Numerical Taxonomy of Actinomadura and Related Actinomycetes
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http://wjst.wu.ac.th Natural Sciences Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria Megga Ratnasari PIKOLI1,*, Irawan SUGORO2 and Suharti3 1Department of Biology, Faculty of Science and Technology, Universitas Islam Negeri Syarif Hidayatullah Jakarta, Ciputat, Tangerang Selatan, Indonesia 2Center for Application of Technology of Isotope and Radiation, Badan Tenaga Nuklir Nasional, Jakarta Selatan, Indonesia 3Department of Chemistry, Faculty of Science and Computation, Universitas Pertamina, Simprug, Jakarta Selatan, Indonesia (*Corresponding author’s e-mail: [email protected], [email protected]) Received: 7 September 2017, Revised: 11 September 2018, Accepted: 29 October 2018 Abstract Studies that explore the diversity of microorganisms in unusual (extreme) environments have become more common. Our research aims to predict the diversity of bacteria that inhabit an extreme environment, a coal mine’s soil with pH of 2.93. Soil samples were collected from the soil at a depth of 12 meters from the surface, which is a clay layer adjacent to a coal seam in Tanjung Enim, South Sumatera, Indonesia. A culture-independent method, the polymerase chain reaction based denaturing gradient gel electrophoresis, was used to amplify the 16S rRNA gene to detect the viable-but-unculturable bacteria. Results showed that some OTUs that have never been found in the coal environment and which have phylogenetic relationships to the rare actinobacteria Actinomadura, Actinoallomurus, Actinospica, Streptacidiphilus, Aciditerrimonas, and Ferrimicrobium. Accordingly, the highly acidic soil in the coal mine is a source of rare actinobacteria that can be explored further to obtain bioactive compounds for the benefit of biotechnology. -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Actinomadura Keratinilytica Sp. Nov., a Keratin- Degrading Actinobacterium Isolated from Bovine Manure Compost
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 828–834 DOI 10.1099/ijs.0.003640-0 Actinomadura keratinilytica sp. nov., a keratin- degrading actinobacterium isolated from bovine manure compost Aaron A. Puhl,1 L. Brent Selinger,2 Tim A. McAllister1 and G. Douglas Inglis1 Correspondence 1Agriculture and Agri-Food Canada Research Centre, 5403 1st Avenue S, Lethbridge, AB T1J G. Douglas Inglis 4B1, Canada [email protected] 2Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada A novel keratinolytic actinobacterium, strain WCC-2265T, was isolated from bovine hoof keratin ‘baited’ into composting bovine manure from southern Alberta, Canada, and subjected to phenotypic and genotypic characterization. Strain WCC-2265T produced well-developed, non- fragmenting and extensively branched hyphae within substrates and aerial hyphae, from which spherical spores possessing spiny cell sheaths were produced in primarily flexuous or straight chains. The cell wall contained meso-diaminopimelic acid, whole-cell sugars were galactose, glucose, madurose and ribose, and the major menaquinones were MK-9(H6), MK-9(H8), MK- 9(H4) and MK-9(H2). These characteristics suggested that the organism belonged to the genus Actinomadura and a comparative analysis of 16S rRNA gene sequences indicated that it formed a distinct clade within the genus. Strain WCC-2265T could be differentiated from other species of the genus Actinomadura by DNA–DNA hybridization, morphological and physiological characteristics and the predominance of iso-C16 : 0, iso-C17 : 0 and 10-methyl C17 : 0 fatty acids. The broad range of phenotypic and genetic characters supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura keratinilytica sp. -
Novel Polyethers from Screening Actinoallomurus Spp
