65 Book 22/7/05 1:19 pm Page i Micro-organisms and Earth systems – advances in geomicrobiology There is growing awareness that important environmental transformations are catalysed, mediated and influenced by micro-organisms, and such knowledge is having an increasing influence on disciplines other than microbiology, such as geology and mineralogy. Geo- microbiology can be defined as the study of the role that microbes have played and are playing in processes of fundamental importance to geology. As such, it is a truly inter- disciplinary subject area, necessitating input from physical, chemical and biological sciences. The book focuses on some important microbial functions in aquatic and terrestrial environments and their influence on ‘global’ processes and includes state-of-the-art approaches to visualization, culture and identification, community interactions and gene transfer, and diversity studies in relation to key processes. Microbial involvement in key global biogeochemical cycles is exemplified by aquatic and terrestrial examples. All major groups ofgeochemically active microbes are represented, including cyanobacteria, bacteria, archaea, microalgae and fungi, in a wide range ofhabitats, reflecting the wealth ofdiversity in both the natural and the microbial world. This book represents environmental microbiology in its broadest sense and will help to promote exciting collaborations between microbiologists and those in complementary physical and chemical disciplines. Geoffrey Michael Gaddis Professor of Microbiology and Head of the Division of Environmental and Applied Biology in the School of Life Sciences at the University of Dundee, UK. Kirk T. Sempleis a Reader in the Department of Environmental Science at Lancaster University, UK. Hilary M. Lappin-Scottis Professor of Environmental Microbiology in the School of Biosciences, University of Exeter, UK. 65 Book 22/7/05 1:19 pm Page ii Symposia of the Society for General Microbiology Managing Editor: Dr Melanie Scourfield, SGM, Reading, UK Volumes currently available: 43 Transposition 45 Control of virus diseases 47 Prokaryotic structure and function – a new perspective 51 Viruses and cancer 52 Population genetics of bacteria 53 Fifty years of antimicrobials: past perspectives and future trends 54 Evolution of microbial life 55 Molecular aspects of host–pathogen interactions 56 Microbial responses to light and time 57 Microbial signalling and communication 58 Transport of molecules across microbial membranes 59 Community structure and co-operation in biofilms 60 New challenges to health: the threat of virus infection 61 Signals, switches, regulons and cascades: control of bacterial gene expression 62 Microbial subversion of host cells 63 Microbe–vector interactions in vector-borne diseases 64 Molecular pathogenesis of virus infections 65 Book 22/7/05 1:19 pm Page iii SIXTY-FIFTH SYMPOSIUM OF THE SOCIETY FOR GENERAL MICROBIOLOGY HELD AT KEELE UNIVERSITY SEPTEMBER 2005 Edited by G. M. Gadd, K. T. Semple & H. M. Lappin-Scott micro-organisms and earth systems – advances in geomicrobiology Published for the Society for General Microbiology cambridge university press Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press TheEdinburghBuilding,Cambridgecb22ru,UK Published in the United States of America by Cambridge University Press, New York www.cambridge.org Informationo n this title: www.cambridge.org/9780521862226 © Society for General Microbiology 2005 Thispublicationisincopyright.Subjecttostatutoryexceptionandtotheprovisionof relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. Firstpublishedinprintformat 2005 isbn-13 978-0-511-14130-0 eBook (NetLibrary) isbn-10 0-511-14130-0 eBook (NetLibrary) isbn-13 978-0-521-86222-6 hardback isbn-10 0-521-86222-1 hardback Cambridge University Press has no responsibility for the persistence or accuracy of urls forexternalorthird-partyinternetwebsitesreferredtointhispublication,anddoesnot guaranteethatanycontentonsuchwebsitesis,orwillremain,accurateorappropriate. 65 Book 22/7/05 1:19 pm Page v CONTENTS Contributors vii Editors’ Preface xi M. Wagner and M. W. Taylor Isotopic-labelling methods for deciphering the function of uncultured micro-organisms 1 L. A. Warren Biofilms and metal geochemistry: the relevance of micro-organism-induced geochemical transformations 11 N. D. Gray and I. M. Head Minerals, mats, pearls and veils: themes and variations in giant sulfur bacteria 35 D. W. Hopkins, B. Elberling, L. G. Greenfield, E. G. Gregorich, P. Novis, A. G. O’Donnell and A. D. Sparrow Soil micro-organisms in Antarctic dry valleys: resource supply and utilization 71 V. R. Phoenix, A. A. Korenevsky, V. R. F. Matias and T. J. Beveridge New insights into bacterial cell-wall structure and physico-chemistry: implications for interactions with metal ions and minerals 85 J. Coombs and T. Barkay Horizontal gene transfer of metal homeostasis genes and its role in microbial communities of the deep terrestrial subsurface 109 L. G. Benning, V. R. Phoenix and B. W. Mountain Biosilicification: the role of cyanobacteria in silica sinter deposition 131 K. H. Nealson and R. Popa Metabolic diversity in the microbial world: relevance to exobiology 151 D. B. Nedwell Biogeochemical cycling