Comparative Evaluation of Four Bacteria-Specific Primer Pairs For
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Proposed Minimal Standards for Describing New Genera and Species of the Suborder Micrococcineae
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1823–1849 DOI 10.1099/ijs.0.012971-0 Proposed minimal standards for describing new genera and species of the suborder Micrococcineae Peter Schumann,1 Peter Ka¨mpfer,2 Hans-Ju¨rgen Busse 3 and Lyudmila I. Evtushenko4 for the Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, P. Schumann 38124 Braunschweig, Germany [email protected] 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t, 35392 Giessen, Germany 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria 4All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Moscow Region 142290, Russia The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names. INTRODUCTION Aureobacterium and Rothia/Stomatococcus) and one pair of homotypic synonyms (Pseudoclavibacter/Zimmer- The suborder Micrococcineae was established by mannella) (Table 1 and http://www.the-icsp.org/taxa/ Stackebrandt et al. -
Schumannella Luteola Gen. Nov., Sp. Nov., a Novel Genus of the Family Microbacteriaceae
J. Gen. Appl. Microbiol., 54, 253‒258 (2008) Full Paper Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae Sun-Young An*, Tian Xiao, and Akira Yokota Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113‒0032, Japan (Received February 28, 2008; Accepted June 24, 2008) An actinobacterial strain KHIAT, isolated from lichen in Tokyo, was taxonomically characterized using a polyphasic approach. The isolate is a Gram-positive, anaerobic, non-motile and rod- shaped bacterium. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolate is represented as an independent lineage distinctive from the Microbacteriaceae genera. The G+C content of DNA was 58.7 mol%. The chemotaxonomic characteristics of the isolate are cell wall peptidoglycan type (2,4-diaminobutyric acid), major cellular fatty acids (anteiso-C15:0 and iso-C16:0) and quinone type (MK-11 and MK-10). On the basis of the phenotypic and phyloge- netic distinctness, it is proposed that strain KHIAT represents a novel species in a new genus of the family Microbacteriaceae, Schumannella luteola gen. nov., sp. nov. The type strain is KHIAT (=JCM 23215T=TISTR 1824T). Key Words—Schumannella luteola gen. nov., sp. nov. Introduction butyric acid in the cell wall. Analyses of the 16S rRNA gene sequences from strain KHIAT showed that it was The family Microbacteriaceae currently contains 24 related to genera such as Leifsonia, Rhodoglobus, and genera, which are characterized by unsaturated major Salinibacterium of the family Microbacteriaceae. menaquinones (Collins and Jones, 1981) and B-type The aim of the present study is to elucidate the taxo- peptidoglycan (Park et al., 1993; Schleifer and Kan- nomic position of the isolate, using polyphasic taxon- dler, 1972; Stackebrandt et al., 1997). -
Systematic Research on Actinomycetes Selected According
Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals. -
Of Bergey's Manual
BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B Michael Goodfellow, Peter Kämpfer, Hans-Jürgen Busse, Martha E. Trujillo, Ken-ichiro Suzuki, Wolfgang Ludwig and William B. Whitman EDITORS, VOLUME FIVE William B. Whitman DIRECTOR OF THE EDITORIAL OFFICE Aidan C. Parte MANAGING EDITOR EDITORIAL BOARD Fred A. Rainey, Chairman, Peter Kämpfer, Vice Chairman, Paul De Vos, Jongsik Chun, Martha E. Trujillo and William B. Whitman WITH CONTRIBUTIONS FROM 116 COLLEAGUES William B. Whitman Bergey’s Manual Trust Department of Microbiology 527 Biological Sciences Building University of Georgia Athens, GA 30602-2605 USA ISBN 978-0-387-95043-3 ISBN 978-0-387-68233-4 (eBook) DOI 10.1007/978-0-387-68233-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012930836 © 2012, 1984–1989 Bergey’s Manual Trust Bergey’s Manual is a registered trademark of Bergey’s Manual Trust. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. -
Plantibacter Flavus Strain 251, Increased A
Identification of Plant Growth-Promoting Bacterial Endophytes Using Culture-Dependent In Vitro and Laboratory In Planta Methods by Evan Mayer A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Cell and Systems Biology University of Toronto ©Copyright by Evan Mayer 2019 Identification of Plant Growth-Promoting Bacterial Endophytes Using Culture-Dependent In Vitro and Laboratory In Planta Methods Evan Mayer Master of Science Cell and Systems Biology University of Toronto 2019 Abstract This study examined a collection of 220 bacterial endophytes isolated from herbaceous plants growing in petroleum-contaminated soils for plant growth promotion abilities. 12% of endophytes tested induced statistically significant growth benefits in Arabidopsis. The strongest plant growth promoting endophyte, Plantibacter flavus strain 251, increased A. thaliana fresh biomass and total root length by 4.7 and 5.8 times respectively over control plants and contained genes for auxin and ACC deaminase production. In vitro tests showed that 26% of endophytes from 19 different genera were potentially capable of nitrogen fixation, while 42% of endophytes from 16 different genera were capable of phosphate solubilization. Of the potential nitrogen fixers, 80% demonstrated free-living nitrogen fixation capability when grown in nitrogen-free media. None of the three endophytes tested improved Arabidopsis tolerance to drought stress. Overall, this study showed that a large variety of bacterial endophytes are capable of direct plant growth promotion. ii Acknowledgements I would like to thank my supervisor, Roberta Fulthorpe, for giving me the opportunity to not just get a Master’s degree, but to also grow as a person. -
Actinobacterial Diversity in Atacama Desert Habitats As a Road Map to Biodiscovery
Actinobacterial Diversity in Atacama Desert Habitats as a Road Map to Biodiscovery A thesis submitted by Hamidah Idris for the award of Doctor of Philosophy July 2016 School of Biology, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom Abstract The Atacama Desert of Northern Chile, the oldest and driest nonpolar desert on the planet, is known to harbour previously undiscovered actinobacterial taxa with the capacity to synthesize novel natural products. In the present study, culture-dependent and culture- independent methods were used to further our understanding of the extent of actinobacterial diversity in Atacama Desert habitats. The culture-dependent studies focused on the selective isolation, screening and dereplication of actinobacteria from high altitude soils from Cerro Chajnantor. Several strains, notably isolates designated H9 and H45, were found to produce new specialized metabolites. Isolate H45 synthesized six novel metabolites, lentzeosides A-F, some of which inhibited HIV-1 integrase activity. Polyphasic taxonomic studies on isolates H45 and H9 showed that they represented new species of the genera Lentzea and Streptomyces, respectively; it is proposed that these strains be designated as Lentzea chajnantorensis sp. nov. and Streptomyces aridus sp. nov.. Additional isolates from sampling sites on Cerro Chajnantor were considered to be nuclei of novel species of Actinomadura, Amycolatopsis, Cryptosporangium and Pseudonocardia. A majority of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of six wild type microorganisms while those screened against Bacillus subtilis reporter strains inhibited sporulation and cell envelope, cell wall, DNA and fatty acid synthesis. -
Nevşehir Bilim Ve Teknoloji Dergisi (2021), 10(1) 44-55
Nevşehir Bilim ve Teknoloji Dergisi (2021), 10(1) 44-55 Nevşehir Bilim ve Teknoloji Dergisi Araştırma Makelesi (Research Article) Makale Doi: 10.17100/nevbiltek.878877 Geliş Tarihi:12-02-2021 Kabul Tarihi:07-05-2021 Lasiocampa trifolii (Denis & Schiffermüller, 1775)’nin Dahili Bakteriyel Çeşitliliği: Yeni Bir Olası Okibacterium sp. Ali SEVİM1* , Elif SEVİM 2 1Kırşehir Ahi Evran Üniversitesi, Ziraat Fakültesi, Bitki Koruma Bölümü, Kırşehir ORCID ID: 0000-0003-2472-599X 2Kırşehir Ahi Evran Üniversitesi, Fen Edebiyat Fakültesi, Moleküler Biyoloji ve Genetik Bölümü, Kırşehir ORCID ID:0000-0002-6455-1333 Öz Böceklerin bağırsak sistemlerinde bulunan mikroorganizmaların bu böceklerin sindirim ve beslenme süreçlerinde faydalı olduğu bilinmektedir. Bu anlamda, böceklerin bağırsak sistemindeki bakterilerin tanımlanması, özellikle ekonomik olarak zararlı veya faydalı böcek türlerinin besleyici ve sindirim özelliklerinin belirlenmesi açısından özellikle önemlidir. Bu çalışmada, Lasiocampa trifolii'nin (Denis & Schiffermüller, 1775) (Lepidoptera: Lasiocampidae) dahili bakteriyel florası kültür bağımlı teknikler kullanarak belirlenmiştir. Bu böceğin larvaları, çeşitli otlar ve çalılar, meşe, kavak ve süpürge çimi gibi bitki yapraklarıyla beslenmektedir. Larvalar Mayıs-Haziran (2019) aylarında Türkiye'nin Kırşehir bölgesinden toplanmış ve bakteri izolasyonu için laboratuvara getirilmiştir. Dört adet 3-4. instar larvalar bakteri izolasyonu için kullanılmıştır. İzole edilen bakteriler, 16S rRNA dizin analizi kullanılarak tanımlanmıştır. On bir bakteri -
Plant Growth-Promoting Actinobacteria: a New Strategy for Enhancing Sustainable Production and Protection of Grain Legumes
3 Biotech (2017) 7:102 DOI 10.1007/s13205-017-0736-3 REVIEW ARTICLE Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes 1 1 1 Arumugam Sathya • Rajendran Vijayabharathi • Subramaniam Gopalakrishnan Received: 2 November 2016 / Accepted: 19 April 2017 Ó Springer-Verlag Berlin Heidelberg 2017 Abstract Grain legumes are a cost-effective alternative for Introduction the animal protein in improving the diets of the poor in South-East Asia and Africa. Legumes, through symbiotic Grain legumes also called ‘Poor man’s meat’ are an nitrogen fixation, meet a major part of their own N demand essential entity in food and feed due to its protein, minerals, and partially benefit the following crops of the system by and other bioactive molecules. Increasing nutritional enriching soil. In realization of this sustainability advan- awareness increased the per-capita consumption of grain tage and to promote pulse production, United Nations had legumes across the world (Amarowicz and Pegg 2008). declared 2016 as the ‘‘International Year of pulses’’. Grain The symbiotic association of leguminous crops with rhi- legumes are frequently subjected to both abiotic and biotic zobia contributes 65% of nitrogen (N) needs. Their better stresses resulting in severe yield losses. Global yields of adaptation as an inter-crop with cereals or tuber crops helps legumes have been stagnant for the past five decades in in increased income generation and livelihood resilience of spite of adopting various conventional and molecular small holder farmers. However, production level of such breeding approaches. Furthermore, the increasing costs and leguminous crops has constraints in various forms such as negative effects of pesticides and fertilizers for crop pro- pest and pathogen attacks, infertile soils, and climate duction necessitate the use of biological options of crop changes. -
Culture-Dependent Microbiome of the Ciona Intestinalis Tunic: Isolation, Bioactivity Profiling and Untargeted Metabolomics
Supplementary Information Culture-dependent microbiome of the Ciona intestinalis tunic: Isolation, bioactivity profiling and untargeted metabolomics Caroline Utermann 1, Vivien A. Echelmeyer 1, Martina Blümel 1, Deniz Tasdemir 1,2* 1 GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany 2 Kiel University, Christian-Albrechts-Platz 4, Kiel 24118, Germany * Corresponding author: Deniz Tasdemir Email: [email protected] This document includes: Supplementary Figures S1-S8 Figure S1. Number of microbial strains isolated from the tunic of C. intestinalis and seawater reference. Figure S2. Distribution of bacterial orders across the sample types and their geographic locations. Figure S3. Distribution of fungal orders across the sample types and their geographic locations. Figure S4. Chemical structures of putatively identified compounds in the crude extracts of five selected microbial strains isolated from the tunic of C. intestinalis. Figure S5. FBMN of the crude extract of Pyrenochaeta sp. strain CHT58 cultivated on PDA medium. Figure S6. FBMN of the crude extract of Pseudogymnoascus destructans strain CHT56 cultivated on CAG medium. Figure S7. FBMN of the crude extract of Penicillium sp. strain CKT35 cultivated on medium PDA. Figure S8. FBMN of the crude extract of Boeremia exigua strain CKT91 cultivated on CAG (blue nodes) and PDA (red nodes) media. Supplementary Tables S1-S10 Table S1. Parameters for MZmine-processing of UPLC-MS/MS data. Table S2. Identification of microbial strains isolated from C. intestinalis and seawater reference in Helgoland and Kiel Fjord. Table S3. Bioactivity (%) of crude extracts derived from tunic-associated microbial strains at a test concentration of 100 µg/mL. -
Rathayibacter Agropyri (Non O’Gara, 1916) Comb
TAXONOMIC DESCRIPTION Schroeder et al., Int J Syst Evol Microbiol DOI 10.1099/ijsem.0.002708 Rathayibacter agropyri (non O’Gara, 1916) comb. nov., nom. rev., isolated from western wheatgrass (Pascopyrum smithii) Brenda K. Schroeder,1 William L. Schneider,2 Douglas G. Luster,2 Aaron Sechler2 and Timothy D. Murray3,* Abstract Aplanobacter agropyri was first described in 1915 by O’Gara and later transferred to the genus Corynebacterium by Burkholder in 1948 but it was not included in the Approved Lists of Bacterial Names in 1980 and, consequently, is not recognized as a validly published species. In the 1980s, bacteria resembling Corynebacterium agropyri were isolated from plant samples stored at the Washington State Mycological Herbarium and from a diseased wheatgrass plant collected in Cardwell, Montana, USA. In the framework of this study, eight additional isolates were recovered from the same herbarium plant samples in 2011. The isolates are slow-growing, yellow-pigmented, Gram-stain-positive and coryneform. The peptidoglycan is type B2g containing diaminobutyric acid, alanine, glycine and glutamic acid, the cell-wall sugars are rhamnose and mannose, the major respiratory quinone is MK-10, and the major fatty acids are anteiso-15 : 0, anteiso 17 : 0 and iso-16 : 0, all of which are typical of the genus Rathayibacter. Phylogenetic analysis of 16S rRNA gene sequences placed the strains in the genus Rathayibacter and distinguished them from the six other described species of Rathayibacter. DNA– DNA hybridization confirmed that the strains were members of a novel species. Based on phenotypic, chemotaxonomic and phylogenetic characterization, it appears that strains CA-1 to CA-12 represent a novel species, and the name Rathayibacter agropyri (non O’Gara, 1916) comb. -
Okibacterium Fritillariae Gen. Nov., Sp. Nov., a Novel Genus of the Family Microbacteriaceae
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 987–993 DOI: 10.1099/ijs.0.02033-0 Okibacterium fritillariae gen. nov., sp. nov., a novel genus of the family Microbacteriaceae 1 VKM – All-Russian Lyudmila I. Evtushenko,1,2 Lubov V. Dorofeeva,1 Valentina I. Krausova,1 Collection of 2 3 4 Microorganisms, G. K. Ekaterina Yu. Gavrish, Svetlana G. Yashina and Mariko Takeuchi Skryabin Institute of Biochemistry and Physiology of Author for correspondence: Lyudmila I. Evtushenko. Tel: j7 095 925 74 48. Fax: j7 095 956 33 70. Microorganisms, Russian e-mail: evtushenko!ibpm.serpukhov.ru Academy of Sciences, Pushchino, Moscow Region, 142290, Russia Okibacterium fritillariae gen. nov., sp. nov. (type strain VKM Ac-2059T l IFO 2 Pushchino State University, 16404T) is proposed for aerobic, oxidase- and catalase-positive, coryneform Pushchino, Moscow bacteria isolated from seeds of Fritillaria ruthenica Wikstr. and Clematis recta Region, 142290, Russia L. Strains of the new genus form a distinct branch within the phylogenetic 3 Institute of Cell Biophysics, cluster composed of members of the family Microbacteriaceae and are Russian Academy of Sciences, Pushchino, characterized by B-type peptidoglycan containing amino acids glycine, Moscow Region, 142290, glutamate, homoserine, alanine and lysine, the glycolyl type of muramic acid, Russia the major menaquinones MK-10 and MK-11, the principal phospholipids 4 Institute for Fermentation, phosphatidylglycerol and diphosphatidylglycerol, and a DNA GMC content of Osaka, 17-85, Juso- approximately 67 mol%. honmachi 2-home, Yudogava-ku, Osaka 532, Japan Keywords: Actinomycetales, Okibacterium fritillariae gen. nov., sp. nov., Fritillaria ruthenica Wikstr., Clematis recta L., plant seeds INTRODUCTION in peptidoglycan amino acid composition but differed from this genus by the major menaquinones. -
Filogenómica Como Un Enfoque Para Comprender El Carácter Anfibionte De Clavibacter Michiganensis
CENTRO DE INVESTIGACIÓN Y DE ESTUDIOS AVANZADOS DEL INSTITUTO POLITÉCNICO NACIONAL UNIDAD IRAPUATO Filogenómica como un enfoque para comprender el carácter anfibionte de Clavibacter michiganensis Tesis que presenta Alan Guillermo Yañez Olvera Para Obtener el Grado de Maestro en Ciencias En la Especialidad de Biotecnología de Plantas Director de la Tesis: Dr. Francisco Barona Gómez Irapuato, Guanajuato Febrero, 2019 AGRADECIMIENTOS Al Consejo Nacional de Ciencia y Tecnología (CONACyT) por el financiamiento durante el tiempo que duró mi maestría (número de registro becario 614044 / número de beca 456308), nada de esto habría sido posible sin su apoyo. A mis sinodales, el Dr. John Paul Délano Frier y el Dr. Rafael Montiel Duarte, por su valiosa ayuda. A mi asesor el Dr. Francisco Barona Gómez por toda su guía, apoyo y aliento para la finalización de este trabajo (¡Muchas gracias Paco!). A todo los miembros del laboratorio 14, también a aquellos que nos visitaron brevemente. A mis amigos, desde el más viejo hasta el más nuevo, gracias por las risas :). Gracias Emi. Especialmente a mi familia, que nunca deja de apoyarme. Los amo. Y a usted que se está tomando el tiempo de leer esto. 2 ÍNDICE RESUMEN 7 ABSTRACT 8 1. INTRODUCCIÓN 9 1.1 La adaptabilidad de las bacterias 9 1.1.1 La filogenómica y la genómica comparativa 9 1.2 Interacciones planta-microorganismo 10 1.3 Anfibionte 11 1.3.1 Lecciones del anfibionte más famoso. 11 1.4 Taxonomía de Clavibacter michiganensis subsp. michiganensis 12 1.5 Clavibacter michiganensis subsp. michiganensis (Cmm) y el cancro bacteriano 13 1.5.1 Infección por Cmm y síntomas del cancro bacteriano 13 1.6 Elementos funcionales asociados al desarrollo del cancro bacteriano 14 1.6.1 Proteasas 15 1.6.2 CAZymes 15 1.6.2.1 PCWDE 15 1.6.2.2 Otras CAZymes 16 1.6.3 Otros elementos asociados al desarrollo del cancro bacteriano 16 2.