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The Journal of the Australian Speleological Federation ICS Down
CAVES The Journal of the Australian Speleological Federation AUSTRALIA ICS Down Under 2017 • White Nose Syndrome Spéléo Secours FranÇais • Khazad-Dum The Thailand Project No. 197 • JUNE 2014 COMING EVENTS This list covers events of interest to anyone seriously interested in caves and http:///www.uis-speleo.org/ or on the ASF website http://www.caves.org. au. For karst. The list is just that: if you want further information the contact details international events, the Chair of International Commission (Nicholas White, ASF for each event are included in the list for you to contact directly. A more exten- [email protected]) may have extra information. This looks like a sive list was published in the last ESpeleo. The relevant websites and details of very busy 2014 and do not forget the ASF conference in Exmouth in mid-2015. other international and regional events may be listed on the UIS/IUS website I hope we have time to go caving! 2014 September 29—October 2 October 25 Climate Change—the Karst Record 7 (KR7) Melbourne. This international Canberra Speleological Society 60th Birthday Lunch. Yowani Country conference at the University of Melbourne will showcase the latest research Club, 455 Northbourne Ave, Lyneham ACT.11.30am for a 12 noon start. Buf- from specialists investigating past climate records from speleothems and cave fet lunch with some drinks provided. Bar facilities available. Cost: $35 per sediments. Pre and post field trips to karst regions of eastern Australia and person. Payment is required by 30th September, 2014. Should you need to northern New Zealand. -
Cave-70-02-Fullr.Pdf
L. Espinasa and N.H. Vuong ± A new species of cave adapted Nicoletiid (Zygentoma: Insecta) from Sistema Huautla, Oaxaca, Mexico: the tenth deepest cave in the world. Journal of Cave and Karst Studies, v. 70, no. 2, p. 73±77. A NEW SPECIES OF CAVE ADAPTED NICOLETIID (ZYGENTOMA: INSECTA) FROM SISTEMA HUAUTLA, OAXACA, MEXICO: THE TENTH DEEPEST CAVE IN THE WORLD LUIS ESPINASA AND NGUYET H. VUONG School of Science, Marist College, 3399 North Road, Poughkeepsie, NY 12601, [email protected] and [email protected] Abstract: Anelpistina specusprofundi, n. sp., is described and separated from other species of the subfamily Cubacubaninae (Nicoletiidae: Zygentoma: Insecta). The specimens were collected in SoÂtano de San AgustõÂn and in Nita Ka (Huautla system) in Oaxaca, MeÂxico. This cave system is currently the tenth deepest in the world. It is likely that A.specusprofundi is the sister species of A.asymmetrica from nearby caves in Sierra Negra, Puebla. The new species of nicoletiid described here may be the key link that allows for a deep underground food chain with specialized, troglobitic, and comparatively large predators suchas thetarantula spider Schizopelma grieta and the 70 mm long scorpion Alacran tartarus that inhabit the bottom of Huautla system. INTRODUCTION 760 m, but no human sized passage was found that joined it into the system. The last relevant exploration was in Among international cavers and speleologists, caves 1994, when an international team of 44 cavers and divers that surpass a depth of minus 1,000 m are considered as pushed its depth to 1,475 m. For a full description of the imposing as mountaineers deem mountains that surpass a caves of the Huautla Plateau, see the bulletins from these height of 8,000 m in the Himalayas. -
Life at Acidic Ph Imposes an Increased Energetic Cost for a Eukaryotic Acidophile Mark A
CORE Metadata, citation and similar papers at core.ac.uk Provided by e-Prints Soton The Journal of Experimental Biology 208, 2569-2579 2569 Published by The Company of Biologists 2005 doi:10.1242/jeb.01660 Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile Mark A. Messerli1,2,*, Linda A. Amaral-Zettler1, Erik Zettler3,4, Sung-Kwon Jung2, Peter J. S. Smith2 and Mitchell L. Sogin1 1The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, 2BioCurrents Research Center, Program in Molecular Physiology, Marine Biological Laboratory, Woods Hole, MA 02543, USA, 3Sea Education Association, PO Box 6, Woods Hole, MA 02543, USA and 4Centro de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain *Author for correspondence (e-mail: [email protected]) Accepted 25 April 2005 Summary Organisms growing in acidic environments, pH·<3, potential difference of Chlamydomonas sp., measured would be expected to possess fundamentally different using intracellular electrodes at both pH·2 and 7, is close molecular structures and physiological controls in to 0·mV, a rare value for plants, animals and protists. The comparison with similar species restricted to neutral pH. 40·000-fold difference in [H+] could be the result of either We begin to investigate this premise by determining the active or passive mechanisms. Evidence for active magnitude of the transmembrane electrochemical H+ maintenance was detected by monitoring the rate of ATP gradient in an acidophilic Chlamydomonas sp. (ATCC® consumption. At the peak, cells consume about 7% more PRA-125) isolated from the Rio Tinto, a heavy metal ATP per second in medium at pH·2 than at pH·7. -
Aerobic Respiration
Life is based on redox • All energy generation in biological systems is due to redox (reduction-oxidation) reactions Aerobic Respiration: + - C6H12O6 + 6 H2O ==> 6 CO2 + 24 H +24 e oxidation electron donor (aka energy source) + - (O2+ 4H + 4e ==> 2H2O) x6 reduction electron acceptor --------------------------------------- C6H12O6 + 6 O2 ==> 6 CO2 + 6 H2O overall reaction (24 electrons) Types of bacterial metabolisms • While eukaryotes only reduce O2 and oxidize organic compounds, prokaryotes can use a variety of electron donors and acceptors, organic and inorganic. - • Aerobic respiration: e acceptor is O2 - • Anaerobic respiration: e acceptor is not O2 • Fermentation: e- donor and acceptor are organic molecules • Chemolithotrophy: e- donor and acceptor are inorganic molecules • Phototrophy: e- donor is light and e- acceptor is either organic or inorganic all microorganisms energy source? chemical light chemotroph phototroph carbon source? carbon source? organic organic CO CO compound 2 compound 2 chemoheterotroph chemoautotroph photoheterotroph photoautotroph e- acceptor? Nitrifying and sulfur- use H O to reduce CO ? oxidizing bacteria 2 2 green non-sulfur and O Other than O 2 2 purple non-sulfur bacteria anoxygenic oxygenic photosynthesis: photosynthesis: green sulfur and most bacteria Organic Inorganic cyanobacteria compound compound purple sulfur bacteria fermentative organism anaerobic respiration: nitrate, sulfate, Fe(III) Aerobic or anaerobic respiration Chemolithotrophy Important molecules Redox Electron Carrier: for example the -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Analyzing Microbial Physiology and Nutrient Transformation in a Model, Acidophilic Microbial Community using Integrated `Omics' Technologies Permalink https://escholarship.org/uc/item/259113st Author Justice, Nicholas Bruce Publication Date 2013 Supplemental Material https://escholarship.org/uc/item/259113st#supplemental Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Analyzing Microbial Physiology and Nutrient Transformation in a Model, Acidophilic Microbial Community using Integrated ‘Omics’ Technologies By Nicholas Bruce Justice A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Jillian Banfield, Chair Professor Mary Firestone Professor Mary Power Professor John Coates Fall 2013 Abstract Analyzing Microbial Physiology and Nutrient Transformation in a Model, Acidophilic Microbial Community using Integrated ‘Omics’ Technologies by Nicholas Bruce Justice Doctor of Philosophy in Microbiology University of California, Berkeley Professor Jillian F. Banfield, Chair Understanding how microorganisms contribute to nutrient transformations within their community is critical to prediction of overall ecosystem function, and thus is a major goal of microbial ecology. Communities of relatively tractable complexity provide a unique opportunity to study the distribution of metabolic characteristics amongst microorganisms and how those characteristics subscribe diverse ecological functions to co-occurring, and often closely related, species. The microbial communities present in the low-pH, metal-rich environment of the acid mine drainage (AMD) system in Richmond Mine at Iron Mountain, CA constitute a model microbial community due to their relatively low diversity and extensive characterization over the preceding fifteen years. -
Functionalized Membrane Domains: an Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger
Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger To cite this version: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger. Functionalized Membrane Domains: An Ancestral Feature of Archaea?. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.526. 10.3389/fmicb.2020.00526. hal-02553764 HAL Id: hal-02553764 https://hal.archives-ouvertes.fr/hal-02553764 Submitted on 20 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-11-00526 March 30, 2020 Time: 21:44 # 1 ORIGINAL RESEARCH published: 31 March 2020 doi: 10.3389/fmicb.2020.00526 Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte1†, Philippe Schaeffer2†, Vincent Grossi3† and Phil M. Oger1*† 1 Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France, 2 Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France, 3 Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. -
EXTREMOPHILES – Vol
EXTREMOPHILES – Vol. I - Extremophiles: Basic Concepts - Charles Gerday EXTREMOPHILES: BASIC CONCEPTS Charles Gerday Laboratory of Biochemistry, University of Liège, Belgium Keywords: extremophiles, thermophiles, halophiles, alkaliphiles, acidophiles, metallophiles, barophiles, psychrophiles, piezophiles, extreme conditions Contents 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Acknowledgments Glossary Bibliography Biographical Sketch Summary Extremophiles are organisms which permanently experience environmental conditions which mayUNESCO be considered as extreme –in comparisonEOLSS to the physico-chemical characteristics of the normal environment of human cells: the latter belonging to the mesophile or temperate world. Some eukaryotic organisms such as fishes, invertebrates, yeasts, fungi, and plants have partially colonized extreme habitats characterized by low temperature and/orSAMPLE of elevated hydrostatic pressure. CHAPTERS In general, however, the organisms capable of thriving at the limits of temperature, pH, salt concentration and hydrostatic pressure, are prokaryotic. In fact, some organisms depend on these extreme conditions for survival and have therefore developed unique adaptations, especially at the level of their membranes and macromolecules, and affecting proteins and nucleic acids in particular. The molecular bases of the various adaptations are beginning to be understood and are briefly described. The study of the extremophile world has contributed greatly to defining, in more precise terms, fundamental concepts such as macromolecule stability and protein folding. -
Obecné Znaky Metabolismu + Bioenergetika
Metabolism • General concept of metabolism + Bioenergetics • Cellular respiration (glykolysis + CKC + oxidative phosphorylation) • Sacharide metabolism + photosynthesis • Lipid metabolism • Metabolism of nitrous compounds Obecné znaky metabolismu + bioenergetika BUNĚČNÁ TEORIE Robert Hook (1667) "buňka" 1. Buňky tvoří veškerou živou hmotu (x viry). 2. Veškeré buňky pocházejí z jiných buněk (x samoplození). 3. Informace se předávají z generace na generaci. 4. V buňkách látky podléhají chemickým přeměnám. 5. Buňky reagují na vnější podněty. Otevřené systémy: tok látek, energie a informací dovnitř a ven dynamická rovnováha → ustálený stav Pravá rovnováha → smrt organismu Metabolic types (trofika, trofé = výživa): Energy source: light→ phototroph chemical reaction(redox) → chemotrophs Proton/electron donor acceptor Anorganic Organic Oxygen Other lithotrophs organotrophs aerobic anaerobic (líthos = stone) Fermentace: „disproporcionace“ Např.: C6H12O6 2 CH3-CH(OH)-COOH C6H12O6 2 CH3-CH2-OH + 2CO2 To be continued…….. Carbon source: anorganic → autotrophs organic → heterotrophs Common metabolic types METABOLISM Carbon source Proton source Proton example acceptor photolithotrophs CO2 H2O CO2 Green parts of (autotrophic) plant photolithotrophs Organic comp H2O (CO2) Some (heterotrophic) photosynthetic bacteria Photoorganotrophs Organic comp. Organic comp CO2 Some algae nad (heterotrophic) bacteria chemoorganotrophs Organic comp Organic comp O2 Animals, aerobic aerobic MO 2- Chemoorganotrophs Organic comp Organic comp SO4 Soil anaerobic - Anaerobic -
A Brief Journey to the Microbial World
2 A Brief Journey to the Microbial World Green sulfur bacteria are I Seeing the Very Small 25 phototrophic microorganisms 2.1 Some Principles of Light Microscopy 25 that form their own phyloge- 2.2 Improving Contrast in Light Microscopy 26 netic lineage and were some 2.3 Imaging Cells in Three Dimensions 29 of the first phototrophs to 2.4 Electron Microscopy 30 evolve on Earth. II Cell Structure and Evolutionary History 31 2.5 Elements of Microbial Structure 31 2.6 Arrangement of DNA in Microbial Cells 33 2.7 The Evolutionary Tree of Life 34 III Microbial Diversity 36 2.8 Metabolic Diversity 36 2.9 Bacteria 38 2.10 Archaea 41 2.11 Phylogenetic Analyses of Natural Microbial Communities 43 2.12 Microbial Eukarya 43 CHAPTER 2 • A Brief Journey to the Microbial World 25 for which resolution is considerably greater than that of the light I Seeing the Very Small microscope. UNIT 1 istorically, the science of microbiology blossomed as the The Compound Light Microscope ability to see microorganisms improved; thus, microbiology H The light microscope uses visible light to illuminate cell struc- and microscopy advanced hand-in-hand. The microscope is the tures. Several types of light microscopes are used in microbiol- microbiologist’s most basic tool, and every student of microbiol- ogy: bright-field, phase-contrast, differential interference contrast, ogy needs some background on how microscopes work and how dark-field, and fluorescence. microscopy is done. We therefore begin our brief journey to the With the bright-field microscope, specimens are visualized microbial world by considering different types of microscopes because of the slight differences in contrast that exist between and the applications of microscopy to imaging microorganisms. -
Geomicrobiology of Biovermiculations from the Frasassi Cave System, Italy
D.S. Jones, E.H. Lyon, and J.L. Macalady ± Geomicrobiology of biovermiculations from the Frasassi Cave System, Italy. Journal of Cave and Karst Studies, v. 70, no. 2, p. 78±93. GEOMICROBIOLOGY OF BIOVERMICULATIONS FROM THE FRASASSI CAVE SYSTEM, ITALY DANIEL S. JONES*,EZRA H. LYON 2, AND JENNIFER L. MACALADY 3 Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA, phone: tel: (814) 865-9340, [email protected] Abstract: Sulfidic cave wallshostabundant, rapidly-growing microbial communiti es that display a variety of morphologies previously described for vermiculations. Here we present molecular, microscopic, isotopic, and geochemical data describing the geomicrobiology of these biovermiculations from the Frasassi cave system, Italy. The biovermiculations are composed of densely packed prokaryotic and fungal cellsin a mineral-organic matrix containing 5 to 25% organic carbon. The carbon and nitrogen isotope compositions of the biovermiculations (d13C 5235 to 243%,andd15N 5 4to 227%, respectively) indicate that within sulfidic zones, the organic matter originates from chemolithotrophic bacterial primary productivity. Based on 16S rRNA gene cloning (n567), the biovermiculation community isextremely diverse,including 48 representative phylotypes (.98% identity) from at least 15 major bacterial lineages. Important lineagesinclude the Betaproteobacteria (19.5% of clones),Ga mmaproteobacteria (18%), Acidobacteria (10.5%), Nitrospirae (7.5%), and Planctomyces (7.5%). The most abundant phylotype, comprising over 10% of the 16S rRNA gene sequences, groupsin an unnamed clade within the Gammaproteobacteria. Based on phylogenetic analysis, we have identified potential sulfur- and nitrite-oxidizing bacteria, as well as both auto- and heterotrophic membersof the biovermiculation community. Additionally ,manyofthe clonesare representativesof deeply branching bacterial lineageswith n o cultivated representatives. -
Protection of Chemolithoautotrophic Bacteria Exposed to Simulated
Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils To cite this version: Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils. Pro- tection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions. Icarus, Elsevier, 2010, 209 (2), pp.482. 10.1016/j.icarus.2010.05.027. hal-00676214 HAL Id: hal-00676214 https://hal.archives-ouvertes.fr/hal-00676214 Submitted on 4 Mar 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Accepted Manuscript Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars En‐ vironmental Conditions Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils PII: S0019-1035(10)00220-4 DOI: 10.1016/j.icarus.2010.05.027 Reference: YICAR 9450 To appear in: Icarus Received Date: 11 August 2009 Revised Date: 14 May 2010 Accepted Date: 28 May 2010 Please cite this article as: Gómez, F., Mateo-Martí, E., Prieto-Ballesteros, O., Martín-Gago, J., Amils, R., Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions, Icarus (2010), doi: 10.1016/j.icarus.2010.05.027 This is a PDF file of an unedited manuscript that has been accepted for publication. -
BIOGEOCHEMICAL INTERACTIONS in FLOODED UNDERGROUND MINES Renee Schmidt Montana Tech
Montana Tech Library Digital Commons @ Montana Tech Graduate Theses & Non-Theses Student Scholarship Summer 2017 BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES Renee Schmidt Montana Tech Follow this and additional works at: http://digitalcommons.mtech.edu/grad_rsch Part of the Geochemistry Commons Recommended Citation Schmidt, Renee, "BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES" (2017). Graduate Theses & Non-Theses. 129. http://digitalcommons.mtech.edu/grad_rsch/129 This Thesis is brought to you for free and open access by the Student Scholarship at Digital Commons @ Montana Tech. It has been accepted for inclusion in Graduate Theses & Non-Theses by an authorized administrator of Digital Commons @ Montana Tech. For more information, please contact [email protected]. BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES by Renée Schmidt A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Geoscience: Geochemistry Option Montana Tech 2017 ii Abstract This study presents a biogeochemical analysis of microbial communities in flooded underground mines in Butte, Montana, USA. Samples were collected from nine mineshafts representing three distinct geochemical zones. These zones consist of the East, West, and Outer Camp mines. The East Camp mines, bordering the Berkeley Pit Superfund site, have the highest concentrations of dissolved metals and the most acidic pH values. Dissolved metal concentrations in the West Camp are one to three orders of magnitude lower than in the East Camp and have nearly neutral pH values. The Outer Camp mines have similar metal concentrations to the West Camp but are neutral to alkaline in pH. Sulfide levels also differ between the zones. In the East Camp, sulfide levels were below detection limits, whereas the West and Outer Camp mines had sulfide -6 -4 18 concentrations ranging from 10 to 10 mol/L.