NGUYEN-DISSERTATION-2017.Pdf (5.044Mb)
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil
THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….………. -
Runella Slithyformis Type Strain (LSU 4(T))
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Permalink https://escholarship.org/uc/item/52p6k8qb Journal Standards in genomic sciences, 6(2) ISSN 1944-3277 Authors Copeland, Alex Zhang, Xiaojing Misra, Monica et al. Publication Date 2012-05-04 DOI 10.4056/sigs.2475579 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2012) 6:145-154 DOI:10.4056/sigs.2485911 Complete genome sequence of the aquatic bacterium T Runella slithyformis type strain (LSU 4 ) Alex Copeland1, Xiaojing Zhang1,2, Monica Misra1,2, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,2, Lynne A. Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Chongle Pan1,4, Cynthia D. Jeffries1,4, John C. Detter1, Evelyne-Marie Brambilla5, Manfred Rohde6, Olivier D. Ngatchou Djao6, Markus Göker5, Johannes Sikorski5, Brian J. Tindall5, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and Konstantinos Mavromatis1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, -
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. -
Eelgrass Sediment Microbiome As a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan
Microbes Environ. Vol. 34, No. 1, 13-22, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18103 Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan TATSUNORI NAKAGAWA1*, YUKI TSUCHIYA1, SHINGO UEDA1, MANABU FUKUI2, and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252–0880, Japan; and 2Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060–0819, Japan (Received July 16, 2018—Accepted October 22, 2018—Published online December 1, 2018) Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. -
Community and Whole Genome Analysis of Wastewater Bacteria
Community and Whole Genome Analysis of Wastewater Bacteria By Daniel Rice BSc(Hons) A thesis submitted in total fulfilment of the requirements for the degree of Master of Science School of Life Sciences College of Science, Health and Engineering La Trobe University Victoria Australia February 2020 1 TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................................ i LIST OF FIGURES ..................................................................................................................... iii LIST OF TABLES ....................................................................................................................... iv LIST OF ABBREVIATIONS .......................................................................................................... v STATEMENT OF AUTHORSHIP ................................................................................................vii ACKNOWLEDGEMENTS ......................................................................................................... viii SUMMARY ..............................................................................................................................ix SECTION 1: INTRODUCTION 1.1 Activated sludge process ................................................................................................... 2 1.2 Community profiling of activated sludge bacterial communities ....................................... 7 1.2.1 Phosphorous removal .......................................................................................... -
Bioflocculation of Wastewater Organic Matter at Short Retention Times
Bioflocculation of Wastewater Organic Matter at Short Retention Times Lena Faust Thesis committee Promotor Prof. dr. ir. H.H.M. Rijnaarts Professor, Chair Environmental Technology Wageningen University Co-promotor Dr. ir. H. Temmink Assistant professor, Sub-department of Environmental Technology Wageningen University Other members Prof. Dr A.J.M. Stams, Wageningen University Prof. Dr. I. Smets, University of Leuven, Belgium Prof. Dr. B.-M. Wilen, Chalmers University of Technology, Sweden Prof. Dr. D.C. Nijmeijer, University of Twente, The Netherlands This research was conducted under the auspices of the Graduate School SENSE (Socio- Economic and Natural Sciences of the Environment) Bioflocculation of Wastewater Organic Matter at Short Retention Times Lena Faust Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 3rd of December 2014 at 1.30 p.m. in the Aula. Lena Faust Bioflocculation of Wastewater Organic Matter at Short Retention Times, 163 pages. PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in English and Dutch ISBN 978-94-6257-171-6 ˮDa steh ich nun, ich armer Tor, und bin so klug als wie zuvor.ˮ Dr. Faust (in Faust I written by Johann Wolgang von Goethe) Contents 1 GENERAL INTRODUCTION ....................................................................................................................1 -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Genome Analysis of Two Bacterial Strains Isolated from Diseased
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 September 2020 doi:10.20944/preprints202009.0144.v1 1 Article 2 Genome analysis of two bacterial strains isolated 3 from diseased freshwater sponge reveals the 4 probable cause of its joint domination in microbial 5 community 6 Ivan Petrushin 1,2,*, Sergei Belikov 1 and Lubov Chernogor 1, 7 1 Limnological institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; 8 [email protected] 9 2 Irkutsk State University, Irkutsk 664003, Russia; [email protected] 10 * Correspondence: [email protected]; 11 12 Abstract: Endemic freshwater sponges (Demosponges, Lubomirskiidae) dominate in Lake Baikal 13 and are multicellular filter-feeding animals represent a complex consortium of many species of 14 eukaryotes and prokaryotes. In recent years, mass disease and death of the L. baicalensis have been 15 an urgent problem of Lake Baikal. The etiology and ecology of these events remain unknown. 16 Bacteria in microbiomes of diseased sponges of the families Flavobacteriaceae and Oxalobacteraceae 17 were dominant. Both species are opportunistic pathogens common for freshwater ecosystems. The 18 aim of our study is to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium 19 sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. The first 20 one attacks the other cells using type VI secretion system, suppress gram-positive bacteria with 21 violacein pigment and regulate its own activity via quorum sensing. It makes the floc and strong 22 biofilm by exopolysaccharide biosynthesis and PEP‐CTERM proteins expression. The second one 23 utilizes the fragments of cell walls produced of polysaccharides. -
Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain
Lawrence Berkeley National Laboratory Recent Work Title RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Permalink https://escholarship.org/uc/item/9f26h2cp Journal Applied and environmental microbiology, 83(14) ISSN 0099-2240 Authors Yu, Dianzhen Xia, Ming Zhang, Liping et al. Publication Date 2017-07-01 DOI 10.1128/aem.00709-17 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RpoN (σσ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain Dianzhen Yu,a,b Ming Xia,a,b Liping Zhang,a Yulong Song,a You Duan,a,b Tong Yuan,d,f Minjie Yao,c Liyou Wu,d Chunyuan Tian,e Zhenbin Wu,a Xiangzhen Li,c Jizhong Zhou,d Dongru Qiua Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Chinaa ; University of Chinese Academy of Sciences, Beijing, Chinab; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Chinac ; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAd; School of Life Sciences and Technology, Hubei Engineering University, Xiaogan, Chinae; College of Life Science, Henan Agricultural University, Zhengzhou, Chinaf ABSTRACT Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincola tertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. -
55Th Annual W.W.O.A. Conference October 5-8, 2021 La Crosse Convention Center, La Crosse Inside This Issue… 2021- 2022 W.W.O.A
VOL. 241, JUNE 2021 WISCONSIN WASTEWATER OPERATORS’ ASSOCIATION, INC. Aerial view of Jefferson Wastewater Treatment Plant, Jefferson, Wisconsin 55th Annual W.W.O.A. Conference October 5-8, 2021 La Crosse Convention Center, La Crosse Inside This Issue… 2021- 2022 W.W.O.A. OFFICIAL DIRECTORY • Presidents message / Page 3 Don Lintner Jenny Pagel President Director (2021) N2511 State Rd 57 Wastewater Foreman • Tribute to Tim Nennig / Page 4 New Holstein, WI 53061 City of Clintonville Cell: 920-418-3869 N9055 Cty Road M [email protected] Shiocton WI 54170 • City of Jefferson Wastewater / Page 6 Work: 715-823-7675 Rick Mealy Cell: 920-606-4634 President Elect [email protected] Independent Contractor Lab • Board meeting minutes & Regulatory Assistance April 2 and 3, 2020 / Page 17 319 Linden Lane Marc Stephanie Delavan WI 53115 Director (2020) Cell: 608-220-9457 Director of Public Works • Collection System seminars / Page 24 [email protected] Village of Valders 1522 Puritan Rd New Holstein WI 53061 Jeremy Cramer Work: 920-629-4970 • Board meeting minutes Vice President Wastewater Treatment Cell: 920-251-8100 March 19, 2020 / Page 25 Director [email protected] City of Sun Prairie Joshua Voigt 300 E Main Street • Reminder: Director (2022) Sun Prairie WI 53590 Direct Sales Representative Awards nominations / Page 26 Work: 608-825-0731 Flygt a Xylem Brand Cell: 608-235-9280 3894 Lake Drive jcramer@ Hartford WI 53027 • Troubleshooting Corner: cityofsunprairie.com Work: 262-506-2343 Zoogloea and Thauera / Page 27 Cell: 414-719-5567 [email protected] Jeff Smudde • Index of advertisers / Page 30 Past President Nate Tillis Director of Environmental Director (2022) Programs Maintenance Supervisor NEW Water (GBMSD) City of Waukesha 2231 N Quincy St. -
DGGE) and PGR Cloning of 16S Rrna Genes
THE UNIVERSITY OF NEW SOUTH thesis/Dissertation Sheet Surname or Family name:LE Rrst ^ I Other narne/s: Abbreviation for degree as given in the University calendar: MSc | ScliooliBiotechnolo^^^^^^ and Biomolecular ScienoBS Faculty: Science Title:Community analysis and physiological characterisation of bacterial isolates from a nitrifying membrane bioreactor Abstract This thesis focuses on the identification of early colonisers on membrane surfaces used in wastewater treatment, as well as the physiological characterisation of bacterial cultures isolated from different micro- environments of a membrane bioreactor (MBR). The bacterial community composition of early biofilms on membrane surfaces under different hydrodynamic conditions (pressurised and non-pressurised) and of the activated sludge in an MBR were examined by culture-independent, molecular-based methods of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and PGR cloning of 16S rRNA genes. A bench-scale, nitrifying MBR treating artificial waste was employed. The hollow fibre ultrafiltration membrane was made of polypropylene with an average pore diameter of 0.04 \im. Analysis of DGGE profiles of the sessile communities on membrane surfaces revealed that Tetrasphaera elongata species were important colonisers due to their ability to bind to membrane surfaces irrespective of the hydrodynamic context and exposure time. Interactions between isolates from the bioreactor and membrane surfaces were further investigated by characterising the physiological traits important in biofilm initiation and proliferation on membrane surfaces such as motility, auto-aggregation, co-aggregation, hydrophobicity and quorum sensing. Bacterial strains were isolated from floes and supernatant phases of the activated sludge as well as from pressurised membrane surfaces. Microbacterium sp. were prevalent in all culture collections. -
Cooperative Interaction of Janthinobacterium Sp. SLB01 and Flavobacterium Sp
International Journal of Molecular Sciences Article Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensis Ivan Petrushin 1,2,* , Sergei Belikov 1 and Lubov Chernogor 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; [email protected] (S.B.); [email protected] (L.C.) 2 Faculty of Business Communication and Informatics, Irkutsk State University, Irkutsk 664033, Russia * Correspondence: [email protected] Received: 31 August 2020; Accepted: 25 October 2020; Published: 30 October 2020 Abstract: Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition.