Do Soil Metagenomes Differ According to Our Expectations?
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Chapter 1.0: Introduction
CHAPTER 1.0: INTRODUCTION 1.1 Why study Antarctica? The Antarctic includes some of the most extreme terrestrial environments by very low temperature, frequent freeze-thaw and wet-dry cycles, low and transient precipitation, reduced humidity, rapid drainage and limited organic nutrients which are considered as unfavorable condition (Yergeau et al., 2006). Located in the Earth‟s south hemisphere, Antarctica has received considerable amount of attention due to its untapped resources. Renowned for its cold, harsh conditions, there is an abundance of microbial life which has undergone their own adaption and evolutionary processes to survive. Since, Antarctic microbial habitats have remained relatively conserved for many years; there are unique opportunities for studying microbial evolution (Vincent, 2000). Besides that, presence of psychrophiles and other extermophiles in the environment are interesting specimens of nature‟s wonder. Psychrophilic enzymes produced have high potential in biotechnology for example the conservation of energy by reducing the need of heat treatment, the application of eurythermal polar cyanobacteria for wastewater treatment in cold climates (Tang et al., 1997) and the integration of proteases, lipases and cellulases into detergents to improve its mode of action in cold water. 1.2 Antarctic microorganisms Although bacterial researches have been conducted since early 1900s by Ekelof (Boyd and Boyd, 1962), little is known about the presence and characteristics of bacteria in the Antarctica. Microorganisms dominate Antarctic biology compare to other continent (Friedmann, 1993) as well as they are fundamental to the functioning of Antarctic ecosystems. Baseline knowledge of prokaryotic biodiversity in Antarctica is still limited (Bohannan 1 and Hughes, 2003). Among these microorganisms, bacteria are an important part of the soil. -
Deinococcus Antarcticus Sp. Nov., Isolated from Soil
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 331–335 DOI 10.1099/ijs.0.066324-0 Deinococcus antarcticus sp. nov., isolated from soil Ning Dong,1,2 Hui-Rong Li,1 Meng Yuan,1,2 Xiao-Hua Zhang2 and Yong Yu1 Correspondence 1SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, Yong Yu PR China [email protected] 2College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China A pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20T, was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m”2) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans. Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. Highest sequence similarities were with Deinococcus ficus CC-FR2-10T (93.5 %), Deinococcus xinjiangensis X-82T (92.8 %), Deinococcus indicus Wt/1aT (92.5 %), Deinococcus daejeonensis MJ27T (92.3 %), Deinococcus wulumuqiensis R-12T (92.3 %), Deinococcus aquaticus PB314T (92.2 %) and T Deinococcus radiodurans DSM 20539 (92.2 %). Major fatty acids were C18 : 1v7c, summed feature 3 (C16 : 1v7c and/or C16 : 1v6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20T was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20T represents a novel species of the genus Deinococcus, for which the name Deinococcus antarcticus sp. -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats: a Comparison Between Bidirectional Pyrosequencing and Cultivation
Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats: A Comparison between Bidirectional Pyrosequencing and Cultivation Bjorn Tytgat1*, Elie Verleyen2, Dagmar Obbels2, Karolien Peeters1¤a, Aaike De Wever2¤b, Sofie D’hondt2, Tim De Meyer3, Wim Van Criekinge3, Wim Vyverman2, Anne Willems1 1 Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium, 2 Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium, 3 Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium Abstract The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1– 22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). -
(12) Patent Application Publication (10) Pub. No.: US 2014/0017724 A1 LEONETT Et Al
