Extreme Environments and High-Level Bacterial Tellurite Resistance
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A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L
JOURNAL OF BACTERIOLOGY, Feb. 1990, p. 756-761 Vol. 172, No. 2 0021-9193/90/020756-06$02.00/0 Copyright © 1990, American Society for Microbiology A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L. HOLMES* AND MICHAEL L. DYALL-SMITH Department of Microbiology, University of Melbourne, Parkville, Victoria 3052, Australia Received 25 May 1989/Accepted 10 November 1989 A mutant resistant to the gyrase inhibitor novobiocin was selected from a halophilic archaebacterium belonging to the genus Haloferax. Chromosomal DNA from this mutant was able to transform wild-type ceils to novobiocin resistance, and these transformants formed visible colonies in 3 to 4 days on selective plates. The resistance gene was isolated on a 6.7-kilobase DNA KpnI fragment, which was inserted into a cryptic multicopy plasmid (pHK2) derived from the same host strain. The recombinant plasmid transformed wild-type cells at a high efficiency (>106/pg), was stably maintained, and could readily be reisolated from transformants. It could also transform Halobacterium volcanii and appears to be a useful system for genetic analysis in halophilic archaebacteria. Archaebacteria are phylogenetically distinct from eubac- cle was the lack of selectable traits, such as antibiotic teria and eucaryotes and can be broadly divided into three resistance. groups: methanogens, sulfur-dependent thermoacidophiles, The aim of this study was to find a selectable marker for and extreme halophiles (for a review, see reference 22). use in constructing plasmid vectors suitable for isolating and Numerous halobacteria have been isolated from hypersaline studying genes in halobacteria. We report the successful environments around the world, but it is only recently that construction of such a vector by using a gene conferring their taxonomy has been analyzed in a rigorous and compre- resistance to novobiocin and a cryptic plasmid from Halo- hensive fashion. -
Biotechnological Potential of Peptides and Secondary Metabolites in Archaea
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Crossref Hindawi Publishing Corporation Archaea Volume 2015, Article ID 282035, 7 pages http://dx.doi.org/10.1155/2015/282035 Review Article Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea James C. Charlesworth1,2 and Brendan P. Burns1,2 1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia 2Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW 2052, Australia Correspondence should be addressed to Brendan P. Burns; [email protected] Received 5 February 2015; Revised 7 July 2015; Accepted 8 July 2015 Academic Editor: Juergen Wiegel Copyright © 2015 J. C. Charlesworth and B. P. Burns. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Archaea are an understudied domain of life often found in “extreme” environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. -
Naming Polyatomic Ions and Acids Oxyanions
Oxyanions Naming Polyatomic Ions and Oxyanions Acids Oxyanions- negative ions containing Oxyanions may contain the prefix oxygen. “hypo-”, less than, or “per-”, more than. These have the suffix “-ate” or “-ite” For example - “-ate” means it has more oxygen atoms ClO4 Perchlorate bonded, “-ite” has less - ClO3 Chlorate For example - ClO2 Chlorite 2- SO4 sulfate ClO- Hypochlorite 2- SO3 sulfite Acids Naming acids Naming Acids Certain compounds produce H+ ions in Does it contain oxygen? water, these are called acids. If it does not, it gets the prefix “hydro-” and If it does contain an oxyanion, then the suffix “-ic acid” replace the ending. You can recognize them because the neutral compound starts with “H”. HCl If the ending was “–ate”, add “-ic acid” Hydrochloric acid If the ending was “–ite”, add “-ous acid” For example HCl, H2SO4, and HNO3. HF Don’t confuse a polyatomic ion with a H2SO4 Sulfuric Acid Hydrofluoric acid neutral compound. H2SO3 Sulfurous Acid HCN HCO - is hydrogen carbonate, not an acid. 3 Hydrocyanic acid Examples Examples Nomenclature (naming) of Covalent compounds HNO3 HNO3 Nitric Acid HI HI Hydroiodic acid H3AsO4 H3AsO4 Arsenic Acid HClO2 HClO2 Chlorous Acid 1 Determining the type of bond Covalent bonding is very Covalent bonding is very First, determine if you have an ionic different from ionic naming compound or a covalent compound. similar to ionic naming A metal and a nonmetal will form an You always name the one that is least Ionic names ignored the subscript ionic bond. electronegative first (furthest from because there was only one possible Compounds with Polyatomic ions form fluorine) ratio of elements. -
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally. -
Some English Terms Used in Microbiology 1
Some English terms used in Microbiology 1 Shapes & Structures General terms Antibiotics and related Bacillus (pl. bacilli) Acid fast (acid fastness) ácido-alcohol resistente Acetylases Capsule Bacterial (adj.) Ampicillin Cell wall pared celular Bacterium (pl., bacteria): Beta-lactamase Coccus (cocci; and hence Staphylococcus, Bench: poyata Beta-lactamic Staphylococci) Biofilm Cephalosporin Core oligosaccharide núcleo oligosacarídico Burner (Bunsen Burner): mechero (Bunsen) Chloramphenicol Cortex Colony: colonia Colistin Fimbria (pl. fimbriae) Coverslip: (vidrio) cubreobjetos D-Cycloserine Flagellum (pl. flagella) Dye colorante DNA-gyrase Glycocalix Eukaryote or eucaryote Erythromycin Lipid A Incubator: estufa de incubación Ethambuthol Lipopolysaccharide Inoculating loop asa de siembra Fluoroquinolone Murein mureína Inoculum (inocula): Gentamicin (formerly gentamycin) Omp: outer membrane major protein proteína To flame: flamear Isoniazide de membrane externa Flask (Erlenmeyer flask): matraz Methicillin Outer membrane membrana externa Volumetric flask: matraz aforado Methylases PAMP (pathogen associated molecular pattern): Microorganism Nalidixic acid patrón molecular asociado a patógeno Motility movilidad Penicillin Peptidoglycan peptidoglucano Mycoplasm Penicillin binding protein (PBP) Periplasm periplasma Negative staining tinción negativa Phosphonomycin Periplasmic space espacio periplásmico Petri dish: placa de Petri Phosphorylases Permeability barrier barrera de permeabilidad Prokaryote or procaryote Polymyxin Pilus (pl. pili) Rack: -
The Regulation of Arsenic Metabolism in Rhizobium Sp. NT-26
The regulation of arsenic metabolism in Rhizobium sp. NT-26 Paula Corsini Madeira University College London Thesis submitted for the degree of Doctor of Philosophy 2016 I, Paula Corsini Madeira, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Date: Signed: II Abstract Arsenic (As) is a toxic metalloid and a major contaminant in terrestrial and aquatic environments. The two soluble forms, arsenite (AsIII) and arsenate (AsV) are toxic to most organisms. A range of phylogenetically distant bacteria are able to oxidize AsIII to the less toxic form, arsenate AsV using the periplasmic arsenite oxidase (AioBA). The two-component signal transduction system AioS/AioR and the AsIII-binding periplasmic protein AioX are required for AsIII oxidation and are involved in the transcriptional regulation of the aioBA operon. Most AsIII oxidisers can also reduce AsV to AsIII via the As (Ars) resistance system. The focus of this work was to understand the regulation of genes involved in AsIII oxidation and As resistance together with those involved in phosphate metabolism in the facultative chemolithoautotrophic AsIII oxidiser NT-26 grown under different conditions. Gene expression was studied by quantitative PCR in cells grown heterotrophically with and without AsIII or AsV in late-log and stationary phases. qPCR was optimised and suitable reference genes were chosen. The expression of genes involved in phosphate transport, sensing As and the genes aioX, aioS, aioR (AsIII-sensing and regulation) and aioB, aioA (AsIII oxidation) and cytC (cytochrome c) were also analysed in NT-26 grown heterotrophically in the presence or absence of AsIII or AsV at different growth stages (i.e., late-log and stationary phases). -
And Inter-Protein Couplings of Backbone Motions Underlie
www.nature.com/scientificreports OPEN Intra- and inter-protein couplings of backbone motions underlie protein thiol-disulfde exchange cascade Received: 26 July 2018 Wenbo Zhang1,3, Xiaogang Niu2,3, Jienv Ding1,3,5, Yunfei Hu2,3,6 & Changwen Jin1,2,3,4 Accepted: 6 October 2018 The thioredoxin (Trx)-coupled arsenate reductase (ArsC) is a family of enzymes that catalyzes the Published: xx xx xxxx reduction of arsenate to arsenite in the arsenic detoxifcation pathway. The catalytic cycle involves a series of relayed intramolecular and intermolecular thiol-disulfde exchange reactions. Structures at diferent reaction stages have been determined, suggesting signifcant conformational fuctuations along the reaction pathway. Herein, we use two state-of-the-art NMR methods, the chemical exchange saturation transfer (CEST) and the CPMG-based relaxation dispersion (CPMG RD) experiments, to probe the conformational dynamics of B. subtilis ArsC in all reaction stages, namely the enzymatic active reduced state, the intra-molecular C10–C82 disulfde-bonded intermediate state, the inactive oxidized state, and the inter-molecular disulfde-bonded protein complex with Trx. Our results reveal highly rugged energy landscapes in the active reduced state, and suggest global collective motions in both the C10–C82 disulfde-bonded intermediate and the mixed-disulfde Trx-ArsC complex. Protein thiol-disulfde exchange reactions play fundamental roles in living systems, represented by the thiore- doxin (Trx) and glutaredoxin (Grx) systems that maintain the cytoplasmic reducing environment, the protein DsbA that catalyzes the formation of protein disulfde bonds in bacterial periplasm, as well as the protein disulfde isomerase (PDI) proteins that facilitate correct disulfde bonding1–5. -
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. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Diversity of Cultivated and Metabolically Active Aerobic Anoxygenic Phototrophic Bacteria Along an Oligotrophic Gradientthe in Mediterranean Sea C
Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 8, 4421–4457, 2011 Biogeosciences www.biogeosciences-discuss.net/8/4421/2011/ Discussions doi:10.5194/bgd-8-4421-2011 © Author(s) 2011. CC Attribution 3.0 License. This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1INSU-CNRS, UMR 7144, Observatoire Oceanologique´ de Roscoff, Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR 7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR 6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Accepted: 29 April 2011 – Published: 5 May 2011 Correspondence to: C. Jeanthon (jeanthon@sb-roscoff.fr) Published by Copernicus Publications on behalf of the European Geosciences Union. 4421 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterio- plankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of 5 AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. -
Shree Nath Singh Editor Microbial Degradation of Synthetic Dyes in Wastewaters Environmental Science and Engineering
Environmental Science Shree Nath Singh Editor Microbial Degradation of Synthetic Dyes in Wastewaters Environmental Science and Engineering Environmental Science Series editors Rod Allan, Burlington, ON, Canada Ulrich Förstner, Hamburg, Germany Wim Salomons, Haren, The Netherlands More information about this series at http://www.springer.com/series/3234 Shree Nath Singh Editor Microbial Degradation of Synthetic Dyes in Wastewaters 123 Editor Shree Nath Singh Plant Ecology and Environmental Science Division CSIR—National Botanical Research Institute Lucknow, Uttar Pradesh India ISSN 1431-6250 ISBN 978-3-319-10941-1 ISBN 978-3-319-10942-8 (eBook) DOI 10.1007/978-3-319-10942-8 Library of Congress Control Number: 2014951157 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer.