Note: Front Cover -- Science for the Protection of Indonesian Coastal Ecosystems (SPICE) -- Science for the Protection of Indonesian Coastal Ecosystems (SPICE) -- Copyright -- Contents -- Contributors -- Reviewers -- Foreword -- 1 - Introduction-Science for the Protection of Indonesian Coastal Ecosystems (SPICE) -- 1.1 Rationale -- 1.2 Development and implementation of the research and education program SPICE -- 1.3 Research, education, and outreach activities -- 1.4 Summary and synthesis of SPICE results -- Acknowledgments -- References -- 2 - Physical environment of the Indonesian Seas with focus on the western region -- 2.1 Introduction -- 2.2 The marine circulation -- 2.2.1 The global context -- 2.2.2 The regional circulation -- 2.2.3 Tides -- 2.3 Seasonal variability and long-term changes -- 2.3.1 Seasonality of circulation -- 2.3.2 Seasonality of temperature and salinity -- 2.3.3 Long-term development of sea surface temperature and sea surface salinity -- 2.4 Water residence times -- 2.5 Sources and sinks of freshwater -- 2.6 Remote sensing methods applied in coastal process studies -- 2.6.1 Available satellite data -- 2.6.2 Ocean color and its variation in Indonesian coastal waters -- 2.6.3 Satellite-based studies of phytoplankton and coastal processes -- 2.6.3.1 Distribution of phytoplankton -- 2.6.3.2 Coastal discharge and influence of tidal and monsoon phases -- 2.6.3.3 Climatological aspects -- Acknowledgments -- References -- 3 - Human interventions in rivers and estuaries of Java and Sumatra -- 3.1 Introduction -- 3.2 Drivers of environmental change affecting river fluxes -- 3.3 Natural factors, human interventions, and extreme events controlling river fluxes -- 3.3.1 The Brantas River, Java, as an example of high suspended matter rivers -- 3.3.1.1 Variations in sources, composition, and fate of nutrients. , 3.3.1.2 Variations in sources, composition, and fate of suspended sediments and particulate organic matter -- 3.3.1.3 Effects on phytoplankton abundance and community composition -- 3.3.1.4 Effects on the dissolved oxygen regime of the lower Brantas -- 3.3.2 The Siak River, Sumatra, as an example of blackwater rivers -- 3.3.2.1 Variations in dissolved organic carbon and dissolved oxygen -- 3.3.2.2 Sources and fate of nutrients -- 3.4 Governance and management programs -- Acknowledgments -- References -- 4 - Carbon cycle in tropical peatlands and coastal seas -- 4.1 Introduction -- 4.2 Background information -- 4.2.1 Peat -- 4.2.2 Peatland types -- 4.2.3 Vegetation and biodiversity -- 4.2.4 Peatland distribution and carbon storage -- 4.3 Indonesian peatlands -- 4.3.1 History of Indonesian peat swamps -- 4.3.2 Peat properties -- 4.3.3 Peat carbon accumulation -- 4.3.4 Land use and cover changes in Indonesia -- 4.3.5 The hydrological cycle of Indonesian peatlands -- 4.4 Peat carbon losses -- 4.4.1 CO2 emissions caused by peat and forest fires -- 4.4.2 CO2 emissions caused by peat soil oxidations -- 4.4.3 Off-site CO2 emission -- 4.5 Land-ocean continuum -- 4.5.1 SPICE study area -- 4.5.2 Dissolved organic carbon -- 4.5.3 Dissolved organic carbon yields -- 4.5.4 CO2 emission from rivers -- 4.5.5 Dissolved inorganic carbon yields -- 4.5.6 Leaching and erosion -- 4.5.7 Priming -- 4.6 Estuaries and the ocean -- 4.6.1 Dissolved organic carbon -- 4.6.1.1 The microbial organic carbon pump in the ocean -- 4.6.1.2 Dissolved organic carbon discharges into the ocean -- 4.6.1.3 The fate of dissolved organic carbon in the ocean -- 4.6.2 CO2 emissions from the coastal ocean -- 4.6.3 Organic carbon burial -- 4.6.4 The