US 20140017724A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0017724 A1 LEONETT et al. (43) Pub. Date: Jan. 16, 2014 (54) METHODS FOR ISOLATING BACTERIA (30) Foreign Application Priority Data (71) Applicants:CENTRE NATIONAL DE LA Jan. 19, 2009 (EP) .................................. O9305041.7 RECHERCHE SCIENTIFIOUE, Paris Cedex 16 (FR); DEINOVE, Paris (FR) Publication Classification (72) Inventors: JEAN-PAUL LEONETTI, Montpellier (51) Int. Cl. (FR); STEPHANIETEXIER, CI2P I/04 (2006.01) Montauban (FR) CI2R I/OI (2006.01) CI2P 23/00 (2006.01) (73) Assignees: CENTRE NATIONAL DE LA (52) U.S. Cl. RECHERCHE SCIENTIFIOUE, Paris CPC, C12P I/04 (2013.01): CI2P 23/00 (2013.01); Cedex 16 (FR); DEINOVE, Paris (FR) CI2R I/01 (2013.01) USPC ........... 435/67; 435/170; 435/71.3; 435/69.4: (21) Appl. No.: 14/030,504 435/101; 435/252.1 (57) ABSTRACT (22) Filed: Sep. 18, 2013 The present invention relates to compositions and methods to identify novel bacteria and metabolites derived therefrom. Related U.S. Application Data More specifically, the invention describes a novel method to isolate bacteria producing metabolites of interest from envi (63) Rsingit. E; ronmental samples. Particularly, the invention discloses a EP2010/05 o 51 3. O Jan 18, 201 p method to select rare antibiotic producing bacteria. The • Y-s invention can be used from any sample and allows the isola (60) Provisional application No. 61/145,606, filed on Jan. tion of bacteria having e.g., pharmaceutical or agrochemical 19, 2009. interest. Patent Application Publication Jan. 16, 2014 US 2014/0017724 A1 igure 1a Figure 1b US 2014/0017724 A1 Jan. -
Microbial Hitchhikers on Intercontinental Dust: Catching a Lift in Chad
The ISME Journal (2013) 7, 850–867 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Microbial hitchhikers on intercontinental dust: catching a lift in Chad Jocelyne Favet1, Ales Lapanje2, Adriana Giongo3, Suzanne Kennedy4, Yin-Yin Aung1, Arlette Cattaneo1, Austin G Davis-Richardson3, Christopher T Brown3, Renate Kort5, Hans-Ju¨ rgen Brumsack6, Bernhard Schnetger6, Adrian Chappell7, Jaap Kroijenga8, Andreas Beck9,10, Karin Schwibbert11, Ahmed H Mohamed12, Timothy Kirchner12, Patricia Dorr de Quadros3, Eric W Triplett3, William J Broughton1,11 and Anna A Gorbushina1,11,13 1Universite´ de Gene`ve, Sciences III, Gene`ve 4, Switzerland; 2Institute of Physical Biology, Ljubljana, Slovenia; 3Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA; 4MO BIO Laboratories Inc., Carlsbad, CA, USA; 5Elektronenmikroskopie, Carl von Ossietzky Universita¨t, Oldenburg, Germany; 6Microbiogeochemie, ICBM, Carl von Ossietzky Universita¨t, Oldenburg, Germany; 7CSIRO Land and Water, Black Mountain Laboratories, Black Mountain, ACT, Australia; 8Konvintsdyk 1, Friesland, The Netherlands; 9Botanische Staatssammlung Mu¨nchen, Department of Lichenology and Bryology, Mu¨nchen, Germany; 10GeoBio-Center, Ludwig-Maximilians Universita¨t Mu¨nchen, Mu¨nchen, Germany; 11Bundesanstalt fu¨r Materialforschung, und -pru¨fung, Abteilung Material und Umwelt, Berlin, Germany; 12Geomatics SFRC IFAS, University of Florida, Gainesville, FL, USA and 13Freie Universita¨t Berlin, Fachbereich Biologie, Chemie und Pharmazie & Geowissenschaften, Berlin, Germany Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bode´le´ Depression in the Republic of Chad has been called the dustiest place on earth. -
Identification and Properties of the Deinococcus Grandis and Deinococcus Proteolyticus Single-Stranded DNA Binding Proteins (SSB)
Vol. 54 No. 1/2007, 79–87 on-line at: www.actabp.pl Regular paper Identification and properties of the Deinococcus grandis and Deinococcus proteolyticus single-stranded DNA binding proteins (SSB) Paweł Filipkowski and Józef Kur Gdańsk University of Technology, Chemical Faculty, Department of Microbiology, Gdańsk, Poland Received: 18 September, 2006; revised: 03 January, 2007; accepted: 18 January, 2007 available on-line: 27 February, 2007 To study the biochemical properties of SSB’s from Deinococcus grandis (DgrSSB) and Deinoc- occus proteolyticus (DprSSB), we have cloned the ssb genes obtained by PCR and have devel- oped Escherichia coli overexpression systems. The genes consist of an open reading frame of 891 (DgrSSB) and 876 (DprSSB) nucleotides encoding proteins of 296 and 291 amino acids with a cal- culated molecular mass of 32.29 and 31.33 kDa, respectively. The amino-acid sequence of DgrSSB exhibits 45%, 44% and 82% identity and the amino-acid sequence of DprSSB reveals 43%, 43% and 69% identity with Thermus aquaticus (TaqSSB), Thermus thermophilus (TthSSB) and Deinoc- occus radiodurans SSBs, respectively. We show that DgrSSB and DprSSB are similar to Thermus/ Deinococcus SSBs in their biochemical properties. They are functional as homodimers, with each monomer encoding two single-stranded DNA binding domains (OB-folds). In fluorescence titra- tions with poly(dT), both proteins bind single-stranded DNA with a binding site size of about 33 nt per homodimer. In a complementation assay in E. coli, DgrSSB and DprSSB took over the in vivo function of EcoSSB. Thermostability with half-lives of about 1 min at 65–67.5°C make DgrSSB and DprSSB similar to the known SSB of Deinococcus radiodurans (DraSSB). -
Distribution and Characterization of Bacterial Communities in Diverse Antarctic Ecosystems by High-Throughput Sequencing
––– Distribution and characterization of bacterial communities in diverse Antarctic ecosystems by high-throughput sequencing Bjorn Tytgat Promotors Prof. Dr. Anne Willems Prof. Dr. Elie Verleyen Dissertation submitted in fulfilment of the requirements for the degree of Doctor (Ph.D) in Sciences, Biology (Ghent University) Tytgat Bjorn | Distribution and characterization of bacterial communities in diverse Antarctic ecosystems by high-throughput sequencing Copyright © 2016, Bjorn Tytgat ISBN-number: 978-9-4619738-8-7 All rights reserved. No part of this thesis protected by its copyright notice may be reproduced or utilized in any form or any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Funding: This thesis was supported by the Special Research Fund BOF of Ghent University (grant 0J28410) and by the Belgian Science Policy Office (BelSPO) project CCAMBIO. Ph.D. Thesis, Faculty of Sciences, Ghent University, Ghent, Belgium Publicly defended in Ghent, Belgium, April 28th, 2016 ii Examination committee Prof. Dr. Koen Sabbe (Chairman) Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Olivier De Clerck (Secretary) Phycology Research Group, Ghent University Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Anne Willems (Promotor) Laboratory of Microbiology Department of Microbiology and Biochemistry, Faculty of Sciences, Ghent University Prof. Dr. Elie Verleyen (Co-promotor) Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Wim Vyverman Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. -
Radiation Resistant of Native Deinococcus Spp. Isolated from the Lout Desert of Iran ‘‘The Hottest Place on Earth’’
Int. J. Environ. Sci. Technol. (2014) 11:1939–1946 DOI 10.1007/s13762-014-0643-7 ORIGINAL PAPER Radiation resistant of native Deinococcus spp. isolated from the Lout desert of Iran ‘‘the hottest place on Earth’’ M. Mohseni • J. Abbaszadeh • A. Nasrollahi Omran Received: 27 January 2014 / Revised: 9 May 2014 / Accepted: 2 July 2014 / Published online: 23 July 2014 Ó Islamic Azad University (IAU) 2014 Abstract Two native ionizing radiation-resistant bacteria Keywords Deinococcus Á Radiation-resistant bacteria Á were isolated and identified from a soil sample collected Ionizing radiation Á Lout desert from extreme conditions of the Lout desert in Iran. The hottest land surface temperature has been recorded in the Lout desert from 2004 to 2009. Also, it is categorized as a Introduction hyper arid place. Both ionizing radiation and desiccation may cause damage on genome. Soil sample was irradiated Members of genus Deinococcus are able to live in extreme in order to eliminate sensitive bacteria then cultured in one- conditions such as arid deserts, under ionizing radiations, tenth-strength tryptic soy broth medium. Bacterial sus- ROS (reactive oxygen species) molecules and other oxi- pension used for radiation treatment. Morphological and dative stress inducing chemicals (Slade and Radman 2011). physiological characterization and phylogenetic studies This astonishing ability in Deinococcus is due to its repair based on 16S rRNA gene sequence were used for identifi- mechanisms (Minton 1994). It is well known that radiation- cation. The cells were rod shape, non-motile, non-spore resistant bacteria have evolved recombination repair and forming and gram positive. The 16S rRNA gene sequence strong antioxidant systems to survive ROS-mediated showed 99.5 % of similarity to Deinococcus ficus. -
Methods for Isolating Bacteria
(19) & (11) EP 2 210 935 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 28.07.2010 Bulletin 2010/30 C12N 1/00 (2006.01) (21) Application number: 09305041.7 (22) Date of filing: 19.01.2009 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Leonetti, Jean-Paul HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL 34170 Castelnau Le Lez (FR) PT RO SE SI SK TR • Texier, Stéphanie Designated Extension States: 34090 Montpellier (FR) AL BA RS (74) Representative: Gallois, Valérie et al (71) Applicants: Cabinet BECKER & ASSOCIES • Deinove 25, rue Louis Le Grand 75010 Paris (FR) 75002 Paris (FR) • Centre National de la Recherche Scientifique 75016 Paris Cedex 16 (FR) (54) Methods for isolating bacteria (57) The present invention relates to compositions ularly, the invention discloses a method to select rare and methods to identify novel bacteria and metabolites antibiotic producing bacteria. The invention can be used derived therefrom. More specifically, the invention de- from any sample and allows the isolation of bacteria hav- scribes a novel method to isolate bacteria producing me- ing e.g., pharmaceutical or agrochemical interest. tabolites of interest from environmental samples. Partic- EP 2 210 935 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 210 935 A1 Description [0001] The present invention relates to compositions and methods to identify novel bacteria and metabolites derived therefrom. More specifically, the invention describes a novel method to isolate bacteria producing metabolites of interest 5 from environmental samples. -
The Role of Photoheterotrophic and Chemoautotrophic
The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Guillaume Tahon Promotor Prof. Dr. Anne Willems Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) of Science: Biotechnology (Ghent University) Tahon Guillaume | The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Copyright © 2017, Tahon Guillaume ISBN-number: 978-94-6197-523-2 All rights are reserved. No part of this thesis protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotor. Printed by University Press | http://www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium This Ph.D. work was supported by the Fund for Scientific Research – Flanders (project G.0146.12) Publically defended in Ghent, Belgium, May 5th, 2017 Examination committee Prof. Dr. Savvas Savvides (Chairman) L-Probe: Laboratory for protein Biochemistry and Biomolecular Engineering Faculty of Sciences, Ghent University, Belgium VIB Inflammation Research Center VIB, Ghent, Belgium Prof. Dr. Anne Willems (Promotor) LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Elie Verleyen (Secretary) Laboratory of Protistology and Aquatic Ecology Faculty of Sciences, Ghent University, Belgium Em. Prof. Dr. Paul De Vos LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Dr. Natalie Leys SCK·CEN: Environment, Health and Safety Belgian Nuclear Research Centre, Mol, Belgium Dr. -
Isolation and Characterization of Aerobic Anoxygenic Phototrophs
Systematic and Applied Microbiology 40 (2017) 357–369 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica ∗ Guillaume Tahon, Anne Willems Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium a r t i c l e i n f o a b s t r a c t Article history: This study investigated the culturable aerobic phototrophic bacteria present in soil samples collected in Received 16 March 2017 the proximity of the Belgian Princess Elisabeth Station in the Sør Rondane Mountains, East Antarctica. Received in revised form 15 May 2017 Until recently, only oxygenic phototrophic bacteria (Cyanobacteria) were well known from Antarctic soils. Accepted 16 May 2017 However, more recent non-cultivation-based studies have demonstrated the presence of anoxygenic phototrophs and, particularly, aerobic anoxygenic phototrophic bacteria in these areas. Approximately Keywords: 1000 isolates obtained after prolonged incubation under different growth conditions were studied and pufLM characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Repre- AAP Proteorhodopsin sentative strains were identified by sequence analysis of 16S rRNA genes. More than half of the isolates Actinorhodopsin grouped among known aerobic anoxygenic phototrophic taxa, particularly with Sphingomonadaceae, Cultivation Methylobacterium and Brevundimonas. In addition, a total of 330 isolates were tested for the presence of key phototrophy genes. While rhodopsin genes were not detected, multiple isolates possessed key genes of the bacteriochlorophyll synthesis pathway. The majority of these potential aerobic anoxygenic phototrophic strains grouped with Alphaproteobacteria (Sphingomonas, Methylobacterium, Brevundimonas and Polymorphobacter).