Article Novel Polyethers from Screening Actinoallomurus spp. Marianna Iorio 1, Arianna Tocchetti 1, Joao Carlos Santos Cruz 2, Giancarlo Del Gatto 1, Cristina Brunati 2, Sonia Ilaria Maffioli 1, Margherita Sosio 1,2 and Stefano Donadio 1,2,* 1 NAICONS Srl, Viale Ortles 22/4, 20139 Milano, Italy; [email protected] (M.I.); [email protected] (A.T.); [email protected] (G.D.G.); [email protected] (S.I.M.); [email protected] (M.S.) 2 KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy; [email protected] (J.C.S.C.); [email protected] (C.B.) * Correspondence: [email protected] Received: 1 May 2018; Accepted: 13 June 2018; Published: 14 June 2018 Abstract: In screening for novel antibiotics, an attractive element of novelty can be represented by screening previously underexplored groups of microorganisms. We report the results of screening 200 strains belonging to the actinobacterial genus Actinoallomurus for their production of antibacterial compounds. When grown under just one condition, about half of the strains produced an extract that was able to inhibit growth of Staphylococcus aureus. We report here on the metabolites produced by 37 strains. In addition to previously reported aminocoumarins, lantibiotics and aromatic polyketides, we described two novel and structurally unrelated polyethers, designated α- 770 and α-823. While we identified only one producer strain of the former polyether, 10 independent Actinoallomurus isolates were found to produce α-823, with the same molecule as main congener. Remarkably, production of α-823 was associated with a common lineage within Actinoallomurus, which includes A. fulvus and A. amamiensis. All polyether producers were isolated from soil samples collected in tropical parts of the world. -
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A Thesis Submitted for the Degree of PhD at the University of Warwick Permanent WRAP URL: http://wrap.warwick.ac.uk/81849 Copyright and reuse: This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. For more information, please contact the WRAP Team at: [email protected] warwick.ac.uk/lib-publications Unlocking the potential of novel taxa – a study on Actinoallomurus João Carlos Santos Cruz Submitted for the degree of Doctor of Philosophy School of Life Sciences, University of Warwick March, 2016 1 TABLE OF CONTENTS Table of Contents .......................................................................................................... i Acknowledgments...................................................................................................... iv List of Figures ................................................................................................................. v List of Tables ................................................................................................................. ix Declaration .................................................................................................................. xi Summary ....................................................................................................................... xii Abbreviations ............................................................................................................. -
Draft Genome of Thermomonospora Sp. CIT 1 (Thermomonosporaceae) and in Silico Evidence of Its Functional Role in Filter Cake Biomass Deconstruction
Genetics and Molecular Biology, 42, 1, 145-150 (2019) Copyright © 2019, Sociedade Brasileira de Genética. Printed in Brazil DOI: http://dx.doi.org/10.1590/1678-4685-GMB-2017-0376 Genome Insight Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction Wellington P. Omori1, Daniel G. Pinheiro2, Luciano T. Kishi3, Camila C. Fernandes3, Gabriela C. Fernandes1, Elisângela S. Gomes-Pepe3, Claudio D. Pavani1, Eliana G. de M. Lemos3 and Jackson A. M. de Souza4 1Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 2Departamento de Tecnologia, Laboratório de Bioinformática, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 3Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 4Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of mi- croorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assem- bled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacte- rium that produces cellulases in compost, and it can survive temperatures of 60 ºC. -
Class Actinobacteria Subclass Actinobacteridae Order Actinomycetales Suborder Streptosporangineae Family Thermomonosporaceae Genus Actinomadura
Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig Class Actinobacteria Subclass Actinobacteridae Order Actinomycetales Suborder Streptosporangineae Family Thermomonosporaceae Genus Actinomadura Copyright: PD Dr. Joachim M. Wink, HZI - Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany, Mail: [email protected]. Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig The Genus Actinomadura To the genus Actinomadura belong 34 species Actinomadura atramentaria , catellatispora, citrea, coerulea, cremea, echinospora, fibrosa, formosensis, fulvescens, glauciflava, hallensis, hibisca, kijaniata, latina, livida, luteofluorescens, macra, madurae, mexicana, meyerae, namibiensis, napirensis, nitritigenes, oligospora, pelletieri rubrobrunnea, rugatobispora, spadix, umbrina, verrucosospora, vinacea , viridilutea, viridis and yumaensis .. In 2001 the species aurantiaca, glomerata, libanotica, longicatena and viridilutea were transferred to the genus Actinocorallia Actinomadura carminata is reclasssificated to Nonomuraea roseoviolacea subsp. carminata by Gyobu and Miyadoh (2001). Excellospora viridilutea is transferred to Actinomadura as A. viridilutea by Zhang et al. 2001. Extensively branching vegetative hyphae form a dense non fragmenting substrate mycelium; aerial mycelium is moderately developed or absent. At maturity, the aerial mycelium forms short or ocassionally long chains of arthrospores. Spore chains are straight, hooked (open loops), -
Bacteriophages
BACTERIOPHAGES Edited by Ipek Kurtböke Bacteriophages Edited by Ipek Kurtböke Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Maja Bozicevic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Bacteriophages, Edited by Ipek Kurtböke p. -
Bioactive Actinobacteria Associated with Two South African Medicinal Plants, Aloe Ferox and Sutherlandia Frutescens
Bioactive actinobacteria associated with two South African medicinal plants, Aloe ferox and Sutherlandia frutescens Maria Catharina King A thesis submitted in partial fulfilment of the requirements for the degree of Doctor Philosophiae in the Department of Biotechnology, University of the Western Cape. Supervisor: Dr Bronwyn Kirby-McCullough August 2021 http://etd.uwc.ac.za/ Keywords Actinobacteria Antibacterial Bioactive compounds Bioactive gene clusters Fynbos Genetic potential Genome mining Medicinal plants Unique environments Whole genome sequencing ii http://etd.uwc.ac.za/ Abstract Bioactive actinobacteria associated with two South African medicinal plants, Aloe ferox and Sutherlandia frutescens MC King PhD Thesis, Department of Biotechnology, University of the Western Cape Actinobacteria, a Gram-positive phylum of bacteria found in both terrestrial and aquatic environments, are well-known producers of antibiotics and other bioactive compounds. The isolation of actinobacteria from unique environments has resulted in the discovery of new antibiotic compounds that can be used by the pharmaceutical industry. In this study, the fynbos biome was identified as one of these unique habitats due to its rich plant diversity that hosts over 8500 different plant species, including many medicinal plants. In this study two medicinal plants from the fynbos biome were identified as unique environments for the discovery of bioactive actinobacteria, Aloe ferox (Cape aloe) and Sutherlandia frutescens (cancer bush). Actinobacteria from the genera Streptomyces, Micromonaspora, Amycolatopsis and Alloactinosynnema were isolated from these two medicinal plants and tested for antibiotic activity. Actinobacterial isolates from soil (248; 188), roots (0; 7), seeds (0; 10) and leaves (0; 6), from A. ferox and S. frutescens, respectively, were tested for activity against a range of Gram-negative and Gram-positive human pathogenic bacteria. -
Proposal of Carbonactinosporaceae Fam. Nov. Within the Class Actinomycetia. Reclassification of Streptomyces Thermoautotrophicus
Systematic and Applied Microbiology 44 (2021) 126223 Contents lists available at ScienceDirect Systematic and Applied Microbiology journal homepage: www.elsevier.com/locate/syapm Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov Camila Gazolla Volpiano a,1, Fernando Hayashi Sant’Anna b,1, Fábio Faria da Mota c, Vartul Sangal d, Iain Sutcliffe d, Madhaiyan Munusamy e, Venkatakrishnan Sivaraj Saravanan f, Wah-Seng See-Too g, ⇑ Luciane Maria Pereira Passaglia a, Alexandre Soares Rosado h,i, a Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil b PROADI-SUS, Hospital Moinhos de Vento, 630, Ramiro Barcelos Porto Alegre, RS, Brazil c Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, 4365, Brasil Ave, Rio de Janeiro, RJ, Brazil d Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom e Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore f Department of Microbiology, Indira Gandhi College of Arts and Science, Kathirkamam, Pondicherry, India g Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia h LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil i BESE, Biological and Environmental Sciences and Engineering Division, KAUST, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia article info abstract Article history: Streptomyces thermoautotrophicus UBT1T has been suggested to merit generic status due to its phyloge- Received 6 April 2021 netic placement and distinctive phenotypes among Actinomycetia. -
