Understanding the Molecular Mechanism of Manganese
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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Aquabacterium Gen. Nov., with Description of Aquabacterium Citratiphilum Sp
International Journal of Systematic Bacteriology (1999), 49, 769-777 Printed in Great Britain Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system Sibylle Kalmbach,’ Werner Manz,’ Jorg Wecke2 and Ulrich Szewzyk’ Author for correspondence : Werner Manz. Tel : + 49 30 3 14 25589. Fax : + 49 30 3 14 7346 1. e-mail : [email protected]. tu-berlin.de 1 Tech nisc he U nive rsit ;it Three bacterial strains isolated from biofilms of the Berlin drinking water Berlin, lnstitut fur system were characterized with respect to their morphological and Tec hn ischen Umweltschutz, Fachgebiet physiological properties and their taxonomic position. Phenotypically, the Okologie der bacteria investigated were motile, Gram-negative rods, oxidase-positive and Mikroorganismen,D-l 0587 catalase-negative, and contained polyalkanoates and polyphosphate as Berlin, Germany storage polymers. They displayed a microaerophilic growth behaviour and 2 Robert Koch-lnstitut, used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfate Nordufer 20, D-13353 Berlin, Germany or ferric iron. The substrates metabolized included a broad range of organic acids but no carbohydrates at all. The three species can be distinguished from each other by their substrate utilization, ability to hydrolyse urea and casein, cellular protein patterns and growth on nutrient-rich media as well as their temperature, pH and NaCl tolerances. Phylogenetic analysis, based on 165 rRNA gene sequence comparison, revealed that the isolates are affiliated to the /I1 -subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44.9 to 51*3O/0. -
Sites in the Virginia-Washington, D.C.-Maryland Metro Area to Observe Or Collect Bacteria That Precipitate Iron and Manganese Oxides1
SITES IN THE VIRGINIA-WASHINGTON, D.C.-MARYLAND METRO AREA TO OBSERVE OR COLLECT BACTERIA THAT PRECIPITATE IRON AND MANGANESE OXIDES1 by Eleanora I. Robbins U.S. Geological Survey Open-File Report 98-202 April 24, 1998 1 This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards. This publication is intended to be used along with U.S. Geological Survey EarthFax (1-800- USA-MAPS) What's the Red in the Water? What's the Black on the Rocks? What's the Oil on the Surface? and < http: //pubs.usgs. gov/publications/text/Norriemicrobes. html > SITES IN THE VIRGINIA-WASHINGTON, D.C.-MARYLAND METRO AREA TO OBSERVE OR COLLECT BACTERIA THAT PRECIPITATE IRON AND MANGANESE OXIDES VIRGINIA VA Site 1A. Fairfax County, Huntley Meadows Park: From the Beltway (495), go south on US 1. Turn right onto Lockheed Blvd.; travel to end of Lockheed Blvd., and then turn CAREFULLY into the Park at the sign. Park in parking lot, walk along the wetland path to the beginning of the boardwalk. Look to the right (north) and see red patches in the water where ground water is discharging. This ground water is anoxic and carries reduced iron. The iron bacteria here (predominantly Leptothrix ochracea^ oxidize the iron and turn it into a red flocculate. If you move the flocculate aside, you can see the underlying black color formed where the reducing bacteria reduce the iron to its black state in the zone of reduction in the mud. As you walk along the boardwalk, you will see much evidence of the iron bacterium, Leptothrix discophora] that forms glassy-looking patches that appear, at first glance, to be an nil-film VA Site IB. -
Leptothrix Cholodnii
This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Article Cite This: ACS Nano 2020, 14, 5288−5297 www.acsnano.org Polyfunctional Nanofibril Appendages Mediate Attachment, Filamentation, and Filament Adaptability in Leptothrix cholodnii ‡ ⊥ † ⊥ ∇ † ‡ § Tatsuki Kunoh,*, , Kana Morinaga, , Shinya Sugimoto, Shun Miyazaki, Masanori Toyofuku, , ∥ ‡ § ‡ § Kenji Iwasaki, Nobuhiko Nomura,*, , and Andrew S. Utada*, , ‡ † § ∥ Faculty and Graduate School of Life and Environmental Sciences, Microbiology Research Center for Sustainability, and Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan ∇ Department of Bacteriology and Jikei Center for Biofilm Research and Technology, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan *S Supporting Information ABSTRACT: Leptothrix is a species of Fe/Mn-oxidizing bacteria known to form long filaments composed of chains of cells that eventually produce a rigid tube surrounding the filament. Prior to the formation of this brittle microtube, Leptothrix cells secrete hair-like structures from the cell surface, called nanofibrils, which develop into a soft sheath that surrounds the filament. To clarify the role of nanofibrils in filament formation in L. cholodnii SP-6, we analyze the behavior of individual cells and multicellular filaments in high-aspect ratio microfluidic chambers using time-lapse and intermittent in situ fluorescent staining of nanofibrils, complemented with atmospheric scanning electron microscopy. We show that in SP-6 nanofibrils are important for attachment and their distribution on young filaments post-attachment is correlated to the directionality of filament elongation. -