invisible carbon footprint -- 4.6.5 The marine peat carbon budget -- 4.6.6 Emission factors -- 4.7 Ecosystem CO2 emissions. , 4.7.1 Net on-site ecosystem CO2 exchange -- 4.7.2 CO2 emission from pristine peat swamps -- 4.7.3 CO2 emission from disturbed peatlands -- 4.8 Evaluation of CO2 emissions -- 4.8.1 Climate response to cumulative emissions of CO2 -- 4.8.2 CO2 reduction potential -- 4.8.3 CO2 emissions and land losses -- 4.8.4 Climate pledges and gaps -- 4.9 Socioeconomic implications -- 4.9.1 REDD+ -- 4.9.2 SPICE field experiments -- 4.10 Outlook -- References -- 5 - Coral reef social-ecological systems under pressure in Southern Sulawesi -- 5.1 Introduction-coral reefs in Indonesia and the Spermonde Archipelago -- 5.2 Functioning of coral reefs -- 5.2.1 Water quality and biogeochemical processes -- 5.2.2 Benthic coral reef community dynamics of Spermonde Archipelago -- 5.2.3 Bacterial communities and biofilms -- 5.2.4 Coral reef recruitment processes -- 5.2.5 Coral physiology -- 5.2.6 Relationships between benthic and fish communities -- 5.2.7 Consequences of disturbances for coral reef functioning -- 5.3 Genetic connectivity of reefs in the Coral Triangle region -- 5.3.1 Large-scale connectivity across the Coral Triangle region -- 5.3.2 Small-scale connectivity in the Spermonde Archipelago -- 5.3.3 Self-recruitment at the islands of Barrang Lompo and Samalona -- 5.3.4 Application of connectivity data in marine-protected area network design -- 5.4 Social systems associated with the use of coral-based resources and reef-specific challenges -- 5.4.1 Participatory assessment of Spermonde's coral reef fisheries -- 5.4.2 Investigating marine social-ecological feedbacks and dynamics -- 5.4.3 Reef-related livelihoods and implications for the present and future health of fishers and reefs -- 5.4.4 Changing target species, perceptions of reef resources, and implications for food security. , 5.4.5 Conclusions for the management of coral reef resources in the Spermonde Archipelago -- 5.5 Modeling to support the management of reef systems -- 5.5.1 Simulating the impact of fisheries on coral reef dynamics -- 5.5.2 A model on gear choices of fishermen -- 5.5.3 Spatial patterns of fishing ground distribution -- 5.6 Summary and outlook -- Acknowledgments -- References -- Appendix A5 -- 6 - Ecology of seagrass beds in Sulawesi-Multifunctional key habitats at the risk of destruction -- 6.1 General introduction to tropical Southeast Asian seagrass meadows -- 6.1.1 High biodiversity of seagrasses in the coral triangle of the tropical Indo-West Pacific -- 6.1.2 Introduction to the Spermonde Archipelago and its seagrasses and mangroves -- 6.2 The current distribution of seagrasses in the Spermonde Archipelago -- 6.2.1 Area estimates and seagrass mapping -- 6.2.2 The structure of tropical seagrass bed systems -- 6.3 Seagrass ecology -- 6.3.1 The historic loss of megaherbivores and today's important role of burrowing shrimp -- 6.3.2 Macrobenthic communities -- 6.3.3 The food web and the trophic pyramid in tropical seagrass beds -- 6.3.4 The function of seagrass meadows as water filters and buffers for land runoff -- 6.3.5 Carbon storage -- 6.3.6 Seagrass beds as carbon sinks -- 6.3.7 Trophic transfers from seagrass meadows to nearby ecosystems -- 6.4 Tropical seagrass beds as key habitat for fish species -- 6.4.1 Tropical seagrasses and their associated fish communities -- 6.4.2 The seagrass canopy as a driver of fish communities -- 6.4.3 Differences in fish habitat utilization across seagrass meadows with distinct canopy structures -- 6.5 Human-seagrass interactions -- 6.5.1 Ecological value and ecosystem services -- 6.5.2 Fisheries on fish and invertebrates in seagrass beds -- 6.5.3 Seaweed farms -- 6.5.4 Human-made infrastructure. , 6.5.5 Current threats -- 6.6 Conclusions and outlook -- Acknowledgments -- References -- 7 - Mangrove ecosystems under threat in Indonesia: the Segara Anakan Lagoon, Java, and other examples -- 7.1 Introduction -- 7.2 The study areas -- 7.3 Environmental setting and natural resource use -- 7.3.1 The physical setting -- 7.3.2 Water quality, biogeochemistry, and pollution -- 7.3.3 Carbon sources and storage -- 7.3.4 Flora and fauna -- 7.3.5 Population and natural resource use in the Segara Anakan region -- 7.4 Environmental change in the Segara Anakan Lagoon region: causes, drivers, and impacts -- 7.4.1 Decline of marine species and fisheries -- 7.4.2 Sedimentation and its causes -- 7.4.3 Reclamation of land and conflicts over new land -- 7.5 Threats to mangrove forests and their ecosystem services in Indonesia -- 7.6 Management programs -- Acknowledgments -- References -- 8 - Impact of megacities on the pollution of coastal areas-the case example Jakarta Bay -- 8.1 Introduction -- 8.2 Hydrological system and nutrient dispersion -- 8.3 Organic and inorganic pollution in Jakarta Bay -- 8.3.1 Types, quantity, and distribution of pollutants -- 8.3.1.1 Trace hazardous elements -- 8.3.1.2 Organic pollutants -- 8.3.2 Characterizing emission sources -- 8.3.2.1 Source apportionment of trace elements -- 8.3.2.2 The insect repellent N,N-diethyl-m-toluamide as tracer for municipal sewage and the implications for coastal management -- 8.3.3 Industrial emissions in the Greater Jakarta area and their role for the contamination of the Jakarta Bay ecosystem -- 8.3.4 The flushing-out phenomenon -- 8.3.5 Accumulation in biota -- 8.4 Water quality and biological responses -- 8.4.1 Water pollution in Jakarta Bay and the Thousand Islands -- 8.4.2 Biological responses to anthropogenic stressors -- 8.4.3 Impacts on the physiology of key coral reef organisms. , 8.4.4 Impacts on reef composition.

Note: Front Cover -- Microbial Communities in Coastal Sediments -- Copyright Page -- Contents -- Introduction -- 1 Source and composition of organic matter and its role in designing sediment microbial communities -- 1.1 Introduction -- 1.2 Organic matter in coastal sediments -- 1.2.1 Types of sedimentary organic matter -- 1.2.1.1 Total organic matter/total organic carbon -- 1.2.1.2 Particulate organic matter/particulate organic carbon -- 1.2.1.3 Dissolved organic matter/dissolved organic carbon -- 1.2.1.4 Dissolved inorganic carbon -- 1.2.1.5 Labile organic matter -- 1.2.1.6 Refractory organic matter -- 1.2.1.7 Microbial biomass carbon -- 1.2.1.8 Biopolymeric carbon -- 1.3 Source of organic matter: autochthonous and allochthonous -- 1.3.1 Autochthonous organic matter -- 1.3.2 Allochthonous organic matter -- 1.3.2.1 Transport by rivers -- 1.3.2.2 Agricultural and urban runoff -- 1.4 Quality of organic matter in sediments -- 1.4.1 Organic matter quality indices -- 1.5 Microbial degradation of organic matter -- 1.6 Role of organic matter in designing sediment microbial communities -- 1.7 Microbial diversity and ecology in coastal sediments -- 1.7.1 Diversity of bacterial communities -- 1.7.1.1 Hydrolytic bacteria -- 1.7.1.2 Denitrifying bacteria -- 1.7.1.3 Iron and manganese reducers -- 1.7.1.4 Sulfate reducers -- 1.8 Diversity of archaeal communities -- 1.8.1 Methanogenic archaea -- References -- 2 Sources, types, and effects of nutrients (N and P) in coastal sediments -- 2.1 Introduction -- 2.2 Nutrient sources of coastal ecosystems -- 2.2.1 Agriculture -- 2.2.2 Animal husbandry and marine aquaculture -- 2.2.3 Fossil fuel burning and atmospheric deposition -- 2.3 Nutrient enrichment: forms and types -- 2.4 Effect of hypernutrification -- 2.4.1 Eutrophication and consequences for ecology -- 2.4.2 Hypoxia and anoxia in water and sediment. , 2.4.3 Eutrophication-induced changes in sediment microbial communities -- References -- 3 Environmental variables and factors regulating microbial structure and functions -- 3.1 Introduction -- 3.2 Spatial and temporal heterogeneity -- 3.3 Geological factors -- 3.3.1 Sediment granulometry -- 3.3.2 Sediment depth -- 3.3.2.1 Shift in substrate availability with depth -- 3.3.2.2 Decrease in lability of organic matter with depth -- 3.4 Hydrological factors -- 3.5 Physicochemical factors -- 3.5.1 pH -- 3.5.2 Salinity -- 3.5.3 Pore water chemistry/presence of nutrients or chemicals -- 3.5.4 Redox potential -- 3.5.5 Changes in availability of electron acceptors -- 3.5.5.1 Aerobic respiration -- 3.5.5.2 Nitrate reduction -- 3.5.5.3 Mn and Fe reduction -- 3.5.5.4 Sulfate reduction -- 3.5.5.5 Methanogenesis -- 3.5.6 Role of electron donors -- 3.6 Biological factors -- 3.6.1 Trophic interactions -- 3.6.1.1 Syntrophy and interspecies hydrogen transfer -- 3.6.2 Evolutionary mechanisms and diversification -- 3.6.3 Ecological coherence -- 3.6.4 Microbial characteristics -- 3.6.5 Bioturbation and ventilation -- 3.6.6 Plant interactions -- 3.7 Nutritional factors -- 3.8 Natural and anthropogenic disturbances -- 3.9 Presence of contaminants/toxic substances -- References -- 4 Biogeocycling of nutrients (C, N, P, S, and Fe) and implications on greenhouse gas emissions -- 4.1 Introduction -- 4.2 Biogeocycling of nutrients -- 4.2.1 Carbon -- 4.2.2 Nitrogen -- 4.2.3 Sulfur -- 4.2.4 Manganese (Mn) and iron (Fe) -- 4.3 Greenhouse gas dynamics in coastal ecosystems -- 4.3.1 Carbon dioxide -- 4.3.2 Methane -- 4.3.3 Nitrous oxide -- References -- 5 Biodegradation and biotransformation of persistent organic pollutants by microbes in coastal sediments -- 5.1 Introduction -- 5.2 Why persistent organic pollutants? -- 5.3 Anaerobic degradation and pathways. , 5.3.1 Phenols and chlorinated phenols -- 5.3.2 3-Chlorobenzoate -- 5.3.3 Polycyclic aromatic hydrocarbons -- 5.3.4 Polychlorinated biphenyls -- 5.3.5 Polychlorinated dibenzo-p-dioxins and dibenzofurans -- 5.4 Anaerobic microorganisms involved -- 5.5 Limitations for anaerobic degradation: electron acceptors -- 5.6 Future prospects -- References -- 6 Assessment of microbial structure and functions in coastal sediments -- 6.1 Introduction -- 6.2 Culture-dependent methods: the "great plate count anomaly" -- 6.3 Molecular tools used to examine microbial diversity of coastal sediments -- 6.3.1 Gene amplification and sequencing of 16S rDNA -- 6.3.2 Fluorescence in situ hybridization -- 6.3.3 Terminal restriction fragment length polymorphism -- 6.3.4 Denaturing gradient gel electrophoresis/temperature gradient gel electrophoresis -- 6.4 High-throughput sequencing technologies -- 6.4.1 Metagenomics: an approach based on small subunit ribosomal RNA -- 6.5 Functional diversity of coastal sediment microbes -- 6.5.1 Stable isotope probing -- 6.6 Microbial activity in coastal sediment: study of biogeochemical reaction rates in laboratory microcosms -- 6.7 Conclusion and future prospects -- References -- Appendix 1: Conclusions and future perspectives -- Index -- Back Cover.

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