Shewanella Algae Relatives Capable of Generating Electricity From
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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. -
Electrochemical Interaction of Shewanella Oneidensis MR-1 and Its Outer Membrane Cytochromes Omca and Mtrc with Hematite Electrodes
Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 73 (2009) 5292–5307 www.elsevier.com/locate/gca Electrochemical interaction of Shewanella oneidensis MR-1 and its outer membrane cytochromes OmcA and MtrC with hematite electrodes Leisa A. Meitl a, Carrick M. Eggleston a,*, Patricia J.S. Colberg b, Nidhi Khare a, Catherine L. Reardon c, Liang Shi c a Department of Geology and Geophysics, University of Wyoming, Laramie, WY 82071, USA b Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY 82071, USA c Microbiology Group, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: P7-50, Richland, WA 99354, USA Received 27 December 2008; accepted in revised form 15 June 2009; available online 28 June 2009 Abstract Bacterial metal reduction is an important biogeochemical process in anaerobic environments. An understanding of elec- tron transfer pathways from dissimilatory metal-reducing bacteria (DMRB) to solid phase metal (hydr)oxides is important for understanding metal redox cycling in soils and sediments, for utilizing DMRB in bioremedation, and for developing tech- nologies such as microbial fuel cells. Here we hypothesize that the outer membrane cytochromes OmcA and MtrC from Shewanella oneidensis MR-1 are the only terminal reductases capable of direct electron transfer to a hematite working elec- trode. Cyclic voltammetry (CV) was used to study electron transfer between hematite electrodes and protein films, S. oneid- ensis MR-1 wild-type cell suspensions, and cytochrome deletion mutants. After controlling for hematite electrode dissolution at negative potential, the midpoint potentials of adsorbed OmcA and MtrC were measured (À201 mV and À163 mV vs. -
The Hybrid Motor in Shewanella Oneidensis MR-1
Flagellar motor tuning The hybrid motor in Shewanella oneidensis MR-1 Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Anja Paulick aus Hoyerswerda Marburg (Lahn), 2012 Die Untersuchungen zur vorliegenden Arbeit wurden von Mai 2008 bis März 2012 am Max-Planck-Institut für terrestrische Mikrobiologie unter der Leitung von Dr. Kai M. Thormann durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg (HKZ: 1180) als Dissertation angenommen am: 03.04.2012 Erstgutachter: Dr. Kai M. Thormann Zweitgutachter: Prof. Dr. Martin Thanbichler Weitere Mitglieder der Prüfungskommission: Prof. Dr. Klaus Lingelbach Prof. Dr. Uwe G. Maier Prof. Dr. Alexander Böhm Tag der mündlichen Prüfung: 06.09.2012 Die während der Promotion erzielten Ergebnisse sind zum Teil in folgenden Originalpublikationen veröffentlicht: Paulick A, Koerdt A, Lassak J, Huntley S, Wilms I, Narberhaus F, Thormann KM: Two different stator systems drive a single polar flagellum in Shewanella oneidensis MR-1. Mol Microbiol 2009, 71:836-850. Koerdt A1, Paulick A1, Mock M, Jost K, Thormann KM: MotX and MotY are required for flagellar rotation in Shewanella oneidensis MR-1. J Bacteriol 2009, 191:5085-5093. Thormann KM, Paulick A: Tuning the flagellar motor. Microbiology 2010, 156:1275-1283. Ergebnisse aus in dieser Promotion nicht erwähnten Projekten sind in folgenden Originalpublikationen veröffentlicht: Bubendorfer S, Held S, Windel N, Paulick A, Klingl A, Thormann KM: Specificity of motor components in the dual flagellar system of Shewanella putrefaciens CN-32. Mol Microbiol 2011. 1 diese Autoren wirkten gleichberechtigt an der Publikation mit Ich versichere, dass ich meine Dissertation: “Flagellar motor tuning The hybrid motor in Shewanella oneidensis MR-1” selbstständig, ohne unerlaubte Hilfe angefertigt und mich dabei keiner anderen als der von mir ausdrücklich bezeichneten Quellen und Hilfen bedient habe. -
Effect of Temperature on a Miniaturized Microbial Fuel Cell (MFC) Hao Ren*, Chenming Jiang and Junseok Chae
Ren et al. Micro and Nano Syst Lett (2017) 5:13 DOI 10.1186/s40486-017-0048-8 LETTER Open Access Effect of temperature on a miniaturized microbial fuel cell (MFC) Hao Ren*, Chenming Jiang and Junseok Chae Abstract A microbial fuel cell (MFC) is a bioinspired energy converter which directly converts biomass into electricity through the catalytic activity of a specific species of bacteria. The effect of temperature on a miniaturized microbial fuel cell with Geobacter sulfurreducens dominated mixed inoculum is investigated in this paper for the first time. The miniatur- ized MFC warrants investigation due to its small thermal mass, and a customized setup is built for the temperature effect characterization. The experiment demonstrates that the