DOCSLIB.ORG

Microbial Influence on the Performance of Subsurface, Salt

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Radioactive Waste Management and Decommissioning 2018 Microbial Influence Microbial Influence on the Performance of Subsurface, Salt-Based Radioactive Waste Repositories Salt-Based Radioactive Waste of Subsurface, Microbial Influence on the Performance on the Performance of Subsurface, Salt-Based Radioactive Waste Repositories An Evaluation Based on Microbial Ecology, Bioenergetics and Projected Repository Conditions Radioactive Waste Management and Decommissioning Microbial Influence on the Performance of Subsurface, Salt-Based Radioactive Waste Repositories An Evaluation Based on Microbial Ecology, Bioenergetics and Projected Repository Conditions © OECD 2018 NEA No. 7387 NUCLEAR ENERGY AGENCY ORGANISATION FOR ECONOMIC CO-OPERATION AND DEVELOPMENT ORGANISATION FOR ECONOMIC CO-OPERATION AND DEVELOPMENT The OECD is a unique forum where the governments of 35 democracies work together to address the economic, social and environmental challenges of globalisation. The OECD is also at the forefront of efforts to understand and to help governments respond to new developments and concerns, such as corporate governance, the information economy and the challenges of an ageing population. The Organisation provides a setting where governments can compare policy experiences, seek answers to common problems, identify good practice and work to co-ordinate domestic and international policies. The OECD member countries are: Australia, Austria, Belgium, Canada, Chile, the Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Israel, Italy, Japan, Korea, Latvia, Luxembourg, Mexico, Netherlands, New Zealand, Norway, Poland, Portugal, Slovak Republic, Slovenia, Spain, Sweden, Switzerland, Turkey, the United Kingdom and the United States. The European Commission takes part in the work of the OECD. OECD Publishing disseminates widely the results of the Organisation’s statistics gathering and research on economic, social and environmental issues, as well as the conventions, guidelines and standards agreed by its members. This work is published on the responsibility of the OECD Secretary-General. NUCLEAR ENERGY AGENCY The OECD Nuclear Energy Agency (NEA) was established on 1 February 1958. Current NEA membership consists of 33 countries: Argentina, Australia, Austria, Belgium, Canada, the Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Japan, Korea, Luxembourg, Mexico, the Netherlands, Norway, Poland, Portugal, Romania, Russia, the Slovak Republic, Slovenia, Spain, Sweden, Switzerland, Turkey, the United Kingdom and the United States. The European Commission also takes part in the work of the Agency. The mission of the NEA is: – to assist its member countries in maintaining and further developing, through international co-operation, the scientific, technological and legal bases required for a safe, environmentally sound and economical use of nuclear energy for peaceful purposes; – to provide authoritative assessments and to forge common understandings on key issues as input to government decisions on nuclear energy policy and to broader OECD analyses in areas such as energy and the sustainable development of low-carbon economies. Specific areas of competence of the NEA include the safety and regulation of nuclear activities, radioactive waste management and decommissioning, radiological protection, nuclear science, economic and technical analyses of the nuclear fuel cycle, nuclear law and liability, and public information. The NEA Data Bank provides nuclear data and computer program services for participating countries. This document, as well as any data and map included herein, are without prejudice to the status of or sovereignty over any territory, to the delimitation of international frontiers and boundaries and to the name of any territory, city or area. Corrigenda to OECD publications may be found online at: www.oecd.org/publishing/corrigenda. © OECD 2018 You can copy, download or print OECD content for your own use, and you can include excerpts from OECD publications, databases and multimedia products in your own documents, presentations, blogs, websites and teaching materials, provided that suitable acknowledgement of the OECD as source and copyright owner is given. All requests for public or commercial use and translation rights should be submitted to [email protected]. Requests for permission to photocopy portions of this material for public or commercial use shall be addressed directly to the Copyright Clearance Center (CCC) at [email protected] or the Centre français d'exploitation du droit de copie (CFC) [email protected]. Cover photos: Geological salt beds deep underground in New Mexico (Courtesy of Carlsbad Department of Development); Halobacterium sp. (noricense) isolated from Salado halite in the Waste Isolation Pilot Plant (United States). FOREWORD Foreword Because of their ability to effectively isolate radioactive waste from the environment and the public, deep geological formations are considered the optimal choice for the disposal of hazardous waste. Granitic rock, basalt, clay, tuff and evaporite salt beds are among the different types of sites that are being considered for radioactive waste repositories. Since it was determined that organisms are active even in deep geological settings, a great deal of research has been undertaken to determine the influence of microorganisms on repository performance (i.e. safety cases). Nonetheless, few data are available on the microbiology of subterranean salt formations in proposed and active locations for radioactive waste repositories. Because the biogeochemistry of other deep geological settings differs significantly from that of subterranean salt, it is not always possible to extrapolate microbial activity from one type of site to another. In lieu of directly applicable data, repository scientists rely on “indirect” information – such as microbial ecology, genomics and the thermodynamic feasibility of certain types of metabolism in hypersaline environments – to predict microbial activity and the potential impact on the performance of the repository. The lack of data and the resulting uncertainty surrounding microbial processes in high ionic strength repository settings has meant that performance assessments and safety cases must be conservative in their predictions of potential microbial impact. While such a conservative approach can be defended in a regulatory process, a better understanding of the system would nonetheless alleviate the need to spend engineering resources on what may only be perceived problems. Microorganisms are predicted to have diverse effects on radioactive waste repository performance. These effects are linked to activities that may affect radionuclide speciation and solubility, or that may enhance mobility and thus the source term used in evaluating repository performance. MICROBIAL INFLUENCE ON THE PERFORMANCE OF SUBSURFACE, SALT-BASED RADIOACTIVE WASTE REPOSITORIES, NEA No. 7387, OECD 2018 3 ACKNOWLEDGEMENTS Acknowledgements The NEA would like to express its appreciation to the principal authors of this report: J.S. Swanson,1 A. Cherkouk,2 T. Arnold,2 A. Meleshyn3 and D.T. Reed.1 The Los Alamos National Laboratory (LANL) – Carlsbad Operations Actinide Chemistry and Repository Science Program in Carlsbad, New Mexico – the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Centre for Resource Ecology in Rossendorf, Germany; and the Gesellschaft für Anlagen und Reaktorsicherheit in Braunschweig, Germany helped in compiling this report. The NEA also wishes to acknowledge the support of Russ Patterson, the US Department of Energy (DOE) programme manager. LANL research described herein was funded by the Department of Energy-Carlsbad Field Office (DOE-CBFO) as part of the ongoing recertification of the Waste Isolation Pilot Plant (WIPP) transuranic repository. HZDR research described herein was funded by the Young Investigators Grant, MicroSALT, and by the German Federal Ministry for Economic Affairs and Energy (BMWi). 1. Los Alamos National Laboratory – Carlsbad Operations; Carlsbad, New Mexico, United States. 2. Helmholtz-Zentrum Dresden-Rossendorf; Dresden, Germany. 3. Gesellschaft für Anlagen und Reaktorsicherheit; Braunschweig, Germany. 4 MICROBIAL INFLUENCE ON THE PERFORMANCE OF SUBSURFACE, SALT-BASED RADIOACTIVE WASTE REPOSITORIES, NEA No. 7387, OECD 2018 TABLE OF CONTENTS Table of contents List of abbreviations and acronyms ................................................................................ 7 Executive summary ............................................................................................................ 9 Chapter 1. Repository performance and the possible effects of microbial activity ............................................................................................................. 11 Chapter 2. Background .................................................................................................... 13 The subterranean salt environment and the potential for microbial life ............ 13 The microbiology of hypersaline systems and the subterranean salt biosphere ....................................................................................................................... 14 Chapter 3. The potential for microbial activity under projected repository conditions ....................................................................................................... 19 Expected conditions ...................................................................................................
Recommended publications
  • Microbial Community Responses to Modern Environmental

    Microbial Community Responses to Modern Environmental

    Originally published as: Genderjahn, S., Alawi, M., Wagner, D., Schüller, I., Wanke, A., Mangelsdorf, K. (2018): Microbial Community Responses to Modern Environmental and Past Climatic Conditions in Omongwa Pan, Western Kalahari: A Paired 16S rRNA Gene Profiling and Lipid Biomarker Approach. - Journal of Geophysical Research, 123, 4, pp. 1333—1351. DOI: http://doi.org/10.1002/2017JG004098 Journal of Geophysical Research: Biogeosciences RESEARCH ARTICLE Microbial Community Responses to Modern Environmental 10.1002/2017JG004098 and Past Climatic Conditions in Omongwa Pan, Western Key Points: Kalahari: A Paired 16S rRNA Gene Profiling • Kalahari pan structures possess high potential to act as geoarchives for and Lipid Biomarker Approach preserved biomolecules in arid to semiarid regions S. Genderjahn1 , M. Alawi1 , D. Wagner1,2 , I. Schüller3, A. Wanke4, and K. Mangelsdorf1 • Past microbial biomarker suggests changing climatic conditions during 1GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany, 2Institute of Earth and the Late Glacial to Holocene transition 3 in the western Kalahari Environmental Science, University of Potsdam, Potsdam, Germany, Marine Research Department, Senckenberg am Meer, 4 • Based on taxonomic investigations, Wilhelmshaven, Germany, Department of Geology, University of Namibia, Windhoek, Namibia the abundance and diversity of the microbial community in the pan is related to near-surface processes Abstract Due to a lack of well-preserved terrestrial climate archives, paleoclimate studies are sparse in southwestern Africa. Because there are no perennial lacustrine systems in this region, this study relies on a Supporting Information: saline pan as an archive for climate information in the western Kalahari (Namibia). Molecular biological and • Supporting Information S1 biogeochemical analyses were combined to examine the response of indigenous microbial communities to modern and past climate-induced environmental conditions.
  • Regeneration of Unconventional Natural Gas by Methanogens Co

    Regeneration of Unconventional Natural Gas by Methanogens Co

    www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.
  • Evaluation of 16S Rrna Primer Sets for Characterisation of Microbiota in Paediatric Patients with Autism Spectrum Disorder L

    Evaluation of 16S Rrna Primer Sets for Characterisation of Microbiota in Paediatric Patients with Autism Spectrum Disorder L

    www.nature.com/scientificreports OPEN Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder L. Palkova1,2, A. Tomova3, G. Repiska3, K. Babinska3, B. Bokor4, I. Mikula5, G. Minarik2, D. Ostatnikova3 & K. Soltys4,6* Abstract intestinal microbiota is becoming a signifcant marker that refects diferences between health and disease status also in terms of gut-brain axis communication. Studies show that children with autism spectrum disorder (ASD) often have a mix of gut microbes that is distinct from the neurotypical children. Various assays are being used for microbiota investigation and were considered to be universal. However, newer studies showed that protocol for preparing DNA sequencing libraries is a key factor infuencing results of microbiota investigation. The choice of DNA amplifcation primers seems to be the crucial for the outcome of analysis. In our study, we have tested 3 primer sets to investigate diferences in outcome of sequencing analysis of microbiota in children with ASD. We found out that primers detected diferent portion of bacteria in samples especially at phylum level; signifcantly higher abundance of Bacteroides and lower Firmicutes were detected using 515f/806r compared to 27f/1492r and 27f*/1495f primers. So, the question is whether a gold standard of Firmicutes/Bacteroidetes ratio is a valuable and reliable universal marker, since two primer sets towards 16S rRNA can provide opposite information. Moreover, signifcantly higher relative abundance of Proteobacteria was detected using 27f/1492r. The beta diversity of sample groups difered remarkably and so the number of observed bacterial genera. An advent of massively parallel sequencing (MPS) technologies has revolutionized an investigating of human microbiota1.
  • The Life of Brine: Halophiles in 2001 Comment Mike Dyall-Smith* and Michael Danson†

    The Life of Brine: Halophiles in 2001 Comment Mike Dyall-Smith* and Michael Danson†

    http://genomebiology.com/2001/2/12/reports/4033.1 Meeting report The life of brine: halophiles in 2001 comment Mike Dyall-Smith* and Michael Danson Addresses: *Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia. Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK. Correspondence: Mike Dyall-Smith. E-mail: [email protected] Published: 21 November 2001 reviews Genome Biology 2001, 2(12):reports4033.1–4033.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2001/2/12/reports/4033 © BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) reports haloarchaea found in salt ponds that have 8% salt (or A report on the International conference on Halophilic 2.3-fold concentrated seawater) but are not detectable at the Microorganisms, Sevilla, Spain, 23-27 September 2001. higher salinities usually associated with haloarchaea (20-35% salt). Discovered using 16S rRNA libraries, the new haloar- chaea are distantly related to Haloarcula. None has been cul- The 2001 halophiles meeting covered archaea, bacteria, tured but these results suggest an optimum salt concentration fungi and algae adapted to living hypersaline environments. for growth far lower than that of known haloarchaea. These deposited research Despite the absence of some American colleagues as a result represent an intermediate group of haloarchaea, not previ- of the recent terrorist attack, the meeting was full of exciting ously suspected, and offer insight into the evolution of advances (as well as pictures of salt lakes, salterns, brines extreme halophiles.
  • Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*

    Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*

    J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past.
  • Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus Dombrowskii and Other Extremely Halophilic Archaebacteria

    Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus Dombrowskii and Other Extremely Halophilic Archaebacteria

    ASTROBIOLOGY Volume 9, Number 1, 2009 © Mary Ann Liebert, Inc. DOI: 10.1089/ast.2007.0234 Special Paper Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus dombrowskii and Other Extremely Halophilic Archaebacteria Sergiu Fendrihan,1 Attila Bérces,2 Helmut Lammer,3 Maurizio Musso,4 György Rontó,2 Tatjana K. Polacsek,1 Anita Holzinger,1 Christoph Kolb,3,5 and Helga Stan-Lotter1 Abstract The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibil- ity of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloar- chaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522T was ex- posed to UV doses over a wavelength range of 200–400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m2, and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m2. The estimated Ն 2 D37 (dose of 37 % survival) for Hcc. dombrowskii was 400 kJ/m . However, exposure of cells to UV flux while 2 in liquid culture reduced D37 by 2 orders of magnitude (to about 1 kJ/m ); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica.
  • 1 Microbial Transformations of Organic Chemicals in Produced Fluid From

    1 Microbial Transformations of Organic Chemicals in Produced Fluid From

    Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem.
  • Extracellular Hydrolases Producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India

    Extracellular Hydrolases Producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India

    Int.J.Curr.Microbiol.App.Sci (2016) 5(11): 51-64 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 5 Number 11 (2016) pp. 51-64 Journal homepage: http://www.ijcmas.com Original Research Article http://dx.doi.org/10.20546/ijcmas.2016.511.006 Extracellular Hydrolases producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India Bhavini N. Rathod1, Harshil H. Bhatt2 and Vivek N. Upasani1* 1Department of Microbiology, M.G. Science Institute, Ahmedabad- 380009, India 2Kadi Sarva Vishwavidyalay Gandhinagar-23, India *Corresponding author ABSTRACT Haloarchaea thrive in hypersaline environments such as marine salterns, saline soils, soda lakes, salted foods, etc. The lysis of marine phyto- and zoo-planktons such as algae, diatoms, shrimps, purple and green bacteria, fish, etc. releases K e yw or ds biopolymers namely cellulose, starch, chitin, proteins, lipids, etc. in the saline Extremozymes , ecosystems. The chemorganotrophic haloarchaea therefore, need to produce haloarchaea, hydrolytic enzymes to utilize these substrates. However, the raw solar salt used for hydrolases, preservation can cause spoilage of foods due to the growth of halobacteria leading Halobacterium, to economic loss. We report here the isolation and identification of extracellular Haloferax, hydrolases (substrates casein, gelatin, starch, and Tweens: 20, 60, 40, 80) Halopetinus, producing haloarchaea isolated from the salt and brine samples collected from Okhamadhi marine salterns at Okhamadhi, Gujarat, India. Morphological,
  • The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

    The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

    biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations.
  • In Vivo Multi-Dimensional Information-Keeping in Halobacterium Salinarum

    In Vivo Multi-Dimensional Information-Keeping in Halobacterium Salinarum

    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.14.949925; this version posted February 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. In vivo multi-dimensional information-keeping in Halobacterium salinarum Davis, J.1,2‡, Bisson-Filho, A.3, Kadyrov, D.4, De Kort, T. M.5,1, Biamonte, M. T.6, Thattai, M.7, Thutupalli, S.7,8, Church, G. M. 1‡ 1 Department of Genetics, Blavatnik Institute, Harvard Medical School, 2 Department of Biology, Massachusetts Institute of Technology 3 Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454. 4 SkBiolab, Technopark Skolkovo, Skolkovo Innovation center, Moscow 143026, Russia 5 Biosciences Master’s programme Molecular & Cellular Life Sciences, Faculty of Science, Utrecht University, Utrecht, the Neth- erlands 6 Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139 7 Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India 8 International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru 560089, India ‡ Corresponding authors. [email protected] (J.D.); [email protected] (G.M.C.) Shortage of raw materials needed to manufacture components for silicon-based digital memory storage has led to a search for alternatives, including systems for storing texts, images, movies and other forms of information in DNA.
  • Determination of Hydrolytic Enzyme Capabilities of Halophilic Archaea Isolated from Hides and Skins and Their Phenotypic and Phylogenetic Identification by S

    Determination of Hydrolytic Enzyme Capabilities of Halophilic Archaea Isolated from Hides and Skins and Their Phenotypic and Phylogenetic Identification by S

    33 DETERMinATION OF HYDROLYTic ENZYME CAPABILITIES OF HALOPHILIC ARCHAEA ISOLATED FROM HIDES AND SKins AND THEIR PHENOTYpic AND PHYLOGENETic IDENTIFicATION by S. T. B LG School of Health, Canakkale Onsekiz Mart University, Terzioglu Campus Canakkale, Turkey, 17100. and B. MER ÇL YaPiCi Biology Department, Faculty of Arts and Science, Canakkale ONSEKIZ MART UNIVERSITY, TERZIOGLU CAMPUS, Canakkale, Turkey, 17100. and İsmail Karaboz Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, İzmi r, Turkey, 35100. ABSTRACT INTRODUCTION This research aims to isolate extremely halophilic archaea The main constituent of the raw hide is protein, mainly from salted hides, to determine the capacities of their collagen (33% w/w), and remainder is moisture and fat. During hydrolytic enzymes, and to identify them by using phenotypic storage of raw hide, collagen’s excessive proteolysis by and molecular methods. Domestic and imported salted hide lysosomal autolysis or proteolytic bacterial enzymes can lead and skin samples obtained from eight different sources were to the disintegration of the structure of collagen fibers.1 used as the research material. 186 extremely halophilic Biodeterioration is among the major causes of impairment of microorganisms were isolated from salted raw hides and aesthetic, functional and other properties of leather and other skins. Some biochemical, antibiotic sensitivity, pH, NaCl, biopolymers or organic materials and the products made from temperature tolerance and quantitative and qualitative them. Due to the fact that prevention of biological degradation hydrolytic enzyme tests were performed on these isolates. In is very important in conservation and processing of leather, our study, taking into account the phenotypic findings of the great effort is being made for decontamination of these research, 34 of 186 isolates were selected.
  • Isolation, Characterization and Phylogenetic Analysis of Halophilic Archaea from a Salt Mine in Central Anatolia (Turkey)

    Isolation, Characterization and Phylogenetic Analysis of Halophilic Archaea from a Salt Mine in Central Anatolia (Turkey)

    Polish Journal of Microbiology 2012, Vol. 61, No 2, 111–117 ORGINAL PAPER Isolation, Characterization and Phylogenetic Analysis of Halophilic Archaea from a Salt Mine in Central Anatolia (Turkey) EVRIM YILDIZ, BIRGUL OZCAN* AND MAHMUT CALISKAN Mustafa Kemal University, Biology Department, 31040 Hatay-Turkey Received 22 October 2011, revised 2 May 2012, accepted 5 May 2012 Abstract !e haloarchaeal diversity of a salt mine, a natural cave in central Anatolia, was investigated using convential microbiological and molecu- lar biology methods. Eight halophilic archaeal isolates selected based on their colony morphology and whole cell protein profiles were taxonomically classified on the basis of their morphological, physiological, biochemical properties, polar lipid and protein profiles and 16S rDNA sequences. From the 16S rDNA sequences comparisons it was established that the isolates CH2, CH3 and CHC resembled Halorubrum saccharovorum by 98.8%, 98.9% and 99.5%, respectively. !ere was a 99.7% similarity between the isolate CH11 and Halobac- terium noricense and 99.2% between the isolate CHA1 and Haloarcula argentinensis . !e isolate CH8K and CH8B revealed a similarity rate of 99.8% and 99.3% to Halococcus dombrowskii , respectively. It was concluded that the isolates named CH2, CH3 and CHC were clustered in the genus Halorubrum and that CHA1 and CH7 in the genus Haloarcula , CH8K and CH8B in the genus Halococcus and CH11 in the genus Halobacterium . K e y w o r d s: Halophilic archaea, Phylogeny, Taxonomy, Salt mine, Turkey Introduction 2006; 2009; Birbir et al ., 2007). Phylogenetic studies revealed that the halophilic archaeal isolates from Tur- !e increasing interest, in recent years, in micro- key clustered closely to genera Halorubrum , Haloarcula , organisms from hypersaline environments has resulted Natrinema , Halobacterium and Natronococcus (Ozcan in the discovery of several new species and genera et al ., 2007; Birbir et al ., 2007).