Metagenomic and Metatranscriptomic Analyses of Lake Vostok Accretion Ice
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Chemical Structures of Some Examples of Earlier Characterized Antibiotic and Anticancer Specialized
Supplementary figure S1: Chemical structures of some examples of earlier characterized antibiotic and anticancer specialized metabolites: (A) salinilactam, (B) lactocillin, (C) streptochlorin, (D) abyssomicin C and (E) salinosporamide K. Figure S2. Heat map representing hierarchical classification of the SMGCs detected in all the metagenomes in the dataset. Table S1: The sampling locations of each of the sites in the dataset. Sample Sample Bio-project Site depth accession accession Samples Latitude Longitude Site description (m) number in SRA number in SRA AT0050m01B1-4C1 SRS598124 PRJNA193416 Atlantis II water column 50, 200, Water column AT0200m01C1-4D1 SRS598125 21°36'19.0" 38°12'09.0 700 and above the brine N "E (ATII 50, ATII 200, 1500 pool water layers AT0700m01C1-3D1 SRS598128 ATII 700, ATII 1500) AT1500m01B1-3C1 SRS598129 ATBRUCL SRS1029632 PRJNA193416 Atlantis II brine 21°36'19.0" 38°12'09.0 1996– Brine pool water ATBRLCL1-3 SRS1029579 (ATII UCL, ATII INF, N "E 2025 layers ATII LCL) ATBRINP SRS481323 PRJNA219363 ATIID-1a SRS1120041 PRJNA299097 ATIID-1b SRS1120130 ATIID-2 SRS1120133 2168 + Sea sediments Atlantis II - sediments 21°36'19.0" 38°12'09.0 ~3.5 core underlying ATII ATIID-3 SRS1120134 (ATII SDM) N "E length brine pool ATIID-4 SRS1120135 ATIID-5 SRS1120142 ATIID-6 SRS1120143 Discovery Deep brine DDBRINP SRS481325 PRJNA219363 21°17'11.0" 38°17'14.0 2026– Brine pool water N "E 2042 layers (DD INF, DD BR) DDBRINE DD-1 SRS1120158 PRJNA299097 DD-2 SRS1120203 DD-3 SRS1120205 Discovery Deep 2180 + Sea sediments sediments 21°17'11.0" -
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…………………………….………. -
Microbial Diversity of Molasses Containing Tobacco (Maassel) Unveils Contamination with Many Human Pathogens
European Review for Medical and Pharmacological Sciences 2021; 25: 4919-4929 Microbial diversity of molasses containing tobacco (Maassel) unveils contamination with many human pathogens M.A.A. ALQUMBER Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia Abstract. – OBJECTIVE: Tobacco smoking drugs in today’s modern world. Different meth- remains a worldwide health issue, and the use of ods are currently used to consume tobacco, in- flavored varieties (maassel) embedded in glyc- cluding cigarettes, cigars and waterpipes1. Water- erine, molasses, and fruit essence via shisha pipe (shisha) smoking continues to rise globally2. paraphernalia (waterpipe) is growing globally. Smoking flavored tobacco (maassel), through the 16S rRNA gene pyrosequencing was conduct- shisha, is becoming a global preventable cause of ed on 18 different varieties representing 16 fla- 3,4 vors and three brands in order to study the mi- morbidity and mortality . crobiota of maassel and find whether it contains Scientists studied the chemical composition of pathogenic bacteria. tobacco for many years and illustrated the total MATERIALS AND METHODS: The samples number of chemicals identified in tobacco during were selected randomly from the most utilized the years from 1954 to 20055. In addition, a com- brands within Albaha, Saudi Arabia as deter- prehensive review of these chemicals’ classifica- mined through a questionnaire of 253 smok- ers. In addition, ten-fold serially diluted sam- tion, concentration and changes with time due ples were inoculated on blood agar, MacConkey to changes in the shape, design and composition agar, half-strength trypticase soy agar and malt of cigarettes was reported almost a decade ago6. -
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. -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Methanogenic Activity in Río Tinto, a Terrestrial Mars Analogue R
Methanogenic activity in Río Tinto, a terrestrial Mars analogue R. Amils Centro de Biología Molecular Severo Ochoa (UAM-CSIC) y Centro de Astrobiología (INTA- CSIC) Frascati, noviembre 2009 new insides in the Mars exploration H2O on Mars methane (PFS) it can be concluded that on Mars there are sedimentary rocks that were formed in acidic conditions (acidic lakes or oceans) • possible terrestrial analogs: - submarine hydrothermalism - acidic environments to explore the deep sea requires expensive equipment (Alvin) natural acidic waters natural acidic environments: - areas with volcanic activity 0 SO2 + H2S ——> S + H2O - metal mining activities 3+ 2- + FeS2 + H2O —> Fe + SO4 + H in this case the extreme acidic conditions are promoted by biological activity geomicrobiology of metallic sulfides pyrite, molibdenite, tungstenite (thiosulfate mec.) 3+ 2- 2+ + FeS2+6Fe +3H2O → S2O3 +7Fe +6H 2- 3+ 2- 2+ + S2O3 +8Fe +5H2O → 2SO4 +8Fe +10H Rest of sulfides (polisulfide mec.) 3+ + 2+ 2+ 8MS+8Fe +8H → 8M +4H2Sn+8Fe (n≥2) 3+ o 2+ + 4H2Sn+8Fe → S8 +8Fe +8H o 2- + S8 +4H2O (S oxidizers) → SO4 +8H Bacterias come-meteoritos role of the microbial activity in the leaching of pyrite chemical 3+ reaction Fe Fe2+ microbial activity 2- + SO4 + H Rio Tinto rise at the heart of the Iberian Pyritic Belt Río Tinto is an acidic river, pH 2.3, 100 km long and with a high concentration of soluble metals the iron concentration at the origin is between 15-20 g/l and the sulfate is constant and around 15 g/l geoMICROBIOLOGY combination of conventional microbial ecology techniques and molecular ecology tools A B Phylogeny of acidophilic microorganisms detected in Rio Tinto Actinobacteria Cyanobacteria . -
Extremozymes of the Hot and Salty Halothermothrix Orenii
Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
SUPPLEMENTARY INFORMATIONARTICLES https://doi.org/10.1038/s41559-020-1221-7 In the format provided by the authors and unedited. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. -
Updating the Taxonomic Toolbox: Classification of Alteromonas Spp
1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp. -
Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor. -
UNIVERSITY of CALIFORNIA, SAN DIEGO Indicators of Iron
UNIVERSITY OF CALIFORNIA, SAN DIEGO Indicators of Iron Metabolism in Marine Microbial Genomes and Ecosystems A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Shane Lahman Hogle Committee in charge: Katherine Barbeau, Chair Eric Allen Bianca Brahamsha Christopher Dupont Brian Palenik Kit Pogliano 2016 Copyright Shane Lahman Hogle, 2016 All rights reserved . The Dissertation of Shane Lahman Hogle is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2016 iii DEDICATION Mom, Dad, Joel, and Marie thank you for everything iv TABLE OF CONTENTS Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents .................................................................................................................v List of Figures ................................................................................................................... vii List of Tables ..................................................................................................................... ix Acknowledgements ..............................................................................................................x Vita .................................................................................................................................. -
Diversity of Culturable Bacteria Including Pantoea in Wild Mosquito Aedes Albopictus Claire Valiente Moro, Florence-Hélène Tran, F
Diversity of culturable bacteria including Pantoea in wild mosquito Aedes albopictus Claire Valiente Moro, Florence-Hélène Tran, F. N. Raharimalala, P. Ravelonandro, Patrick Mavingui To cite this version: Claire Valiente Moro, Florence-Hélène Tran, F. N. Raharimalala, P. Ravelonandro, Patrick Mavin- gui. Diversity of culturable bacteria including Pantoea in wild mosquito Aedes albopictus. BMC Microbiology, BioMed Central, 2013, 13 (1), pp.70. 10.1186/1471-2180-13-70. hal-02522192 HAL Id: hal-02522192 https://hal-univ-lyon1.archives-ouvertes.fr/hal-02522192 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Valiente Moro et al. BMC Microbiology 2013, 13:70 http://www.biomedcentral.com/1471-2180/13/70 RESEARCH ARTICLE Open Access Diversity of culturable bacteria including Pantoea in wild mosquito Aedes albopictus Claire Valiente Moro1,2*, Florence Hélène Tran1,2, Fara Nantenaina Raharimalala3,5, Pierre Ravelonandro4 and Patrick Mavingui1,2 Abstract Background: The microbiota has been shown to play an important role in the biology of insects. In recent decades, significant efforts have been made to better understand the diversity of symbiotic bacteria associated with mosquitoes and assess their influence on pathogen transmission.