archaea and bacteria can thrive in extreme environment (heat, cold, acidity, high pressure) and can use unusual energy source Distinguish between growth and survival (e.g., seeds, spores) Analogs for extraterrestrial environments Origin of life in extreme environments? Origin of Yellowstone National Park pH scale pH 3 Temperature 60 C Rich in sulfur Nymph Creek Hydrogenobacter gets energy by reacting oxygen from the air with hydrogen gas and/or sulfide in the water. It uses the energy to make carbohydrate (sugar) from atmospheric carbon dioxide and hydrogen in the water: CO2 + 2 H2 = CH2O + H2O (where CH2O is part of a carbohydrate). Nymph Creek flowing into Nymph Lake, Yellowstone National Park; green mat of Cyanidium (pH 3, 40 to 45oC) Nymph Lake Hydrogenobacter acidocaldarius Hyperthermophile (T > 80 C), pH ≈ 3 H2 metabolism, low nutrient tolerant Hot springs in YNP, New Zealand & Australia + oil wells “Boiling Lake” Grand Prismatic 70 C Filled with thermophiles Sulphobus: optimum T~80C Orange “mats” of pigmented Minimum 60 C, maaximum extremophiles 90C. Lives by oxidizing sulfur (carotenoids) which is abundant near hot springs Adaptations of Thermophilies Similar to “ordinary” archaea and bacteria (DNA, same amino acids) Subtle differences: Cell membranes are made of lipids that are more stable to high temperature Additional enzyme (reverse DNA gyrase) causes DNA to fold up in a way that is more stable against heat The absolute maximum temperature is around 150 C--- DNA breaks up very readily above this temperature Slow growth of bacteria in thermafrost down to -20C YNP-Octopus Spring (White Creek area) Microbial mat. -
Exploring the Taxonomical and Functional Profile of As Burgas Hot Spring Focusing on Thermostable Β-Galactosidases
www.nature.com/scientificreports OPEN Exploring the taxonomical and functional profle of As Burgas hot spring focusing on thermostable β‑galactosidases María‑Eugenia DeCastro1, Michael P. Doane2,4, Elizabeth Ann Dinsdale2,3, Esther Rodríguez‑Belmonte1 & María‑Isabel González‑Siso1* In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquifcae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta‑galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o‑Nitrophenyl‑β‑d‑galactopyranoside (ONPG) and p‑Nitrophenyl‑ β‑d‑fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This fnding highlights the challenge of fnding novel active enzymes based only on their sequence. Termophiles, growing optimally at temperatures over 55 °C, are found in hot environments such as fumaroles, hydrothermal vents, hot springs, or deserts1–4. -
Phylogeny Based on 16S Rrna/DNA
Phylogeny Based on Secondary article 16S rRNA/DNA Article Contents . Introduction Erko Stackebrandt, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, . Semantic Macromolecules: a Basis for Phylogenetic Braunschweig, Germany Studies . Sequence Determination, Sequence Alignment and Determination of Sequence Similarities Modern systematics of prokaryotes is based on comparative analysis of the evolutionarily . Recognition of the Higher Taxa of Prokaryotes conservative genes coding for 16S ribosomal RNA. Dendrograms of phylogenetic . Polyphasic Approach to Bacterial Systematics relatedness show the order in which organisms evolved in time, thus providing a basis for . The Taxonomic Rank ‘Species’ in Bacteriology their classification. Introduction are the historical record of evolution, and the determina- In contrast to more highly evolved eukaryotes, in which tion of their primary structure provides a powerful means complex morphologies visibly reflect their evolutionary by which evolutionary relationships can be measured. In history, the microscopic and ultrastructural features of essence, two organisms possessing a given stretch of microorganisms cannot be used to deduce the way in which semantides which differ in only a few changes (mutations, the prokaryotes and the morphologically simple eukar- nucleotide order or amino acid positions) are more closely yotic forms evolved. Before 1960 taxonomists were unable related to each other than those organisms in which a to appreciate the complexity of microbial systematics and higher number of changes have accumulated. Thus these to recognize that groups based on superficial properties molecules can be considered as chronometers. As different alone did not necessarily reflect those which arose due to genes are subjected to different rates of changes (same evolutionary processes. -
Novel Nitrite Reductase Domain Structure Suggests a Chimeric
Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in Phylum Chloroflexi Sarah Schwartz1, Lily Momper1, L. Thiberio Rangel1, Cara Magnabosco2, Jan Amend3, and Gregory Fournier1 1Massachusetts Institute of Technology 2ETH Zurich 3University of Southern California June 11, 2021 Abstract Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of Phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported nitric oxide reductase subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported. RESEARCH PAPER TITLE: Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in Phylum Chloroflexi SHORT TITLE: Novel Denitrification Architecture in Chloroflexi Sarah L. Schwartz1,2*, Lily M. Momper2,3, L. Thiberio Rangel2, Cara Magnabosco4, Jan P. Amend5,6, and Gregory P. Fournier2 1. Microbiology Graduate Program, Massachusetts Institute of Technology 2. Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology 3. Exponent, Inc., Pasadena, CA 4. Department of Earth Sciences, ETH Zurich 5. Department of Earth Sciences, University of Southern California 6. Department of Biological Sciences, University of Southern California *Correspondence: [email protected], +1 (415) 497-1747 SUMMARY Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from ma- rine and terrestrial ecosystems. -
Metagenome-Assembled Genomes Provide New Insight Into The
www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.