Lesson 35. Spore Forming Anaerobes
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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…………………………….………. -
The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Catalogue of Bacteria Shapes
We first tried to use the most general shape associated with each genus, which are often consistent across species (spp.) (first choice for shape). If there was documented species variability, either the most common species (second choice for shape) or well known species (third choice for shape) is shown. Corynebacterium: pleomorphic bacilli. Due to their snapping type of division, cells often lie in clusters resembling chinese letters (https://microbewiki.kenyon.edu/index.php/Corynebacterium) Shown is Corynebacterium diphtheriae Figure 1. Stained Corynebacterium cells. The "barred" appearance is due to the presence of polyphosphate inclusions called metachromatic granules. Note also the characteristic "Chinese-letter" arrangement of cells. (http:// textbookofbacteriology.net/diphtheria.html) Lactobacillus: Lactobacilli are rod-shaped, Gram-positive, fermentative, organotrophs. They are usually straight, although they can form spiral or coccobacillary forms under certain conditions. (https://microbewiki.kenyon.edu/index.php/ Lactobacillus) Porphyromonas: A genus of small anaerobic gram-negative nonmotile cocci and usually short rods thatproduce smooth, gray to black pigmented colonies the size of which varies with the species. (http:// medical-dictionary.thefreedictionary.com/Porphyromonas) Shown: Porphyromonas gingivalis Moraxella: Moraxella is a genus of Gram-negative bacteria in the Moraxellaceae family. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli or, as in the case of Moraxella catarrhalis, diplococci in morphology (https://en.wikipedia.org/wiki/Moraxella). *This one could be changed to a diplococcus shape because of moraxella catarrhalis, but i think the short rods are fair given the number of other moraxella with them. Jeotgalicoccus: Jeotgalicoccus is a genus of Gram-positive, facultatively anaerobic, and halotolerant to halophilicbacteria. -
Bacillus Pycnus Spa Nov. and Bacillus Neidei Spa Nov., Round-Spored
674 International Journal ofSystematic and Evolutionary Microbiology (2002),52,501-505 DOl: 10.1099/ijs.0.01836-0 Bacillus pycnus Spa nov. and Bacillus neidei Spa NOTE nov., round-spored bacteria from soil 1 Microbial Properties L. K. Nakamura,1 O. Shida/ H. Takagi2 and K. Komagata3 Research Unit, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, Author for correspondence: L K. Nakamura. Tel: + 13096816395. Fax: + 13096816672. IL 61604, USA e-mail: nakamulki"mail.ncaur.usda.gov 2 Research Laboratory, Higeta Shoyu Co. Ltd, Bacillus sphaericus sensu lato currently consists of seven or more groups of Choshi, Chiba 288, Japan unrelated taxa, one of which is B. sphaericus sensu stricto and another of 3 Department of which is Bacillus fusiformis. Members of two groups (groups 6 and 7), in Agricultural Chemistry, Tokyo University of common with all other B. sphaericus-like organisms, are unable to grow Agriculture, Setagaya-ku, anaerobically or to use common hexoses, pentoses and hexitols as sources of Tokyo 156, Japan carbon, have G+C contents of 34-36 mol % and form round spores. Groups 6 and 7 can be differentiated from other B. sphaericus-like organisms by low DNA relatedness and by variations in whole-cell fatty acid composition. Unique characteristics of group 6 include the ability to oxidize fi-hydroxybutyrate, the non-requirement for biotin and thiamin and failure to grow in 5 % NaCI. Distinctive traits of group 7 include the inability to oxidize pyruvate and a requirement for biotin, thiamin and cystine for growth. These data show that groups 6 and 7 represent two novel species, for which the names Bacillus pycnus sp. -
Micromasters of the Earth
Micromasters of the Earth Anna WĘGRZYN – the Department of Environmental Biotechnology at the Faculty of Energy and Environmental Engineering at the Silesian University of Technology, Gliwice Please cite as: CHEMIK 2011, 65, 11, 1182-1189 Introduction membrane constitutes about 25% of the whole bacterium mass. It is estimated that our planet was formed about 4.6 billion Peptidoglycan (murein) is a fundamental substance of the bacterial cell years ago. At the very beginning, it was just a lifeless ball of melted wall. In their cell walls, bacteria can contain different quantities of murein magma. The Earth surface was gradually getting cool until reaching which is connected with a diversified sensitivity to dyes. Depending the temperature at which water and other chemical compounds on the number of peptidoglycan layers, the applied dyes (e.g. crystal could have been created. First traces of life are being discovered in violet) are retained inside the cell wall or leached from it. This is the rocks formed about 3.85 billion years ago. Stromatolites - biogenic basis for classifying bacteria into a group of Gram-positive or Gram- rocks dated at about 3.4 billion years which formation was connected negative bacteria (originating from the name of the Danish scientist with activities of cyanobacteria – autotrophic organisms being able to Gram who was the first person to perform the complex staining with XII Conference Environmental produce oxygen in the process of photosynthesis, constitute the fossil crystal violet in 1884). The cells of Gram-negative bacteria contain trace of the prokaryotic structure1 of primitive forms. The creation of lower quantities of murein than in case of Gram-positive bacteria. -
Antonie Van Leeuwenhoek Journal of Microbiology
Antonie van Leeuwenhoek Journal of Microbiology Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients --Manuscript Draft-- Manuscript Number: ANTO-D-15-00548R1 Full Title: Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients Article Type: Original Article Keywords: Kroppenstedtia species, Kroppenstedtia pulmonis, Kroppenstedtia sanguinis, polyphasic taxonomy, 16S rRNA gene, thermoactinomycetes Corresponding Author: Melissa E Bell, MS Centers for Disease Control and Prevention Atlanta, Georgia UNITED STATES Corresponding Author Secondary Information: Corresponding Author's Institution: Centers for Disease Control and Prevention Corresponding Author's Secondary Institution: First Author: Melissa E Bell, MS First Author Secondary Information: Order of Authors: Melissa E Bell, MS Brent A. Lasker, PhD Hans-Peter Klenk, PhD Lesley Hoyles, PhD Catherine Spröer Peter Schumann June Brown Order of Authors Secondary Information: Funding Information: Abstract: Three human clinical strains (W9323T, X0209T and X0394) isolated from lung biopsy, blood and cerebral spinal fluid, respectively, were characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequences showed the three strains belonged to two novel branches within the genus Kroppenstedtia: 16S rRNA gene sequence analysis of W9323T showed closest sequence similarity to Kroppenstedtia eburnea JFMB-ATE T (95.3 %), Kroppenstedtia guangzhouensis GD02T (94.7 %) and strain X0209T (94.6 %); sequence analysis of strain X0209T showed closest sequence similarity to K. eburnea JFMB-ATE T (96.4 %) and K. guangzhouensis GD02T (96.0 %). Strains X0209T and X0394 were 99.9 % similar to each other by 16S rRNA gene sequence analysis. The DNA-DNA relatedness was 94.6 %, confirming that X0209T and X0394 belong to the same species. -
Aerobic Endospore Procedure
Office of Research and Development Photos Aerobic Endospore Procedure Laura A. Boczek Microbiologist US EPA – Office of Research and Development Aerobic Endospore Background Aerobic endospores are protective structures that some genera of bacteria have the ability to produce in response to a stressful environment. These genera are in general harmless to humans and are saprophytic organisms that are ubiquitous in many soil and water environments. These organisms can stay in the endospore form until conditions are favorable for them to germinate out of the endospore state to a vegetative state. This allows them to persist in their environment and resist many environmental stressors such as heat, desiccation, disinfection, and irradiation. 2 Aerobic Endospores Procedure Standard Methods 9218 A & B – outlines how to culture and measure aerobic endospores. Basic steps : 1. Obtaining a representative sample 2. Killing off any vegetative cells that could be in the sample by heat treatment 3. Using membrane filtration to concentrate endopsores in sample and then allow them to grow to enumerate Representative sample Samples should be collected using sterile wide mouth containers and care should be taken not to contaminate the samples during collection by using aseptic technique. Samples that contain a disinfectant residual such as chlorine should have sodium thiosulfate added to the sample bottle prior to collection in order to quench the chlorine. Samples should include a sufficient volume that can be processed to adequately determine treatment efficacy. • Sample waters will contain various amounts of endospores. Therefore if treatment efficacy is the reason why aerobic endospores are being measured a larger volume of sample may need to be collected and processed to determine efficacy. -
Description of Bacillus Laevolacticus (Ex Nakayarna and Yanoshi 1967) Sp
INTERNATIONAL JOURN~OF SYSTEMATIC BACTERIOLOGY,OCt. 1994, p. 659-664 Vol. 44, No. 4 0020-7713/94/$04.00 + 0 Copyright 0 1994, International Union of Microbiological Societies Description of Bacillus laevolacticus (ex Nakayarna and Yanoshi 1967) sp. nov., norn. rev. I. ANDERSCH,? S. PIANKA, D. FRITZE,* AND D. CLAUS DSM-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 0-38124 Braunschweig, Germany The name “Bacillus laevolacticus” Nakayama and Yanoshi 1967 was not included on the Approved Lists of Bacterial Names and therefore has no standing in bacteriological nomenclature. In this study 22 catalase- positive, acid-tolerant, facultatively anaerobic, lactic acid-producingBacillus strains were examined taxonom- ically and compared with a number of strains belonging to phenetically similar Bacillus species (Bacillus coagulans, Bacillus smithii, “Bacillus vesiculiferous”) and with Sporolactobacillus. The G+ C contents (43 to 45 mol%), DNA-DNA homology values (72 to 98%), and results of phenetic similarity analyses revealed that the members of the 44B.laevolacticus” group were very homogeneous in their phenotypic and genotypic character- istics and clearly distinguishable from other Bacillus and SporolactobaciUus species. On the basis of these findings, revival of the name Bacillus laevolacticus is proposed. Traditionally, production of lactic acid is observed in micro- walls containing diaminopimelic acid were consistent with organisms which are grouped under the term “lactic acid the description of the genus Bacillus. Accordingly, these bacteria.” However, a considerable number of lactic acid- organisms were placed in a new genus, Sporolactobacillus, as producing, aerobic, spore-forming organisms have been de- Sporolactobacillus inulinus. Similar organisms, including scribed. These bacteria have been isolated from food or in “Sporolactobacillus laevas,” “Sporolactobacillus laevas var. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions. -
Unraveling the Underlying Heavy Metal Detoxification Mechanisms Of
microorganisms Review Unraveling the Underlying Heavy Metal Detoxification Mechanisms of Bacillus Species Badriyah Shadid Alotaibi 1, Maryam Khan 2 and Saba Shamim 2,* 1 Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; [email protected] 2 Institute of Molecular Biology and Biotechnology (IMBB), Defence Road Campus, The University of Lahore, Lahore 55150, Pakistan; [email protected] * Correspondence: [email protected] Abstract: The rise of anthropogenic activities has resulted in the increasing release of various contaminants into the environment, jeopardizing fragile ecosystems in the process. Heavy metals are one of the major pollutants that contribute to the escalating problem of environmental pollution, being primarily introduced in sensitive ecological habitats through industrial effluents, wastewater, as well as sewage of various industries. Where heavy metals like zinc, copper, manganese, and nickel serve key roles in regulating different biological processes in living systems, many heavy metals can be toxic even at low concentrations, such as mercury, arsenic, cadmium, chromium, and lead, and can accumulate in intricate food chains resulting in health concerns. Over the years, many physical and chemical methods of heavy metal removal have essentially been investigated, but their disadvantages like the generation of chemical waste, complex downstream processing, and the uneconomical cost of both methods, have rendered them inefficient,. Since then, microbial bioremediation, particularly the Citation: Alotaibi, B.S.; Khan, M.; use of bacteria, has gained attention due to the feasibility and efficiency of using them in removing Shamim, S. Unraveling the heavy metals from contaminated environments. Bacteria have several methods of processing heavy Underlying Heavy Metal metals through general resistance mechanisms, biosorption, adsorption, and efflux mechanisms. -
Product Sheet Info
Product Information Sheet for HM-331 Sporosarcina sp., Strain 2681 Incubation: Temperature: 37°C Atmosphere: Aerobic Catalog No. HM-331 Propagation: 1. Keep vial frozen until ready for use, then thaw. For research use only. Not for human use. 2. Transfer the entire thawed aliquot into a single tube of broth. Contributor: 3. Use several drops of the suspension to inoculate an Kimberlee A. Musser, Ph.D., Chief, Bacterial Diseases, agar slant and/or plate. Division of Infectious Diseases, Wadsworth Center, New York 4. Incubate the tubes and plate at 37°C for 48 hours. State Department of Health, Albany, New York Citation: Manufacturer: NIH Biodefense and Emerging Infections Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Research Resource Repository Emerging Infections Research Resources Repository, NIAID, NIH as part of the Human Microbiome Project: Sporosarcina Product Description: sp., Strain 2681, HM-331.” Bacteria Classification: Planococcaceae, Sporosarcina Species: Sporosarcina sp. Biosafety Level: 2 Strain: 2681 Original Source: Sporosarcina sp., strain 2681 was isolated Appropriate safety procedures should always be used with 1 this material. Laboratory safety is discussed in the following from human blood. Comments: Sporosarcina sp., strain 2681 is a reference publication: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and genome for The Human Microbiome Project (HMP). HMP Prevention, and National Institutes of Health. Biosafety in is an initiative to identify and characterize human microbial flora. The complete genome of Sporosarcina sp., strain Microbiological and Biomedical Laboratories. 5th ed. Washington, DC: U.S. Government Printing Office, 2007; see 2681 is currently being sequenced at the Human Genome www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. -
Sporosarcina Aquimarina Sjam16103 Isolated from the Pneumatophores of Avicennia Marina L
Hindawi Publishing Corporation International Journal of Microbiology Volume 2012, Article ID 532060, 10 pages doi:10.1155/2012/532060 Research Article Plant Growth Promoting of Endophytic Sporosarcina aquimarina SjAM16103 Isolated from the Pneumatophores of Avicennia marina L. S. Rylo Sona Janarthine1 and P. Eganathan2 1 Faculty of Marine Science, Annamalai University, Chidambaram 608 502, India 2 Biotechnology Division, M S Swaminathan Research Foundation, Chennai 600 113, India Correspondence should be addressed to S. Rylo Sona Janarthine, jana [email protected] Received 17 October 2011; Revised 12 January 2012; Accepted 20 April 2012 AcademicEditor:A.J.M.Stams Copyright © 2012 S. R. S. Janarthine and P. Eganathan. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Endophytic Sporosarcina aquimarina SjAM16103 was isolated from the inner tissues of pneumatophores of mangrove plant Avicennia marina along with Bacillus sp. and Enterobacter sp. Endophytic S. aquimarina SjAM16103 was Gram variable, and motile bacterium measured 0.6–0.9 μm wide by 1.7–2.0 μm long and light orange-brown coloured in 3-day cultures on tryptone broth at 26◦C. Nucleotide sequence of this strain has been deposited in the GenBank under accession number GU930359. This endophytic bacterium produced 2.37 μMol/mL of indole acetic acid and siderophore as it metabolites. This strain could solubilize phosphate molecules and fixes atmospheric nitrogen. Endophytic S. aquimarina SjAM16103 was inoculated into four different plants under in vitro method to analyse its growth-promoting activity and role inside the host plants.