Eukaryota Fungi Bacteria
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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 -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
Acidovorax Citrulli
Bulletin OEPP/EPPO Bulletin (2016) 46 (3), 444–462 ISSN 0250-8052. DOI: 10.1111/epp.12330 European and Mediterranean Plant Protection Organization Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes PM 7/127 (1) Diagnostics Diagnostic PM 7/127 (1) Acidovorax citrulli Specific scope Specific approval and amendment This Standard describes a diagnostic protocol for Approved in 2016-09. Acidovorax citrulli.1 This Standard should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols. strain, were mainly isolated from non-watermelon, cucurbit 1. Introduction hosts such as cantaloupe melon (Cucumis melo var. Acidovorax citrulli is the causal agent of bacterial fruit cantalupensis), cucumber (Cucumis sativus), honeydew blotch and seedling blight of cucurbits (Webb & Goth, melon (Cucumis melo var. indorus), squash and pumpkin 1965; Schaad et al., 1978). This disease was sporadic until (Cucurbita pepo, Cucurbita maxima and Cucurbita the late 1980s (Wall & Santos, 1988), but recurrent epi- moschata) whereas Group II isolates were mainly recovered demics have been reported in the last 20 years (Zhang & from watermelon (Walcott et al., 2000, 2004; Burdman Rhodes, 1990; Somodi et al., 1991; Latin & Hopkins, et al., 2005). While Group I isolates were moderately 1995; Demir, 1996; Assis et al., 1999; Langston et al., aggressive on a range of cucurbit hosts, Group II isolates 1999; O’Brien & Martin, 1999; Burdman et al., 2005; Har- were highly aggressive on watermelon but moderately ighi, 2007; Holeva et al., 2010; Popovic & Ivanovic, 2015). aggressive on non-watermelon hosts (Walcott et al., 2000, The disease is particularly severe on watermelon (Citrullus 2004). -
Rivadalve Coelho Gonçalves Etiologia Da Mancha
RIVADALVE COELHO GONÇALVES ETIOLOGIA DA MANCHA BACTERIANA DO EUCALIPTO NO BRASIL Tese apresentada à Universidade Federal de Viçosa, como parte das exigências do Programa de Pós- Graduação em Fitopatologia, para obtenção do título de Doctor Scientiae. VIÇOSA MINAS GERAIS – BRASIL 2003 Ficha catalográfica preparada pela Seção de Catalogação e Classificação da Biblioteca Central da UFV T Gonçalves, Rivadalve Coelho, 1970- G635e Etiologia da mancha bacteriana do eucalipto no Brasil / 2003 Rivadalve Coelho Gonçalves. – Viçosa : UFV, 2003. xiii, 79f. : il. ; 29cm. Inclui apêndice. Orientador: Acelino Couto Alfenas. Tese (doutorado) - Universidade Federal de Viçosa. Inclui bibliografia. 1. Mancha bacteriana - Etiologia. 2. Xanthomonas. 3. Eucalipto - Doenças e pragas. I. Universidade Federal de Viçosa. II.Título. CDD 20.ed. 632.32 RIVADALVE COELHO GONÇALVES ETIOLOGIA DA MANCHA BACTERIANA DO EUCALIPTO NO BRASIL Tese apresentada à Universidade Federal de Viçosa, como parte das exigências do Programa de Pós- Graduação em Fitopatologia, para obtenção do título de Doctor Scientiae. APROVADA: 6 de novembro de 2003. _______________________________ _______________________________ Prof. Luiz Antonio Maffia Prof. José Rogério de Oliveira (Conselheiro) (Conselheiro) _______________________________ _______________________________ Prof. Júlio Cézar Mattos Cascardo Dr. Miguel Angel Dita Rodríguez _______________________________ Prof. Acelino Couto Alfenas (Orientador) Ao professor Acelino Couto Alfenas DEDICO ii AGRADECIMENTOS A Deus, provedor de vida, inteligência -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES .............................................................................................................................. -
Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax As Acidovorax Avenae Subsp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 107-119 Vol. 42, No. 1 0020-7713/92/010107-13$02 .OO/O Copyright 0 1992, International Union of Microbiological Societies Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov. , Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci A. WILLEMS,? M. GOOR, S. THIELEMANS, M. GILLIS,” K. KERSTERS, AND J. DE LEY Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit Gent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenue, Pseudomonas rubrilineans, “Pseudomonas setariae, ” Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudo- monas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenue. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenue and Acidovorax konjaci. Within Acidovorax avenue we distinguished the following three subspecies: Acidovorax avenue subsp. -
DEEPT Genomics) Reveals Misclassification of Xanthomonas Species Complexes Into Xylella, Stenotrophomonas and Pseudoxanthomonas
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. 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. Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification of Xanthomonas species complexes into Xylella, Stenotrophomonas and Pseudoxanthomonas Kanika Bansal1,^, Sanjeet Kumar1,$,^, Amandeep Kaur1, Shikha Sharma1, Prashant Patil1,#, Prabhu B. Patil1,* 1Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh. $Present address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. #Present address: Department of Microbiology, School of Medicine, University of Washington, Seattle, WA, USA. ^Equal Contribution *Corresponding author Running Title: Comprehensive phylo-taxono-genomics of Xanthomonas and its relatives. Correspondence: Prabhu B. Patil Email: [email protected] Principal Scientist CSIR- Institute of Microbial Technology Sector 39-A, Chandigarh, India- 160036 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. 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. Abstract Genus Xanthomonas encompasses specialized group of phytopathogenic bacteria with genera Xylella, Stenotrophomonas and Pseudoxanthomonas being its closest relatives. While species of genera Xanthomonas and Xylella are known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species of Stenotrophomonas are multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genus Pseudoxanthomonas and further in-depth comparative studies with publically available genome resources of other three genera. -
1 a Horizontally Acquired Expansin Gene Increases Virulence of the Emerging Plant
bioRxiv preprint doi: https://doi.org/10.1101/681643; this version posted July 2, 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 1 A horizontally acquired expansin gene increases virulence of the emerging plant 2 pathogen Erwinia tracheiphila 3 Jorge Rochaa,b*#, Lori R. Shapiroa,c*, Roberto Koltera 4 5 #Address correspondence to Jorge Rocha, [email protected] 6 a Department of Microbiology, Harvard Medical School, Boston MA. 7 b Present Address: Conacyt-Centro de Investigación y Desarrollo en Agrobiotecnología 8 Alimentaria, San Agustin Tlaxiaca, Mexico 9 c Present Address: Department of Applied Ecology, North Carolina State University, 10 Raleigh, NC 11 12 * JR and LRS contributed equally to this work. 13 Word count: Abstract 219, Main Text (Introduction, Results, Discussion) 4354 14 15 Running title: An expansin increases Erwinia tracheiphila virulence 16 #Address correspondence to Jorge Rocha, [email protected] 17 Keywords: expansin, virulence, glycoside hydrolase, Cucurbita, Erwinia, squash, plant 18 cell wall, cellulose, pectin, horizontal gene transfer, plant pathogen, xylem 19 20 Author Contributions: JR and LRS conceived of the study. JR designed and conducted 21 molecular protocols and lab experiments. LRS conducted computational analyses and 22 performed experiments. JR, LRS and RK interpreted experimental data. JR and LRS 23 wrote the first draft of the manuscript, and JR, LRS and RK added critical revisions. bioRxiv preprint doi: https://doi.org/10.1101/681643; this version posted July 2, 2019. -
Complete Assembly of the Genome of an Acidovorax Citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
fmicb-10-01400 June 19, 2019 Time: 15:19 # 1 ORIGINAL RESEARCH published: 20 June 2019 doi: 10.3389/fmicb.2019.01400 Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species Rongzhi Yang1, Diego Santos Garcia2, Francisco Pérez Montaño1,3, Gustavo Mateus da Silva1, Mei Zhao4, Irene Jiménez Guerrero1, Tally Rosenberg1, Gong Chen4, Inbar Plaschkes5, Shai Morin2, Ron Walcott4 and Saul Burdman1* 1 Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel, 2 Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel, 3 Department of Microbiology, University of Seville, Seville, Spain, 4 Department of Plant Pathology, University of Georgia, Athens, GA, United States, 5 Bioinformatics Unit, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel Edited by: Martin G. Klotz, Washington State University, Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat United States to cucurbit crop production worldwide. Based on genetic and phenotypic properties, Reviewed by: A. citrulli strains are divided into two major groups: group I strains have been generally Robert Wilson Jackson, isolated from melon and other non-watermelon cucurbits, while group II strains are University of Reading, United Kingdom closely associated with watermelon. In a previous study, we reported the genome Tingchang Zhao, of the group I model strain, M6. At that time, the M6 genome was sequenced by Chinese Academy of Agricultural Sciences, China MiSeq Illumina technology, with reads assembled into 139 contigs. -
A Comparative Genomics Study of the Genes Involved in the Catabolic Pathways of Naphthalene”
