Note: 9780323899925v1_WEB -- Front Cover -- Molecular Medical Microbiology -- Copyright Page -- Contents -- List of contributors -- About the editors -- Preface -- 1 Molecular medical microbiology-from bench to bedside -- 1.1 The concept -- 1.2 The evolving concept -- 1.3 From bench to bedside -- References -- 1 Bacterial structure -- 2 Classification of medically important bacteria -- 2.1 Introduction -- 2.2 Basics of bacterial taxonomy -- 2.3 Gram-negative bacteria -- 2.3.1 Enterobacterales -- 2.3.1.1 Enterobacter spp -- 2.3.1.2 Klebsiella spp -- 2.3.1.3 Citrobacter spp -- 2.3.1.4 Escherichia and Shigella -- 2.3.1.5 Pseudomonas spp -- 2.3.1.6 Other glucose nonfermenting gram-negative bacilli -- 2.3.1.7 Acinetobacter spp -- 2.3.1.8 Burkholderia spp -- 2.4 Gram-positive bacteria -- 2.4.1 Mycobacterium -- 2.4.1.1 Staphylococci -- 2.4.1.2 Viridans group streptococci -- 2.5 Conclusion and summary -- References -- 3 Bacterial ultrastructure -- 3.1 Introduction -- 3.2 Overview of bacterial ultrastructures -- 3.3 Surface appendages -- 3.4 Flagella -- 3.5 Pili and fimbriae -- 3.6 Capsules and S-layers -- 3.7 Membrane vesicles -- 3.8 Bacterial cell walls -- 3.9 Gram-negative bacterial cell wall -- 3.10 Gram-positive bacterial cell walls -- 3.11 Mycobacteria -- 3.12 Cell wall-deficient bacteria -- 3.13 Cell walls of Archea and surface appendages -- 3.14 Cytoplasmic membrane -- 3.15 Nucleoid -- 3.16 Bacterial cell division -- 3.17 Cytoplasmic inclusions -- 3.18 Outlook -- References -- 4 Bacterial cell walls: peptidoglycan -- 4.1 Introduction -- 4.2 The basic chemical structure of peptidoglycan -- 4.2.1 The glycan strands in peptidoglycan -- 4.2.2 The stem peptides in peptidoglycan -- 4.2.3 Peptide cross-links -- 4.2.4 Variation of the fine structure -- 4.3 Biophysical properties of peptidoglycan -- 4.3.1 Thickness of peptidoglycan -- 4.3.2 Elasticity of sacculi. , 4.3.3 Pores in the sacculus -- 4.4 Architecture of peptidoglycan -- 4.5 Peptidoglycan biosynthesis and modifications -- 4.5.1 Cytoplasmic steps to UDP-MurNAc pentapeptide -- 4.5.2 Synthesis of the lipid-linked precursor -- 4.5.3 Variation in the lipid II structure -- 4.5.4 Peptidoglycan synthases -- 4.5.5 Peptidoglycan hydrolases -- 4.5.6 Secondary modifications in the peptidoglycan structure -- 4.6 Covalent attachment of secondary cell wall polymers to peptidoglycan -- 4.7 Covalent attachment of proteins to peptidoglycan -- 4.8 Peptidoglycan synthesis during the cell cycle -- 4.8.1 Peptidoglycan synthesis complexes active in cell elongation and division -- 4.8.2 Molecular mechanism of peptidoglycan growth: the 3-for-1 growth model -- 4.8.3 Regulation of peptidoglycan growth from the inside and outside -- Acknowledgments -- References -- 5 Bacterial capsules -- 5.1 Introduction -- 5.2 Chemical and structural properties of the capsules -- 5.2.1 Primary structures -- 5.2.2 Secondary structures -- 5.2.3 Other properties of capsular polysaccharides -- 5.3 Genetics of capsule biosynthesis -- 5.3.1 Gram-negative bacteria -- 5.3.2 Gram-positive bacteria -- 5.4 Biosynthesis of the capsules -- 5.4.1 Wzy-dependent polymerization -- 5.4.2 ABC transporter-dependent polymerization -- 5.4.3 Synthase-dependent polymerization -- 5.4.4 Attachment of bacterial capsules to the cell surface -- 5.5 Regulation of capsule production -- 5.5.1 Modulation at the DNA level -- 5.5.2 Modulation at the transcriptional level -- 5.5.3 Posttranscriptional regulation -- 5.5.4 Metabolic regulation -- 5.6 Biological functions of the capsules -- 5.6.1 Capsules as a virulence factors -- 5.6.2 Capsules as an immune evasion factor -- 5.6.3 Other functions of capsules -- 5.7 The capsules as targets for host immunity and therapeutics. , 5.7.1 Molecular recognition of bacterial capsules by host immune systems -- 5.7.2 Capsules as vaccine antigens -- 5.7.3 Capsules as therapeutic targets -- 5.8 Conclusion and prospect -- Acknowledgments -- References -- 6 Flagella -- 6.1 Flagellar function -- 6.1.1 Estimation of torque -- 6.1.2 Tumbling -- 6.1.3 Energy source -- 6.2 Flagellar structure -- 6.2.1 Filament -- 6.2.1.1 Flagellin (Hag or FliC) -- 6.3 Phase variation -- 6.4 Filament structure -- 6.5 Filament helicity -- 6.5.1 Polymorphism -- 6.6 Calladine model -- 6.6.1 Flagella family -- 6.7 Hook -- 6.7.1 Hook protein -- 6.7.2 Universal joint -- 6.7.3 Hook length control -- 6.8 Hook-associated proteins -- 6.8.1 Basal body -- 6.9 Rod -- 6.10 The LP ring complex -- 6.10.1 The MS ring complex -- 6.11 The cytoplasmic ring -- 6.12 Flagellar protein export apparatus -- 6.13 Chaperones -- 6.14 The Mot proteins -- 6.15 Assembly system of flagella -- 6.15.1 Morphogenesis -- 6.15.2 Distal growth -- 6.15.3 Cap proteins -- 6.16 Protein export apparatus -- 6.16.1 Type 3 secretion system -- 6.16.2 Substrate specificity switching -- 6.17 Morphological pathway -- 6.18 In the cytoplasm -- 6.19 In the periplasmic space -- 6.20 Outside the cell -- 6.21 Origin of flagella -- 6.21.1 Type 3 secretion system -- 6.21.2 FOF1-ATPase -- 6.22 Conclusion -- Acknowledgment -- References -- 7 Bacterial pili and fimbriae -- 7.1 Introduction -- 7.2 Chaperone-usher pathway pilus represented by type I fimbriae and P pilus of Escherichia coli -- 7.2.1 Structure of type I fimbriae and pili -- 7.2.2 Biogenesis model of type I fimbriae and P pili -- 7.2.3 Alternative chaperone/usher pathways -- 7.2.4 Regulation of type I fimbriae and P pili -- 7.2.5 Function of type I fimbriae and pili -- 7.3 Type IV fimbriae and P pilus -- 7.3.1 Structure and biogenesis of type IV fimbriae and pili. , 7.3.2 Regulation of type IV fimbriae and pili -- 7.3.3 Function of type IV fimbriae and pili -- 7.3.4 Type V pilus -- 7.3.5 Structure of type V fimbriae and pili -- 7.3.6 Biogenesis model of type V fimbriae and pili -- 7.3.7 Regulation of type V fimbriae and pili -- 7.3.8 Function of type V fimbriae and pili -- 7.4 Development of novel therapeutics via targeting the pilus biogenesis -- 7.5 Emerging themes and future directions -- Acknowledgment -- References -- 8 Endospores, sporulation, and germination -- 8.1 Introduction -- 8.2 Sporulation as a survival strategy -- 8.3 The endospore structure and resistance -- 8.4 Endospore formation -- 8.5 Spore awakening: germination -- 8.6 Endospore formers pathogens -- 8.7 Pathogenic spore formers control -- 8.8 Endospore detection -- 8.9 Endospore-based technology -- 8.9.1 Probiotics -- 8.9.2 Biocides -- 8.9.3 Biofuels and organic compounds -- 8.9.4 Bioparticles -- References -- 2 Bacterial cell function -- 9 Bacterial growth and cultivation -- 9.1 Introduction -- 9.2 Bacterial growth -- 9.2.1 Patterns of growth and sources of information -- 9.2.2 Molecular information related to bacterial growth -- 9.2.2.1 Ribosomal RNA -- 9.2.2.2 Chromosome replication -- 9.2.2.3 Cell division -- 9.2.2.4 Global regulatory proteins -- 9.2.3 Growth and stasis -- 9.2.3.1 Lag phase -- 9.2.3.2 Exponential phase -- 9.2.3.3 Stationary phase -- 9.2.3.4 Death phase -- 9.2.3.5 Exit from dormant or stationary cellular states and re-entry into growth -- 9.2.4 The Environmental factors that affect bacterial growth -- 9.2.4.1 Temperature -- 9.2.4.2 Oxygen -- 9.2.4.3 pH -- 9.2.4.4 Osmotic pressure -- 9.2.5 Unique growth forms: spores, biofilms, and persisters -- 9.3 Bacterial growth and antibiotics treatment -- 9.4 Bacterial cultivations -- 9.4.1 Historic perspective of cultivation -- 9.4.2 "As-yet-unculturable" bacteria. , 9.4.3 The renaissance of bacterial cultivation -- 9.4.3.1 Cocultivation -- 9.4.3.2 Community cultivation -- 9.4.3.3 In situ cultivation -- 9.4.3.4 Single-cell isolation and cultivation -- 9.4.3.5 High-throughput cultivation -- 9.4.3.6 Culturomics -- 9.5 Final remarks -- Acknowledgments -- References -- 10 Bacterial energy metabolism -- 10.1 Introduction -- 10.1.1 Scope of chapter -- 10.2 Fermentation -- 10.2.1 Bacterial fermentation of sugars -- 10.2.2 Bacterial ethanol fermentation -- 10.2.3 Bacterial lactate fermentation -- 10.2.4 Propionate fermentation -- 10.2.5 Bacterial organic acid fermentation -- 10.2.6 Bacterial biogas fermentation -- 10.2.7 Its role in human health -- 10.2.8 Industrial bacterial fermentation -- 10.2.8.1 Chemiosmosis -- 10.2.9 Complete steps of chemiosmosis and adenosine triphosphate synthesis -- 10.2.10 Adenosine triphosphate synthase -- 10.2.11 Evolutionary significance -- 10.2.11.1 Aerobic respiration -- 10.2.12 Glycolysis -- 10.2.13 Formation of acetyl-CoA -- 10.2.14 Tricarboxylic acid cycle -- 10.2.15 Pyruvate dehydrogenase complex -- 10.2.16 Citrate synthase -- 10.2.17 Isocitrate dehydrogenase -- 10.2.18 α-Ketoglutarate dehydrogenase complex -- 10.2.18.1 Anaerobic respiration -- 10.2.19 Nitrate respiration -- 10.2.20 Denitrification -- 10.2.21 Applications of denitrification -- 10.2.22 Sulfate respiration -- 10.2.23 Fumaric acid respiration -- 10.2.23.1 Metabolism of complex carbohydrates -- 10.2.24 Starch metabolism -- 10.2.25 Cellulose degradation -- 10.2.26 Lignin degradation -- 10.2.27 Xylan degradation -- 10.2.27.1 Energy metabolism in selected bacteria -- 10.2.28 Obligate aerobes -- 10.2.29 Obligate anaerobes -- 10.2.30 Facultative anaerobes -- 10.2.31 Microaerophile -- References -- 11 Biofilms, quorum sensing, and crosstalk -- 11.1 Communal behavior of bacteria -- 11.2 A conceptual overview of quorum sensing. , 11.3 Quorum signals and circuits.

Note: Intro -- Preface -- Prologue -- Contents -- Editor Biography and Contributors -- 1 Land--Ocean Interactions Between the Changjiang (Yangtze River) Watersheds to the East China Sea Continental Margin -- Abstract -- 1.1 Geographic Setting -- 1.1.1 Watersheds of the Changjiang -- 1.1.2 The Changjiang (Yangtze River) Estuary -- 1.1.3 East China Sea -- 1.2 Natural and Anthropogenic Forcings -- 1.3 An Overview of Previous Studies in the Region -- 1.4 Scientific Research and Relevance to Human Society -- 1.5 Scope and Structure of the Monograph -- 1.6 Looking Forward to the Future: Challenges and Opportunities for Ongoing Research -- Acknowledgments -- References -- 2 Hydrodynamics of the Changjiang Estuary and Adjacent Seas -- Abstract -- 2.1 Introduction -- 2.2 Tides and Residual Water Transport -- 2.2.1 Tides -- 2.2.1.1 Tidal Elevation and Tidal Range -- 2.2.1.2 Harmonic Analysis -- 2.2.2 Residual Water Transport -- 2.2.2.1 Numerical Model -- 2.2.2.2 Residual Water Transport in Winter -- 2.2.2.3 Residual Water Transport in Summer -- 2.3 Saltwater Intrusion -- 2.3.1 Impacts of Wind Stress on the SSO -- 2.3.2 Numerical Simulations -- 2.3.3 Mechanisms of Wind Impact on Saltwater Intrusion -- 2.4 Dispersal of Riverine Plumes in the East China Sea -- 2.4.1 Extension of the CDW in Winter -- 2.4.2 Extension of the CDW in Summer -- 2.4.3 Numerical Simulation of Tidal Modulation on the Extension of the CDW -- 2.5 Summary -- Acknowledgments -- References -- 3 Changjiang Estuary Sediment Transport Dynamics -- Abstract -- 3.1 Introduction -- 3.2 Riverine Sediment Transport -- 3.2.1 Water and Sediment Discharge -- 3.2.2 Sediment Grain Sizes -- 3.2.3 Flocculation of Suspended Sediment -- 3.2.4 Discussion -- 3.3 Estuarine Sediment Transport -- 3.3.1 Suspended Sediment -- 3.3.2 Bottom Sediment -- 3.3.3 Exchange Between Suspended and Bottom Sediments. , 3.3.3.1 Grain Size Distributions -- 3.3.3.2 Quantification Methods of the Sediment Exchange -- 3.3.3.3 Evidence of Sediment Exchange -- 3.3.4 Discussion -- 3.4 Impacts of Engineering Works -- 3.4.1 Introduction -- 3.4.2 Model Setup -- 3.4.3 Changes in Estuarine Circulation -- 3.4.4 Changes in Transport Timescales -- 3.4.5 Discussion -- 3.5 Summary -- Appendix A: Summary of Data Sources -- References -- 4 Temporal Variations in Water and Sediment Discharge from the Changjiang (Yangtze River) and Downstream Sedimentary Responses -- Abstract -- 4.1 Introduction -- 4.2 Temporal Variation in Riverine Water and Sediment Discharge -- 4.2.1 Water Discharge -- 4.2.1.1 Long-term Variation in Water Discharge -- Periodicity of Water Discharge -- Temporal Trends in Water Discharge -- 4.2.1.2 Seasonal Variation in Precipitation and Water Discharge -- 4.2.1.3 Extreme Water Discharge Events -- 4.2.1.4 Predictions of Future Water Discharge -- 4.2.2 Sediment Discharge -- 4.2.2.1 Long-term Variation -- Increase in Sediment Discharge Before the 1960s -- Decrease in Sediment Discharge Since the 1960s -- 4.2.2.2 Seasonal Variation -- 4.2.2.3 Predictions of Future Sediment Discharge -- 4.2.3 Suspended Sediment Concentration -- 4.2.3.1 Long-term Variation -- 4.2.3.2 Seasonal Variation -- 4.3 Delta Response to Variations in Riverine Sediment Supply -- 4.3.1 Intertidal Wetland Response -- 4.3.2 Subaqueous Delta Response -- 4.3.3 Complexity of Delta Response -- 4.4 Variations in Surface Suspended Sediment Concentration in the Estuary and Adjacent Coastal Waters -- 4.4.1 Spatial Pattern of Suspended Sediment Concentration -- 4.4.2 Temporal Variation in Suspended Sediment Concentration -- 4.4.2.1 Neap--Spring Tide Variation -- 4.4.2.2 Seasonal Variation -- 4.4.2.3 Long-term Trends -- 4.5 Summary and Conclusions -- Acknowledgments -- References. , 5 Plant Nutrients and Trace Elements from the Changjiang Watersheds to the East China Sea -- Abstract -- 5.1 Introduction -- 5.2 Materials, Methods, and Data Collection -- 5.2.1 Field and Oceanic Observations, Sample Collection, and Analysis -- 5.2.2 Simulation of Element Partitioning Between Water and Particulate Phases -- 5.3 Plant Nutrients and Trace Elements from the Watershed to the River Mouth of the Changjiang -- 5.3.1 Longitudinal Profiles of Plant Nutrient Concentrations -- 5.3.2 Temporal Changes in Plant Nutrient Concentrations -- 5.3.3 Concentrations of Trace Elements in the Changjiang -- 5.4 Results of Laboratory Simulations -- 5.5 Modification of Chemical Species in the Changjiang Estuary and Adjacent Coastal Environment -- 5.6 Biogeochemical Dynamics of Chemical Elements in the East China Sea -- 5.6.1 Anthropogenic Impacts on Coastal Ecosystems from Land-Based Activities -- 5.6.2 Chemical Element Budgets and Their Impacts on Ecosystems -- 5.7 Summary and Prospects for the Future -- Acknowledgments -- References -- 6 Organic Matter and Biomarkers of the Changjiang Estuary and East China Sea Shelf -- Abstract -- 6.1 Introduction -- 6.2 Sampling and Methods -- 6.2.1 Field Observations and Sample Collection -- 6.2.2 Laboratory Analysis -- 6.3 Particulate and Dissolved Organic Carbon from the Watershed to the Shelf -- 6.3.1 Spatial and Temporal Variations in Particulate and Dissolved Organic Carbon in the Changjiang -- 6.3.2 Characterization of DOM with EEMs -- 6.3.3 Dynamics of POC and DOC in the East China Sea -- 6.4 Characterization of Organic Matter with Various Biomarkers -- 6.4.1 Temporal Variation in Riverine Organic Matter from Pigments and Amino Acids -- 6.4.2 Delivery of Particulate Terrigenous Organic Matter from the River to the Shelf -- 6.4.3 Distribution of Organic Matter in the Sediments Over the East China Sea. , 6.5 Anthropogenic Impacts on the River, Estuary, and Adjacent Regions -- 6.5.1 Impacts of Dams on the Transportation of Terrestrial Organic Matter to the Lower Stream -- 6.5.2 Distribution of Pollutants and Their Impacts -- 6.6 Summary -- Acknowledgments -- References -- 7 Coastal Wetlands in the Changjiang Estuary -- Abstract -- 7.1 General Characteristics of Coastal Wetlands in the Changjiang Estuary -- 7.2 Spatial and Temporal Dynamics of Salt marsh Vegetation -- 7.2.1 Succession of Salt marsh Vegetation in the Changjiang Estuary -- 7.2.2 Spatiotemporal Dynamics of Salt marsh Vegetation in the Changjiang Estuary -- 7.2.3 Spatiotemporal Salt marsh Dynamics in the Chongming Dontan National Nature Reserve -- 7.2.4 Spatiotemporal Dynamics of Salt marsh in the Jiuduansha National Nature Reserve -- 7.3 Biological Invasion in the Coastal Wetlands -- 7.3.1 Impacts of the S. alterniflora Invasion on Benthic Communities in the Wetlands -- 7.3.2 CA Model for Simulation of the Expansion of S. alterniflora -- 7.3.3 Population Expansion on the Middle Shoal -- 7.3.4 Population Expansion on the Lower Shoal -- 7.3.5 Implications for Strategic Control of Invasive Plants -- 7.4 Management and Conservation of Coastal Wetlands in the Changjiang Estuary -- 7.4.1 Stresses on the Coastal Wetlands in the Changjiang Estuary -- 7.4.2 Management and Conservation of the Coastal Wetlands -- 7.5 Summary and Conclusions -- References -- 8 Marine Biology of the Changjiang (Yangtze River) Estuary and Adjacent East China Sea Shelf -- Abstract -- 8.1 Introduction -- 8.2 Materials and Methods -- 8.3 Phytoplankton in the Changjiang Estuary -- 8.3.1 Species Composition and Dominant Species -- 8.3.2 Phytoplankton Along Estuarine Gradients -- 8.3.3 Phytoplankton Communities -- 8.4 Zooplankton Communities of the Changjiang Estuary and the Shelf Waters of the East China Sea. , 8.4.1 Variations in Species Composition and Diversity Among Subregions of the Changjiang Estuary -- 8.4.2 Seasonal Succession of Zooplankton Populations -- 8.4.3 Zooplankton Along the Salinity Gradients -- 8.4.4 Changes in Zooplankton in the Changjiang Estuary and the Adjacent East China Sea -- 8.5 The Benthic Macro-Invertebrate Community of the Changjiang Estuary -- 8.6 Fish Communities of the Changjiang Estuary and the Adjacent East China Sea -- 8.6.1 Species Composition -- 8.6.2 Temporal--Spatial Distributions of Fishes -- 8.6.3 Fish Migration Patterns -- 8.6.4 Fishery Resources in the East China Sea -- 8.6.5 Fish Migratory Routes in the East China Sea -- 8.6.5.1 Large Yellow Croaker -- 8.6.5.2 Small Yellow Croaker -- 8.6.5.3 White Croaker -- 8.6.6 The Ichthyoplanktonic Community in the Changjiang Estuary and the Adjacent East China Sea -- 8.7 A General View of Ecocatastrophe in the Marine Ecosystems of the Changjiang Estuary and the Adjacent East China Sea -- 8.8 Overall Evaluation -- Acknowledgments -- References -- 9 Socioeconomic Dimensions of the Coastal Environment of the East China Sea -- Abstract -- 9.1 Introduction -- 9.2 Urbanization and Environmental Quality -- 9.2.1 Temporal Variations in the Urbanization Rate in Each Region -- 9.2.2 Impact of Urbanization on the Coastal Environment -- 9.2.2.1 Urban Sewage Discharge -- 9.2.2.2 Industrial Wastewater Discharge -- 9.2.2.3 Solid Waste -- 9.2.2.4 Public Transportation and Private Car Use -- 9.2.2.5 Reclamation and the Quality of the Coastal Environment -- 9.2.3 Environmental Investigation -- 9.3 Economy and Environmental Quality -- 9.3.1 GDP -- 9.3.1.1 Value of Agricultural Planting and Crop Production -- 9.3.1.2 Animal Husbandry -- 9.3.1.3 Fisheries and Marine Aquaculture -- 9.3.1.4 Industrial GDP Structure -- 9.3.2 Impact of the Economy on the Environment -- 9.3.2.1 Changing Land Use. , 9.3.2.2 Fertilizer Application.

Note: Intro -- Contents -- Contributors -- 1: Introduction and Background -- 1.1 International Workshops -- 1.2 IOC/WESTPAC Summer Training Courses Were Organised -- 1.3 This Monograph Is an Output from These Activities! -- References -- 2: Anthropogenic Environmental Impacts on Coral Reefs in the Western and South-Western Pacific Ocean -- 2.1 Introduction -- 2.1.1 The Western and South-Western Pacific Region and the Coral Reefs -- 2.1.2 Population Change and Migration of People to Coastal Areas -- 2.1.3 Subsistence Living and Impacts of the Global Economic Situation on Reef Resources -- 2.1.4 Pollution from Small-Scale Developments -- 2.1.5 Shipping Impacts -- 2.1.6 Coastal City Expansion -- 2.1.7 Large Industry Impacts -- 2.1.7.1 Agriculture and Forestry -- 2.1.8 Tourism -- 2.1.9 Commercial Fishing Including Marine and Coastal Mariculture -- 2.1.10 Mining -- 2.1.11 Military Activities and Atomic Bomb Testing -- 2.1.12 Dredging and Dumping of Dredge Materials (Spoils) -- 2.2 Hydrodynamic Impacts of Anthropogenic Activities on Coral Reefs -- 2.3 Climate Change -- 2.4 Conclusions -- Appendix:Tribute to Dr. William G. L. (Bill) AALBERSBERG (1949-2018) -- References -- 3: Advances in Coral Biology -- 3.1 Introduction -- 3.2 Coral Biology -- 3.2.1 Reproduction, Development, and Recruitment of Larvae -- 3.2.1.1 Coral Spawning -- 3.2.1.2 Fertilization -- 3.2.1.3 Hybridization -- 3.2.1.4 Embryonic Development -- 3.2.1.5 Recruitment -- 3.2.2 Coral Taxonomy and Species Identification -- 3.2.2.1 Molecular Taxonomy and Systematics -- 3.2.2.2 Population Genetics -- 3.3 Current Threats on the Health of Reef Corals -- 3.3.1 Coral Bleaching -- 3.3.1.1 Spatial and Temporal Variation -- 3.3.1.2 Causes, Mechanisms, and Consequences -- 3.3.2 Coral Diseases -- 3.3.2.1 Identification and Prevalence -- 3.3.2.2 Disease Transmission -- 3.3.2.3 Prevention and Therapy. , 3.4 Management Consideration Based on Coral Biology -- References -- 4: Reef Ecology in the Western Pacific for Adaptation to Global Change -- 4.1 Introduction -- 4.2 Coral Reef Biodiversity Decline and Extinction Risk -- 4.2.1 Coral Reef Biodiversity Loss -- 4.2.2 Extinction Risk of Corals -- 4.3 Coral Reef Recovery After Disturbances -- 4.3.1 Disturbance Types and Impacts -- 4.3.2 Coral Reef Recovery -- 4.4 Coral Reef Resilience -- 4.4.1 Ecological Resilience -- 4.4.2 Coral Reef Resilience Indicators -- 4.4.3 Coral Reef Resilience Assessment -- 4.4.4 Coral Reef Resilience-Based Management -- 4.5 Coral Reef Connectivity -- 4.5.1 Concepts of Marine Population Connectivity -- 4.5.2 Ocean Circulation Drives Population Connectivity -- 4.5.3 Population Connectivity Among Corals and Reef Fishes -- 4.5.4 Applied Population Connectivity -- 4.6 Coral Reef Bioerosion -- 4.6.1 The Role of Bioerosion in Reef Development -- 4.6.2 Endolithic Bioerosion -- 4.6.3 External Bioerosion -- 4.6.4 Environmental Impacts on Bioerosion -- 4.7 Coral Reef Refugia Under Global Change -- 4.7.1 Coral Reef Refugia Concepts -- 4.7.2 Coral Reef Refugia from Thermal Stress -- 4.7.3 Coral Reef Refugia from Ocean Acidification -- 4.8 Marine Protected Area Networks (MPA Networks) -- 4.8.1 MPA Network Design Principles -- 4.8.2 Spatial Variations in MPA Networks -- 4.8.3 Fisheries in MPA Networks -- 4.8.4 Assessment and Conservation in MPA Networks -- 4.9 Passive and Active Restoration of Degraded Coral Reefs -- 4.9.1 Passive Coral Restoration -- 4.9.2 Direct Coral Transplantation -- 4.9.3 Coral Gardening -- 4.9.4 Substratum Addition (Artificial Reefs) -- 4.9.5 Substratum Stabilization and Enhancement -- 4.9.6 Coral Larval Enhancement -- References -- 5: Biogeochemical Dynamics of Coral Reef Systems -- 5.1 Introduction -- 5.2 External Driving Forces of Coral Reefs. , 5.2.1 Solar Radiation -- 5.2.2 Tide and Waves -- 5.2.3 Winds and Monsoon -- 5.2.4 Water Circulation and Currents -- 5.2.5 Land-Sourced Influxes -- 5.3 Sources of Chemical Elements in Coral Reef Systems -- 5.3.1 Terrestrial Material Inputs -- 5.3.2 Atmospheric Depositions -- 5.3.3 Coastal Upwelling -- 5.3.4 Recycling Within the System -- 5.4 Major Pathways of Biogeochemical Cycles -- 5.4.1 Autotrophic Production and Symbiosis -- 5.4.2 Heterotrophic Processes -- 5.4.3 Coupling Between Pelagic and Benthic Sub-systems -- 5.4.4 Food Web Dynamics -- 5.5 Interactions Between Biogeochemistry and Coral Reef Ecosystems -- 5.5.1 Impact of Nutrients on the Coral Ecosystems -- 5.5.2 Carbon Chemistry and Calcification -- 5.5.3 Mass Flow and Relationship with Energy Budgets -- 5.5.4 Discussion -- 5.6 Prospect of Climate Change and Anthropogenic Perturbations -- 5.6.1 Global Warming and Ocean Acidification -- 5.6.2 Impacts of Sea Level Rise -- 5.6.3 Roles of Human Society from Land- and Marine-Based Activities -- 5.6.4 Feedbacks to the Earth System -- 5.7 Modeling Approach to the Biogeochemistry of Coral Reefs -- 5.7.1 Quantitative Description of the Coral Symbiosis -- 5.7.2 Reef-Scale Model for Coral Ecosystems -- 5.7.3 Examples of Numerical Simulations in Coral System -- 5.7.4 Future Perspectives -- 5.8 Summary and Way Forward -- References -- 6: Environmental and Climate Proxies Embedded in Coral Skeletons -- 6.1 Introduction -- 6.1.1 Anatomy of Coral Skeleton -- 6.1.2 Basic Chemical Reactions Leading to Aragonite Formation in Coral -- 6.1.3 Solubility of CaCO3 and Water Temperature -- 6.1.4 Biomineralization Process for Aragonite Precipitation in Coral -- 6.1.5 Organic Matter in Coral Skeleton -- 6.2 Coral Core Sampling and Handling for Further Chemical and Isotopic Measurements -- 6.2.1 Retrieval of Coral Core and Slab Cutting -- 6.2.2 Slab Cleaning. , 6.2.3 Micro-Sampling -- 6.2.4 Subsample Cleaning for Chemical and Isotope Analysis -- 6.3 Intra- and Inter-skeletal and Colony Variability in the Chemical and Isotope Compositions -- 6.3.1 Intra-skeletal Variations -- 6.3.2 Inter-colony and Gender Variability -- 6.3.3 Calcite Formation Within the Aragonite Lattice -- 6.4 Age Model -- 6.4.1 Annual Growth Band -- 6.4.2 14C Dating (t1/2 = 5730 Years) (Valid for < -- 5 x t1/2 Years Old Coral) -- 6.4.3 230Th Dating (Valid < -- 123,000 Years Old Coral) -- 6.4.4 210Pb Dating (Valid < -- 100 Years Old Coral) -- 6.4.5 228Th Dating (Valid < -- 30 Years Old Coral) -- 6.4.6 90Sr Dating (Valid Since the 1950s) -- 6.4.7 Amino Acid Racemization (Valid Up to 40,000 Years Old Coral) -- 6.5 Principles of Application of Proxies/Tracers to the Past Climate and Environment -- 6.6 Chemical Elements and Isotopes Proxies -- 6.6.1 Lithium (Li) and Lithium Isotopes -- 6.6.2 Boron (B) and Boron Isotopes -- 6.6.3 Carbon (C) Isotopes -- 6.6.4 Nitrogen (N) Isotopes -- 6.6.5 Oxygen (O) Isotopes and Carbonate Clumped Isotopes -- 6.6.6 Fluorine (F) -- 6.6.7 Sodium (Na) -- 6.6.8 Magnesium (Mg) and Magnesium Isotopes -- 6.6.9 Phosphorus (P) -- 6.6.10 Sulfur (S) and Sulfur Isotopes -- 6.6.11 Calcium (Ca) Isotopes -- 6.6.12 Vanadium (V), Chromium (Cr), Manganese (Mn), Iron (Fe), Nickel (Ni), Copper (Cu), and Zinc (Zn) -- 6.6.13 Strontium (Sr) and Sr Isotopes -- 6.6.14 Yttrium -- 6.6.15 Molybdenum (Mo) Isotopes -- 6.6.16 Cadmium (Cd) -- 6.6.17 Iodine (I) and Iodine Isotopes -- 6.6.18 Barium (Ba) and Barium Isotopes -- 6.6.19 Rare Earth Elements (REEs) -- 6.6.20 Neodymium (Nd) -- 6.6.21 Lead (Pb) and Lead Isotopes -- 6.6.22 Uranium (U) -- 6.6.23 Plutonium (Pu) Isotopes -- 6.7 Discussion and Summary -- References -- 7: Synthesis and Future Perspectives on the Coral Reefs in the Western Pacific Region -- 7.1 Introduction. , 7.2 Function of Coral Reefs in a Sustainable Anthropocene -- 7.3 Coral Reefs in the Western Pacific Region and Comparison to Other Areas -- 7.4 External Forcings and Systems Response Threats to Coral Reefs in the Indo-Western Pacific Region -- 7.5 Summary and Main Conclusions of This Study -- 7.5.1 Anthropogenic Impacts Become Dominant Issues for the Sustainable Development of Coral Reef Systems -- 7.5.2 Coral Biology Is Critical in Our Knowledge of Tropical and Subtropical Environments -- 7.5.3 Coral Reef Ecology Bridges System Functions and Adaptive Management Towards a Sustainable Development -- 7.5.4 Biogeochemical Processes of Coral Reefs Play a Key Role in Understanding the Element Cycles and Connectivity Between Dif... -- 7.5.5 Proxies Embedded in Coral Skeletons Are Powerful Tool to Track the Impact of Environmental and Climate Variabilities -- 7.6 Challenges for the Ecosystem-Based Management (EbM) -- 7.7 Future Scientific Research Priorities on Coral Reefs -- References -- Postscript.

Note: Förderkennzeichen BMBF 1501414 , Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden , Text in Deutsch, mit englischen und deutschen Zusammenfassungen

Note: Zugl.: Aachen, Techn. Hochsch., Diss., 2010