Gravity-Driven Microfiltration Pretreatment for Reverse
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Sphingopyxis Italica, Sp. Nov., Isolated from Roman Catacombs 1 2
View metadata, citation and similar papers at core.ac.uk brought to you by CORE IJSEM Papers in Press. Published December 21, 2012 as doi:10.1099/ijs.0.046573-0 provided by Digital.CSIC 1 Sphingopyxis italica, sp. nov., isolated from Roman catacombs 2 3 Cynthia Alias-Villegasª, Valme Jurado*ª, Leonila Laiz, Cesareo Saiz-Jimenez 4 5 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 6 Apartado 1052, 41080 Sevilla, Spain 7 8 * Corresponding author: 9 Valme Jurado 10 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC 11 Apartado 1052, 41080 Sevilla, Spain 12 Tel. +34 95 462 4711, Fax +34 95 462 4002 13 E-mail: [email protected] 14 15 ª These authors contributed equally to this work. 16 17 Keywords: Sphingopyxis italica, Roman catacombs, rRNA, sequence 18 19 The sequence of the 16S rRNA gene from strain SC13E-S71T can be accessed 20 at Genbank, accession number HE648058. 21 22 A Gram-negative, aerobic, motile, rod-shaped bacterium, strain SC13E- 23 S71T, was isolated from tuff, the volcanic rock where was excavated the 24 Roman Catacombs of Saint Callixtus in Rome, Italy. Analysis of 16S 25 rRNA gene sequences revealed that strain SC13E-S71T belongs to the 26 genus Sphingopyxis, and that it shows the greatest sequence similarity 27 with Sphingopyxis chilensis DSMZ 14889T (98.72%), Sphingopyxis 28 taejonensis DSMZ 15583T (98.65%), Sphingopyxis ginsengisoli LMG 29 23390T (98.16%), Sphingopyxis panaciterrae KCTC12580T (98.09%), 30 Sphingopyxis alaskensis DSM 13593T (98.09%), Sphingopyxis 31 witflariensis DSM 14551T (98.09%), Sphingopyxis bauzanensis DSM 32 22271T (98.02%), Sphingopyxis granuli KCTC12209T (97.73%), 33 Sphingopyxis macrogoltabida KACC 10927T (97.49%), Sphingopyxis 34 ummariensis DSM 24316T (97.37%) and Sphingopyxis panaciterrulae T 35 KCTC 22112 (97.09%). -
Prevotella Jejuni Sp. Nov., Isolated from the Small Intestine of a Child with Coeliac Disease
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4218–4223 DOI 10.1099/ijs.0.052647-0 Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease Maria E. Hedberg,1 Anne Israelsson,1 Edward R. B. Moore,2,3 Liselott Svensson-Stadler,2 Sun Nyunt Wai,4 Grzegorz Pietz,1 Olof Sandstro¨m,5 Olle Hernell,5 Marie-Louise Hammarstro¨m1 and Sten Hammarstro¨m1 Correspondence 1Department of Clinical Microbiology, Immunology, Umea˚ University, SE-90187 Umea˚, Sweden Maria E. Hedberg 2CCUG – Culture Collection University of Gothenburg, Department of Clinical Bacteriology, [email protected] Sahlgrenska University Hospital, SE-41345 Go¨teborg, Sweden Sten Hammarstro¨m 3 [email protected] Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40530 Go¨teborg, Sweden 4Department of Molecular Biology, Umea˚ University, SE-90187 Umea˚, Sweden 5Department of Clinical Sciences, Pediatrics, Umea˚ University, SE-90187 Umea˚, Sweden Five obligately anaerobic, Gram-stain-negative, saccharolytic and proteolytic, non-spore-forming bacilli (strains CD3 : 27, CD3 : 28T, CD3 : 33, CD3 : 32 and CD3 : 34) are described. All five strains were isolated from the small intestine of a female child with coeliac disease. Cells of the five strains were short rods or coccoid cells with longer filamentous forms seen sporadically. The organisms produced acetic acid and succinic acid as major metabolic end products. Phylogenetic analysis based on comparative 16S rRNA gene sequence analysis revealed close relationships between CD3 : 27, CD3 : 28T and CD3 : 33, between CD3 : 32 and Prevotella histicola CCUG 55407T, and between CD3 : 34 and Prevotella melaninogenica CCUG 4944BT. -
Shifting the Genomic Gold Standard for the Prokaryotic Species Definition
Shifting the genomic gold standard for the prokaryotic species definition Michael Richter and Ramon Rossello´ -Mo´ ra1 Marine Microbiology Group, Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), E-07190 Esporles, Spain Edited by James M. Tiedje, Center for Microbial Ecology, East Lansing, MI, and approved September 16, 2009 (received for review June 11, 2009) DNA-DNA hybridization (DDH) has been used for nearly 50 years as of diversity among prokaryotes, the circumscription of each geno- the gold standard for prokaryotic species circumscriptions at the species would, in addition, be dependent on each group being genomic level. It has been the only taxonomic method that offered studied (2, 6). Nevertheless, the use of DDH has mainly driven the a numerical and relatively stable species boundary, and its use has construction of the current prokaryotic taxonomy, as it has become had a paramount influence on how the current classification has the gold standard for genomically circumscribing species. This been constructed. However, now, in the era of genomics, DDH parameter has had a similar impact in prokaryotic taxonomy as the appears to be an outdated method for classification that needs to interbreeding premise that is the basis for the biological species be substituted. The average nucleotide identity (ANI) between two concept for animal and plant taxonomies (1). In the late 1980’s (5), genomes seems the most promising method since it mirrors DDH taxonomists already believed that the reference standard for de- closely. Here we examine the work package JSpecies as a user- termining taxonomy would be full genome sequences. friendly, biologist-oriented interface to calculate ANI and the Despite being a traditional method, DDH has been often criti- correlation of the tetranucleotide signatures between pairwise cized as being inappropriate to circumscribe prokaryotic taxa genomic comparisons. -
Entwicklung Eines Datenbank-Gestützten Computerprogramms Zur Taxonomischen Identifizierung Von Mikrobiellen Populationen Auf Molekularbiologischer Basis
Entwicklung eines Datenbank-gestützten Computerprogramms zur taxonomischen Identifizierung von mikrobiellen Populationen auf molekularbiologischer Basis Anwendung dieses Programms auf die Charakterisierung der Diversität stickstofffixierender und denitrifzierender Mikroorganismen in Abhängigkeit einer Stickstoffdüngung Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Christopher Rösch aus München Hundt Druck Köln, 2005 Berichterstatter: Prof. Dr. H. Bothe Prof. Dr. D. Schomburg Tag der mündlichen Prüfung: 11. Juli 2005 Meinen Eltern Abstract The present work aimed at developing a novel method which allows to characterize microbial communities from environmental samples in a comprehensive and rapid way. Approaches tried so far either supplied information about the identity of a small fraction of organisms within the total community (e. g. by sequencing of clone libraries), or demonstrated the diversity of organisms without identifying them (e. g. community profiling). In the approach presented here, a method for determining such profiles (by tRFLP analysis) was combined with an automatic analysis by a computer program (TReFID) newly developed for the current study. For the characterization of microorganisms, three different data bases have been constructed: (1) for denitrifying bacteria: a nosZ data base with 607 entries (2) for dinitrogen fixing bacteria: a nifH data base with 1,318 entries (3) for bacteria in general: a 16S rDNA data base with 22,145 entries Thus a comprehensive data set has been developed particularly for the 16S rRNA gene. The use of the TReFID program now allows investigators to characterize bacterial communities from any environmental sample in a rather comprehensive way. Several control analyses showed that the TReFID program is suited for the analysis of environmental samples. -
Variability of Photosynthesis Genes in Purple Bacteria and Molecular Determinants of Their Spectral Properties
Variability of photosynthesis genes in purple bacteria and molecular determinants of their spectral properties Von der Fakultät für Mathematik und Naturwissenschaften der Carl von Ossietzky Universität Oldenburg zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften angenommene Dissertation von Christian Tuschak geboren am 12. Dezember 1969 in Recklinghausen Oldenburg, September 2003 Erstreferent: Prof. Dr. Heribert Cypionka Korreferent: Prof. Dr. Jörg Overmann Tag der Disputation: 17.12.2003 Für meine Eltern Für Judit List of Abbreviations [32P]dCTP deoxy cytidine triphosphate, labled with radioactive phosphor 32P aa amino acids ATCC American type culture collection ATP adenosine