Título del Trabajo Final “Bacterial degradation of petroleum hydrocarbons; a comparative genomics study of the genes involved in the catabolic pathways of naphthalene” Nombre Estudiante: Athanasía Varsaki Plan de Estudios del Estudiante: Bioinformática Área del trabajo final: Microbiología, biotecnología y biología molecular Nombre Consultor/a: Paloma Pizarro Tobías Nombre Profesor/a responsable de la asignatura: Paloma Pizarro Tobías Fecha Entrega: 02/01/2018 Esta obra está sujeta a una licencia de Reconocimiento-NoComercial- SinObraDerivada 3.0 España de Creative Commons Licencias alternativas (elegir alguna de las siguientes y sustituir la de la página anterior) A) Creative Commons: Esta obra está sujeta a una licencia de Reconocimiento-NoComercial- SinObraDerivada 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-NoComercial-CompartirIgual 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-NoComercial 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-SinObraDerivada 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-CompartirIgual 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento 3.0 España de Creative Commons B) GNU Free Documentation License (GNU FDL) Copyright © AÑO TU-NOMBRE. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back- Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License". -
Seed Treatments for Control of Acidovorax Citrulli
Biological watermelon (Citrullus lanatus L.) seed treatments for control of Acidovorax citrulli Rachel Klein Major Project/Report submitted to the faculty of Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Master of Agriculture and Life Sciences In Plant Sciences and Pest Management Gregory E. Welbaum, School of Plant and Environmental Sciences Anton Baudoin, School of Plant and Environmental Sciences Jim Westwood, School of Plant and Environmental Sciences May 15, 2020 Blacksburg, VA Keywords: organic agriculture, cucurbits, watermelon, melon, bacterial fruit blotch, antimicrobial, antibacterial, catechin, green tea, seed treatment, Acidovorax citrulli 1 Contents Abstract…………………………………………………………….3 Introduction………………………………………………………..4 Purpose………………………………………………….………….7 Review of Literature………………………………………….…...7 Materials and Methods………………………….………….……10 Results....................................………………………………….....16 Discussion……………………………………………………...….27 References………………………………………...………………33 2 ABSTRACT Acidovorax citrulli is a seedborne pathogen responsible for bacterial fruit blotch (BFB), an economically important disease in melon and watermelon throughout the world. BFB is highly virulent and in affected fields can cause yield reduction of up to 95%, which has resulted in over $100,000 in losses to melon growers in some cases. The efficacy of green tea as an antimicrobial seed treatment against A. citrulli was tested. Watermelon seeds were treated with green tea after inoculation with transgenic A. citrulli expressing green fluorescent protein (GFP). Forty five percent of watermelon seedlings inoculated with a high level (OD600:1.0, ~8 x 108 cells/ml) of A. citrulli displayed GFP in their cotyledons. When these seeds were treated with green tea, only 11.2% displayed GFP in their cotyledons. None of the treated watermelon seedlings inoculated with a low level (OD600:0.001, ~8 x 105 cells/ml) of A. -
Molecular Characterisation of the Causal Agent of Bacterial Leaf Streak of Maize
Molecular characterisation of the causal agent of bacterial leaf streak of maize NJJ Niemann 21114900 Dissertation submitted in fulfilment of the requirements for the degree Magister Scientiae in Environmental Sciences at the Potchefstroom Campus of the North-West University Supervisor: Prof CC Bezuidenhout Co-supervisor: Prof BC Flett May 2015 Declaration I declare that this dissertation submitted for the degree of Master of Science in Environmental Sciences at the North-West University, Potchefstroom Campus, has not been previously submitted by me for a degree at this or any other university, that it is my own work in design and execution, and that all material contained herein has been duly acknowledged. __________________________ __________________ NJJ Niemann Date ii Acknowledgements Thank you God for giving me the strength and will to complete this dissertation. I would like to thank the following people: My father, mother and brother for all their contributions and encouragement. My family and friends for their constant words of motivation. My supervisors for their support and providing me with the platform to work independently. Stefan Barnard for his input and patience with the construction of maps. Dr Gupta for his technical assistance. Thanks to the following organisations: The Maize Trust, the ARC and the NRF for their financial support of this research. iii Abstract All members of the genus Xanthomonas are considered to be plant pathogenic, with specific pathovars infecting several high value agricultural crops. One of these pathovars, X. campestris pv. zeae (as this is only a proposed name it will further on be referred to as Xanthomonas BLSD) the causal agent of bacterial leaf steak of maize, has established itself as a widespread significant maize pathogen within South Africa.