Secondary Metabolites and Biodiversity of Actinomycetes Manal Selim Mohamed Selim, Sayeda Abdelrazek Abdelhamid* and Sahar Saleh Mohamed
Selim et al. Journal of Genetic Engineering and Biotechnology (2021) 19:72 Journal of Genetic Engineering https://doi.org/10.1186/s43141-021-00156-9 and Biotechnology REVIEW Open Access Secondary metabolites and biodiversity of actinomycetes Manal Selim Mohamed Selim, Sayeda Abdelrazek Abdelhamid* and Sahar Saleh Mohamed Abstract Background: The ability to produce microbial bioactive compounds makes actinobacteria one of the most explored microbes among prokaryotes. The secondary metabolites of actinobacteria are known for their role in various physiological, cellular, and biological processes. Main body: Actinomycetes are widely distributed in natural ecosystem habitats such as soil, rhizosphere soil, actinmycorrhizal plants, hypersaline soil, limestone, freshwater, marine, sponges, volcanic cave—hot spot, desert, air, insects gut, earthworm castings, goat feces, and endophytic actinomycetes. The most important features of microbial bioactive compounds are that they have specific microbial producers: their diverse bioactivities and their unique chemical structures. Actinomycetes represent a source of biologically active secondary metabolites like antibiotics, biopesticide agents, plant growth hormones, antitumor compounds, antiviral agents, pharmacological compounds, pigments, enzymes, enzyme inhibitors, anti-inflammatory compounds, single-cell protein feed, and biosurfactant. Short conclusions: Further highlight that compounds derived from actinobacteria can be applied in a wide range of industrial applications in biomedicines and the -
Morphological Identification of Actinobacteria
Chapter 3 Morphological Identification of Actinobacteria Qinyuan Li, Xiu Chen, Yi Jiang and Chenglin Jiang Additional information is available at the end of the chapter http://dx.doi.org/10.5772/61461 Abstract Actinobacteria is a phylum of gram-positive bacteria with high G+C content. Among gram-positive bacteria, actinobacteria exhibit the richest morphological differentia‐ tion, which is based on a filamentous degree of organization like filamentous fungi. The actinobacteria morphological characteristics are basic foundation and informa‐ tion of phylogenetic systematics. Classic actinomycetes have well-developed radial mycelium, which can be divided into substrate mycelium and aerial mycelium according to morphology and function. Some actinobacteria can form complicated structures, such as spore, spore chain, sporangia, and sporangiospore. The structure of hyphae and ultrastructure of spore or sporangia can be observed with microscopy. Actinobacteria have different cultural characteristics in various kinds of culture media, which are important in the classification identification, general with spores, aerial hyphae, with or without color and the soluble pigment, different growth condition on various media as the main characteristics. The morphological differen‐ tiation of actinobacteria, especially streptomycetes, is controlled by relevant genes. Both morphogenesis and antibiotic production in the streptomycetes are initiated in response to starvation, and these events are coupled. Keywords: Actinobacteria, Morphology, Morphological characteristics, Cultural charac‐ teristics 1. Introduction The history of the classification of prokaryote clearly demonstrates that changes were caused by the availability of new techniques [1]. The development of prokaryotic classification has experienced different stages: (i) the classical or traditional classification mainly based on © 2016 The Author(s). Licensee InTech.