optimal temperature for the miniaturized MFC is 322–326 K (49–53 °C). When the temperature is increased from 294 to 322 K, a remarkable current density improve- 2 ment of 282% is observed, from 2.2 to 6.2 Am− . Furthermore, we perform in depth analysis on the effect of tempera- ture on the miniaturized MFC, and found that the activation energy for the current limiting mechanism of the MFC is approximately between 0.132 and 0.146 eV, and the result suggest that the electron transfer between cytochrome c is the limiting process for the miniaturized MFC. Keywords: Microbial fuel cell (MFC), Micro-electro-mechanical systems (MEMS), Temperature effect, Activation energy, Extracellular electron transfer (EET), Cytochrome c, Rate limiting step Background and power density than other types of exoelectrogen. The A microbial fuel cell electrochemically converts bio- effect of temperature on microbial fuel cells with Geo- mass into electricity through the catalytic activity of bacter as exoelectrogen has been investigated by many specific species of bacteria, named exoelectrogen or researchers, and it is reported that the optimal temper- anode-respiring bacteria, which are capable of transfer ature to be 298–303 K (25–30 °C) for macro/mesoscale electrons outside their outer membrane [1–3]. -
Microbial Structure and Energy Generation in Microbial Fuel Cells Powered with Waste Anaerobic Digestate
energies Article Microbial Structure and Energy Generation in Microbial Fuel Cells Powered with Waste Anaerobic Digestate Dawid Nosek * and Agnieszka Cydzik-Kwiatkowska Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45 G, 10-709 Olsztyn, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-89-523-4144; Fax: +48-89-523-4131 Received: 19 July 2020; Accepted: 7 September 2020; Published: 10 September 2020 Abstract: Development of economical and environment-friendly Microbial Fuel Cells (MFCs) technology should be associated with waste management. However, current knowledge regarding microbiological bases of electricity production from complex waste substrates is insufficient. In the following study, microbial composition and electricity generation were investigated in MFCs powered with waste volatile fatty acids (VFAs) from anaerobic digestion of primary sludge. Two anode sizes were tested, resulting in organic loading rates (OLRs) of 69.12 and 36.21 mg chemical oxygen demand (COD)/(g MLSS d) in MFC1 and MFC2, respectively. Time of MFC operation affected the microbial · structure and the use of waste VFAs promoted microbial diversity. High abundance of Deftia sp. and Methanobacterium sp. characterized start-up period in MFCs. During stable operation, higher OLR in MFC1 favored growth of exoelectrogens from Rhodopseudomonas sp. (13.2%) resulting in a higher and more stable electricity production in comparison with MFC2. At a lower OLR in MFC2, the percentage of exoelectrogens in biomass decreased, while the abundance of genera Leucobacter, Frigoribacterium and Phenylobacterium increased. In turn, this efficiently decomposed complex organic substances, favoring high and stable COD removal (over 85%). -
Biofilm Engineering Approaches for Improving the Performance Of
REVIEW published: 05 July 2018 doi: 10.3389/fenrg.2018.00063 Biofilm Engineering Approaches for Improving the Performance of Microbial Fuel Cells and Bioelectrochemical Systems Maria Joseph Angelaalincy 1, Rathinam Navanietha Krishnaraj 2, Ganeshan Shakambari 1, Balasubramaniem Ashokkumar 3, Shanmugam Kathiresan 4 and Perumal Varalakshmi 1* 1 Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, India, 2 Department of Chemical and Biological Engineering, Composite and Nanocomposite Advanced Manufacturing – Biomaterials Center, Rapid City, SD, United States, 3 Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India, 4 Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India Microbial fuel cells (MFCs) are emerging as a promising future technology for a wide range Edited by: Abudukeremu Kadier, of applications in addition to sustainable electricity generation. Electroactive (EA) biofilms National University of Malaysia, produced by microorganisms are the key players in the bioelectrochemical systems Malaysia involving microorganism mediated electrocatalytic reactions. Therefore, genetically Reviewed by: modifying the organism for increased production of EA biofilms and improving the extra G. Velvizhi, Indian Institute of Chemical electron transfer (EET) mechanisms may attribute to increase in current density of a MFC Technology (CSIR), India and an increased COD removal in wastewater treatment plant coupled MFC systems. Özlem Onay, Anadolu University, Turkey Extracellular polysaccharides (EPS) produced by the organisms attribute to both biofilm *Correspondence: formation and electron transfer. Although cell surface modification, media optimization Perumal Varalakshmi and operation parameters validation are established as enhancement strategies for a fuel [email protected] cell performance, engineering the vital genes involved in electroactive biofilm formation Specialty section: is the future hope. -
DOE-ERSP PI MEETING 2007 Abstracts
DOE-ERSP PI MEETING: Abstracts April 16–19, 2007 Lansdowne, Virginia Environmental Remediation Sciences Program (ERSP) This work was supported by the Office of Science, Biological and Environmental Research, Environmental Remediation Sciences Division (ERSD), U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Table of Contents Introduction.............................................................................................................................5 ERSP Contacts.......................................................................................................................7 ERSP Annual PI Meeting Preliminary Agenda .......................................................................9 ABSTRACTS .......................................................................................................................13 GENERAL ERSP ABSTRACTS.......................................................................................15 Allen-King ......................................................................................................................17 Apel ...............................................................................................................................18 Baer...............................................................................................................................19 Baldwin..........................................................................................................................20 Bargar............................................................................................................................21 -
The Physiological Role and Characterization of Melanin Produced by Shewanella Algae Bry
University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Spring 2001 The physiological role and characterization of melanin produced by Shewanella algae BrY Charles Edwin Turick University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Turick, Charles Edwin, "The physiological role and characterization of melanin produced by Shewanella algae BrY" (2001). Doctoral Dissertations. 28. https://scholars.unh.edu/dissertation/28 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Hal 89-106 Alimuddin Enzim
Microbial community of black band disease on infection ... (Ofri Johan) MICROBIAL COMMUNITY OF BLACK BAND DISEASE ON INFECTION, HEALTHY, AND DEAD PART OF SCLERACTINIAN Montipora sp. COLONY AT SERIBU ISLANDS, INDONESIA Ofri Johan*)#, Dietriech G. Bengen**), Neviaty P. Zamani**), Suharsono***), David Smith****), Angela Mariana Lusiastuti*****), and Michael J. Sweet******) *) Research and Development Institute for Ornamental Fish Culture, Jakarta **) Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Bogor Agricultural University ***) Research Center for Oceanography, The Indonesian Institute of Science ****) School of Biology, Newcastle University, NE1 7RU, United Kingdom *****) Center for Aquaculture Research and Development ******) Biological Sciences Research Group, University of Derby, Kedleston Road, Derby, DE22 1GB, United Kingdom (Received 19 March 2014; Final revised 12 September 2014; Accepted 10 November 2014) ABSTRACT It is crucial to understand the microbial community associated with the host when attempting to discern the pathogen responsible for disease outbreaks in scleractinian corals. This study determines changes in the bacterial community associated with Montipora sp. in response to black band disease in Indonesian waters. Healthy, diseased, and dead Montipora sp. (n = 3 for each sample type per location) were collected from three different locations (Pari Island, Pramuka Island, and Peteloran Island). DGGE (Denaturing Gradient Gel Electrophoresis) was carried out to identify the bacterial community associated with each sample type and histological analysis was conducted to identify pathogens associated with specific tissues. Various Desulfovibrio species were found as novelty to be associated with infection samples, including Desulfovibrio desulfuricans, Desulfovibrio magneticus, and Desulfovibrio gigas, Bacillus benzoevorans, Bacillus farraginis in genus which previously associated with pathogenicity in corals. -
Effect of Electrode Spacing on Electron Transfer and Conductivity of Geobacter Sulfurreducens Biofilms
Bioelectrochemistry 131 (2020) 107395 Contents lists available at ScienceDirect Bioelectrochemistry journal homepage: www.elsevier.com/locate/bioelechem Effect of electrode spacing on electron transfer and conductivity of Geobacter sulfurreducens biofilms Panpan Liu a,b, Abdelrhman Mohamed b,PengLianga, Haluk Beyenal b,⁎ a State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment, Tsinghua University, Beijing 100084, PR China b The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99163, USA article info abstract Article history: To understand electron transport in electrochemically active biofilms, it is necessary to elucidate the heteroge- Received 15 April 2019 neous electron transport across the biofilm/electrode interface and in the interior of G. sulfurreducens biofilms Received in revised form 12 September 2019 bridging gaps of varying widths. The conductivity of Geobacter sulfurreducens biofilm bridging nonconductive Accepted 13 September 2019 gaps with widths of 5 µm, 10 µm, 20 µm and 50 µm is investigated. Results of electrochemical gating measure- Available online 4 October 2019 ment show that biofilm conductivity peaks at the potential of −0.35 V vs. Ag/AgCl. The biofilm conductivity in- creases with gap width (10.4 ± 0.2 µS cm−1 in 5 µm gap, 13.3 ± 0.2 µS cm−1 in 10 µm gap, 16.7 ± 1.4 µS cm−1 in Keywords: −1 Electrochemically active biofilm 20 µm gap and 41.8 ± 2.02 µS cm in 50 µm gap). These results revealed that electron transfer in Exoelectrogens G. sulfurreducens biofilm is a redox-driven. In addition, higher biofilm conductivities and lower charge transfer Biofilm conductivity resistances are observed in all gaps under a turnover condition than in those under a non-turnover condition. -
Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature
microorganisms Review Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature Klaudia Tutka, Magdalena Zychowska˙ and Adam Reich * Department of Dermatology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-055 Rzeszow, Poland; [email protected] (K.T.); [email protected] (M.Z.)˙ * Correspondence: [email protected]; Tel.: +48-605076722 Received: 30 August 2020; Accepted: 6 November 2020; Published: 8 November 2020 Abstract: Rosacea is a chronic inflammatory skin disorder of a not fully understood pathophysiology. Microbial factors, although not precisely characterized, are speculated to contribute to the development of the condition. The aim of the current review was to summarize the rosacea-associated alterations in the skin, blood, and gut microbiome, investigated using culture-independent, metagenomic techniques. A systematic review of the PubMed, Web of Science, and Scopus databases was performed, according to PRISMA (preferred reporting items for systematic review and meta-analyses) guidelines. Nine out of 185 papers were eligible for analysis. Skin microbiome was investigated in six studies, and in a total number of 115 rosacea patients. Blood microbiome was the subject of one piece of research, conducted in 10 patients with rosacea, and gut microbiome was studied in two papers, and in a total of 23 rosacea subjects. Although all of the studies showed significant alterations in the composition of the skin, blood, or gut microbiome in rosacea, the results were highly inconsistent, or even, in some cases, contradictory. Major limitations included the low number of participants, and different study populations (mainly Asians). Further studies are needed in order to reliably analyze the composition of microbiota in rosacea, and the potential application of microbiome modifications for the treatment of this dermatosis. -
Genomic Signatures of Sex, Selection and Speciation in the Microbial World
Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro B.Sc. Biology McGill University, 2003 M.Sc. Integrative Bioscience Oxford University, 2004 SUBMITTED TO THE PROGRAM IN COMPUTATIONAL AND SYSTEMS BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTATIONAL AND SYSTEMS BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY SEPTEMBER 2010 © 2010 Massachusetts Institute of Technology All rights reserved Signature of Author:...……………………………………………………………………………………….. Program in Computational and Systems Biology August 6, 2010 Certified by:…………………………………………………………………………………………………. Eric J. Alm Assistant Professor of Civil and Environmental Engineering and Biological Engineering Thesis Supervisor Accepted by:………………………………………………………………………………………………… Christopher B. Burge Professor of Biology and Biological Engineering Chair, Computational and Systems Biology Ph.D. Graduate Committee 1 Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro Submitted to the Program in Computational and Systems Biology on August 6, 2010 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Computational and Systems Biology ABSTRACT Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes.