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This chapter summarizes the physiology of bacterial respiration with an emphasis on topics relevant for understanding processes at a cellular level, as well as for understanding the larger-scale implications of respiration within aquatic ecosystems. The analysis begins with definitions and examples of respiratory systems, and reviews essential aspects of their biochemistry. Modes of respiration and aspects of their dynamics are surveyed next, with a brief consideration of the organisms involved, their distribution, and constraints on their activity.

This chapter provides a brief historical account of the success and limitations of using chemical biomarkers in aquatic ecosystems. It also introduces the general concepts of chemical biomarkers as they relate to global biogeochemical cycling. The application of chemical biomarkers in modern and/or ancient ecosystems is largely a function of the inherent structure and stability of the molecule, as well as the physicochemical environment of the system wherein it exists. In some cases, redox changes in sediments have allowed for greater preservation of biomarker compounds; in well-defined laminated sediments; for example, a strong case can be made for paleo-reconstruction of past organic matter composition sources. However, many of the labile chemical biomarkers may be lost or transformed within minutes to hours of being released from the cell from processes such as bacterial and/or metazoan grazing, cell lysis, and photochemical breakdown. The role of trophic effects versus large-scale physiochemical gradients in preserving or destroying the integrity of chemical biomarkers varies greatly across different ecosystems. These effects are discussed as they relate to aquatic systems such as lakes, estuaries, and oceans.

Studies conducted in a wide range of freshwater ecosystems have revealed specific suites of attributes that predispose certain ecosystems to being sites of elevated MeHg bioaccumulation in fish and piscivorous birds and mammals. These hotspots result from a complex sequence of biotic and abiotic mechanisms that occur at critical points in the transfer of Hg in the environment from Hg supply, methylation, transport, bioaccumulation, and transfer in food webs. System-specific case studies are described in which Hg concentrations in biotic endpoints are known to be elevated. These studies highlight mercury sensitivity factors in natural lakes and ponds occupying sensitive landscapes, small and large managed reservoirs, the Florida Everglades, the Great Lakes, and in industrially impacted rivers.

This chapter first explores the current perspective of fires in watersheds and the social and ecological reactions to changes to the historic fire regimes. It then discusses issues surrounding the restoration of fire regimes within watersheds, and ends with the concept of integrated watershed restoration. Rehabilitation and restoration are not mutually exclusive, and most of the tools and practices used in rehabilitation are often used for restoration. Post-fire rehabilitation and other post-fire activities treat fire as an emergency, not as an expression of the ecosystem process. The most important issues that form obstacles to restoring fire regimes, and a possible approach to overcome them are addressed. Fire is a natural process within most of California watersheds and must be considered when managing for riparian, aquatic, and water resources. Fires out of their natural regime can and do cause serious damage to ecological assets.

Chapter 10 focuses on ecosystem services as a key concept to study the conservation of high altitude waters. Despite their limited area, these ecosystems provide important provisioning, regulating, and cultural services on both local and global scales. They are water towers for mountain and lowland populations, serve as important carbon dioxide sinks, constitute the most extensive high altitude pastoral regions worldwide, and serve as refugia for unique species and communities. The chapter argues that the sustainable use and effective conservation of these ecosystems requires developing sound indicators and scenarios of temporal environmental changes. It also requires uncovering ecosystems’ macroeconomic dimension (i.e. identifying and quantifying causal interactions among biodiversity, water use changes, and socio-economic drivers at different scales), and developing strategies combining biodiversity conservation (e.g. through the protection of umbrella species and extensive areas), livelihood protection and development, and the maintenance of cultural diversity and traditional values.

Chapter 7 elucidates the relationships between the structure and functioning of aquatic ecosystems at high altitude through the description of material cycles and food webs. Following the landscape continuum model, material cycling is profoundly influenced by the physical structure of the waterscape (e.g. vegetation cover); as a result a great diversity of energetic pathways characterize high altitude waterscapes, along an autotrophy–heterotrophy gradient. Similarly, high altitude aquatic food webs embrace a great diversity of trophic compartments, feeding strategies, and processes (trophic cascades and terrestrial subsidiarity) that are profoundly shaped by environmental harshness. Harsh conditions also generate stress gradients along which the strength and direction of species interactions (from competition to facilitation) and their functional role (e.g. as ecosystem engineers) are modified. The resulting structural and functional changes affect in turn species coexistence and trigger potential ecosystem shifts.

In evolutionary terms, insects have been in existence for over 400 million years and unequivocal evidence of insects with aquatic habits dates from approximately 320 million years ago. Exactly when and how insects began to occupy aquatic environments is open to debate; unravelling the ecological roles of insects in ancient aquatic ecosystems is even more challenging. Insect fossils are vital in trying to unravel evolutionary histories, but the fossil record is incomplete. This chapter discusses the fossil record and how it can inform our understanding of evolutionary events. Major events in insect evolution are reviewed at the coarse taxonomic level of insect orders and with emphasis on the evolution of aquatic and semi-aquatic groups. In a necessarily speculative manner, there are discussions of the history and evolution of aquatic habits, and the biogeography of the major aquatic insect groups as revealed by plate tectonics. The final section describes some of the many different environments occupied by aquatic insects and their characteristic faunas.

This chapter discusses biodiversity-ecosystem function studies in aquatic ecosystems in which additional biotic or abiotic drivers have been taken into account as mediators of ecosystem responses. It examines the impact of species richness relative to abiotic or biotic drivers of change or other biodiversity measures, including species composition and species evenness. It assesses the influence of model systems and ecosystem type of the experimental study on the strength of the relationship between species richness and ecosystem properties, as well as other drivers of change and ecosystem properties. Finally, it illustrates how ecosystem properties are mediated across aquatic ecosystems by analysing the effects of abiotic, biodiversity, and other biotic drivers of change combined.

This chapter describes the geologic, geographic, and ecological context of the location of Luquillo Mountains, particularly the factors affecting the response mechanisms of terrestrial and aquatic ecosystems to disturbance. It describes the existing conditions of the physical environment, chemical environment, and the biota of the Luquillo Mountains as they respond to disturbances. It then merges the decade-long research about the Mountains with the other tropical ecosystems around the globe.

Chapter 9 reviews the threats imposed by human activities to aquatic life at high altitude. High altitude regions of the inter-tropical belt are generally much more densely populated than their temperate counterparts. Therefore, they are directly affected by a number of human-related disturbances such as land use changes, water contamination, use and diversion, and the introduction of invasive species. The chapter details several unique environmental conditions of high altitude environments that make their aquatic biota particularly at risk in the face of anthropogenic disturbances. Among others, glaciers concentrate pollutants, low oxygen concentrations affect the response of aquatic fauna to stress, ultraviolet B modifies the bioavailability of contaminants, high primary productivity of grasslands encourages cattle ranching and fuels fires over large scales, and isolated watersheds favour species extinction following biological invasions.

Chapter 8 focuses on the effects of warming and changes in precipitation patterns on aquatic life at high altitude. Located near the edge of their climatic limits, in regions where the rate of warming is generally amplified compared with lowlands, high altitude aquatic systems present a high sensitivity to climate change. Changes in mountain climate create a number of indirect effects on aquatic life through the control of hydrological systems and processes, particularly those associated with the cryosphere (e.g. permafrost and ice melting) and the soil–vegetation interface (e.g. treeline expansion). The chapter then presents the three basic options faced by all aquatic organisms as their environmental conditions alter as a result of climate change: adapt, migrate, or perish. At an ecosystem level, small changes in physical, chemical, or biological characteristics can be amplified into major shifts in limnological properties.

Park and wildlife managers are facing an ironic dilemma as they work to restore and protect aquatic ecosystems — must amphibians be sacrificed if native fish are to return? Over the past century throughout the United States, resource managers sought to enhance the recreational value of lakes and streams by stocking non-native (exotic) game fish. The “success” of this effort is now recognized as a serious impediment to conserving natural aquatic biodiversity. Introduced fish endanger and replace native fish species through predation, competition, hybridization, and disease transmission. In many cases, bringing back the natives is doomed unless the introduced fish are eradicated. In Yellowstone National Park, four species of non-native trout were introduced, have become established, and threaten the survival of indigenous fish. A program to remove non-native trout has begun, but techniques used to remove these fish also threaten amphibians. Recommendations are made to eliminate or reduce the threat to amphibians, including making managers aware of the presence of amphibians, and offering strategies for reducing amphibian vulnerability to fish removal techniques.

Chapter 6 presents the interaction between space and time in determining the organization of natural communities in high altitude heterogeneous waterscapes. After explaining why high altitude waters represent suitable models for examining metacommunity organization, the chapter focuses on dispersal—a central process to allow colonization and establishment of populations in remote localities and to counter local extinctions. Community organization patterns are then described for a variety of organisms living in high altitude waters, from microbes to invertebrates to fish and birds. These patterns reveal that both environmental and spatial variables are generally involved in species assembling. Examples of studies on directional spatial processes (e.g. through wind and water flow), waterscape genetics, and temporal variability (synchrony/asynchrony) are highlighted as promising research areas to increase the current knowledge on high altitude metacommunity dynamics.

Aquatic ecosystems are particularly sensitive to climate change due to the high heat capacity of water, the probability of altered thermal regimes, and changes to coupled thermal-hydrological variability. This chapter draws together the strategies, options, and processes available to protect and restore vulnerable aquatic ecosystems and threatened species. Options include freshwater protected area management; restoring flow regimes; improved dam operations and floodplain management; coherent approaches to legislation, policy, and governance to support environmental flow management; and greater indigenous engagement and learning. A vigorous global river and catchment restoration effort is needed to help restore and protect ecosystems and species threatened by climatic and human stressors. Much can be achieved if humans can learn to live with and celebrate variability, diversity, and change.

This chapter discusses the Yellowstone fires and relates these to the physical landscape. Fires such as those of 1988 in the Greater Yellowstone ecosystem clearly have major ecological significance through changes in age structure and composition of vegetation, but their impacts on the physical landscape can be equally profound. Both transient and persistent alterations of terrestrial and aquatic ecosystems may result from post-fire geomorphic processes. Fire is particularly important as a catalyst of landscape change in mountain regions, where high-severity burns markedly increase the potential for surface runoff, soil erosion, and landslides on steep slopes, resulting in debris flows and floods during intense storms and rapid snowmelt. Such events account for a large proportion of long-term sediment export in many mountain drainage basins.

Our knowledge of the distribution of most Wisconsin nongame fishes is limited because they have not been frequently surveyed. Between 1974 and 1980, the Wisconsin Department of Natural Resources (WDNR) conducted the Fish Distribution Study. More recently, the WDNR began a new statewide fish survey in part to allow a rewrite of the landmark Fishes of Wisconsin book. This chapter compares the results of these two surveys to examine how nongame fishes have declined in selected small streams and lakes in the southernmost quarter of Wisconsin. This region is generally the most densely populated with a landscape dominated by intensive agriculture and urbanization. Although some high-quality aquatic ecosystems remain, findings suggest that, if current trends continue, the future of these ecosystems is precarious. A conservation strategy is proposed to help protect these ecosystems and their fish faunas.