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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. -
Characterization of Stress Tolerance and Metabolic Capabilities of Acidophilic Iron-Sulfur-Transforming Bacteria and Their Relevance to Mars
Characterization of stress tolerance and metabolic capabilities of acidophilic iron-sulfur-transforming bacteria and their relevance to Mars Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften – Dr. rer. nat. – vorgelegt von Anja Bauermeister aus Leipzig Im Fachbereich Chemie der Universität Duisburg-Essen 2012 Die vorliegende Arbeit wurde im Zeitraum von März 2009 bis Dezember 2012 im Arbeitskreis von Prof. Dr. Hans-Curt Flemming am Biofilm Centre (Fakultät für Chemie) der Universität Duisburg-Essen und in der Abteilung Strahlenbiologie (Institut für Luft- und Raumfahrtmedizin, Deutsches Zentrum für Luft- und Raumfahrt, Köln) durchgeführt. Tag der Einreichung: 07.12.2012 Tag der Disputation: 23.04.2013 Gutachter: Prof. Dr. H.-C. Flemming Prof. Dr. W. Sand Vorsitzender: Prof. Dr. C. Mayer Erklärung / Statement Hiermit versichere ich, dass ich die vorliegende Arbeit mit dem Titel „Characterization of stress tolerance and metabolic capabilities of acidophilic iron- sulfur-transforming bacteria and their relevance to Mars” selbst verfasst und keine außer den angegebenen Hilfsmitteln und Quellen benutzt habe, und dass die Arbeit in dieser oder ähnlicher Form noch bei keiner anderen Universität eingereicht wurde. Herewith I declare that this thesis is the result of my independent work. All sources and auxiliary materials used by me in this thesis are cited completely. Essen, 07.12.2012 Table of contents Abbreviations ....................................................................................... -
Deinococcus Radiodurans : La Recombinaison Entre S´Equencesr´Ep´Et´Eeset La Transformation Naturelle Solenne Ithurbide
Variabilit´eg´en´etiquechez la bact´erieradior´esistante Deinococcus radiodurans : la recombinaison entre s´equencesr´ep´et´eeset la transformation naturelle Solenne Ithurbide To cite this version: Solenne Ithurbide. Variabilit´eg´en´etiquechez la bact´erieradior´esistante Deinococcus radio- durans : la recombinaison entre s´equencesr´ep´et´eeset la transformation naturelle. Biologie mol´eculaire.Universit´eParis Sud - Paris XI, 2015. Fran¸cais. <NNT : 2015PA112193>. <tel- 01374867> HAL Id: tel-01374867 https://tel.archives-ouvertes.fr/tel-01374867 Submitted on 2 Oct 2016 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE 426 GÈNES GÉNOMES CELLULES Institut de Biologie Intégrative de la Cellule THÈSE DE DOCTORAT SCIENCES DE LA VIE ET DE LA SANTÉ par Solenne ITHURBIDE Variabilité génétique chez la bactérie radiorésistante Deinococcus radiodurans : La recombinaison entre séquences répétées et la transformation naturelle Soutenue le 23 Septembre 2015 Composition du jury : Directeur de thèse : Suzanne SOMMER Professeur -
A Moderately Boron-Tolerant Candidatus Novel Soil Bacterium Lysinibacillus Pakistanensis Sp
Pak. J. Bot., 45(SI): 41-50, January 2013. A MODERATELY BORON-TOLERANT CANDIDATUS NOVEL SOIL BACTERIUM LYSINIBACILLUS PAKISTANENSIS SP. NOV. CAND., ISOLATED FROM SOYBEAN (GLYCINE MAX L.) RHIZOSPHERE RIFAT HAYAT1,2,3*, IFTIKHAR AHMED2*, JAYOUNG PAEK4, MUHAMMAD EHSAN1, 2, MUHAMMAD IQBAL2 AND YOUNG H. CHANG4* 1Department of Soil Science & SWC, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan 2Plant Biotechnology Program, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad-45500, Pakistan 3Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan 4Korean Collection of Type Cultures, Biological Resource Center, KRIBB, 52 Oeundong, Daejeon 305-806, Republic of Korea *Correspondence E-mail: [email protected]; [email protected]; [email protected] Abstract A Gram-positive, motile, rod-shaped, endospore-forming and moderately boron (B) tolerant novel candidatus strain, designated as NCCP-54T, was isolated from rhizospheric soil of soybean (Glycine max L.) sampled from the experimental area of Research Farm, PMAS Arid Agriculture University, Rawalpindi, Pakistan. To delineate its taxonomic position, the strain was subject to polyphasic characterization. Cells of the strain NCCP-54T can grow at 10-45○C (optimum at 28○C) at pH ranges of 6.5-9.0 (optimum at pH 7.0) and in 0-6% NaCl (w/v) in tryptic soya agar medium. It can also tolerate 150 mM boric acid in agar medium; however, optimum growth occurs in the absence of boric acid. Based on 16S rRNA gene sequence analysis, strain NCCP-54T showed highest similarity to Lysinibacillus xylanilyticus KCTC13423T (99.1%), Lysinibacillus fusiformis KCTC3454T (98.5%), Lysinibacillus boronitolerans KCTC13709T (98.4%), Lysinibacillus parviboronicapiens KCTC13154T (97.8%), and Lysinibacillus sphaericus KCTC3346T (97.5%) and less than 97% with other closely related taxa. -
Experimental and Statistical Analysis of Nutritional Requirements for the Growth of the Extremophile Deinococcus Geothermalis DSM 11300
Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300 Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gorret To cite this version: Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gor- ret. Experimental and statistical analysis of nutritional requirements for the growth of the ex- tremophile Deinococcus geothermalis DSM 11300. Extremophiles, Springer Verlag, 2014, 18 (6), pp.1009-1021. 10.1007/s00792-014-0671-8. hal-01268947 HAL Id: hal-01268947 https://hal.archives-ouvertes.fr/hal-01268947 Submitted on 11 Mar 2019 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. OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible This is an author’s version published in: http://oatao.univ-toulouse.fr/22999 Official URL: https://doi.org/10.1007/s00792-014-0671-8 To cite this version: Bornot, Julie and Aceves-Lara, César-Arturo and Molina-Jouve, Carole and Uribelarrea, Jean-Louis and Gorret, Nathalie Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. -
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. -
Bacillus Safensis FO-36B and Bacillus Pumilus SAFR-032: a Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates
bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: A Whole Genome 2 Comparison of Two Spacecraft Assembly Facility Isolates 3 Madhan R Tirumalai1, Victor G. Stepanov1, Andrea Wünsche1, Saied Montazari1, 4 Racquel O. Gonzalez1, Kasturi Venkateswaran2, George. E. Fox1§ 5 1Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001. 6 2 Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California 7 Institute of Technology, Pasadena, CA, 91109. 8 9 §Corresponding author: 10 Dr. George E. Fox 11 Dept. Biology & Biochemistry 12 University of Houston, Houston, TX 77204-5001 13 713-743-8363; 713-743-8351 (FAX); email: [email protected] 14 15 Email addresses: 16 MRT: [email protected] 17 VGS: [email protected] 18 AW: [email protected] 19 SM: [email protected] 20 ROG: [email protected] 21 KV: [email protected] 22 GEF: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide 24 resistance, genome comparison, phage insertions 25 26 Background 27 Microbial persistence in built environments such as spacecraft cleanroom facilities [1-3] is often 28 characterized by their unusual resistances to different physical and chemical factors [1, 4-7]. -
The Effects of Natural Variation in Background Radioactivity on Humans, Animals and Other Organisms
Biol. Rev. (2012), pp. 000–000. 1 doi: 10.1111/j.1469-185X.2012.00249.x The effects of natural variation in background radioactivity on humans, animals and other organisms Anders P. Møller1,∗ and Timothy A. Mousseau2 1Laboratoire d’Ecologie, Syst´ematique et Evolution, CNRS UMR 8079, Universit´e Paris-Sud, Bˆatiment 362, F-91405, Orsay Cedex, France 2Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA ABSTRACT Natural levels of radioactivity on the Earth vary by more than a thousand-fold; this spatial heterogeneity may suffice to create heterogeneous effects on physiology, mutation and selection. We review the literature on the relationship between variation in natural levels of radioactivity and evolution. First, we consider the effects of natural levels of radiation on mutations, DNA repair and genetics. A total of 46 studies with 373 effect size estimates revealed a small, but highly significant mean effect that was independent of adjustment for publication bias. Second, we found different mean effect sizes when studies were based on broad categories like physiology, immunology and disease frequency; mean weighted effect sizes were larger for studies of plants than animals, and larger in studies conducted in areas with higher levels of radiation. Third, these negative effects of radiation on mutations, immunology and life history are inconsistent with a general role of hormetic positive effects of radiation on living organisms. Fourth, we reviewed studies of radiation resistance among taxa. These studies suggest that current levels of natural radioactivity may affect mutational input and thereby the genetic constitution and composition of natural populations. -
Dynamic Consolidated Bioprocessing for Innovative Lab-Scale Production of Bacterial Alkaline Phosphatase from Bacillus Paraliche
www.nature.com/scientificreports OPEN Dynamic consolidated bioprocessing for innovative lab‑scale production of bacterial alkaline phosphatase from Bacillus paralicheniformis strain APSO Soad A. Abdelgalil1,2*, Nadia A. Soliman1, Gaber A. Abo‑Zaid1 & Yasser R. Abdel‑Fattah1 To meet the present and forecasted market demand, bacterial alkaline phosphatase (ALP) production must be increased through innovative and efcient production strategies. Using sugarcane molasses and biogenic apatite as low‑cost and easily available raw materials, this work demonstrates the scalability of ALP production from a newfound Bacillus paralicheniformis strain APSO isolated from a black liquor sample. Mathematical experimental designs including sequential Plackett– Burman followed by rotatable central composite designs were employed to select and optimize the concentrations of the statistically signifcant media components, which were determined to be molasses, (NH4)2NO3, and KCl. Batch cultivation in a 7‑L stirred‑tank bioreactor under uncontrolled pH conditions using the optimized medium resulted in a signifcant increase in both the volumetric and specifc productivities of ALP; the alkaline phosphatase throughput 6650.9 U L−1, and µ = 0.0943 h−1; respectively, were obtained after 8 h that, ameliorated more than 20.96, 70.12 and 94 folds compared to basal media, PBD, and RCCD; respectively. However, neither the increased cell growth nor enhanced productivity of ALP was present under the pH‑controlled batch cultivation. Overall, this work presents novel strategies for the statistical optimization and scaling up of bacterial ALP production using biogenic apatite. Te bioeconomy represents the value chain of sustainable manufacturing using renewable, low-cost biological resources to sustainably produce food, energy, and industrial products1. -
Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms
Chapter 5 Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms Matías Giménez, Gastón Azziz, Paul R. Gill, and Silvia Batista Abstract Plasmids play an important role in the evolution of microbial communi- ties. These mobile genetic elements can improve host survival and may also be involved in horizontal gene transfer (HGT) events between individuals. Diverse culture-dependent and culture-independent approaches have been used to character- ize these mobile elements. Culture-dependent methods are usually associated with classical microbiological techniques. In the second approach, development of spe- cific protocols for analysis of metagenomes involves many challenges, including assembly of sequences and availability of a reliable database, which are crucial. In addition, alternative strategies have been developed for the characterization of plas- mid DNA in a sample, generically referred to as plasmidome. The Antarctic continent has environments with diverse characteristics, including some with very low temperatures, humidity levels, and nutrients. The presence of microorganisms and genetic elements capable of being transferred horizontally has been confirmed in these environments, and it is generally accepted that some of these elements, such as plasmids, actively participate in adaptation mechanisms of host microorganisms. Information related to structure and function of HGT elements in Antarctic bac- teria is very limited compared to what is known about HGT in bacteria from temper- ate/tropical environments. Some studies are done with biotechnological objectives. The search for mobile elements, such as plasmids, may be related to improve the expression of heterologous genes in host organisms growing at very low tempera- tures. More recently, however, additional studies have been done to detect plasmids in isolates, associated or not with specific phenotypes such as drug resistance. -
Isolation and Characterization of a Biosurfactant from Deinococcus Caeni PO5 Using Jackfruit Seed Powder As a Substrate
Ann Microbiol (2014) 64:1007–1020 DOI 10.1007/s13213-013-0738-2 ORIGINAL ARTICLE Isolation and characterization of a biosurfactant from Deinococcus caeni PO5 using jackfruit seed powder as a substrate Chanika Saenge Chooklin & Sirirat Petmeaun & Suppasil Maneerat & Atipan Saimmai Received: 15 April 2013 /Accepted: 18 October 2013 /Published online: 22 January 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract Biosurfactant-producing bacteria were isolated Keywords Deinococcus caeni . Isolation . Jackfruit seed from various sources in the south of Thailand. Isolates were powder . Surface tension . Biosurfactant . Polyaromatic screened for biosurfactant production using jackfruit seed hydrocarbons . Microbial oil recovery powder (JSP) as a novel and promising substrate. The highest biosurfactant activity was obtained with a bacterial strain which was identified by 16S rRNA gene sequence analysis Introduction as Deinococcus caeni PO5. D. caeni PO5 was able to grow and reduce the surface tension of the culture supernatant from Biosurfactants are a diverse group of surface-active agents 67.0 to 25.0 mN/m after 87 h of cultivation when 40 g/l of JSP with both hydrophilic and hydrophobic moieties and are pro- and 1 g/l of commercial monosodium glutamate were used as duced by many living microorganisms, such as bacteria and carbon and nitrogen sources, respectively. The biosurfactant fungi (Desai and Banat 1997). Biosurfactants have many obtained by ethyl acetate extraction showed high surface advantages over synthetic surfactants. These include a lower tension reduction (47.0 mN/m), a small critical micelle con- toxicity and higher biodegradability, which makes them more centration value (8 mg/l), thermal and pH stability with re- environmentally friendly, better foaming properties, milder spect to surface tension reduction and emulsification activity, production conditions, lower critical micelle concentration, and a high level of salt tolerance. -
Marine Extremophiles: a Source of Hydrolases for Biotechnological Applications
Mar. Drugs 2015, 13, 1925-1965; doi:10.3390/md13041925 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications Gabriel Zamith Leal Dalmaso 1,2, Davis Ferreira 3 and Alane Beatriz Vermelho 1,* 1 BIOINOVAR—Biotechnology laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] 2 Graduate Program in Plant Biotechnology, Health and Science Centre, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil 3 BIOINOVAR—Biotechnology Laboratories: Virus-Cell Interaction, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-(21)-3936-6743; Fax: +55-(21)-2560-8344. Academic Editor: Kirk Gustafson Received: 1 December 2014 / Accepted: 25 March 2015 / Published: 3 April 2015 Abstract: The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons.