521 Organism Index
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide
antioxidants Review Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide Ivan Kushkevych 1,* , Veronika Bosáková 1,2 , Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 3,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (V.B.); [email protected] (M.V.) 2 Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic 3 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: Hydrogen sulfide is a toxic compound that can affect various groups of water microorgan- isms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as Citation: Kushkevych, I.; Bosáková, well as the conditions for isolation and cultivation of these microorganisms will be presented. V.; Vítˇezová,M.; Rittmann, S.K.-M.R. -
The Position of Cyanobacteria in the World of Phototrophs
Carlsberg Res. Commun. Vol. 42, p. 77-98, 1977 THE POSITION OF CYANOBACTERIA IN THE WORLD OF PHOTOTROPHS. by ROGER Y STANIER D~partementde Biochimieet G6n6tiqueMicrobienne 28, rue du Dr Roux, 75015 Paris, France EMIL CHR. nANSENlecture delivered at the Carlsberg Laboratory Centennial and the Inauguration of the Carlsberg Research Center on September 28th, 1976 Key words: prokaryotic photosynthetic apparatus; obligate photoautotrophy; oxidative and reductive pentose phosphate cycles; nitrogen fixation; oxygenic photosynthesis; facultative anoxygenic photosynthesis; cyanobacterial ecology; cyanobacterial developmental patterns Recent advances in our knowledge of the biological properties of the cyanobacteria (former ,blue-green algae,) are reviewed. The subjects discussed include: cyanobacterial cell structure and development; comparative as- pects of photosyntetic structure and function in prokaryotes; carbon metabolism and its relation to obligate photoautotrophy; and special properties of cyanobacteria that are of ecological significance (temperature rela- tionships, nitrogen fixation and facultative anoxygenicphotosynthesis). 1. INTRODUCTION seated functional differences between the two The largest evolutionary discontinuity among kinds of cells could be appreciated only after contemporary organisms lies at the cellular the molecular biological revolution. level; it permits us to distinguish two biological In addition to the organisms long recognized superkingdoms, eukaryotes and prokaryotes as bacteria, the superkingdom of prokaryotes -
The Complete Genome Sequence of Chlorobium Tepidum TLS, a Photosynthetic, Anaerobic, Green-Sulfur Bacterium
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium Jonathan A. Eisen*†, Karen E. Nelson*, Ian T. Paulsen*, John F. Heidelberg*, Martin Wu*, Robert J. Dodson*, Robert Deboy*, Michelle L. Gwinn*, William C. Nelson*, Daniel H. Haft*, Erin K. Hickey*, Jeremy D. Peterson*, A. Scott Durkin*, James L. Kolonay*, Fan Yang*, Ingeborg Holt*, Lowell A. Umayam*, Tanya Mason*, Michael Brenner*, Terrance P. Shea*, Debbie Parksey*, William C. Nierman*, Tamara V. Feldblyum*, Cheryl L. Hansen*, M. Brook Craven*, Diana Radune*, Jessica Vamathevan*, Hoda Khouri*, Owen White*, Tanja M. Gruber‡, Karen A. Ketchum*§, J. Craig Venter*, Herve´ Tettelin*, Donald A. Bryant¶, and Claire M. Fraser* *The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850; ¶Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; and ‡Department of Stomatology, Microbiology and Immunology, University of California, San Francisco, CA 94143 Communicated by Alexander N. Glazer, University of California System, Oakland, CA, March 28, 2002 (received for review January 8, 2002) The complete genome of the green-sulfur eubacterium Chlorobium Here we report the determination and analysis of the complete tepidum TLS was determined to be a single circular chromosome of genome of C. tepidum TLS, the type strain of this species. 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosyn- Materials and Methods thesis by the reductive tricarboxylic acid cycle. Genome comparisons Genome Sequencing. C. tepidum genomic DNA was isolated as have identified genes in C. tepidum that are highly conserved among described (5). -
New Finds of Skeletal Fossils in the Terminal Neoproterozoic of the Siberian Platform and Spain
New finds of skeletal fossils in the terminal Neoproterozoic of the Siberian Platform and Spain ANDREY YU. ZHURAVLEV, ELADIO LIÑÁN, JOSÉ ANTONIO GÁMEZ VINTANED, FRANÇOISE DEBRENNE, and ALEKSANDR B. FEDOROV Zhuravlev, A.Yu., Liñán, E., Gámez Vintaned, J.A., Debrenne, F., and Fedorov, A.B. 2012. New finds of skeletal fossils in the terminal Neoproterozoic of the Siberian Platform and Spain. Acta Palaeontologica Polonica 57 (1): 205–224. A current paradigm accepts the presence of weakly biomineralized animals only, barely above a low metazoan grade of or− ganization in the terminal Neoproterozoic (Ediacaran), and a later, early Cambrian burst of well skeletonized animals. Here we report new assemblages of primarily calcareous shelly fossils from upper Ediacaran (553–542 Ma) carbonates of Spain and Russia (Siberian Platform). The problematic organism Cloudina is found in the Yudoma Group of the southeastern Si− berian Platform and different skeletal taxa have been discovered in the terminal Neoproterozoic of several provinces of Spain. New data on the morphology and microstructure of Ediacaran skeletal fossils Cloudina and Namacalathus indicate that the Neoproterozoic skeletal organisms were already reasonably advanced. In total, at least 15 skeletal metazoan genera are recorded worldwide within this interval. This number is comparable with that known for the basal early Cambrian. These data reveal that the terminal Neoproterozoic skeletal bloom was a real precursor of the Cambrian radiation. Cloudina,the oldest animal with a mineralised skeleton on the Siberian Platform, characterises the uppermost Ediacaran strata of the Ust’−Yudoma Formation. While in Siberia Cloudina co−occurs with small skeletal fossils of Cambrian aspect, in Spain Cloudina−bearing carbonates and other Ediacaran skeletal fossils alternate with strata containing rich terminal Neoprotero− zoic trace fossil assemblages. -
Evolution of Oxygenic Photosynthesis
EA44CH24-Fischer ARI 17 May 2016 19:44 ANNUAL REVIEWS Further Click here to view this article's online features: • Download figures as PPT slides • Navigate linked references • Download citations Evolution of Oxygenic • Explore related articles • Search keywords Photosynthesis Woodward W. Fischer, James Hemp, and Jena E. Johnson Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125; email: wfi[email protected] Annu. Rev. Earth Planet. Sci. 2016. 44:647–83 Keywords First published online as a Review in Advance on Great Oxidation Event, photosystem II, chlorophyll, oxygen evolving May 11, 2016 complex, molecular evolution, Precambrian The Annual Review of Earth and Planetary Sciences is online at earth.annualreviews.org Abstract This article’s doi: The origin of oxygenic photosynthesis was the most important metabolic 10.1146/annurev-earth-060313-054810 innovation in Earth history. It allowed life to generate energy and reducing Copyright c 2016 by Annual Reviews. power directly from sunlight and water, freeing it from the limited resources All rights reserved of geochemically derived reductants. This greatly increased global primary productivity and restructured ecosystems. The release of O2 as an end prod- Access provided by California Institute of Technology on 07/14/16. For personal use only. Annu. Rev. Earth Planet. Sci. 2016.44:647-683. Downloaded from www.annualreviews.org uct of water oxidation led to the rise of oxygen, which dramatically altered the redox state of Earth’s atmosphere and oceans and permanently changed all major biogeochemical cycles. Furthermore, the biological availability of O2 allowed for the evolution of aerobic respiration and novel biosynthetic pathways, facilitating much of the richness we associate with modern biology, including complex multicellularity. -
The Cyanobacterial Genome Core and the Origin of Photosynthesis
The cyanobacterial genome core and the origin of photosynthesis Armen Y. Mulkidjanian*†‡, Eugene V. Koonin§, Kira S. Makarova§, Sergey L. Mekhedov§, Alexander Sorokin§, Yuri I. Wolf§, Alexis Dufresne¶, Fre´ de´ ric Partensky¶, Henry Burdʈ, Denis Kaznadzeyʈ, Robert Haselkorn†**, and Michael Y. Galperin†§ *School of Physics, University of Osnabru¨ck, D-49069 Osnabru¨ck, Germany; ‡A. N. Belozersky Institute of Physico–Chemical Biology, Moscow State University, Moscow 119899, Russia; §National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; ¶Station Biologique, Unite´Mixte de Recherche 7144, Centre National de la Recherche Scientifique et Universite´Paris 6, BP74, F-29682 Roscoff Cedex, France; ʈIntegrated Genomics, Inc., Chicago, IL 60612; and **Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637 Contributed by Robert Haselkorn, July 14, 2006 Comparative analysis of 15 complete cyanobacterial genome se- to trace the conservation of these genes among other taxa. We quences, including ‘‘near minimal’’ genomes of five strains of analyzed the phylogenetic affinities of genes in this set and Prochlorococcus spp., revealed 1,054 protein families [core cya- identified previously unrecognized candidate photosynthetic nobacterial clusters of orthologous groups of proteins (core Cy- genes. We further used this gene set to address the identity of the OGs)] encoded in at least 14 of them. The majority of the core first phototrophs, a subject of intense discussion in recent years CyOGs are involved in central cellular functions that are shared (8, 9, 12–33). We show that cyanobacteria and plants share with other bacteria; 50 core CyOGs are specific for cyanobacteria, numerous photosynthesis-related genes that are missing in ge- whereas 84 are exclusively shared by cyanobacteria and plants nomes of other phototrophs. -
Phylogeny and Molecular Signatures (Conserved Proteins and Indels) That Are Specific for the Bacteroidetes and Chlorobi Species Radhey S Gupta* and Emily Lorenzini
BMC Evolutionary Biology BioMed Central Research article Open Access Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species Radhey S Gupta* and Emily Lorenzini Address: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, L8N3Z5, Canada Email: Radhey S Gupta* - [email protected]; Emily Lorenzini - [email protected] * Corresponding author Published: 8 May 2007 Received: 21 December 2006 Accepted: 8 May 2007 BMC Evolutionary Biology 2007, 7:71 doi:10.1186/1471-2148-7-71 This article is available from: http://www.biomedcentral.com/1471-2148/7/71 © 2007 Gupta and Lorenzini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them. Results: Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum) DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum) TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. -
PROJECT SUMMARY the Overall Goals of This Proposal Are to Obtain
Principal Investigator: Loftus, Brendan J PROJECT SUMMARY The overall goals of this proposal are to obtain a high-coverage, high-quality draft of the Acanthamoeba castellanii Neff (Ac) genome and annotate and analyze the genome sequence data. We intend to use the whole genome shotgun method followed by whole genome assembly to construct a high-quality genome assembly for Ac. The project team is well suited to undertake this work. The PI, Brendan Loftus is a faculty member at The Institute for Genomic Research (TIGR) and PI on the Entamoeba histolytica genome effort amongst other eukaryotic projects, and has publications in genome assembly and analysis. The Co-PI, Michael Gray, is Canada Research Chair in Genomics and Genome Evolution at Dalhousie University in Halifax, Nova Scotia, Canada. Dr. Gray also holds an appointment as Fellow in the Program in Evolutionary Biology, Canadian Institute for Advanced Research. Dr. Gray has extensive experience in protist mitochondrial genomics, is currently Project Leader of the Protist EST Program (PEP), a large- scale genomics initiative managed and partly funded by Genome Canada and has specific responsibility for several of the individual PEP EST projects, including that for Ac. The intellectual merit of the proposal stems from the significant position of Ac as one of the few well-studied members of the free-living amoebae, which play an important role in a variety of terrestrial and aquatic environments. As such, Ac is one of the most commonly found amoebae in soil. From an evolutionary perspective Ac is proposed to be a member of the ancient subphylum Protamoebae. -
Photosynthesis 481
Photosynthesis 481 C3 plants, which regulate the opening of stomatal in the dark by using respiration to utilize organic pores for gas exchange in leaves, also lack rubisco compounds from the environment. They are ther- and apparently use PEP carboxylase exclusively to mophilic bacteria found in hot springs around the fix CO2. world. They also distinguish themselves among the Contributions of the late Martin Gibbs to this arti- photosynthetic bacteria by possessing mobility. An cleare acknowledged. example is Chloroflexus aurantiacus. Gerald A. Berkowitz; Archie R. Portis, Jr.; Govindjee 4. Heliobacteria (Heliobacteriaceae). These are strictly anaerobic bacteria that contain bacterio- Bacterial Photosynthesis chlorophyll g. They grow primarily using organic Certain bacteria have the ability to perform photo- substrates and have not been shown to carry out synthesis. This was first noticed by Sergey Vinograd- autotrophic growth using only light and inorganic sky in 1889 and was later extensively investigated substrates. An example is Heliobacterium chlorum. by Cornelis B. Van Niel, who gave a general equa- Like plants, algae, and cyanobacteria, anoxygenic tion for bacterial photosynthesis. This is shown in photosynthetic bacteria are capable of photophos- reaction (9). phorylation, which is the production of adeno- sine triphosphate (ATP) from adenosine diphosphate bacteriochlorophyll 2H2A + CO2 + light −−−−−−−−−→ {CH2O}+2A + H2O (ADP) and inorganic phosphate (Pi) using light as the enzymes (9) primary energy source. Several investigators have suggested that the sole function of the light reaction where A represents any one of a number of reduc- in bacteria is to make ATP from ADP and Pi. The hy- tants, most commonly S (sulfur). drolysis energy of ATP (or the proton-motive force Photosynthetic bacteria cannot use water as the that precedes ATP formation) can then be used to hydrogen donor and are incapable of evolving oxy- drive the reduction of CO2 to carbohydrate by H2A gen. -
~Nalla~R~C (CANADA a GEOLOGY FIELD "GUIDE to SELECTED SITES in NEWFOUNDLAND, NOVA SCOTIA
D~s)COVER~NGROCK~~ ~j!NERAl~ ~NfO)FOs)S~l5) ~NAllA~r~C (CANADA A GEOLOGY FIELD "GUIDE TO SELECTED SITES IN NEWFOUNDLAND, NOVA SCOTIA, PRINCE EDV\JARDISLAND7 AND NEW BRUNSWICK 7_".-- ~ _. ...._ .•-- ~.- Peter Wallace. Editor Atlantic Geoscience Society Department of Earth Sciences La Societe G60scientifique Dalhousie University de L'Atlantique Halifax, Nova Scotia AGS Special Publication 14 • DISCOVERING ROCKS, MINERALS AND FOSSILS IN ATLANTIC CANADA A Geology Field Guide to Selected Sites in Newfoundland, Nova Scotia, Prince Edward Island and New Brunswick • Peter Wallace, editor Department of Earth Sciences Dalhousie University, Halifax, Nova Scotia Atlantic Geoscience Society La Societe Geoscientifique de L'Atlantique • AGS Special Publication • @ 1998 Atlantic Geoscience Society Department of Earth Sciences Dalhousie University 1236 Henry Street, Halifax Nova Scotia, Canada B3H3J5 This book was produced with help from The Canadian Geological Foundation, The Department of Earth Sciences, Dalhousie University, and The Atlantic Geoscience Society. ISBN 0-9696009-9-2 AGS Special Publication Number . 14.. I invite you to join the Atlantic Geoscience Society, write clo The Department of Earth Sciences, Dalhousie University (see above) Cover Photo Cape Split looking west into the Minas Channel, Nova Scotia. The split is caused by erosion along North-South faults cutting the Triassic-Jurassic-aged North Mountain Basalt and is the terminal point of a favoured hike of geologists and non-geologists alike. Photo courtesy of Rob • Fensome, Biostratigrapher, -
Metabolism of Carbochidrates in the Cell of Green Photosintesis Sulfur Bacteria
Chapter 10 Metabolism of Carbochidrates in the Cell of Green Photosintesis Sulfur Bacteria M. B. Gorishniy and S. P. Gudz Additional information is available at the end of the chapter http://dx.doi.org/10.5772/50629 1. Introduction Green bacteria - are phylogenetic isolated group photosyntetic microorganisms. The peculiarity of the structure of their cells is the presence of special vesicles - so-called chlorosom containing bacteriochlorofils and carotenoids. These microorganisms can not use water as a donor of electrons to form molecular oxygen during photosynthesis. Electrons required for reduction of assimilation CO2, green bacteria are recovered from the sulfur compounds with low redox potential. Ecological niche of green bacteria is low. Well known types of green bacteria - a common aquatic organisms that occur in anoxic, was lit areas of lakes or coastal sediments. In some ecosystems, these organisms play a key role in the transformation of sulfur compounds and carbon. They are adapted to low light intensity. Compared with other phototrophic bacteria, green bacteria can lives in the lowest layers of water in oxygen-anoxic ecosystems. Representatives of various genera and species of green bacteria differ in morphology of cells, method of movement, ability to form gas vacuoles and pigment structure of the complexes. For most other signs, including metabolism, structure photosyntetic apparats and phylogeny, these families differ significantly. Each of the two most studied families of green bacteria (Chlorobium families and Chloroflexus) has a unique way of assimilation of carbon dioxide reduction. For species of the genus Chlorobium typical revers tricarboxylic acids cycle, and for members of the genus Chloroflexus - recently described 3- hidrocsypropionatn cycle. -
Morphological and Behavioural Evolution Through
MORPHOLOGICAL AND BEHAVIOURAL EVOLUTION THROUGH THE EDIACARAN AND BASAL CAMBRIAN OF THE MACKENZIE MOUNTAINS, NW CANADA by Calla Agnes Carbone A thesis submitted to the Department of Geological Sciences and Geological Engineering In conformity with the requirements for the Degree of Master of Science Queen’s University Kingston, Ontario, Canada (January, 2014) Copyright © Calla Agnes Carbone, 2014 i Abstract The Mackenzie Mountains of NW Canada contains a superb record of biotic evolution through the late Ediacaran-early Cambrian that is ideal for studying the biological, ecological, behavioural, and environmental innovations that occurred during the Ediacaran and basal Cambrian. Newly discovered Ediacara-type megafossils in the uppermost Blueflower Formation at Sekwi Brook include tubes possibly attributable to suspension-feeding annelids, the preserved top of a large frond holdfast, and several problematica. These fossils represent the youngest and shallowest Ediacaran fossils known from NW Canada, and differ significantly from the communities of deep-water rangeomorphs preserved lower in the succession. Behavioural evolution of the infauna through the Ediacaran and earliest Cambrian can be observed in the rich trace fossil records of the Blueflower and Ingta formations. Trace fossils in the lower part of the Blueflower Formation are characterized by millimeter-diameter, simple, horizontal burrows of microbial grazers and deposit feeders that demonstrated very primitive and inconsistent two-dimensional avoidance strategies. Upper Blueflower trace fossils additionally include three-dimensional avoidance burrows and oblique burrows of filter-feeders or predators, reflecting new behavioural innovations and increased three-dimensional use of the substrate. The Cambrian strata of the Ingta Formation further include probing, U-shaped, and radiating burrows, irregular networks, and arthropod trails.