Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus Dombrowskii and Other Extremely Halophilic Archaebacteria
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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. -
Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies
Protocol Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies Mirko Stauffer 1 , Stephan Hirschi 1 , Zöhre Ucurum 1, Daniel Harder 1 , Ramona Schlesinger 2,* and Dimitrios Fotiadis 1,* 1 Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; mirko.stauff[email protected] (M.S.); [email protected] (S.H.); [email protected] (Z.U.); [email protected] (D.H.) 2 Department of Physics, Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany * Correspondence: [email protected] (R.S.); [email protected] (D.F.) Received: 6 July 2020; Accepted: 19 July 2020; Published: 22 July 2020 Abstract: The light-driven proton pump bacteriorhodopsin (BR) from the extreme halophilic archaeon Halobacterium salinarum is a retinal-binding protein, which forms highly ordered and thermally stable 2D crystals in native membranes (termed purple membranes). BR and purple membranes (PMs) have been and are still being intensively studied by numerous researchers from different scientific disciplines. Furthermore, PMs are being successfully used in new, emerging technologies such as bioelectronics and bionanotechnology. Most published studies used the wild-type form of BR, because of the intrinsic difficulty to produce genetically modified versions in purple membranes homologously. However, modification and engineering is crucial for studies in basic research and, in particular, to tailor BR for specific applications in applied sciences. We present an extensive and detailed protocol ranging from the genetic modification and cultivation of H. -
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. -
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, -
Emended Descriptions of Genera of the Family Halobacteriaceae
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 637–642 DOI 10.1099/ijs.0.008904-0 Taxonomic Emended descriptions of genera of the family Note Halobacteriaceae Aharon Oren,1 David R. Arahal2 and Antonio Ventosa3 Correspondence 1Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, Aharon Oren The Hebrew University of Jerusalem, Jerusalem 91904, Israel [email protected] 2Departamento de Microbiologı´a y Ecologı´a and Coleccio´n Espan˜ola de Cultivos Tipo (CECT), Universidad de Valencia, 46100 Burjassot, Valencia, Spain 3Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain The family Halobacteriaceae currently contains 96 species whose names have been validly published, classified in 27 genera (as of September 2008). In recent years, many novel species have been added to the established genera but, in many cases, one or more properties of the novel species do not agree with the published descriptions of the genera. Authors have often failed to provide emended genus descriptions when necessary. Following discussions of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteriaceae, we here propose emended descriptions of the genera Halobacterium, Haloarcula, Halococcus, Haloferax, Halorubrum, Haloterrigena, Natrialba, Halobiforma and Natronorubrum. The family Halobacteriaceae was established by Gibbons rRNA gene sequence-based phylogenetic trees rather than (1974) to accommodate the genera Halobacterium and on true polyphasic taxonomy such as recommended for the Halococcus. At the time of writing (September 2008), the family (Oren et al., 1997). As a result, there are often few, if family contained 96 species whose names have been validly any, phenotypic properties that enable the discrimination published, classified in 27 genera. -
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
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. -
An Overview of Saltpan Halophilic Bacterium
ntimicrob A ia f l o A l g a e Manikandan and Senthilkumar, J Antimicrob n n r t u s o Agents 2017, 3:4 J Journal of Antimicrobial Agents DOI: 10.4172/2472-1212.1000151 ISSN: 2472-1212 Review Article Open Access An Overview of Saltpan Halophilic Bacterium Manikandan P* and Senthilkumar PK Department of Microbiology, Faculty of Science, Annamalai University, Tamilnadu, India *Corresponding author: Perumal Manikandan, Asst. Professor, Department of Microbiology, Annamalai, University, Annamalainagar, Tamilnadu, India, Tel: +04144-238248; E-mail: [email protected] Received date: August 18, 2017; Accepted date: October 17, 2017; Published date: October 18, 2017 Copyright: © 2017 Manikandan P, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Hypersaline environments provide an excellent medium for natural microbial communities which serve as a potential source of pharmaceutical substances. Salt is widely present in the earth. Almost 73% of earth was covered with marine water which contains 2.5% of common salt. Protease enzyme activity widespread in microorganisms, plant and animals. Proteolytic enzymes used in the industrial application and bioremediation process. In recent years’ new mutant’s microbe resistant to commonly used antibiotics. Protease inhibitors used as potential antibiotics for controlling microbial infections. A Hypersaline environment such as salt pans and salt lakes has high salt concentration and pH. The saltpan provides a diversity of different environmental conditions of alkalinity, salinity, temperature, pH and nutrition. Halophilic organisms growing between 0.5 and 3.0 M salt concentration. -
Study of the Archaeal Motility System of H. Salinarum by Cryo-Electron Tomography
Technische Universität München Max Planck-Institut für Biochemie Abteilung für Molekulare Strukturbiologie “Study of the archaeal motility system of Halobacterium salinarum by cryo-electron tomography” Daniel Bollschweiler Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. B. Reif Prüfer der Dissertation: 1. Hon.-Prof. Dr. W. Baumeister 2. Univ.-Prof. Dr. S. Weinkauf Die Dissertation wurde am 05.11.2015 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 08.12.2015 angenommen. “REM AD TRIARIOS REDISSE” - Roman proverb - Table of contents 1. Summary.......................................................................................................................................... 1 2. Introduction ..................................................................................................................................... 3 2.1. Halobacterium salinarum: An archaeal model organism ............................................................ 3 2.1.1. Archaeal flagella ...................................................................................................................... 5 2.1.2. Gas vesicles .............................................................................................................................. 8 2.2. The challenges of high salt media and low dose tolerance in TEM ......................................... -
Studies on the Chemotaxis Network in Halobacterium Salinarum and Helicobacter Pylori
Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München Studies on the Chemotaxis Network in Halobacterium salinarum and Helicobacter pylori von Andreas Schaer aus Freiburg i. Br. 2002 Erklärung Diese Dissertation wurde im Sinne von § 13 Abs 3 bzw. 4 der Promotionsordnung vom 29. Januar 1998 von Herrn Prof. Dr. Dieter Oesterhelt betreut. Ehrenwörtliche Versicherung Diese Dissertation wurde selbstständig, ohne unerlaubte Hilfe angefertigt. München, den 18. August 2002. Dissertation eingereicht am: 30. August 2002 1. Berichterstatter: Hon.-Prof. Dr. D. Oesterhelt 2. Berichterstatter: Univ.-Prof. Dr. L.-O. Essen Tag der mündlichen Prüfung: 12. Februar 2003 Danksagung Die vorliegende Arbeit wurde am Max-Planck-Institut für Biochemie unter Anleitung von Prof. Dr. D. Oesterhelt angefertigt. Mein besonderer Dank gilt Herrn Prof. Dr. D. Oesterhelt für die Überlassung des sehr interessanten Themas, für sein reges Interesse am Fortgang der Arbeit und sein stetes Bemühen, optimale Arbeitsbedingungen zu schaffen. Darüber hinaus weiß ich das in mich gesetzte Vertrauen, die mir gewährte große wissenschaftliche Freiheit und die Hilfe beim Erstellen vorliegender Arbeit sehr zu schätzen. Ganz besonders möchte ich auch Herrn Prof. Dr. L.-O. Essen danken. Während der gesamten Promotionszeit stand er mir bei kleineren und größeren Problemen als Betreuer immer zur Seite. Ihm verdanke ich viele Anregungen, fruchtbare Diskussionen und Erläuterungen und die Einführung in viele biochemischen Arbeitsmethoden. Danken möchte ich auch allen Laborkollegen und Mitgliedern der Abteilung Membranbiochemie für die fröhliche Arbeitsatmosphäre, die so manchen Fehlschlag zu verkraften half. Mein herzlicher Dank gilt auch meinen Eltern sowie meinen Freunden, die nicht zuletzt durch ihre moralische Unterstützung wesentlich zum Gelingen dieser Arbeit beigetragen haben. -
Bacteria and Archaea - Aharon Oren
PHYLOGENETIC TREE OF LIFE - Bacteria And Archaea - Aharon Oren BACTERIA AND ARCHAEA Aharon Oren The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. Keywords: Archaea, Bacteria, Bacteriological Code, Bergey‟s Manual, Nomenclature, Phylogenetic tree, Polyphasic taxonomy, Prokaryotes, 16S rRNA, Taxonomy, Species concept, Systematics Contents 1. Prokaryotes: The unseen majority 2. The species concept for the Prokaryotes 3. Bacteria and Archaea, the two domains of the prokaryotic world 4. The differences between Bacteria and Archaea 5. The Prokaryotes – a taxonomic overview 5.1. General considerations 5.2. The phyla of Bacteria 5.3. The phyla of Archaea 6. Prokaryotes: The uncultured majority Glossary Bibliography Biographical sketch Summary With an estimated number of 4-6x1030 cells, the prokaryotes are the most numerous organisms on earth. They inhabited our planet long before the eukaryotes evolved, and metabolically they are the most diverse group. Compared to the number of eukaryotic taxa the number of prokaryote genera and species described is surprisingly small. A little over 9,000 different species of prokaryotes have been named, and classified in nearly 2,000 genera. The naming of prokaryotes is regulated by the International Code of Nomenclature of Prokaryotes. Internationally approved rules for naming species exist, but there is no universally accepted species concept for the prokaryotes. For the description of new representatives a polyphasic approach is used, which includes determination of numerous phenotypic and genotypic properties. If necessary, the genomes of related strains are compared by DNA-DNA hybridization or full or partial genome sequence comparison. Since the 1970s comparative sequence analysis of small- subunit ribosomal RNA has revolutionized our views of prokaryote taxonomy. -
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.