Micro-organisms and earth systems- -advances in geomicrobiology: sixty-fifth Symposium of the Society for General Microbiology held at Keele University, September 2005

There is growing awareness that important environmental transformations are catalysed, mediated and influenced by microorganisms, and geomicrobiology can be defined as the influence of microorganisms on geologic processes. This is probably the most rapidly growing area of microbiology at present, combining environmental and molecular microbiology together with significant areas of mineralogy, geochemistry and hydrology. This volume focuses on the function of microorganisms in the environment and their influence on 'global' processes. It will include state-of-the art approaches to visualisation, culture and identification, community interactions and gene transfer, and diversity studies in relation to key processes. This overview for researchers and graduate students will represent environmental microbiology in its broadest sense and help to promote exciting collaborations between microbiologists and those in complementary physical and chemical disciplines. HALF-TITLE......Page 2 TITLE......Page 4 COPYRIGHT......Page 5 CONTENTS......Page 6 CONTRIBUTORS......Page 8 EDITORS’ PREFACE......Page 12 INTRODUCTION......Page 14 IDENTIFICATION OF PLAYERS THAT INCORPORATE LABELLED SUBSTRATES......Page 15 OUTLOOK......Page 20 REFERENCES......Page 22 INTRODUCTION......Page 24 AQUEOUS METAL GEOCHEMISTRY: FUNDAMENTALS......Page 25 Important solid phases......Page 26 Sorption reactions......Page 28 The role of redox status......Page 31 Relevance of microbial functional metabolism......Page 32 Biofilms: existence, structure and function......Page 35 Environmental biofilm metal geochemistry......Page 36 CONCLUSIONS......Page 39 REFERENCES......Page 41 Achromatium......Page 48 Beggiatoa......Page 50 Thioploca......Page 51 Thiothrix......Page 53 Thiomargarita......Page 55 GIANT SULFUR BACTERIA: ENERGY AND GEOCHEMICAL SIGNIFICANCE......Page 56 Energetic considerations of sulfur oxidation......Page 57 Geochemical significance of giant sulfur bacteria......Page 62 EVOLUTIONARY AND ECOLOGICAL DIVERSITY IN THE GIANT SULFUR BACTERIA......Page 69 Within-genus diversity in morphology and physiology......Page 70 Genetic and ecological diversity in the genus Achromatium......Page 73 GENOMICS MEETS ECOLOGY: UNDERSTANDING ECOLOGICAL DIVERSITY BY USING METAGENOMICS......Page 74 REFERENCES......Page 77 INTRODUCTION......Page 84 MICROBIAL ACTIVITY IN DRY VALLEY SOILS......Page 86 SOURCES OF RESOURCES IN DRY VALLEY SOILS......Page 89 ACKNOWLEDGEMENTS......Page 94 REFERENCES......Page 95 INTRODUCTION......Page 98 Freeze-substitution......Page 99 Freeze-substitution and Gram-positive (Bacillus subtilis) cell walls......Page 100 Frozen hydrated thin sections......Page 101 Correlation of freeze-substitution and frozen hydrated images......Page 103 How does this new interpretation of wall structure correlate with metal-ion interaction and mineralization?......Page 104 POTENTIOMETRIC PROPERTIES OF CELL SURFACES......Page 106 Cell-surface complexity and its impact on potentiometric properties......Page 107 Hydrophobicity studies......Page 112 REFERENCES......Page 117 INTRODUCTION......Page 122 Microbial metabolism in the subsurface......Page 123 THE INTERACTIONS OF SUBSURFACE BACTERIA WITH HEAVY METALS......Page 125 Gene transfer among microbes in the subsurface environment......Page 127 P -type ATPases and their roles in metal homeostasis and HGT......Page 128 Evolution of P -type ATPases by HGT in a subsurface microbial community......Page 129 Evidence for HGT of P -type ATPases in complete prokaryotic genomes......Page 132 HGT gene microarray......Page 135 REFERENCES......Page 137 INTRODUCTION......Page 144 THE CHEMISTRY OF SILICA......Page 146 CYANOBACTERIAL SURFACE PROPERTIES AND FUNCTION......Page 151 CYANOBACTERIAL BIOMINERALIZATION PATHWAYS AND COLLOID AGGREGATION......Page 154 CONCLUSIONS......Page 157 ACKNOWLEDGEMENTS......Page 158 REFERENCES......Page 159 INTRODUCTION......Page 164 Metabolic diversity......Page 165 Prokaryotic mineral formation......Page 170 Eukaryotic mineral formation......Page 172 Biomagnetite and the death of a generalization......Page 173 TIME: LINKING THE PAST WITH THE PRESENT......Page 174 Kinetic biosignatures and layered communities......Page 178 EXTREME ENVIRONMENTS: WHY DO WE GO THERE?......Page 179 CONCLUSIONS......Page 180 REFERENCES......Page 181 PHYSICO-CHEMICAL DIFFERENCES BETWEEN LATITUDINAL REGIONS......Page 186 PRIMARY PRODUCTION......Page 188 ORGANIC MATTER DEGRADATION AND BIOGEOCHEMICAL RECYCLING......Page 195 EFFECT OF TEMPERATURE ON ABILITY TO SEQUESTER SUBSTRATES BY ACTIVE TRANSPORT......Page 196 FUNCTIONAL GROUPS......Page 201 ROLE OF COASTAL WETLANDS......Page 204 REFERENCES......Page 206 INTRODUCTION......Page 214 WEATHERING PROCESSES AND THE INFLUENCE OF MICROBES......Page 215 MICROBES IN ROCK AND MINERAL HABITATS......Page 216 FUNGI IN THE TERRESTRIAL ENVIRONMENT......Page 218 Biomechanical deterioration......Page 219 Biochemical deterioration......Page 220 FUNGAL DETERIORATION OF ROCK AND BUILDING STONE......Page 221 METAL BINDING AND ACCUMULATION BY FUNGI......Page 224 MYCOGENIC MINERAL FORMATION......Page 225 Oxalate precipitation......Page 226 Carbonate precipitation: calcified fungal filaments in limestone and calcareous soils......Page 227 Reduction or oxidation of metals and metalloids......Page 228 Clay mineral formation and impact on soil properties......Page 229 Clay and silicate weathering by fungi......Page 230 Concrete biodeterioration and radioactive waste disposal......Page 232 Bioremediation......Page 233 REFERENCES......Page 234 INTRODUCTION......Page 246 VARIABILITY OF INTRATERRESTRIAL ENVIRONMENTS......Page 247 STRATEGIES FOR EXPLORING INTRATERRESTRIAL ENVIRONMENTS......Page 249 ORGANISMS THAT LIVE IN INTRATERRESTRIAL ENVIRONMENTS......Page 251 RANGE OF BIOMASS IN VARIOUS INTRATERRESTRIAL ENVIRONMENTS......Page 252 INTRATERRESTRIAL SPECIES DIVERSITY......Page 253 ENERGY SOURCES FOR INTRATERRESTRIAL LIFE......Page 254 ACTIVITY OF INTRATERRESTRIAL LIFE FORMS......Page 255 REFERENCES......Page 256 INTRODUCTION......Page 260 Nitrogen......Page 262 Iron......Page 265 Phosphorus......Page 268 Zinc......Page 270 Interactions among Fe, N, P and Zn......Page 271 Interactions of Fe, N, P and Zn with the assimilation of inorganic C......Page 272 Interaction of Fe, N, P and Zn supply with the fate of marine primary producers......Page 274 REFERENCES......Page 278 INTRODUCTION......Page 286 REDUCTION OF Fe(III) AND Mn(IV)......Page 287 Diversity of Fe(III)-reducing organisms......Page 288 Mechanisms of Fe(III) and Mn(IV) reduction: electron transfer to insoluble minerals......Page 290 Vanadium reduction......Page 291 Chromium reduction......Page 292 Cobalt reduction......Page 293 Gold and silver reduction......Page 294 Mercury reduction......Page 295 Arsenic reduction: a role in mass poisoning worldwide?......Page 296 Reduction of Se(VI) and Se(IV) and other group VIB elements......Page 298 REDUCTION OF ACTINIDES AND FISSION PRODUCTS AND THE BIOREMEDIATION OF RADIOACTIVE WASTE......Page 299 Uranium reduction......Page 300 Reduction of other actinides (plutonium and neptunium)......Page 302 Technetium reduction......Page 303 DEGRADATION OF XENOBIOTICS BY METAL-REDUCING BACTERIA......Page 304 REFERENCES......Page 307 INTRODUCTION......Page 316 HISTORY OF AOM......Page 318 MICRO-ORGANISMS INVOLVED IN AOM......Page 319 HOT SPOTS FOR THE STUDY OF AOM......Page 321 Black Sea......Page 322 ENVIRONMENTAL REGULATION OF AOM......Page 323 MECHANISM OF AOM......Page 325 CONCLUSIONS......Page 328 REFERENCES......Page 329 THE NATURE OF MARINE ENVIRONMENTS......Page 334 MARINE FUNGAL DIVERSITY IN MARINE ECOSYSTEMS......Page 337 FUNGAL ADAPTATION TO MARINE ENVIRONMENTS......Page 341 MARINE BIOGEOCHEMICAL PROCESSES......Page 343 Biogeochemical cycling......Page 344 FUNGAL CONTRIBUTION TO CYCLING IN MARINE ECOSYSTEMS......Page 349 REFERENCES......Page 351 INTRODUCTION......Page 358 Sulfur-based cave ecosystems......Page 360 Coupled C and S metabolism......Page 361 MICROBIAL GEOCHEMISTRY METHODS......Page 362 Microbial-community analysis......Page 363 In situ microcosms......Page 365 The example of Lower Kane Cave......Page 366 CONCLUSIONS......Page 372 REFERENCES......Page 373 INDEX......Page 378 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 Of Geochemically Active Microbes Are Represented, Including Cyanobacteria, Bacteria, Archaea, Microalgae And Fungi, In A Wide Range Of Habitats, Reflecting The Wealth Of Diversity 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.--book Jacket. 1. Isotopic-labelling Methods For Deciphering The Function Of Uncultured Micro-organisms / M. Wagner And M. W. Taylor-- 2. Biofilms And Metal Geochemistry : The Relevance Of Micro-organism-induced Geochemical Transformations / L. A. Warren -- 3. Minerals, Mats, Pearls And Veils : Themes And Variations In Giant Sulfur Bacteria / N. D. Gray And I. M. Head -- 4. Soil Micro-organisms In Antarctic Dry Valleys : Resource Supply And Utilization / D. W. Hopkins, B. Elberling, L. G. Greenfield, E. G. Gregorich, P. Novis, A. G. O'donnell And A. D. Sparrow -- 5. New Insights Into Bacterial Cell-wall Structure And Physico-chemistry : Implications For Interactions With Metal Ions And Minerals / V. R. Phoenix, A. A. Korenevsky, V. R. F. Matias And T. J. Beveridge -- 6. Horizontal Gene Transfer Of Metal Homeostasis Genes And Its Role In Microbial Communities Of The Deep Terrestrial Subsurfaces / J. Coombs And T. Barkay --^ 7. Biosilicification : The Role Of Cyanobacteria In Silico Sinter Deposition L. G. Benning, V. Phoenix And B. W. Mountain -- 8. Metabolic Diversity In The Microbial World : Relevance To Exobiology / K. H. Nealson And R. Popa -- 9. Biogeochemical Cycling In Polar, Temperate And Tropical Coastal Zones : Similarities And Differences / D. B. Nedwell -- 10. Fungal Roles And Function In Rock, Mineral And Soil Transformations / G. M. Gadd, M. Fomina And E. P. Burford -- 11. The Deep Intraterrestrial Biosphere / K. Pedersen -- 12. Iron, Nitrogen, Phosphorus And Zinc Cycling And Consequences For Primary Productivity In The Oceans / J. A. Raven, K. Brown, M. Mackay, J. Beardall, M. Giordano, E. Granum, R. C. Leegood, K. Kilminster And D. I. Walker -- 13. Mechanisms And Environmental Impact Of Microbial Metal Reduction / J. R. Lloyd -- 14. New Insights Into The Physiology And Regulation Of The Anaerobic Oxidation Of Methane M. Kruger And T. Treude --^ 15. Biogeochemical Roles Of Fungi In Marine And Estuarine Habitats / N. Clipson, E. Landy And M. Otte -- 16. Role Of Micro-organisms In Karstification / P. C. Bennett And A. S. Engel. Edited By G.m. Gadd, K.t. Semple & H.m. Lappin-scott. Published For The Society For General Microbiology. Includes Bibliographical References And Index. Geomicrobiology can be defined as the influence of microorganisms on geologic processes and is probably the most rapidly growing area of microbiology, combining environmental and molecular microbiology together with significant areas of mineralogy, geochemistry and hydrology. This volume provides an overview of the subject for graduate students and researchers With the benefit of hindsight, the last 20 years in microbial ecology will probably be referred to as the census period that dramatically changed our perception of biodiversity within the three domains of life.