This volume features chapters by an internationally recognized group of authors, here photographed at Alta by Prof. J. Akai (Niigata University, Japan).
The authors as shown (left to right) are: Sue Welch, Liesbeth DeVrind-de Jong, Bill Barker, Jill Banfield (behind me, not especially visible, are Dave Stahl, Patty Sierling), David DesMarais (behind him, not visible, Danielle Fortin), Gordon Southam, Cathy Skinner, Simon Silver, Kirk Nordstrom (standing), Alan Stone, Brad Tebo (white shirt), Bill Ghiorse, (particpant in brown shirt), Sue Barns, (participant in white shirt, standing), Ken Nealson (squatting), Sandra Nierswicki-Bauer (Blue sweatshirt, standing).
Preface H. Catherine W. Skinner
Chapter 1 K. H. Nealson & D. A. Stahl
Microorganisms and Biogeochemical Cycles: What Can We Learn from Layered Microbial Communities?
Introduction
Properties of Prokaryotes
Size
Structure
Metabolic versatility
Mechanisms of energy conservation and patterns of metabolism
The Processes
Aerobic respiration
Nitrification and dentrification
Methane oxidation
Manganese and iron oxidation
Sulfur oxidation
Manganese and iron reduction
Sulfate reduction
Methanogenesis
The Organisms
Aerobic heterotrophs
Chemolithotrophs
Hydrogen-oxidizing bacteria
Sulfur-oxidizing bacteria
Iron-oxidizing bacteria
Nitrifying bacteria and methanotrophs
Methanogens
Acetogens
Fermentative bacteria
Nitrate respiring bacteria
Metal respiring bacteria
Sulfur- and sulfate-reducing bacteria
Proton reducers (syntrophic bacteria)
New Methods and Approaches
Molecular approaches to the microbiology of sediments
Ribosomal RNA-based approaches
Isolation of new organismsQmetal active microbes
Iron-oxidizing bacteria
The iron-reducing bacteria
Mineral and microbes
New microscopic techniques
New microbial ecosystems
Summary
Acknowledgments
References
Chapter 2 S. M. Barns & S. Nierzwicki-Bauer
Microbial Diversity in Modern Subsurface, Ocean, Surface Environments
Introduction
Phylogenetic Introduction to the Diversity and Evolution of Microorganisms
Molecular phylogeny of the microbial world
The origin of life and the Last Common Ancestor
Beyond the Last Common AncestorQDiversification of the domains
Eucarya
Archaea
Bacteria
Geomicrobiological Agents in Depth
Eucarya: Fungi, lichens, algae and protozoa
Archaea
Introduction
Hyperthermophiles
Physiology
Ecology
Halophiles
Physiology
Ecology
Methanogens
Physiology
Ecology
Bacteria: Abundance and diversity
Biogeochemical cycling by bacteria: Introduction
Iron-oxidizing and -reducing organisms
Sulfur-oxidizing and -reducing bacteria
Manganese-oxidizing and -reducing bacteria
Nitrifying and denitrifying bacteria
Bacteria in the lithosphere and hydrosphere: Introduction
Bacteria in the lithosphere
Bacteria in the hydrosphere
Molecular studies of bacterial diversity and abundance in the hydrosphere
Freshwater
Subterranean groundwater ecosystems
Techniques for Studying Geologically Important Microorganisms
Culture-based techniques
Identification and physiological studies
API tests
Biolog tests
Analysis of microbial populations without cultivation
Introduction
Molecular sequence-based phylogenic analysis of microbial populationsQMolecular microbial ecology
Survey of constituent species
rRNA sequence-based in situ methods
PCR-based analyses
DNA probe hybridization analyses
Microscopic techniques for the examination of environmental samples
Signature lipid biomarker (SLB) profiles
Identification of cultured microorganisms and in situ microbial community structure
Nutritional and physiological status of microorganisms
Non-viable and viable biomass determinations
Case Studies
Microbiology of the terrestrial subsurfaceQGEMHEX
Crenarchaeota in hot and not-so-hot environments
Introduction
Crenarchaeal diversity in Obsidian Pool hot spring
Crenarchaeota are widespread and abundant in low-temperature environments
Summary and Conclusions
References
Chapter 3 J. F. Banfield & R. J. Hamers
Processes at Minerals and Surfaces with Relevance to Microorganisms and Prebiotic Synthesis
Introduction
Microbial Access to Mineral Surfaces
Factors that Control Mineralogy
Principles behind Assembly of Crystals
Surfaces and Interfaces
Crystal form
Morphology modification
Defects and surface reactivity
Charge and Protonation at Surfaces
pH dependence of charge at surfaces
Protonation of surfaces
Reactions at Surfaces
Dissolution
Dissolution rate analysis
Adsorption, precipitation, and growth
Silicate Minerals and Their Reactivity: Examples
Silica
Structure and composition
Reactivity
Feldspars
Composition, structure, and microstructure
Reactivity
Layer silicates
Structures and compositions of different types of layer silicates
Compositions and structures of clay minerals
Reactivity of layer silicates
Chain silicates
Structure and chemistry
Reactivity
Orthosilicates
Structures and compositions
Reactivity
Surface phenomena in the laboratory vs. natural weathering
Non-silicate Mineral Reactivity: Examples
Carbonate minerals
Structures and compositions
Reactivity
Oxides and oxyhydroxides
Structures and compositions
Reactivity
Sulfides and sulfates
Structures and compositions
Reactivity
Phosphates
Compositions and structures
Reactivity
Geochemical Reactions and Bioavailability
Prebiotic Synthesis and the Role of Mineral Surfaces in the Origin of Life
Prebiotic synthesis of basic building blocks
Abiotic assembly of the first self-replicating molecules
Problems with the RRNA worldS and alternatives
Minerals as alternative early genetic systems
Conclusion
Concluding Comments Regarding Future Work
Acknowledgments
References
Chapter 4 B. J. Little, P. A. Wagner & Z. Lewandowski
Spatial Relationships between Bacteria and Mineral Surfaces
Introduction
Overview of Biofilm Formation
Initial events of biofilm formation
Biofilm accumulation
Biofilm architecture
Spatial Relationships between Biofilms and Minerals
Mineral deposition
Oxides
Manganese
Iron
Sulfides
Iron
Copper
Silver
Other metals
Carbonates
Mineral dissolution
Conclusions
Acknowledgments
References
Chapter 5 D. Fortin, F. G. Ferris & T. J. Beveridge
Surface-mediated Mineral Development by Bacteria
Introduction
General Overview
Bacterial cell walls
Additional layers above eubacterial cell walls
Biofilms
Sorption of Metal and Silicate Ions to Bacterial Surfaces
Bacterial Mineral Precipitation
Carbonates
Sulfides and paragenetic minerals that form in anaerobic environments
Iron and manganese oxides
Enzymatic reactions
Non-enzymatic reactions
Silicates
Conclusions
Acknowledgments
References
Chapter 6 D.A. Bazylinksi & B.M. Moscowitz
Microbial Biomineralization of Magnetic Iron Minerals: Microbiology, Magnetism and Environmental Significance
Introduction
Biologically Induced Mineralization
General features
Magnetite
Greigite and pyrrhotite
Other non-magnetic iron minerals produced by BIM
Biologically-controlled Mineralization
General features
The magnetotactic bacteria
Classification, phylogeny and general features of the magnetotactic bacteria
Ecology of magnetotactic bacteria
Function of magnetotaxis
Composition and morphology of the magnetosome mineral phase
Effect of environmental conditions on the biomineralization in magnetotactic bacteria
Chemistry and biochemistry of magnetosome formation
Physiology of magnetotactic bacteria
Control over BCM of magnetite
Molecular biology of magnetosome formation and genetics of magnetotactic bacteria
Magnetic Properties of Biogenic Magnetic Minerals
Fundamental principles
Saturation magnetization and Curie temperature
Thermomagnetic analysis
Magnetic hysteresis analysis
Magnetism of Magnetosomes
Particle sizes of magnetosomes
Crystallographic orientation of magnetosomes
Chain assembly of magnetosomes
Physics of Magnetotaxis
Magnetic Microstates of Biogenic Magnetic Minerals
Single domain and multidomain states
Superparamagnetic state
Theoretical domain calculations: Butler-Banerjee model
Local energy minima and metastable SD states: Micromagnetic models
Magnetosomes and micromagnetism
Magnetic Characteristics of BCM- and BIM-type Magnetite
Room temperature magnetic measurements
Low-temperature magnetic properties
Magnetic and geochemical study of magnetotactic bacteria in chemically stratified environments
Biogenic Magnetic Minerals in Sediments
Magnetofossils and natural remanent magnetization
Magnetochemical alteration and preservation of biogenic magnetic minerals
Magnetosomes, Magnetite and Mars
Acknowledgments
References
Chapter 7 B.M. Tebo, W.C. Ghiorse, L.G. van Waasbergen, P.L. Siering, & R. Caspi
Bacterially mediated mineral formation :
Insights into Manganese(II) Oxidation from Molecular Genetic and Biochemical Studies
Introduction
Background
Manganese geochemistry
Manganese mineralogy
Abiotic Mn(II) oxidation
Biological Mn(II) oxidation
Rates of Mn Oxidation/Mineral Formation
Mineralogy of Microbially-produced Manganese Oxides
Model Systems for the Study of Genetics and Biochemistry of Mn(II) oxidation
Pseudomonas putida strain MnB1
Biochemistry
Genetics
Possible mechanism for the oxidation of Mn(II) by SG-1
Surface chemistry of SG-1 spores
Leptothrix discophora strains SS-1 and SP-6
Biochemistry
Genetics
Marine Bacillus sp. strain SG-1
Biochemistry
Genetics
Mn(II) oxidation and cytochromes
Possible mechanisms for the oxidation of Mn(II) by strain MnB1
A molecular ecological study of the mofA gene in its native habitat
Possible mechanisms for oxidation of Mn(II) by Leptothrix spp.
Comparative Aspects of Mn(II)-oxidizing Proteins
Interactions of Mn(II)-oxidizing Bacteria with Other Metals
Conclusions
Acknowledgments
References
Chapter 8 E. W. de Vrind-de Jong & J. P. M. de Vrind
Algal Deposition of Carbonates and Silicates
Introduction
Calcifying and silicifying algae: Occurrence and impact on element
Coccolithophoridae
Principles of biomineralization: Biologically induced or controlled
Supersaturation and nucleation
Crystal growth
Termination of crystal growth
Biomineralization: Biological interference with mineralization
Algal Deposition of Calcium Carbonate
Biologically induced calcification: Chara and Halimeda
Some aspects of photosynthesis
The example of Chara
The example of Halimeda
Biologically controlled calcification: Three coccolithophorid species
Coccolith formation in Pleurochrysis carterae: Ultrastructure of cells and coccoliths
Mechanisms of coccolith synthesis in Pleurochrysis carterae: Role of cell organelles and organic constituents
Relation between photosynthesis and coccolith formation in Pleurochrysis carterae
Coccolith formation in Emiliania huxleyi: Ultrastructure of cells and coccoliths
Coccolith formation in Emiliania huxleyi: Role of cell organelles and organic constituents
Relation between photosynthesis and coccolith formation in Emiliania huxleyi
Coccolith formation in Coccolithus pelagicus: An example of extracellular- controlled biomineralization
Algal Deposition of Silica
Cell wall formation in diatoms
The cell cycle
Cell wall formation: Ultrastructure of frustules
Mechanisms of frustule formation
Scale and stomatocyst formation in Chrysophyta
Stomatocyst formation
Scale formation
Concluding Remarks
Recent developments: The molecular genetical approach
Recent developments: The interdisciplinary approach
Acknowledgments
References
Chapter 9 A. T. Stone
Reactions of Extracellular Organic Ligands with Dissolved Metal Ions and Mineral Surfaces
Introduction
Metal Ions and Ligands: Speciation and Inventory
Lewis Base Functional Groups
Metal Ion Properties Affecting Complex Formation
Physiological Functions that Benefit from Extracellular Organic Ligand Release
Complexation of +II Metal Ions
Complexation of CuII
Metal-to-metal comparisons
Complexation of +III Metal Ions
Solubility limitations
Solubilization of FeIII
Sequestration of AlIII
Complexation and Redox Equilibria
Eh when Fe(OH)3(s) serves as the solubility-limiting phase
Organic Ligand Adsorption
Remaining Challenges towards Understanding Metal Ion and Extracellular Organic Ligand Speciation
Slow rates of +II metal ion desorption from mineral surfaces
Kinetics of ligand exchange reactions
Ternary complex formation in solution and on mineral surfaces
Organic ligand adsorption versus ligand-assisted dissolution
Breakdown of free and metal ion-coordinated organic ligands
A Survey of Extracellular Organic Ligands
Conclusions
References
Chapter 10 S. Silver
The Bacterial View of the Periodic Table: Specific Functions for All Elements
Strategies for Metal Handling by Microorganisms
Mechanisms of Metal Resistance
Plasmid and chromosomal genes
Efflux pumps
Metal Resistance in Bacteria: Case Studies
Mercury
Mercury in the environment
Mercury resistance in bacteria
Arsenic
Arsenic in the environment
Arsenic resistance
Copper resistance in bacteria
Bacterial metallothionein in cyanobacteria
Cadmium resistance in Gram-positive bacteria
Chromate resistance and chromate reduction in Gram-negative bacteria
Tellurite resistance in Gram-negative bacteria
Silver resistance in enteric bacteria
Other toxic metal resistances
Final Comment
Acknowledgments
References
Chapter 11 D. K. Nordstrom & G. Southam
Geomicrobiology of Sulfide Mineral Oxidation
Introduction
Summary of Sulfide Mineral Oxidation Reactions
Compilation of sulfide mineral oxidation studies
Role of bacteria
Aqueous Fe(II) Oxidation Kinetics
Sulfide Metal Oxidation Kinetics
Microbial Oxidation of Sulfide Minerals
General physiology of Thiobacillus ferroxidans
Direct vs. indirect oxidation of non-ferrous sulfide minerals
Thiobacillus spp.-mineral interaction in natural systems
Effects of temperature
Microbial Ecology in Mine Waste Environments
Summary and Future Work
References
Chapter 12 W. W. Barker, S. A. Welch & J. F. Banfield
Biogeochemical Weathering of Silicate Minerals
Introduction
Methods
Lab studies
Field studies
Mechanisms
Physical disaggregation
Soil stabilization
Inorganic acids
Organic acids
Oxalate
Lichen acids
Siderophores
Polysaccharides
Proteins
Nutrient adsorption
Mineral Weathering Studies
Quartz
Feldspars
Micas
Chain silicates
Biogeochemical Weathering over Time
Suggestions for Further Research
Conclusion
References
Chapter 13 D. J. DesMarais
Long-term Evolution of the Biogeochemical Carbon Cycle
Introduction
The Biochemical C Cycle Today
The hydrosphere-atmosphere-biosphere (HAB) subcycle
The sedimentary (SED) subcycle
The metamorphic (MET) subcycle
The mantle-crust (MAN) subcycle
The Carbon Isotope Perspective
Isotope discrimination
Isotopic mass balance
Nonbiological Agents of Long-term Change
The Sun
Impacts
Heat flow
Mantle outgassing
Subduction
Metamorphism
Continental architecture
Role of continents
Ancient continents and the C cycle
Coevolution of the C Cycle and Early Life
The Archean
The MAN subcycle
LifeUs early role in the C cycle
Climate, atmospheric composition and weathering
Stability of the crust
Oxygenic photosynthesis
The late Archean and early Proterozoic
Changes in the MAN subcycle
Tectonic effects on the SED and MET subcycles
Changes in the HAB and SED subcycles
Evolution of the Proterozoic biosphere and its environment
Carbon isotopic evidence
Changing patterns of mineral deposition
Organic C concentrations in sedimentary rocks
Summary
The C cycle, O2 and the evolution of Eukarya
The biosphere-C cycle connection: Future work
Acknowledgments
References
