Diversification and Niche Adaptations of Nitrospina-Like Bacteria in The
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Nitrobacter As an Indicator of Toxicity in Wastewater
State Water Survey Division WATER QUALITY SECTION AT Illinois Department of PEORIA, ILLINOIS Energy and Natural Resources SWS Contract Report 326 NITROBACTER AS AN INDICATOR OF TOXICITY IN WASTEWATER by Wuncheng Wang and Paula Reed Prepared for and funded by the Illinois Department of Energy and Natural Resources September 1983 CONTENTS PAGE Abstract 1 Introduction 1 Scope of study 3 Acknowledgments 3 Literature review 3 Microbial nitrification 3 Influence of toxicants on nitrification 5 Materials and methods 10 Culture 10 Methods 11 Results 12 Preliminary tests 13 Metal toxicity 13 Organic compounds toxicity 16 Time effect 22 Discussion 22 References 27 NITROBACTER AS AN INDICATOR OF TOXICITY IN WASTEWATER by Wuncheng Wang and Paula Reed ABSTRACT This report presents the results of a study of the use of Nitrobacter as an indicator of toxicity. Nitrobacter are strictly aerobic, autotrophic, and slow growing bacteria. Because they convert nitrite to nitrate, the effects that toxins have on them can be detected easily by monitoring changes in their nitrite consumption rate. The bacterial cultures were obtained from two sources — the Peoria and Princeton (Illinois) wastewater treatment plants — and tests were con• ducted to determine the effects on the cultures of inorganic ions and organic compounds. The inorganic ions included cadmium, copper, lead, and nickel. The organic compounds were phenol, chlorophenol (three derivatives), dichlo- rophenol (two derivatives), and trichlorophenol. The bioassay procedure is relatively simple and the results are repro• ducible . The effects of these chemical compounds on Nitrobacter were not dramatic. For example, of the compounds tested, 2,4,6-trichlorophenol was the most toxic to Nitrobacter. -
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. -
Multiple Genome Sequences Reveal Adaptations of a Phototrophic Bacterium to Sediment Microenvironments
Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments Yasuhiro Odaa, Frank W. Larimerb, Patrick S. G. Chainc,d,e, Stephanie Malfattic,d, Maria V. Shinc,d, Lisa M. Vergezc,d, Loren Hauserb, Miriam L. Landb, Stephan Braatschf, J. Thomas Beattyf, Dale A. Pelletierb, Amy L. Schaefera, and Caroline S. Harwooda,1 aDepartment of Microbiology, University of Washington, Seattle, WA 98195; bGenome Analysis and Systems Modeling, Oak Ridge National Laboratory, Oak Ridge, TN 37831; cJoint Genome Institute, Walnut Creek, CA 94598; dLawrence Livermore National Laboratory, Livermore, CA 94550; eDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824; and fDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Edited by Robert Haselkorn, University of Chicago, Chicago, IL, and approved October 14, 2008 (received for review September 13, 2008) The bacterial genus Rhodopseudomonas is comprised of photo- exist in soils and sediments, but on a microscale that is generally synthetic bacteria found widely distributed in aquatic sediments. too small for human observation. The genus Rhodopseudomonas Members of the genus catalyze hydrogen gas production, carbon consists of photosynthetic Alphaproteobacteria of extreme met- dioxide sequestration, and biomass turnover. The genome se- abolic versatility. Members of the genus are ubiquitous in quence of Rhodopseudomonas palustris CGA009 revealed a sur- temperate aquatic sediments (7–9), and isolates classified as prising richness of metabolic versatility that would seem to explain Rhodopseudomonas spp. can grow with or without light or its ability to live in a heterogeneous environment like sediment. oxygen, fix nitrogen, and have highly developed biodegradation However, there is considerable genotypic diversity among Rhodo- abilities. -
Differential Depth Distribution of Microbial Function and Putative Symbionts Through Sediment-Hosted Aquifers in the Deep Terrestrial Subsurface
ARTICLES https://doi.org/10.1038/s41564-017-0098-y Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface Alexander J. Probst1,5,7, Bethany Ladd2,7, Jessica K. Jarett3, David E. Geller-McGrath1, Christian M. K. Sieber1,3, Joanne B. Emerson1,6, Karthik Anantharaman1, Brian C. Thomas1, Rex R. Malmstrom3, Michaela Stieglmeier4, Andreas Klingl4, Tanja Woyke 3, M. Cathryn Ryan 2* and Jillian F. Banfield 1* An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome- resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep- branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface. -
Recycling of Vitamin B12 and NAD+ Within the Pdu Microcompartment of Salmonella Enterica Shouqiang Cheng Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2010 Recycling of vitamin B12 and NAD+ within the Pdu microcompartment of Salmonella enterica Shouqiang Cheng Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Cheng, Shouqiang, "Recycling of vitamin B12 and NAD+ within the Pdu microcompartment of Salmonella enterica" (2010). Graduate Theses and Dissertations. 11713. https://lib.dr.iastate.edu/etd/11713 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. + Recycling of vitamin B12 and NAD within the Pdu microcompartment of Salmonella enterica by Shouqiang Cheng A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Biochemistry Program of Study Committee: Thomas A. Bobik, Major Professor Alan DiSpirito Basil Nikolau Reuben Peters Gregory J. Phillips Iowa State University Ames, Iowa 2010 Copyright © Shouqiang Cheng, 2010. All rights reserved. ii Table of contents Abstract............................................................................................................................. -
Organic Matter Decomposition in Simulated Aquaculture Ponds Group Fish Culture and Fisheries Daily Supervisor(S) Dr
O rganic matter decomposition in simulated aquaculture ponds Beatriz Torres Beristain Promotor: Prof. Dr. J.A .J. V erreth H oogleraar in de V isteelt en V isserij W ageningen U niversiteit C o-promotor: Dr. M .C .J. V erdegem U niversitair docent bij the Leerstoelgroep V isteelt en V isserij W ageningen U niversiteit Samenstelling promotiecommissie: Prof. Dr. Y . A vnimelech Technion, Israel Institute of Technology Prof. Dr. Ir. H .J. Gijzen U N ESC O -IH E, Delf, N etherlands Prof. Dr. Ir. M . W .A . V erstegen W ageningen U niversiteit Prof. Dr. Ir. A .A . K oelmans W ageningen U niversiteit Dit onderzoek is uitgevoerd binnen de onderzoekschool W IA S O rganic matter decomposition in simulated aquaculture ponds Beatriz Torres Beristain Proefschrift Ter verkrijging van de graad van doctor O p gezag van de rector magnificus van W ageningen U niversiteit, Prof. Dr. Ir. L. Speelman, In het openbaar te verdedigen O p dinsdag 15 A pril 2005 des namiddags te half tw ee in de A ula Torres Beristain, B. O rganic matter decomposition in simulated aquaculture ponds PhD thesis, Fish C ulture and Fisheries Group, W ageningen Institute of A nimal Sciences. W ageningen U niversity, P.O . Box 338, 6700 A H W ageningen, The N etherlands. - W ith R ef. œW ith summary in Spanish, Dutch and English ISBN : 90-8504-170-8 A Domingo, Y olanda y A lejandro Table of contents C hapter 1 General introduction. 1 C hapter 2 R eview microbial ecology and role in aquaculture ponds. -
Revealing the Full Biosphere Structure and Versatile Metabolic Functions In
Chen et al. Genome Biology (2021) 22:207 https://doi.org/10.1186/s13059-021-02408-w RESEARCH Open Access Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep Ping Chen1†, Hui Zhou1,2†, Yanyan Huang3,4†, Zhe Xie5†, Mengjie Zhang1,2†, Yuli Wei5, Jia Li1,2, Yuewei Ma3, Min Luo5, Wenmian Ding3, Junwei Cao5, Tao Jiang1,2, Peng Nan3*, Jiasong Fang5* and Xuan Li1,2* * Correspondence: nanpeng@fudan. edu.cn; [email protected]; lixuan@ Abstract sippe.ac.cn †Ping Chen, Hui Zhou, Yanyan Background: The full biosphere structure and functional exploration of the microbial Huang, Zhe Xie and Mengjie Zhang communities of the Challenger Deep of the Mariana Trench, the deepest known contributed equally to this work. hadal zone on Earth, lag far behind that of other marine realms. 3Ministry of Education Key Laboratory for Biodiversity Science Results: We adopt a deep metagenomics approach to investigate the microbiome and Ecological Engineering, School in the sediment of Challenger Deep, Mariana Trench. We construct 178 of Life Sciences, Fudan University, Shanghai, China metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are 5Shanghai Engineering Research reported from hadal sediment for the first time. Based on the MAGs, we find the Center of Hadal Science and microbial community functions are marked by enrichment and prevalence of Technology, College of Marine Sciences, Shanghai Ocean mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is University, Shanghai, China found to be dominated by six fungal groups that are characterized for the first time 1CAS-Key Laboratory of Synthetic in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute reduction, and hydrogen sulfide oxidation pathways. -
Metabolic Versatility of the Nitrite-Oxidizing Bacterium Nitrospira
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. 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-NC 4.0 International license. 1 Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira 2 marina and its proteomic response to oxygen-limited conditions 3 Barbara Bayer1*, Mak A. Saito2, Matthew R. McIlvin2, Sebastian Lücker3, Dawn M. Moran2, 4 Thomas S. Lankiewicz1, Christopher L. Dupont4, and Alyson E. Santoro1* 5 6 1 Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 7 CA, USA 8 2 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 9 Woods Hole, MA, USA 10 3 Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands 11 4 J. Craig Venter Institute, La Jolla, CA, USA 12 13 *Correspondence: 14 Barbara Bayer, Department of Ecology, Evolution and Marine Biology, University of California, 15 Santa Barbara, CA, USA. E-mail: [email protected] 16 Alyson E. Santoro, Department of Ecology, Evolution and Marine Biology, University of 17 California, Santa Barbara, CA, USA. E-mail: [email protected] 18 19 Running title: Genome and proteome of Nitrospira marina 20 21 Competing Interests: The authors declare that they have no conflict of interest. 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. 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. -
Food Waste Composting and Microbial Community Structure Profiling
processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. -
(Antarctica) Glacial, Basal, and Accretion Ice
CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa. -
55631756.Pdf
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universidade do Minho: RepositoriUM Chemosphere 117 (2014) 295–302 Contents lists available at ScienceDirect Chemosphere journal homepage: www.elsevier.com/locate/chemosphere Influence of tetracycline on the microbial community composition and activity of nitrifying biofilms ⇑ Maria Matos a, , Maria A. Pereira a, Pier Parpot b, António G. Brito a,d, Regina Nogueira c a CEB – Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal b Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal c ISAH – Institute of Sanitary Engineering and Waste Management, University of Hannover, Welfengarten 1, D-30167 Hannover, Germany d Institute of Agronomy, Department of Biosystems Sciences and Engineering, University of Lisbon, Tapada da ajuda, 1349-017 Lisboa, Portugal highlights Tetracycline did not affect the removal of carbon and nitrogen. The antibiotic affected the bacterial composition of the biofilms. The tetracycline removal was poor (28%). Biodegradation was probably the main removal mechanism of the antibiotic. The occurrence of tet(S) was influenced by the presence of tetracycline. article info abstract Article history: The present work aims to evaluate the bacterial composition and activity (carbon and nitrogen removal) Received 14 February 2014 of nitrifying biofilms exposed to 50 lgLÀ1 of tetracycline. The tetracycline removal efficiency and the Received in revised form 27 June 2014 occurrence of tetracycline resistance (tet) genes were also studied. Two sequencing batch biofilm reactors Accepted 28 June 2014 (SBBRs) fed with synthetic wastewater were operated without (SBBR1) and with (SBBR2) the antibiotic. -
Nutrient Control Design Manual: State of Technology Review Report,” Were
United States Office of Research and EPA/600/R‐09/012 Environmental Protection Development January 2009 Agency Washington, DC 20460 Nutrient Control Design Manual State of Technology Review Report EPA/600/R‐09/012 January 2009 Nutrient Control Design Manual State of Technology Review Report by The Cadmus Group, Inc 57 Water Street Watertown, MA 02472 Scientific, Technical, Research, Engineering, and Modeling Support (STREAMS) Task Order 68 Contract No. EP‐C‐05‐058 George T. Moore, Task Order Manager United States Environmental Protection Agency Office of Research and Development / National Risk Management Research Laboratory 26 West Martin Luther King Drive, Mail Code 445 Cincinnati, Ohio, 45268 Notice This document was prepared by The Cadmus Group, Inc. (Cadmus) under EPA Contract No. EP‐C‐ 05‐058, Task Order 68. The Cadmus Team was lead by Patricia Hertzler and Laura Dufresne with Senior Advisors Clifford Randall, Emeritus Professor of Civil and Environmental Engineering at Virginia Tech and Director of the Occoquan Watershed Monitoring Program; James Barnard, Global Practice and Technology Leader at Black & Veatch; David Stensel, Professor of Civil and Environmental Engineering at the University of Washington; and Jeanette Brown, Executive Director of the Stamford Water Pollution Control Authority and Adjunct Professor of Environmental Engineering at Manhattan College. Disclaimer The views expressed in this document are those of the individual authors and do not necessarily, reflect the views and policies of the U.S. Environmental Protection Agency (EPA). Mention of trade names or commercial products does not constitute endorsement or recommendation for use. This document has been reviewed in accordance with EPA’s peer and administrative review policies and approved for publication.