in polar, temperate and tropical coastal zones: similarities and differences 173 G. M. Gadd, M. Fomina and E. P. Burford Fungal roles and function in rock, mineral and soil transformations 201 K. Pedersen The deep intraterrestrial biosphere 233 SGM symposium 65 65 Book 22/7/05 1:19 pm Page vi vi Contents J. A. Raven, K. Brown, M. Mackay, J. Beardall, M. Giordano, E. Granum, R. C. Leegood, K. Kilminster and D. I. Walker Iron, nitrogen, phosphorus and zinc cycling and consequences for primary productivity in the oceans 247 J. R. Lloyd Mechanisms and environmental impact of microbial metal reduction 273 M. Krüger and T. Treude New insights into the physiology and regulation of the anaerobic oxidation of methane 303 N. Clipson, E. Landy and M. Otte Biogeochemical roles of fungi in marine and estuarine habitats 321 P. C. Bennett and A. S. Engel Role of micro-organisms in karstification 345 Index 365 SGM symposium 65 65 Book 22/7/05 1:19 pm Page vii CONTRIBUTORS Barkay, T. Department of Biochemistry and Microbiology, Cook College, Rutgers University, 76 Lipman Dr., New Brunswick, NJ 08901, USA Beardall, J. School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia Bennett, P. C. Department of Geological Sciences, The University of Texas at Austin, Austin, TX 78712, USA Benning, L. G. Earth and Biosphere Institute, School of Earth and Environment, University of Leeds, UK Beveridge, T. J. Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Brown, K. Plant Research Unit, Division of Environmental and Applied Biology, School of Life Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK Burford, E. P. Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, UK Clipson, N. Department of Industrial Microbiology, University College Dublin, Belfield, Dublin 4, Ireland Coombs, J. Department of Biochemistry and Microbiology, Cook College, Rutgers University, 76 Lipman Dr., New Brunswick, NJ 08901, USA Elberling, B. Institute of Geography, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen K., Denmark Engel, A. S. Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA Fomina, M. Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, UK Gadd, G. M. Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, UK SGM symposium 65 65 Book 22/7/05 1:19 pm Page viii viii Contributors Giordano, M. Department of Marine Science, Università Politecnica delle Marche, 60131 Ancona, Italy Granum, E. Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK Gray, N. D. School of Civil Engineering and Geosciences, Institute for Research on the Environment and Sustainability and Centre for Molecular Ecology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK Greenfield, L. G. School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand Gregorich, E. G. Agriculture Canada, Central Experimental Farm, Ottawa, Canada K1A 0C6 Head, I. M. School of Civil Engineering and Geosciences, Institute for Research on the Environment and Sustainability and Centre for Molecular Ecology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK Hopkins, D. W. School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK Kilminster, K. School of Plant Biology, University of Western Australia, M090 35 Stirling Highway, Crawley, WA 6009, Australia Korenevsky, A. A. Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Krüger, M. Federal Institute for Geosciences and Resources (BGR), Stilleweg 2, D-30655 Hannover, Germany, and Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany Landy, E. School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK Leegood, R. C. Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK Lloyd, J. R. The Williamson Research Centre for Molecular Environmental Studies and the School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK SGM symposium 65 65 Book 22/7/05 1:19 pm Page ix Contributors ix Mackay, M. Plant Research Unit, Division of Environmental and Applied Biology, School of Life Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK Matias, V. R. F. Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Mountain, B. W. Institute of Geological and Nuclear Sciences, Wairakei Research Centre, Taupo, New Zealand Nealson, K. H. Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA Nedwell, D. B. Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK Novis, P. Manaaki Whenua – Landcare Research, PO Box 69, Lincoln 8152, New Zealand O’Donnell, A. G. Institute for Research on Environment and Sustainability, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK Otte, M. Department of Botany, University College Dublin, Belfield, Dublin 4, Ireland Pedersen, K. Deep Biosphere Laboratory, Department of Cell & Molecular Biology, Göteborg University, Box 462, SE-405 30 Göteborg, Sweden Phoenix, V. R. Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Popa, R. Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA Raven, J. A. Plant Research Unit, Division of Environmental and Applied Biology, School of Life Sciences, University of Dundee at SCRI, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK Sparrow, A. D. School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, and Department of Natural Resources and Environmental Sciences, University of Nevada, 1000 Valley Rd, Reno, NV 89512, USA SGM symposium 65