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The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil
THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….………. -
Pseudonocardia Acaciae Sp. Nov., Isolated from Roots of Acacia Auriculiformis A
Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. Page 1 of 2 Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. 123 Kannika Duangmal , Arinthip Thamchaipenet , Atsuko Matsumoto and 3 Yoko Takahashi - Author Affiliations 1Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand 2Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand 3Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan Correspondence Kannika Duangmal [email protected] or [email protected] Abstract A novel Gram-positive-staining actinomycete designated strain GMKU095T was isolated from surface-sterilized roots of Acacia auriculiformis A. Cunn. ex Benth. (earpod wattle). The organism produced branching mycelium. The spores were non-motile and had a spiny surface. Growth of strain GMKU095T occurred at 18– 42 °C, pH 5.0–8.0 and at NaCl concentrations up to 5 %. Whole-cell hydrolysates contained arabinose and galactose as major characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The menaquinone was MK-8(H4); mycolic acids were not detected. The G+C content of the DNA was 71.6 mol%. iso- C16 : 0 was detected as the major cellular fatty acid. Comparative studies of 16S rRNA gene sequences indicated that the strain was phylogenetically related to members of the genus Pseudonocardia. The most closely related type strain is Pseudonocardia spinosispora IMSNU 50581T , which is 96.2 % similar in 16S rRNA gene sequence. -
Pseudonocardia Pini Sp. Nov., an Endophytic Actinobacterium Isolated from Roots of the Pine Tree Callitris Preissii
Pseudonocardia Pini Sp. Nov., An Endophytic Actinobacterium Isolated From Roots of the Pine Tree Callitris Preissii Onuma Kaewkla ( [email protected] ) Mahasarakham University https://orcid.org/0000-0001-7630-7074 Christopher Milton Mathew Franco Flinders University of South Australia: Flinders University Research Article Keywords: Pseudonocardia pini sp. nov., an endophytic actinobacterium Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-274242/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Archives of Microbiology on April 23rd, 2021. See the published version at https://doi.org/10.1007/s00203-021-02309-3. Page 1/16 Abstract A Gram positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47RT, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), South Australia is described. The major cellular fatty acid of this strain was iso-H-C16:1 and major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was identied as meso- diaminopimelic acid. These chemotaxonomic data conrmed the aliation of strain CAP47RT to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Pseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906T (98.8%), Pseudonocardia oroxyli DSM 44984T (98.7%), Pseudonocardia thailandensis CMU-NKS-70T (98.7%), and Pseudonocardia ailaonensis DSM 44979T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm and digital DNA-DNA hybridization revealed the differentiation of strain CAP47RT from the closest species with validated names. -
Production, Purification, and Characterization of Bioactive Metabolites Produced from Rare Actinobacteria Pseudonocardia Alni
Online - 2455-3891 Vol 9, Suppl. 3, 2016 Print - 0974-2441 Research Article PRODUCTION, PURIFICATION, AND CHARACTERIZATION OF BIOACTIVE METABOLITES PRODUCED FROM RARE ACTINOBACTERIA PSEUDONOCARDIA ALNI RABAB OMRAN1*, MOHAMMED FADHIL KADHEM2 1Department of Biology, College of Science, University of Babylon, Babel, Al-Hillah, Iraq. 2Department of Pharmacology, Ibn Hayyan College, Karbala, Iraq. Email: [email protected], [email protected] Received: 30 August 2016, Revised and Accepted: 12 September 2016 ABSTRACT Objectives: Pseudonocardia alni exhibits antimicrobial activity against tested pathogenic Staphylococcus aureus, Microsporum canis, and Trichophyton mentagrophyte. The present paper aimed to optimize various cultural conditions for antimicrobial metabolite production, purification, and characterization of the active substance. Methods: The effects of various parameters such as culture media, carbon and nitrogen sources, phosphate concentration, pH, temperature, incubation period, and agitation rate on bioactive metabolite production were studied using a flask scale with varying single parameter. The active substances were purified by adsorption chromatography using Silica gel column and Sephadex LH 20 column, and the physical, chemical, and biological properties were characterized. Results: The metabolite production by P. alni was greatly influenced by various cultural conditions. It produced high levels of the antimicrobial substance in International Streptomyces project-2 broth compared with that in potato dextrose broth. The optimum parameters for antimicrobial production from the actinobacterium occurred in the production medium consisting of glucose (1%) and tryptone (1%), 0.001 M of K2HPO4 and the bioactive production. The purified active substance had relative factor Rf=0.53 in the mobile phase of a thin layer chromatography system and 0.05M glycine at initial pH 8.5 and incubated at 30°C for 4 d in stand incubator. -