International Code of Nomenclature of Prokaryotes
2019, volume 69, issue 1A, pages S1–S111 International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision) Charles T. Parker1, Brian J. Tindall2 and George M. Garrity3 (Editors) 1NamesforLife, LLC (East Lansing, Michigan, United States) 2Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) 3Michigan State University (East Lansing, Michigan, United States) Corresponding Author: George M. Garrity ([email protected]) Table of Contents 1. Foreword to the First Edition S1–S1 2. Preface to the First Edition S2–S2 3. Preface to the 1975 Edition S3–S4 4. Preface to the 1990 Edition S5–S6 5. Preface to the Current Edition S7–S8 6. Memorial to Professor R. E. Buchanan S9–S12 7. Chapter 1. General Considerations S13–S14 8. Chapter 2. Principles S15–S16 9. Chapter 3. Rules of Nomenclature with Recommendations S17–S40 10. Chapter 4. Advisory Notes S41–S42 11. References S43–S44 12. Appendix 1. Codes of Nomenclature S45–S48 13. Appendix 2. Approved Lists of Bacterial Names S49–S49 14. Appendix 3. Published Sources for Names of Prokaryotic, Algal, Protozoal, Fungal, and Viral Taxa S50–S51 15. Appendix 4. Conserved and Rejected Names of Prokaryotic Taxa S52–S57 16. Appendix 5. Opinions Relating to the Nomenclature of Prokaryotes S58–S77 17. Appendix 6. Published Sources for Recommended Minimal Descriptions S78–S78 18. Appendix 7. Publication of a New Name S79–S80 19. Appendix 8. Preparation of a Request for an Opinion S81–S81 20. Appendix 9. Orthography S82–S89 21. Appendix 10. Infrasubspecific Subdivisions S90–S91 22. Appendix 11. The Provisional Status of Candidatus S92–S93 23. -
Discovery of Sheath-Forming, Iron-Oxidizing Zetaproteobacteria at Loihi Seamount, Hawaii, USA Emily J
RESEARCH ARTICLE Hidden in plain sight: discovery of sheath-forming, iron-oxidizing Zetaproteobacteria at Loihi Seamount, Hawaii, USA Emily J. Fleming1, Richard E. Davis2, Sean M. McAllister3,, Clara S. Chan4, Craig L. Moyer3, Bradley M. Tebo2 & David Emerson1 1Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA; 2Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR, USA; 3Department of Biology, Western Washington University, Bellingham, WA, USA and 4Department of Geological Sciences, University of Delaware, Newark, DE, USA Correspondence: David Emerson, Bigelow Abstract Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME 04544, USA. Tel.: +1 207 Lithotrophic iron-oxidizing bacteria (FeOB) form microbial mats at focused 315 2567; fax: +1 207 315 2329; flow or diffuse flow vents in deep-sea hydrothermal systems where Fe(II) is a e-mail: [email protected] dominant electron donor. These mats composed of biogenically formed Fe(III)-oxyhydroxides include twisted stalks and tubular sheaths, with sheaths Present address: Sean M. McAllister, typically composing a minor component of bulk mats. The micron diameter Department of Geological Sciences, Fe(III)-oxyhydroxide-containing tubular sheaths bear a strong resemblance to University of Delaware, Newark, DE, USA sheaths formed by the freshwater FeOB, Leptothrix ochracea. We discovered that Received 20 December 2012; revised 28 veil-like surface layers present in iron-mats at the Loihi Seamount were domi- – February 2013; accepted 28 February 2013. nated by sheaths (40 60% of total morphotypes present) compared with deeper Final version published online 15 April 2013. (> 1 cm) mat samples (0–16% sheath). By light microscopy, these sheaths appeared nearly identical to those of L. -
Fluctuation Analysis of Oxidation-Reduction Potential in Circumneutral Ph Iron-Oxidizing Microbial Systems
Fluctuation Analysis of Oxidation-Reduction Potential in Circumneutral pH Iron-Oxidizing Microbial Systems by Allison Marie Leigh Enright A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Earth Sciences University of Toronto © Copyright by Allison M.L. Enright 2015 Fluctuation Analysis of Oxidation-Reduction Potential in Circumneutral pH Iron-Oxidizing Microbial Systems Allison M.L. Enright Doctor of Philosophy Department of Earth Sciences University of Toronto 2015 Abstract The goal of this thesis was to assess the utility of using small-scale fluctuations in oxidation- reduction (redox) potential to distinguish microbial from chemical iron oxidation. Fluctuations in potential arise from the motion of particles in a fluid; measuring fluctuations is therefore a system- scale observable property of micro-scale chemical behaviour, as such particle motion constitutes diffusion. Fluctuations are described by the strength of their correlation, as measured by scaling exponents. A method for the calculation of scaling-exponents of long-range correlation in redox potential measurements was developed, including new instrumentation and the modification of an existing physiological processing algorithm for use with environmental microbiological data sets. Steady-state biological and chemical systems were compared, and scaling exponents calculated from each system were found to differ significantly. In a final study, a series of microcosms were used to determine the relationship between scaling exponent, measuring correlation strength, and oxidation rate. The biological systems are governed by the rate of reaction, while the chemical systems appear to be diffusion-controlled. Because in these systems, Fe(II) is a metabolite, redox potential can then be interpreted as a physically-constrained proxy for metabolic activity. -
Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon
Western Washington University Western CEDAR WWU Graduate School Collection WWU Graduate and Undergraduate Scholarship Summer 2020 Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon Amanda Stromecki [email protected] Follow this and additional works at: https://cedar.wwu.edu/wwuet Part of the Biology Commons Recommended Citation Stromecki, Amanda, "Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon" (2020). WWU Graduate School Collection. 969. https://cedar.wwu.edu/wwuet/969 This Masters Thesis is brought to you for free and open access by the WWU Graduate and Undergraduate Scholarship at Western CEDAR. It has been accepted for inclusion in WWU Graduate School Collection by an authorized administrator of Western CEDAR. For more information, please contact [email protected]. Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon By Amanda Stromecki Accepted in Partial Completion of the Requirements for the Degree Master of Science ADVISORY COMMITTEE Dr. Craig Moyer, Chair Dr. Shawn Arellano Dr. Dietmar Schwarz GRADUATE SCHOOL David L. Patrick, Dean Master’s Thesis In presenting this thesis in partial fulfillment of the requirements for a master’s degree at Western Washington University, I grant to Western Washington University the non- exclusive royalty-free right to archive, reproduce, distribute, and display the thesis in any and all forms, including electronic format, via any digital library mechanisms maintained by WWU. I represent and warrant this is my original work, and does not infringe or violate any rights of others. I warrant that I have obtained written permissions from the owner of any third party copyrighted material included in these files. -
Efficiency of the Biological System for Iron and Manganese Removals from Water
INTERNATIONAL JOURNAL OF SCIENTIFIC & TECHNOLOGY RESEARCH VOLUME 5, ISSUE 07, JULY 2016 ISSN 2277-8616 Efficiency Of The Biological System For Iron And Manganese Removals From Water Fawazy G. Khedr, Khalid A. Shaaban, Said M. Ezzat, Mohamed Maher Abstract: Fifty ground water samples were collected from five different localities in El-Sharkia Province, Egypt during 2014. Leptothrix discophora W19 was isolated from the collected ground water samples, purified and grown on nutrient agar media supplemented with 1mg/L of each of iron and manganese. Conventional identification of Leptothrix discophora W19 isolate following the key of Bergey's manual. Standard water containing different +2 +2 concentrations of Fe and Mn had been examined for both tested metals removal capacity using Leptothrix discophora W19 as a bioleaching. The biological system for iron and manganese removal had provided overall removal efficiency up to 95.25% and 95% for iron and manganese respectively. Key words: Leptothrix discophora W19, Ground water, Iron, Manganese, Biological treatment, Bioleaching. ———————————————————— Introduction sampling cooled box to the laboratory to be examined. Water is the life secret of every living creature on earth. Ground water samples were collected from depth ranged There are two sources of water namely, surface water and between 35 to 65 m under earth’s surface. ground water. Fifty percent of the world's population depends daily on ground water for their drinking water [1]. Isolation and purification of Leptothrix discophora: In a global scale, ground water represents a potential Leptothrix discophora W19 was isolated from collected resource of drinking water. In Egypt, the ground water is ground water samples using nutrient agar medium widely used for drinking, agricultural and other domestic supplemented with 1 mg/L of each of iron and manganese purpose. -
Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal
microorganisms Article Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal Agnia Dmitrievna Galachyants 1,*, Andrey Yurjevich Krasnopeev 1 , Galina Vladimirovna Podlesnaya 1 , Sergey Anatoljevich Potapov 1 , Elena Viktorovna Sukhanova 1 , Irina Vasiljevna Tikhonova 1 , Ekaterina Andreevna Zimens 1, Marsel Rasimovich Kabilov 2 , Natalia Albertovna Zhuchenko 1, Anna Sergeevna Gorshkova 1, Maria Yurjevna Suslova 1 and Olga Ivanovna Belykh 1,* 1 Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; [email protected] (A.Y.K.); [email protected] (G.V.P.); [email protected] (S.A.P.); [email protected] (E.V.S.); [email protected] (I.V.T.); [email protected] (E.A.Z.); [email protected] (N.A.Z.); [email protected] (A.S.G.); [email protected] (M.Y.S.) 2 Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia; [email protected] * Correspondence: [email protected] (A.D.G.); [email protected] (O.I.B.); Citation: Galachyants, A.D.; Tel.: +73-952-425-415 (A.D.G. & O.I.B.) Krasnopeev, A.Y.; Podlesnaya, G.V.; Potapov, S.A.; Sukhanova, E.V.; Abstract: The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bac- Tikhonova, I.V.; Zimens, E.A.; teria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for Kabilov, M.R.; Zhuchenko, N.A.; the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity.