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ENCYCLOPEDIA of GEOBIOLOGY Encyclopedia of Earth Sciences Series ENCYCLOPEDIA OF GEOBIOLOGY Volume Editors Joachim Reitner is Professor of Paleontology, Head of the Department of Geobiology, and Managing Director of the Museum, Collections and Geopark, at the University of Göttingen, Germany. He is also Editor-in-Chief of Lecture Notes in Earth Sciences (Springer), Co-Editor of Facies (Springer), and Associate Editor of the Geomicrobiology Journal (Taylor & Francis). Dr. Reitner’s research focuses on the interplay between organ- isms and their metabolic processes with various abiotic parameters. Many geological processes can be understood as geo-physiological processes, allowing chemical reactions to proceed that would never occur under standard thermodynamic conditions. Therefore, a major thrust of Dr. Reitner’s research is the investigation of the evolution of these processes, which are visible in biosignatures and biomineralization patterns, and in their interaction with biogeochemical cycles. Among his many honors and accolades, Dr. Reitner is the recipient of the G. W. Leibniz Award from the Deutsche Forschungsgemeinschaft. Volker Thiel is Professor of Organic Geochemistry in the Geoscience Center at the University of Göttingen, Germany. Dr. Thiel has been involved in geobiological research for some 15 years, with a focus on the use of organic molecules as chemical tracers (biomarkers) for biogeochemical path- ways. His research interests include lipid biomarkers as indicators for biogeochemical processes, molecular fossils, biological formation, and turn- over of methane, and microbial control on mineral formation. The results of his studies have significantly contributed to the characterization of microbial processes associated with methane turnover in modern and ancient environments. Much of Dr. Thiel’s current work is devoted to new approaches to enhance the spatial resolution of biomarker analysis in geobiological systems. He is member of the Editorial Board of the journal Geobiology (Wiley-Blackwell). Editorial Board Hans-Joachim Fritz Pamela Reid Courant Research Centre Geobiology Rosenstiel School of Marine and Atmospheric Science University of Göttingen University of Miami Goldschmidtstr.3 4600 Rickenbacker Cswy 37077 Göttingen Miami FL 33149 Germany USA Andreas Kappler Xingliang Zhang Center for Applied Geoscience (ZAG) Department of Geology Sigwartstraße 10 Northwest University 72076 Tübingen Xian 710069 Germany China Kurt O. Konhauser Department of Earth and Atmospheric Sciences University of Alberta, Edmonton Alberta, T6G 2E3 Canada Aims of the Series The Encyclopedia of Earth Sciences Series provides comprehensive and authoritative coverage of all the main areas in the Earth Sciences. Each volume comprises a focused and carefully chosen collection of contributions from leading names in the subject, with copious illustrations and reference lists. These books represent one of the world’s leading resources for the Earth Sciences community. Previous volumes are being updated and new works published so that the volumes will continue to be essential reading for all professional earth scientists, geologists, geophysicists, climatolo- gists, and oceanographers as well as for teachers and students. See http://www.springer.com for a current list of titles in the Encyclopedia of Earth Sciences Series.Gotohttp://www.springerlink.com/reference-works/ to visit the “Encyclopedia of Earth Sciences Series” on-line. About the Series Editor Professor Charles W. Finkl has edited and/or contributed to more than 8 volumes in the Encyclopedia of Earth Sciences Series. For the past 25 years he has been the Executive Director of the Coastal Education & Research Foundation (CERF) and Editor-in-Chief of the international Journal of Coastal Research. In addition to these duties, he is Research Professor at Florida Atlantic University in Boca Raton, Florida, USA. He is a graduate of the University of Western Australia (Perth) and previously worked for a wholly owned Australian subsidiary of the International Nickel Company of Canada (INCO). During his career, he acquired field experience in Australia; the Caribbean; South America; SW Pacific islands; south- ern Africa; Western Europe; and the Pacific Northwest, Midwest, and Southeast USA. Founding Series Editor Professor Rhodes W. Fairbridge (deceased) has edited more than 24 Encyclopedias in the Earth Sciences Series. During his career he has worked as a petroleum geologist in the Middle East, been a WW II intelligence officer in the SW Pacific and led expeditions to the Sahara, Arctic