Generalized Antifungal Activity and 454-Screening of Pseudonocardia and Amycolatopsis Bacteria in Nests of Fungus-Growing Ants
Generalized antifungal activity and 454-screening SEE COMMENTARY of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants Ruchira Sena,1, Heather D. Ishaka, Dora Estradaa, Scot E. Dowdb, Eunki Honga, and Ulrich G. Muellera,1 aSection of Integrative Biology, University of Texas, Austin, TX 78712; and bMedical Biofilm Research Institute, 4321 Marsha Sharp Freeway, Lubbock, TX 79407 Edited by Raghavendra Gadagkar, Indian Institute of Science, Bangalore, India, and approved August 14, 2009 (received for review May 1, 2009) In many host-microbe mutualisms, hosts use beneficial metabolites origin (12–14). Many of the ant-associated Pseudonocardia species supplied by microbial symbionts. Fungus-growing (attine) ants are show antibiotic activity in vitro against Escovopsis (13–15). A thought to form such a mutualism with Pseudonocardia bacteria to diversity of actinomycete bacteria including Pseudonocardia also derive antibiotics that specifically suppress the coevolving pathogen occur in the ant gardens, in the soil surrounding attine nests, and Escovopsis, which infects the ants’ fungal gardens and reduces possibly in the substrate used by the ants for fungiculture (16, 17). growth. Here we test 4 key assumptions of this Pseudonocardia- The prevailing view of attine actinomycete-Escovopsis antago- Escovopsis coevolution model. Culture-dependent and culture- nism is a coevolutionary arms race between antibiotic-producing independent (tag-encoded 454-pyrosequencing) surveys reveal that Pseudonocardia and Escovopsis parasites (5, 18–22). Attine ants are several Pseudonocardia species and occasionally Amycolatopsis (a thought to use their integumental actinomycetes to specifically close relative of Pseudonocardia) co-occur on workers from a single combat Escovopsis parasites, which fail to evolve effective resistance nest, contradicting the assumption of a single pseudonocardiaceous against Pseudonocardia because of some unknown disadvantage strain per nest. -
Genome-Wide Studies of Mycolic Acid Bacteria: Computational Identification And
Genome-wide Studies of Mycolic Acid Bacteria: Computational Identification and Analysis of a Minimal Genome Dissertation by Frederick Kinyua Kamanu In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia December, 2012 2 EXAMINATION COMMITTEE APPROVALS FORM The dissertation of Frederick Kinyua Kamanu is approved by the examination committee. Committee Chairperson: Prof. Vladimir B. Bajic Committee Co-Chair: Dr. John A.C. Archer Committee Member: Prof. Pierre Magistretti Committee Member: Prof. Xin Gao Committee Member: Prof. Christoph Gehring Committee Member: Prof. Kothandaraman Narasimhan 3 COPYRIGHT © December, 2012 Frederick Kinyua Kamanu All Rights Reserved 4 ABSTRACT Genome wide studies of mycolic acid bacteria: Computational Identification and Analysis of a Minimal Genome Frederick Kinyua Kamanu The mycolic acid bacteria are a distinct suprageneric group of asporogenous Gram- positive, high GC-content bacteria, distinguished by the presence of mycolic acids in their cell envelope. They exhibit great diversity in their cell and morphology; although primarily non-pathogens, this group contains three major pathogens Mycobacterium leprae, Mycobacterium tuberculosis complex, and Corynebacterium diphtheria. Although the mycolic acid bacteria are a clearly defined group of bacteria, the taxonomic relationships between its constituent genera and species are less well defined. Two approaches were tested for their suitability in describing the taxonomy of the group. First, a Multilocus Sequence Typing (MLST) experiment was assessed and found to be superior to monophyletic (16S small ribosomal subunit) in delineating a total of 52 mycolic acid bacterial species. Phylogenetic inference was performed using the neighbor- joining method. -
Pseudonocardia Parietis Sp. Nov., from the Indoor Environment
This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of ‘Fair Use of Copyrighted Materials’ (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://ijs.sgmjournals.org, and is freely available without a subscription 24 months after publication. First published in: Int J Syst Evol Microbiol, 2009. 59(10) 2449-52. doi:10.1099/ijs.0.009993-0 Pseudonocardia parietis sp. nov., from the indoor environment J. Scha¨fer,1 H.-J. Busse2 and P. Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, P. Ka¨mpfer Germany [email protected] 2Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, giessen.de Austria A Gram-positive, rod-shaped, non-endospore-forming, mycelium-forming actinobacterium (04- St-002T) was isolated from the wall of an indoor environment colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 04-St-002T was shown to belong to the family Pseudonocardiaceae, and to be most closely related to Pseudonocardia antarctica (99.2 %) and Pseudonocardia alni (99.1 %). -
Potential Use of Soil-Born Fungi Isolated from Treated Soil in Indonesia to Degrade Glyphosate Herbicide
JOURNAL OF DEGRADED AND MINING LANDS MANAGEMENT ISSN: 2339-076X, Volume 1, Number 2 (January 2014): 63-68 Research Article Potential use of soil-born fungi isolated from treated soil in Indonesia to degrade glyphosate herbicide N. Arfarita1*, T. Imai 2, B. Prasetya3 1 Faculty of Agriculture, Malang Islamic University, Jl. M.T. Haryono, Malang 65144, Indonesia 2 Division of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi 755-8611, Japan 3 Faculty of Agriculture, Brawijaya University, Jl. Veteran, Malang 65145, Indonesia. * Corresponding author: [email protected] Abstract: The glyphosate herbicide is the most common herbicides used in palm-oil plantations and other agricultural in Indonesial. In 2020, Indonesian government to plan the development of oil palm plantations has reached 20 million hectares of which now have reached 6 million hectares. It means that a huge chemicals particularly glyphosate has been poured into the ground and continues to pollute the soil. However, there is no report regarding biodegradation of glyphosate-contaminated soils using fungal strain especially in Indonesia. This study was to observe the usage of Round Up as selection agent for isolation of soil-born fungi capable to grow on glyphosate as a sole source of phosphorus. Five fungal strains were able to grow consistently in the presence of glyphosate as the sole phosphorus source and identified as Aspergillus sp. strain KRP1, Fusarium sp. strain KRP2, Verticillium sp. strain KRP3, Acremoniumsp. strain GRP1 and Scopulariopsis sp. strain GRP2. This indicates as their capability to utilize and degrade this herbicide. We also used standard medium as control and get seventeen fungal strains. -
Induction of Secondary Metabolism Across Actinobacterial Genera
Induction of secondary metabolism across actinobacterial genera A thesis submitted for the award Doctor of Philosophy at Flinders University of South Australia Rio Risandiansyah Department of Medical Biotechnology Faculty of Medicine, Nursing and Health Sciences Flinders University 2016 TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................ ii TABLE OF FIGURES ............................................................................................. viii LIST OF TABLES .................................................................................................... xii SUMMARY ......................................................................................................... xiii DECLARATION ...................................................................................................... xv ACKNOWLEDGEMENTS ...................................................................................... xvi Chapter 1. Literature review ................................................................................. 1 1.1 Actinobacteria as a source of novel bioactive compounds ......................... 1 1.1.1 Natural product discovery from actinobacteria .................................... 1 1.1.2 The need for new antibiotics ............................................................... 3 1.1.3 Secondary metabolite biosynthetic pathways in actinobacteria ........... 4 1.1.4 Streptomyces genetic potential: cryptic/silent genes .......................... -
Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products. -
Influence of Growth Medium on Diagnostic Characters of Aspergillus and Penicillium Species
African Journal of Microbiology Research Vol. 3 (5) pp. 280-286 May, 2009 Available online http://www.academicjournals.org/ajmr ISSN 1996-0808 ©2009 Academic Journals Full Length Research Paper Influence of growth medium on diagnostic characters of aspergillus and penicillium species M. E. Zain, A. A. Razak, H. H. El-Sheikh, H. G. Soliman and A. M. Khalil Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt. Accepted 27 April, 2009 Three fungal strains; namely, Aspergillus terreus, Penicillium janthinellum and Penicillium duclauxii were cultured on different growth media including yeast extract, malt extract, yeast-malt extract, Czapek's Dox, Sabourod's, Harrlod's, and potato dextrose. The growth and secondary metabolites of the three fungal strains were greatly affected by the growth medium. The colour of the culture and secondary metabolites were noticeably altered and changed according to the growth medium used. Key words: Growth medium, Aspergillus, Penicillium, Secondary metabolites, Culture characteristics. INTRODUCTION The taxonomy of the fungi is in a state of rapid flux at on their sexual reproductive structures. Currently, four present, especially due to recent papers based on DNA divisions are recognized (Alexopolous et al., 1996). comparisons, which often overturn the assumptions of On the other hand, secondary metabolites are com- the older systems of classification (Hibbett, 2007). pounds neither essential for growth nor key intermediates The simple morphology, the lack of a useful fossil re- of the organism’s basic metabolism but presumably play- cord, and fungal diversity has been major impediments to ing some other role in the life of fungi. -
Microorganisms
microorganisms Article Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits Daniel Garrido-Sanz , Miguel Redondo-Nieto , Marta Martín and Rafael Rivilla * Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain; [email protected] (D.G.-S.); [email protected] (M.R.-N.); [email protected] (M.M.) * Correspondence: [email protected] Received: 15 April 2020; Accepted: 20 May 2020; Published: 21 May 2020 Abstract: The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp.