Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
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Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts
Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts Carla Gonçalvesa and Paula Gonçalvesa,1 aApplied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 22, 2019 (received for review June 14, 2019) Horizontal acquisition of bacterial genes is presently recognized as nisms presumed to have facilitated a transition from bacterial an important contribution to the adaptation and evolution of operon transcription to eukaryotic-style gene expression were eukaryotic genomes. However, the mechanisms underlying ex- proposed, such as gene fusion giving rise to multifunctional pro- pression and consequent selection and fixation of the prokaryotic teins (6, 23, 24), increase in intergenic distances between genes to genes in the new eukaryotic setting are largely unknown. Here we generate room for eukaryotic promoters, and independent tran- show that genes composing the pathway for the synthesis of the scription producing mRNAs with poly(A) tails have been dem- essential vitamin B1 (thiamine) were lost in an ancestor of a yeast onstrated (22). In the best documented study, which concerns a lineage, the Wickerhamiella/Starmerella (W/S) clade, known to bacterial siderophore biosynthesis operon acquired by yeasts be- harbor an unusually large number of genes of alien origin. The longing to the Wickerhamiella/Starmerella (W/S) clade, the bacte- thiamine pathway was subsequently reassembled, at least twice, rial genes acquired as an operon were shown to be functional (22). by multiple HGT events from different bacterial donors involving Thiamine, commonly known as vitamin B1, is essential for all both single genes and entire operons. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Genetic Diversity of Bartonella Species in Small Mammals in the Qaidam
www.nature.com/scientificreports OPEN Genetic diversity of Bartonella species in small mammals in the Qaidam Basin, western China Huaxiang Rao1, Shoujiang Li3, Liang Lu4, Rong Wang3, Xiuping Song4, Kai Sun5, Yan Shi3, Dongmei Li4* & Juan Yu2* Investigation of the prevalence and diversity of Bartonella infections in small mammals in the Qaidam Basin, western China, could provide a scientifc basis for the control and prevention of Bartonella infections in humans. Accordingly, in this study, small mammals were captured using snap traps in Wulan County and Ge’ermu City, Qaidam Basin, China. Spleen and brain tissues were collected and cultured to isolate Bartonella strains. The suspected positive colonies were detected with polymerase chain reaction amplifcation and sequencing of gltA, ftsZ, RNA polymerase beta subunit (rpoB) and ribC genes. Among 101 small mammals, 39 were positive for Bartonella, with the infection rate of 38.61%. The infection rate in diferent tissues (spleens and brains) (χ2 = 0.112, P = 0.738) and gender (χ2 = 1.927, P = 0.165) of small mammals did not have statistical diference, but that in diferent habitats had statistical diference (χ2 = 10.361, P = 0.016). Through genetic evolution analysis, 40 Bartonella strains were identifed (two diferent Bartonella species were detected in one small mammal), including B. grahamii (30), B. jaculi (3), B. krasnovii (3) and Candidatus B. gerbillinarum (4), which showed rodent-specifc characteristics. B. grahamii was the dominant epidemic strain (accounted for 75.0%). Furthermore, phylogenetic analysis showed that B. grahamii in the Qaidam Basin, might be close to the strains isolated from Japan and China. -
Phyllosphere Microbiome
http://researchcommons.waikato.ac.nz/ Research Commons at the University of Waikato Copyright Statement: The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). The thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: Any use you make of these documents or images must be for research or private study purposes only, and you may not make them available to any other person. Authors control the copyright of their thesis. You will recognise the author’s right to be identified as the author of the thesis, and due acknowledgement will be made to the author where appropriate. You will obtain the author’s permission before publishing any material from the thesis. Environmental and biogeographical drivers of the Leptospermum scoparium (mānuka) phyllosphere microbiome A thesis submitted in partial fulfilment of the requirements for the degree of Master of Science (Research) at The University of Waikato by Anya Sophia Noble 2018 ii Abstract A substantial body of research exists on the physiology and genetics of Leptospermum scoparium (mānuka); however, the mānuka phyllosphere has not yet been investigated. This research, therefore, provides the first exploration of the bacterial communities comprising the mānuka phyllosphere. In total, 89 samples were collected from five native mānuka forests during the November 2016 – January 2017 mānuka flowering season, and examined alongside spatial, environmental, and host- tree related metadata. Cultivation-independent methods, including DNA extraction and 16S rRNA gene PCR amplicon sequencing analysis, were used to characterise phyllosphere communities. Using a combination of statistical tests, the BLAST algorithm, and a PICRUSt analysis, a habitat-specific core microbiome comprising members of Acidobacteria, Alphaproteobacteria, Bacteroidetes, and Verrucomicrobia, was present in all samples. -
Novel Small Rnas Expressed by Bartonella Bacilliformis Under Multiple Conditions 2 Reveal Potential Mechanisms for Persistence in the Sand Fly Vector and Human 3 Host
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.04.235903; this version posted August 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 4.0 International license. 1 Novel small RNAs expressed by Bartonella bacilliformis under multiple conditions 2 reveal potential mechanisms for persistence in the sand fly vector and human 3 host 4 5 6 Shaun Wachter1, Linda D. Hicks1, Rahul Raghavan2 and Michael F. Minnick1* 7 8 9 10 1 Program in Cellular, Molecular & Microbial Biology, Division of Biological Sciences, 11 University of Montana, Missoula, Montana, United States of America 12 2 Department of Biology and Center for Life in Extreme Environments, Portland State 13 University, Portland, Oregon, United States of America 14 15 16 17 * Corresponding author 18 E-mail: [email protected] (MFM) 19 20 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.04.235903; this version posted August 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 4.0 International license. 21 Abstract 22 Bartonella bacilliformis, the etiological agent of Carrión’s disease, is a Gram-negative, 23 facultative intracellular alphaproteobacterium. Carrión’s disease is an emerging but neglected 24 tropical illness endemic to Peru, Colombia, and Ecuador. B. bacilliformis is spread between 25 humans through the bite of female phlebotomine sand flies. -
09 Piqueras.Qxp
PERSPECTIVES INTERNATIONAL MICROBIOLOGY (2007) 10:217-226 DOI: 10.2436/20.1501.01.30 ISSN: 1139-6709 www.im.microbios.org Microbiology: a dangerous profession? Mercè Piqueras President, Catalan Association for Science Communication (ACCC), Barcelona, Spain The history of science contains many cases of researchers eases in Minorca from the year 1744 to 1749 to which is pre- who have died because of their professional activity. In the fixed, a short account of the climate, productions, inhabi- field of microbiology, some have died or have come close to tants, and endemical distempers of that island (T. Cadell, D. death from infection by agents that were the subject of their Wilson and G. Nicol, London, 1751), which he dedicated to research (Table 1). Infections that had a lethal outcome were the Society of Surgeons of His Majesty’s Royal Navy. usually accidental. Sometimes, however, researchers inocu- Minorcan historian of science Josep M. Vidal Hernández has lated themselves with the pathogen or did not take preventive described and carefully analyzed Cleghorn’s work in measures against the potential pathogen because they wanted Minorca and his report [43]. According to Vidal, what to prove their hypotheses—or disprove someone else’s— Cleghorn describes is “tertian” fever, which was the name regarding the origin of the infection. Here is an overview of given at the time to fever caused by malaria parasites with a several episodes in the history of microbiology since the mid periodicity of 48 hours. In fact, Cleghorn used quinine to nineteenth century involving researchers or workers in fields treat tertian fever (i.e, malaria), which was not eradicated related to microbiology who have become infected. -
Azorhizobium Doebereinerae Sp. Nov
ARTICLE IN PRESS Systematic and Applied Microbiology 29 (2006) 197–206 www.elsevier.de/syapm Azorhizobium doebereinerae sp. Nov. Microsymbiont of Sesbania virgata (Caz.) Pers.$ Fa´tima Maria de Souza Moreiraa,Ã, Leonardo Cruzb,Se´rgio Miana de Fariac, Terence Marshd, Esperanza Martı´nez-Romeroe,Fa´bio de Oliveira Pedrosab, Rosa Maria Pitardc, J. Peter W. Youngf aDepto. Cieˆncia do solo, Universidade Federal de Lavras, C.P. 3037 , 37 200–000, Lavras, MG, Brazil bUniversidade Federal do Parana´, C.P. 19046, 81513-990, PR, Brazil cEmbrapa Agrobiologia, antiga estrada Rio, Sa˜o Paulo km 47, 23 851-970, Serope´dica, RJ, Brazil dCenter for Microbial Ecology, Michigan State University, MI 48824, USA eCentro de Investigacio´n sobre Fijacio´n de Nitro´geno, Universidad Nacional Auto´noma de Mexico, Apdo Postal 565-A, Cuernavaca, Mor, Me´xico fDepartment of Biology, University of York, PO Box 373, York YO10 5YW, UK Received 18 August 2005 Abstract Thirty-four rhizobium strains were isolated from root nodules of the fast-growing woody native species Sesbania virgata in different regions of southeast Brazil (Minas Gerais and Rio de Janeiro States). These isolates had cultural characteristics on YMA quite similar to Azorhizobium caulinodans (alkalinization, scant extracellular polysaccharide production, fast or intermediate growth rate). They exhibited a high similarity of phenotypic and genotypic characteristics among themselves and to a lesser extent with A. caulinodans. DNA:DNA hybridization and 16SrRNA sequences support their inclusion in the genus Azorhizobium, but not in the species A. caulinodans. The name A. doebereinerae is proposed, with isolate UFLA1-100 ( ¼ BR5401, ¼ LMG9993 ¼ SEMIA 6401) as the type strain. -
Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. -
Bartonella Henselae Detected in Malignant Melanoma, a Preliminary Study
pathogens Article Bartonella henselae Detected in Malignant Melanoma, a Preliminary Study Marna E. Ericson 1, Edward B. Breitschwerdt 2 , Paul Reicherter 3, Cole Maxwell 4, Ricardo G. Maggi 2, Richard G. Melvin 5 , Azar H. Maluki 4,6 , Julie M. Bradley 2, Jennifer C. Miller 7, Glenn E. Simmons, Jr. 5 , Jamie Dencklau 4, Keaton Joppru 5, Jack Peterson 4, Will Bae 4, Janet Scanlon 4 and Lynne T. Bemis 5,* 1 T Lab Inc., 910 Clopper Road, Suite 220S, Gaithersburg, MD 20878, USA; [email protected] 2 Intracellular Pathogens Research Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; [email protected] (E.B.B.); [email protected] (R.G.M.); [email protected] (J.M.B.) 3 Dermatology Clinic, Truman Medical Center, University of Missouri, Kansas City, MO 64108, USA; [email protected] 4 Department of Dermatology, University of Minnesota, Minneapolis, MN 55455, USA; [email protected] (C.M.); [email protected] (A.H.M.); [email protected] (J.D.); [email protected] (J.P.); [email protected] (W.B.); [email protected] (J.S.) 5 Department of Biomedical Sciences, Duluth Campus, Medical School, University of Minnesota, Duluth, MN 55812, USA; [email protected] (R.G.M.); [email protected] (G.E.S.J.); [email protected] (K.J.) 6 Department of Dermatology, College of Medicine, University of Kufa, Kufa 54003, Iraq 7 Galaxy Diagnostics Inc., Research Triangle Park, NC 27709, USA; [email protected] Citation: Ericson, M.E.; * Correspondence: [email protected]; Tel.: +1-720-560-0278; Fax: +1-218-726-7906 Breitschwerdt, E.B.; Reicherter, P.; Maxwell, C.; Maggi, R.G.; Melvin, Abstract: Bartonella bacilliformis (B. -
Bartonella Spp. Infection Rate and B. Grahamii in Ticks
LETTERS 8. Reif KE, Macaluso KR. Ecology which is common in Europe, may nlm.nih.gov/Blast.cgi) comparison to of Rickettsia felis: a review. J Med also transmit zoonotic Bartonella spp. published sequences. Entomol. 2009;46:723–36. http://dx.doi. org/10.1603/033.046.0402 Evidence of possible tick transmission On the basis of the amplicon- 9. Reif KE, Stout RW, Henry GC, Foil LD, of bartonellae to humans under natural specifi c melting temperature and DNA Macaluso KR. Prevalence and infection conditions was provided by Eskow et bands representing the specifi c size load dynamics of Rickettsia felis in al. (3) and Angelakis et al. (4), who of 249-bp after gel electrophoresis, actively feeding cat fl eas. PLoS ONE. 2008;3:e2805. http://dx.doi.org/10.1371/ identifi ed Bartonella spp. in tissue results of qPCR showed 100 (4.76%) journal.pone.0002805 samples of patients who were recently infected I. ricinus ticks (Table). 10. Mitchell CJ. The role of Aedes albopictus bitten by ticks. We determined the Positive results did not vary by as an arbovirus vector. Parassitologia. prevalence of Bartonella spp. in developmental tick stages; 4.84% 1995;37:109–13. questing I. ricinus ticks in the city (18/372) adult ticks (5.08% [9/177] Address for correspondence: Didier Raoult, of Hanover, Germany, which is female and 4.62% [9/195] male), URMITE, UMR CNRS 7278, IRD 198, nicknamed The Green Metropolis and 4.71% (80/1,698) nymphs, and 6.67% INSERM 1095, Faculté de Médecine, 27 Bd was selected the German Capital of (2/30) larvae were infected (Table). -
(12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub
US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae -
Microbial Community Composition During Degradation of Organic Matter
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Bodenökologie Microbial community composition during degradation of organic matter Stefanie Elisabeth Wallisch Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Göttlein Prüfer der Dissertation: 1. Hon.-Prof. Dr. M. Schloter 2. Univ.-Prof. Dr. S. Scherer Die Dissertation wurde am 14.04.2015 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 03.08.2015 angenommen. Table of contents List of figures .................................................................................................................... iv List of tables ..................................................................................................................... vi Abbreviations .................................................................................................................. vii List of publications and contributions .............................................................................. viii Publications in peer-reviewed journals .................................................................................... viii My contributions to the publications ....................................................................................... viii Abstract