Canada, Arctic Scandinavia, Brazil and New Guinea. He was Emeritus Professor of Geology at Columbia University and was affiliated with the Goddard Institute for Space Studies. ENCYCLOPEDIA OF EARTH SCIENCES SERIES ENCYCLOPEDIA of GEOBIOLOGY edited by JOACHIM REITNER VOLKER THIEL University of Göttingen Germany Library of Congress Control Number: 2010936497 ISBN: 978-1-4020-9211-4 This publication is available also as: Electronic publication under ISBN 978-1-4020-9212-1 and Print and electronic bundle under ISBN 978-1-4020-9213-8 Published by Springer P.O. Box 17, 3300 AA Dordrecht, The Netherlands Printed on acid-free paper Cover illustration: Iron- and sulfide-oxidizing microbial mats in the Äspö Hard Rock Laboratory, Oskarshamn, Sweden (photograph by Joachim Reitner) Every effort has been made to contact the copyright holders of the figures and tables which have been reproduced from other sources. Anyone who has not been properly credited is requested to contact the publishers, so that due acknowledgment may be made in subsequent editions. All Rights Reserved © Springer Science þ Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Contents Contributors xiii Animal Biocalcification, Evolution 53 Gert Wörheide and Daniel J. Jackson Preface xxvii Animal Skeletons, Advent 58 Acetogens 1 Guoxiang Li, Maoyan Zhu and Zhe Chen Kirsten Küsel and Harold L. Drake Acid Rock Drainage 5 Archaea 64 Lesley A. Warren Volker Thiel Acidophiles 8 Arsenic 69 John F. Stolz and Ronald S. Oremland Acritarchs 8 Asteroid and Comet Impacts 69 Charles S. Cockell Aerobic Metabolism 8 Heribert Cypionka Astrobiology 73 Jack D. Farmer Algae (Eukaryotic) 10 Thomas Friedl, Nicole Brinkmann and Kathrin I. Mohr Bacteria 81 Michael Hoppert Alkalinity 20 Andreas Reimer and Gernot Arp Bacterioplankton 89 Thomas Pommier Amber 24 Eugenio Ragazzi and Alexander R. Schmidt Banded Iron Formations 92 Nicole R. Posth, Kurt O. Konhauser and Anaerobic Oxidation of Methane with Sulfate 36 Andreas Kappler Katrin Knittel and Antje Boetius Basalt (Glass, Endoliths) 103 Anaerobic Transformation Processes, Microbiology 48 Ingunn H. Thorseth Bernhard Schink Beggiatoa 111 Anammox 53 Heide N. Schulz-Vogt Entries without author names are glossary terms vi CONTENTS Biodeterioration (of Stone) 112 Calcite Precipitation, Microbially Induced 223 Christina Beimforde Tanja Bosak Bioerosion 117 Calcium Biogeochemistry 227 Aline Tribollet, Gudrun Radtke and Anton Eisenhauer Stjepko Golubic Cap Carbonates 229 Biofilms 134 Joachim Reitner Joachim Reitner Carbon (Organic, Cycling) 230 Biofilms and Fossilization 136 Amber K. Hardison and Elizabeth A. Canuel Joachim Reitner Carbon (Organic, Degradation) 234 Biogeochemical Cycles 137 Steven T. Petsch Biological Control on Diagenesis: Influence Carbon Cycle 238 of Bacteria and Relevance to Ocean Acidification 137 Carbon Isotopes 238 Fred T. Mackenzie and Andreas J. Andersson Carbonate Environments 238 Biological Volcanic Rock Weathering 143 Eberhard Gischler Charles S. Cockell Carbonates 261 Biomarkers (Molecular Fossils) 147 Martin Dietzel Jochen J. Brocks and Kliti Grice Cathodoluminescence Microscopy 266 Biomarkers (Organic, Compound-Specific Walter Vortisch Isotopes) 167 Kliti Grice and Jochen J. Brocks Chemolithotrophy 271 Volker Thiel Biomining (Mineral Bioleaching, Mineral Biooxidation) 182 Cherts 272 Douglas Eric Rawlings Volker Thiel Bioprotection 185 Chondrites 273 Carlos Rodriguez-Navarro, Maria T. González-Muñoz, Concepción Chroococcidiopsis 273 Jimenez-Lopez and Manuel Rodriguez-Gallego Burkhard Büdel Biosignatures in Rocks 189 Clay Authigenesis, Bacterial 274 Frances Westall and Barbara Cavalazzi Kurt O. Konhauser Biosilicification 201 Coccolithophores 277 Volker Thiel Black Shales 201 Wolfgang Oschmann Cold Seeps 278 Robert G. Jenkins Breakup of Rodinia 206 Zheng-Xiang Li Comets 290 Calcareous Algae 211 Commensalism 290 Calcification 211 Community 290 Calcified Cyanobacteria 211 Copper 290 Robert Riding Stephan M. Kraemer CONTENTS vii Cosmic Molecular Clouds 292 Endoliths 348 Joachim Reitner Bettina Weber and Burkhard Büdel Critical Intervals in Earth History 293 Endosymbiosis 355 Frank Wiese and Joachim Reitner Evaporites 355 Cryobiosphere 306 Exoenzymes 355 Cyanobacteria 306 Kathrin Riedel and Alexander Grunau Kathrin I. Mohr, Nicole Brinkmann and Thomas Friedl Extracellular Polymeric Substances (EPS) 359 Alan W. Decho Deep Biosphere of Salt Deposits 313 Helga Stan-Lotter and Sergiu Fendrihan Extreme Environments 362 Volker Thiel Deep Biosphere of Sediments 317 Fe(II)-Oxidizing Prokaryotes 367 Deep Biosphere of the Oceanic
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