triphosphate bp base pairs bch bacteriochlorophyll biosynthesis genes BChl bacteriochlorophyll crt carontenoid biosynthesis genes DSM / DSMZ Deutsche Sammlung für Mikroorganismen und Zellkulturen EDTA ethylendiamine tetraacetic acid iPCR inverse polymerase chain reaction LH1 light harvesting complex 1 (core antenna) LH2, LH3 light harvesting complexes 2 and 3 (peripheral antennae) MOPS 3-(N-morpholino)propanesulfonic acid NIR near infrared nt nucleotides orf open reading frame PCR polymerase chain reaction PDB protein database PS I, PS II photosystem I and II puc structural and regulatory genes for the peripheral antenna puf photosynthetic unit forming genes (reaction center + light harvesting core antenna) puh structural gene for the reaction center H subunit (photosynthetic unit H protein) QA, QB acceptor quinones A and B in the purple bacterial reaction center Qy long wavelength transition of bacteriochlorophylls RC reaction center SDS sodium dodecyl sulfate SSC sodium chloride-sodium citrate TBE Tris-boric acid-EDTA TE Tris-EDTA Tris Tris(hydroxymethyl)aminomethane i Abbreviations of genus names Acp. Acidiphilium Alc. Allochromatium Amb. Amoebobacter Blc. -
Recommended Standards for the Description of New Species of Anoxygenic Phototrophic Bacteria
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by OceanRep International Journal of Systematic and Evolutionary Microbiology (2004), 54, 1415–1421 DOI 10.1099/ijs.0.03002-0 Recommended standards for the description of new species of anoxygenic phototrophic bacteria Johannes F. Imhoff1 and Pierre Caumette2 Correspondence 1Institut fu¨r Meereswissenschaften, Du¨sternbrooker Weg 20, D-24105 Kiel, Germany Johannes F. Imhoff 2Laboratoire d’Ecologie Mole´culaire, Microbiologie, EA 3525, Universite´ de Pau, F-64000 Pau, [email protected] France Recommended standards for the description of new species of the anoxygenic phototrophic bacteria are proposed in accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria. These standards include information on the natural habitat, ecology and phenotypic properties including morphology, physiology and pigments and on genetic information and nucleic acid data. The recommended standards were supported by the Subcommittee on the taxonomy of phototrophic bacteria of the International Committee on Systematics of Prokaryotes. They are considered as guidelines for authors to prepare descriptions of new species. Introduction complete database of 16S rDNA sequences of available type Four major phenotypically and phylogenetically well- strains (and additional other strains) of the species of distinguished groups of bacteria are able to perform Chlorobiaceae (Overmann & Tuschack, 1997; Alexander anoxygenic photosynthesis and to grow phototrophically -
Diverse Spatial Organization of Photosynthetic Membranes Among Purple Nonsulfur
bioRxiv preprint doi: https://doi.org/10.1101/248997; this version posted January 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Diverse spatial organization of photosynthetic membranes among purple nonsulfur 2 bacteria 3 4 Breah LaSarre1*, David T. Kysela1, Barry D. Stein1, Adrien Ducret1,2, Yves V. Brun1, James B. 5 McKinlay1* 6 1Department of Biology, Indiana University, Bloomington IN 7 2 Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, UMR 5086, 7 passage du 8 Vercors, 69367, Lyon Cedex 07, France. [current] 9 *Co-corresponding authors. 1001 E 3rd Street, Jordan Hall, Bloomington, IN 47405 10 11 Phone: 812-855-0359 12 Email: [email protected] 13 Phone: 812-855-9332 14 Email: [email protected] 15 16 Conflict of interest. 17 The authors declare no conflict of interest. 18 19 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/248997; this version posted January 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 24 ABSTRACT 25 In diverse bacteria, proper cellular physiology requires the utilization of protein- or membrane- 26 bound compartments that afford specific metabolic capabilities. One such compartment is the 27 light-harvesting intracytoplasmic membrane (ICM) of purple nonsulfur bacteria (PNSB). Here we 28 reveal that ICMs are subject to differential spatial organization among PNSB. We visualized 29 ICMs in live cells of fourteen PNSB species by exploiting the natural autofluorescence of the 30 photosynthetic machinery. -
Characterization of Anoxygenic Phototrophs That Grow Using Infrared Radiation (>800 Nm) (Sampling Location: Little Sippewissett Marsh, Woods Hole, Ma)
Characterization Of Anoxygenic Phototrophs That Grow Using Infrared Radiation (>800 Nm) (Sampling Location: Little Sippewissett Marsh, Woods Hole, Ma) Martina Cappelletti, PhD University of Bologna, e-mail: [email protected] Microbial Diversity Course Marine Biological Laboratory, June-July 2011 1 ABSTRACT In this study I performed two enrichment cultures for purple bacteria from a mat soil sample collected in Little Sippewissett marsh. I obtained two mixed culture that were named LWS_880 and LWS_960 as they could grow absorbing light at 880 nm and 960 nm. The molecular analysis of the culturable bacteria obtained by using two different isolation techniques was performed with two primer sets, one specific for the 16S rDNA and the other for the pufM gene. As a result, culturable bacteria in LWS_880 were identified as purple non- sulphur bacteria belonging to the following genera Rhodobacter, Rhodospirillum, Rhodovulum and Rhodobium. The culturable bacteria in LW_960 were shown to belong to the genera Thioroducoccus, Allochromatium, Marichromatium of purple sulfur bacteria and to the purple non-sulfur Rhodovolum genus. CARD-FISH hybridization technique allowed measuring the relative abundance of each group of Proteobacteria in each microbial community pointing out interesting differences between the two samples. Further biochemical assay identified the bacterioclorophyll present in each consortium and chemotaxis activity was detected in the sample LWS_960. INTRODUCTION Most of the fossil fuels utilized as energy source on earth is the result of photosynthesis process occurred many hundreds of millions of years ago. Moreover, the evolution of oxygenic photosynthesis resulted in the oxygenation of Earth’s atmosphere creating a radical new environment for all life. -
Complete Genome Sequence of Parvibaculum Lavamentivorans Type Strain (DS-1T)
Erschienen in: Standards in Genomic Sciences ; 5 (2011), 3. - S. 298-310 Standards in Genomic Sciences (2011) 5:298-310 DOI:10.4056/sigs.2215005 Complete genome sequence of Parvibaculum T lavamentivorans type strain (DS-1 ) David Schleheck1*, Michael Weiss1, Sam Pitluck2, David Bruce3, Miriam L. Land4, Shunsheng Han3, Elizabeth Saunders3, Roxanne Tapia3, Chris Detter3, Thomas Brettin4, James Han2, Tanja Woyke2, Lynne Goodwin3, Len Pennacchio2, Matt Nolan2, Alasdair M. Cook1, Staffan Kjelleberg5, Torsten Thomas5 1 Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia *Corresponding author: [email protected] Keywords: Parvibaculum lavamentivorans DS-1, aerobic, Gram-negative, Rhodobiaceae, sur- factant biodegradation Parvibaculum lavamentivorans DS-1T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Al- phaproteobacteria. Strain DS-1T is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that cata- lyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first com- pleted genome sequence of the genus Parvibaculum, and the first genome sequence of a rep- resentative of the family Rhodobiaceae. -
Rhodovulum Marinum Sp. Nov., a Novel Phototrophic Purple Non-Sulfur Alphaproteobacterium from Marine Tides of Visakhapatnam, India
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 1651–1656 DOI 10.1099/ijs.0.64005-0 Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India T. N. R. Srinivas,1 P. Anil Kumar,1 Ch. Sasikala,1 Ch. V. Ramana,2 J. Su¨ling3 and J. F. Imhoff3 Correspondence 1Environmental Microbial Biotechnology Laboratory, Centre for Environment, Institute of Ch. V. Ramana Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 072, India [email protected] 2Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central [email protected] University, Hyderabad 500 046, India 3Leibniz-Institut fu¨r Meereswissenschaften, Marine Mikrobiologie, Du¨sternbrooker Weg 20, 24105 Kiel, Germany A yellowish-brown bacterium was isolated from enrichment cultures inoculated with seawater samples from the eastern coast of India (Visakhapatnam) under photoheterotrophic conditions. Enrichment and isolation in a medium containing 2 % NaCl (w/v) yielded strain JA128T, which has ovoid to rod-shaped cells, also forms chains and is non-motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA128T clusters with the Alphaproteobacteria and the sequence similarity with its closest relatives, Rhodovulum iodosum and Rhodovulum sulfidophilum, was 95 %. Strain JA128T contained vesicular intracytoplasmic membranes, bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA128T was mesophilic, slightly acidophilic, slightly halophilic and grew photoheterotrophically with a number of organic compounds as carbon source and electron donor. It was unable to grow photoautotrophically, chemoautotrophically or by fermentative modes. It did not utilize sulfide, thiosulfate or hydrogen as electron donors. -
Diversity of Purple Nonsulfur Bacteria in Shrimp Ponds and Mercury Resistant Mechanisms of Selected Strains Kanokwan Mukkata
i Diversity of Purple Nonsulfur Bacteria in Shrimp Ponds and Mercury Resistant Mechanisms of Selected Strains Kanokwan Mukkata A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Microbiology Prince of Songkla University 2016 Copyright of Prince of Songkla University i Diversity of Purple Nonsulfur Bacteria in Shrimp Ponds and Mercury Resistant Mechanisms of Selected Strains Kanokwan Mukkata A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Microbiology Prince of Songkla University Copyright of Prince of Songkla University 2016 ii Thesis Title Diversity of Purple Nonsulfur Bacteria in Shrimp Ponds and Mercury Resistant Mechanisms of Selected Strains Author Miss Kanokwan Mukkata Major Program Microbiology _____________________________________________________________________ Major Advisor Examining Committee: ...................................................... ................................................Chairperson (Assoc. Prof. Dr. Duangporn Kantachote) (Asst. Prof. Dr. Pimonsri Mittraparp-Arthorn) Co-advisor: ..................................................Committee (Assoc. Prof. Dr. Duangporn Kantachote) ...................................................... (Assoc. Prof. Dr. Banjong Wittayaweerasak) ..................................................Committee (Assoc. Prof. Dr. Wanna Choorit) ...................................................... (Prof. Dr. Megharaj Mallavarapu) ..................................................... -
Microbiologically Influenced Corrosion of 1018 Carbon Steel in Static Seawater/Fuel (Petroleum-Based and Renewable) Mixtures
MICROBIOLOGICALLY INFLUENCED CORROSION OF 1018 CARBON STEEL IN STATIC SEAWATER/FUEL (PETROLEUM-BASED AND RENEWABLE) MIXTURES A THESIS SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAIʻI AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN MICROBIOLOGY AUGUST 2017 By Jan A. N. Kealoha Thesis Committee: Stuart Donachie, Chairperson Lloyd Hihara Anne Alvarez Keywords: Microbiologically-Influenced Corrosion (MIC), 1018 carbon steel, Diesel, F-76, HRD, Tubercle Acknowledgements I am extremely grateful for… … the support of the Hawaiʻi Natural Energy Institute (HNEI) for funding this project though the Asia Pacific Research Initiative for Sustainable Energy Systems (APRISES), which is a grant from the U.S. Naval Research Laboratory (award number N00014-13-1-0463), particularly Dr. Scott Turn of HNEI. ... Dr. Shengxi Li for the long hours/days/months of corrosion analysis (XRD, Raman, FTIR, SEM, and EDXA). … Drs. Anthony Amend and Richard O'Rorke for their guidance with Illumina sequencing. … Hawaiʻi Ocean Time-series Program, especially Susan Curless and Brett Updyke … Aaron Toyama and Gavin Taketa of the UH College of Engineering Machine Shop for cutting over 700 steel coupons and moving my samples around with the forklift. … The Hawaiʻi Corrosion Lab members for their support; especially Ryan Sugamoto, Daniel Hong, Jeff Nelson, Raghu Srinivasan and Corey Kaneshiro for all the extra helping hands and advice to keep me sane. … Undergraduate students: Alex Park, Andrew Rogitz, Kate Quiambao, Justin Shortell, James Miller, Shekinah Eugenio, Jenna Maligro, Ashlyn Tanaka who helped process my samples. …My Thesis committee, Drs. Stuart Donachie, Lloyd Hihara and Anne Alvarez, for their guidance, patience and enthusiasm that got me though the massive undertaking of this project.