Microbial Dynamics in the Aquatic Environments of a Nuclear Reactor
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Proquest Dissertations
Approaches to assessing microbial communities in soil, two examples: Biosurfactant production and phenanthrene degradation Item Type text; Dissertation-Reproduction (electronic) Authors Bodour, Adria Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 01/10/2021 06:55:39 Link to Item http://hdl.handle.net/10150/280136 INFORMATION TO USERS This manuscript has been reproduced from the microfiinn 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 corner and continuing from left to right in equal -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Afipia Clevelandensis Sp
JOURNAL OF CLINICAL MICROBIOLOGY, Nov. 1991, p. 2450-2460 Vol. 29, No. 11 0095-1137/91/112450-11$02.00/0 Copyright © 1991, American Society for Microbiology Proposal of Afipia gen. nov., with Afipia felis sp. nov. (Formerly the Cat Scratch Disease Bacillus), Afipia clevelandensis sp. nov. (Formerly the Cleveland Clinic Foundation Strain), Afipia broomeae sp. nov., and Three Unnamed Genospecies DON J. BRENNER,'* DANNIE G. HOLLIS,' C. WAYNE MOSS,' CHARLES K. ENGLISH,2 GERALDINE S. HALL,3 JUDY VINCENT,4 JON RADOSEVIC,5 KRISTIN A. BIRKNESS,1 WILLIAM F. BIBB,' FREDERICK D. QUINN,' B. SWAMINATHAN,1 ROBERT E. WEAVER,' MICHAEL W. REEVES,' STEVEN P. O'CONNOR,6 PEGGY S. HAYES,' FRED C. TENOVER,7 ARNOLD G. STEIGERWALT,' BRADLEY A. PERKINS,' MARYAM I. DANESHVAR,l BERTHA C. HILL,7 JOHN A. WASHINGTON,3 TONI C. WOODS,' SUSAN B. HUNTER,' TED L. HADFIELD,2 GLORIA W. AJELLO,1 ARNOLD F. KAUFMANN,8 DOUGLAS J. WEAR,2 AND JAY D. WENGER' Meningitis and Special Pathogens Branch,' Respiratory Diseases Branch,6 and Bacterial Zoonoses Activity,8 Division of Bacterial and Mycotic Diseases, and Hospital Infections Program,7 Center for Infectious Diseases, Centers for Disease Control, Atlanta, Georgia 30333; Department ofInfectious and Parasitic Diseases Pathology, Armed Forces Institute ofPathology, Washington, DC 20306-60002; Department of Microbiology, Cleveland Clinic Foundation, Cleveland, Ohio 441953; Department ofPediatrics, Tripler Army Medical Center, Tripler AMC, Hawaii 968594; and Indiana State Board of Health, Disease Control Laboratory Division, Indianapolis, Indiana 46206-19645 Received 3 June 1991/Accepted 5 August 1991 On the basis of phenotypic characterization and DNA relatedness determinations, the genus Afipia gen. -
Genome Sequencing and Annotation of Afipia Septicemium Strain OHSU II
ÔØ ÅÒÙ×Ö ÔØ Genome sequencing and annotation of Afipia septicemium strain OHSU II Philip Yang, Guo-Chiuan Hung, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai, Shyh-Ching Lo PII: S2213-5960(14)00033-6 DOI: doi: 10.1016/j.gdata.2014.06.001 Reference: GDATA 43 To appear in: Genomics Data Received date: 13 May 2014 Revised date: 2 June 2014 Accepted date: 2 June 2014 Please cite this article as: Philip Yang, Guo-Chiuan Hung, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai, Shyh-Ching Lo, Genome sequencing and annotation of Afipia septicemium strain OHSU II, Genomics Data (2014), doi: 10.1016/j.gdata.2014.06.001 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT Data in Brief Title: Genome sequencing and annotation of Afipia septicemium strain OHSU_II Authors: Philip Yang1, Guo-Chiuan Hung1, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai and Shyh-Ching Lo* 1 Both are first authors, equally contributed * Corresponding author Tel/Fax +1-301-827-3170/+1-301-827-0449 Email address: [email protected] Affiliations: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA Abstract We report the 5.1 Mb noncontiguous draft genome of Afipia septicemium strain OHSU_II, isolated from blood of a female patient. -
Periodontite Crônica Generalizada (PCG) E Periodontite Agressiva Generalizada (PAG) Para Avaliar Diferenças Entre Suas Microbiotas
SÉRGIO EDUARDO BRAGA DA CRUZ ANÁLISE BIOMOLECULAR DE COMUNIDADES MICROBIANAS SUBGENGIVAIS ASSOCIADAS ÀS PERIODONTITES CRÔNICA E AGRESSIVA GENERALIZADAS Tese apresentada à Faculdade de Odontologia de Piracicaba, da Universidade Estadual de Campinas, para obtenção do Título de Doutor em Biologia Buco-Dental, área de Microbiologia Oral e Imunologia. Orientador: Prof. Dr. Reginaldo Bruno Gonçalves Co-orientador: Prof. Dr. Daniel Saito PIRACICABA, 2010 I II Dedico este trabalho aos meus pais Marilene e João Batista que sempre me apoiaram em todos meus momentos e decisões e por todo amor que sempre me deram. Vocês serão sempre exemplos de vida, dignidade, luta e honra! Às minhas irmãs Monalisa e Renata Karina pela amizade, carinho e amor. Muito obrigado! Eu vos amo! III AGRADECIMENTOS Agradeço a Deus, por cada dia a mim oferecido e pelas oportunidades que tenho a cada dia para crescer e aprender. Ao Prof. Dr. Reginaldo Bruno Gonçalves, meus sinceros e eternos agradecimentos pela orientação, pelo exemplo de batalha profissional, e por todo apoio aqui no Brasil e no Canadá. Ao Prof. Dr. Daniel Saito por todo apoio, co-orientação, ensinamentos e ajuda durante o meu doutorado. Ao Prof. Dr. José Franciso Höfling pelos ensinamentos e conhecimentos laboratoriais e por todo apoio oferecido. À Profª. Drª. Renata de Oliveira Mattos-Graner pelos conhecimentos repassados, pela orientação durante o meu programa de estágio docente (PED) e por todo apoio. Ao Rafael Nóbrega Stipp pela amizade, companheirismo, exemplo profissional, por todos os ensinamentos na área de biologia molecular e microbiologia e, obviamente, pelos grandes momentos de churrascos que em muito fizeram minha história aqui em Piracicaba. -
Isolation of Novel Afipia Septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium Sp
Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses Shyh-Ching Lo1*, Guo-Chiuan Hung1, Bingjie Li1, Haiyan Lei1, Tianwei Li1, Kenjiro Nagamine1¤, Jing Zhang1, Shien Tsai1, Richard Bryant2 1 Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America, 2 Department of Infectious Diseases, Oregon Health and Science University, Portland, Oregon, United States of America Abstract Cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. We re-initiated a set of 3 cultures for analysis of the "uncultivable" or poorly- grown microbes using NGS technology. Broth of cultures from 3 blood samples, submitted from OHSU between 2000 and 2004, were inoculated into culture flasks containing fresh modified SP4 medium and kept at room temperature (RT), 30uC and 35uC. The cultures showing evidence of microbial growth were expanded and subjected to DNA analysis by genomic sequencing using Illumina MiSeq. Two of the 3 re-initiated blood cultures kept at RT after 7–8 weeks showed evidence of microbial growth that gradually reached into a cell density with detectable turbidity. The microbes in the broth when streaked on SP4 agar plates produced microscopic colonies in , 2 weeks. Genomic studies revealed that the microbes isolated from the 2 blood cultures were a novel Afipia species, tentatively named Afipia septicemium. -
A Novel Pathway Producing Dimethylsulphide in Bacteria Is Widespread in Soil Environments
ARTICLE Received 26 Sep 2014 | Accepted 9 Feb 2015 | Published 25 Mar 2015 DOI: 10.1038/ncomms7579 A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments O. Carrio´n1, A.R.J. Curson2, D. Kumaresan3,Y.Fu4, A.S. Lang4, E. Mercade´1 & J.D. Todd2 The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterization of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments and could represent a shift from the notion that DMSP is the only significant precursor of DMS. 1 Laboratori de Microbiologia, Facultat de Farma`cia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain. 2 School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK. 3 School of Earth and Environment, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia. 4 Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St John’s, Newfoundland and Labrador, A1B 3X9, Canada. -
Investigation of Geosmin Removal Efficiency by Microorganism Isolated from Biological Activated Carbon 생물활성탄에서 분리한 미생물의 지오스민 제거효율 평가
ISSN(Print): 1225-7672 / ISSN(Online): 2287-822X DOI http://dx.doi.org/10.11001/jksww.2015.29.1.047 Investigation of geosmin removal efficiency by microorganism isolated from biological activated carbon 생물활성탄에서 분리한 미생물의 지오스민 제거효율 평가 Dawoon Baek1・Jaewon Lim1・Yoonjung Cho1・Yong-Tae Ahn2・Hyeyoung Lee1・ Donghee Park2・Dongju Jung3・Tae-Ue Kim1* 백다운1・임재원1・조윤정1・안용태2・이혜영1・박동희2・정동주3・김태우1* 1Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Kangwon-do, 220-710, Republic of Korea 2Department of Environmental Engineering, Yonsei University, Wonju, Kangwon-do, 220-710, Republic of Korea 3Department of Biomedical Laboratory Science, College of Natural Sciences, Hoseo University, Asan, Chungcheongnam-do 336-795, Republic of Korea 1연세대학교 보건과학대학 임상병리학과, 2연세대학교 보건과학대학 환경공학과, 3호서대학교 자연과학대학 임상병리학과 ABSTRACT Recently, the production of taste and odor (T&O) compounds is a common problem in water industry. Geosmin is one of the T&O components in drinking water. However, geosmin is hardly eliminated through the conventional water treatment systems. Among various advanced processes capable of removing geosmin, adsorption process using granular activated carbon (GAC) is the most commonly used process. As time passes, however GAC process changes into biological activated carbon (BAC) process. There is little information on the BAC process in the literature. In this study, we isolated and identified microorganisms existing within various BAC processes. The microbial concentrations of BAC processes examined were 3.5×105 colony forming units (CFU/g), 2.2×106 CFU/g and 7.0×105 CFU/g in the Seongnam plant, Goyang plant and Goryeong pilot plant, respectively. -
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated
bioRxiv preprint doi: https://doi.org/10.1101/776849; this version posted September 20, 2019. 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-ND 4.0 International license. 1 Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated 2 Study of a Serpentinization-Influenced Aquifer 3 4 L.M. Seyler, W.J. Brazelton, C. McLean, L.I. Putman, A. Hyer, M.D.Y. Kubo, T. Hoehler, D. 5 Cardace, M.O. Schrenk 6 7 Abstract 8 Serpentinization is a low-temperature metamorphic process by which ultramafic rock 9 chemically reacts with water. These reactions provide energy and materials that may be 10 harnessed by chemosynthetic microbial communities at hydrothermal springs and in the 11 subsurface. However, the biogeochemistry of microbial populations that inhabit these 12 environments are understudied and are complicated by overlapping biotic and abiotic processes. 13 We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to 14 environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), 15 a subsurface observatory consisting of twelve wells drilled into the ultramafic and serpentinite 16 mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA 17 sequence data and mass spectrometry data, we determined that several carbon assimilation 18 strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the 19 reductive acetyl-CoA pathway, and methylotrophy are used by the microbial communities 20 inhabiting the serpentinite-hosted aquifer. -
Quantitative PCR Analysis of the Bartonella Henselae Card Gene During Bacterial Stress
Quantitative PCR Analysis of the Bartonella henselae carD Gene during Bacterial Stress Jacob Simmonds A thesis submitted to the Victoria University of Wellington in fulfilment for the degree of Master of Science Victoria University of Wellington Te Whare Wānanga o te Ūpoko o te Ika a Māui 2016 Abstract The Bartonella genus is comprised of arthropod-borne, intracellular bacterial pathogens that colonise the mammalian bloodstream. A large number of mammalian species are hosts for one or more Bartonella species, as either reservoir or incidental hosts. Bartonella species are only able to invade and replicate in host red blood cells in the reservoir host, and to be taken up by an associated haematophagous arthropod vector to complete transmission and the bacterial life cycle. Humans are the reservoir hosts for B. quintana and B. bacilliformis, and are incidental hosts for more than 16 additional zoonotic Bartonella species, including B. henselae, which is normally carried by cats. B. henselae infection, usually acquired through cat scratches or bites, can result in several clinical manifestations, with varying degrees of severity; the most common of these is cat scratch disease, where symptoms commonly range from enlarged lymph nodes to severe fever. Although usually a mild illness, B. henselae infection can occasionally lead to severe symptoms, affecting neurological and other major organ systems. During their life cycle the Bartonellae must adapt to various toxic host environments; such adaptation is mediated by several bacterial stress pathways, which modify bacterial transcription. However, many gaps remain in the understanding of B. henselae stress response pathways. The object of this study, the carD gene, was identified as a possible component of the Bartonella stress response. -
The Microbiology of Lean and Obese Soil
The microbiology of lean and obese soil Frances Patricia Jones September 2016 Department of Geography and Environmental Science, University of Reading, UK Department of AgroEcology, Rothamsted Research, UK Submitted in partial fulfilment of the requirement for the degree of Doctor of Philosophy Abstract The bacterial genus Bradyrhizobium is biologically important within soils, with different representatives found to perform a range of functions including nitrogen fixation through symbioses, photosynthesis and denitrification. The Highfield experiment at Rothamsted provides an opportunity to study the impact of plants on microbial communities as it has three long-term contrasting regimes; permanent grassland, arable and bare fallow (devoid of plants). The bare fallow plots have a significant reduction in soil carbon and microbial biomass. Bradyrhizobium has been shown by metagenomic studies on soil to be one of the most abundant and active groups including in bare fallow soil indicating that some phenotypes are adapted to survive in the absence of plants. A culture collection was created with isolates obtained from contrasting soil types from Highfield in addition to woodland soil, gorse (Ulex europeaus) and broom (Cytisus scoparius) root nodules. The collection’s phylogeny has been explored by sequencing housekeeping genes to determine whether soil treatment affects the core genome. One grassland and one bare fallow isolate had their genome sequenced and differences have been assessed to establish their potential for a range of functions and to direct future experiments. The functional diversity of the collection has been investigated using carbon metabolism assays to identify key substrates and determine whether the isolates group according to soil treatment. -
Oxidizing Bacteria Are Prevalent in Drinking Water Systems
Environmental Microbiology Reports (2017) 9(2), 120–128 doi:10.1111/1758-2229.12508 Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems Daniel N. Marcus,1,2 Ameet Pinto,3 how microbial communities influence the quality of Karthik Anantharaman,1 Steven A. Ruberg,4 drinking water. Eva L. Kramer,1 Lutgarde Raskin2 and Gregory J. Dick1* 1Department of Earth and Environmental Science, Introduction University of Michigan, Ann Arbor, MI, USA. The presence of manganese (Mn) in source waters 2Department of Civil and Environmental Engineering, used for drinking water (DW) production is a common University of Michigan, Ann Arbor, MI, USA. concern, primarily due to the impact of Mn on the aes- 3Department of Civil and Environmental Engineering, thetic quality of finished water (Kohl and Medlar, 2006). Northeastern University, Boston, MA, USA. Mn is regulated by the U.S. Environmental Protection 4Great Lakes Environmental Research Laboratory, Agency at a nonenforceable secondary maximum con- National Oceanic and Atmospheric Administration, taminant level (MCL) of 0.05 mg/l (EPA, 2013). Regard- Ann Arbor, MI, USA less of the possible direct effects of Mn on human health (Bouchard et al., 2011; Khan et al., 2012), the Summary presence of Mn oxides in DW can strongly alter other aspects of water chemistry (Tebo et al., 2004), thus they Manganese (Mn) oxides are highly reactive minerals may indirectly influence the quality of DW. that influence the speciation, mobility, bioavailability Mn oxides can rapidly oxidize other metals and metal- and toxicity of a wide variety of organic and inorganic loids (metal(loid)s hereafter), affecting their speciation, compounds.