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Polar aquatic ecosystems are excellent laboratories for biogeochemical research. The polar regions are among the least modified by human activities, so there are opportunities to study biogeochemical processes in the absence of overwhelming anthropogenic influences. In addition, there are abundant freshwater ecosystems in which comparative or experimental work can be conducted, and increasing evidence for environmental change is driving a rapid expansion in polar research. This chapter draws upon extensive surveys of lake chemistry to summarize the biogeochemical composition of polar lakes, and to illustrate the growing potential for cross-system comparisons. It describes the general features of biogeochemical cycles in polar aquatic environments, and the important and sometimes unique controls over biogeochemical processes.

This chapter illustrates how the activities of soil biota, especially their trophic interactions, influence the processes of decomposition and nutrient cycling, and examines the significance of this for material flow and plant production in terrestrial ecosystems. The focus is on the availability of nitrogen and phosphorus since they are the two nutrients that most limit primary productivity in natural and managed terrestrial ecosystems. First, the issue of how soil microbes regulate the internal cycling of nutrients in terrestrial ecosystems is discussed. This is followed by a discussion of how soil animals influence nutrient cycling and plant growth through their feeding activities on microbes and other fauna.

This chapter discusses ocean productivity, focusing on the factors controlling primary production. It describes the basic principle of nutrient cycling and estimates sea productivity based on phytoplankton abundance and chlorophyll content of surface waters. Production is controlled by nutrient supply and availability of sunlight, and fish depend on the primary producers or photosynthesizing organisms for sustenance. These primary producers include phytoplanktons such as diatoms, dinoflagellates, and coccolithophorids.

This chapter explores the ecological theories built from the proposed ecological laws. It focuses on theories influencing major subdisciplines of ecology starting with physiological ecology, then moving to populations, communities, and ecosystems. It discusses theories of evolution, nutrient cycling, community interaction, ecological stoichiometry, and ecological diffusion. It also considers some major predictions based on the theory and limits to prediction.

Landscape ecosystem ecology is concerned with the study of how landscape structure affects ecosystem structure and function, and how landscape heterogeneity in turn is generated or sustained by the redistribution of nutrients or organisms within and among ecosystems. This chapter begins with an overview of how landscape context influences ecosystem processes, including the effects of land management and land-cover change on nutrient dynamics and productivity. Next, the chapter considers the linkages among systems (metaecosystems) and how spatial subsidies are important for understanding ecosystem function in a landscape context. The chapter then explores under what conditions landscape function becomes disrupted, possibly precipitating irreversible system state changes, before concluding with a clarion call for landscape sustainability; that is, landscape management that preserves the productivity, multifunctionality, and ecological resilience of landscapes in the face of future societal demands, intensifying land use, and rapid climate change.

In this chapter, we explore birds as drivers of nutrient dynamics across ecosystems. For example, seabirds transport nutrients from pelagic regions to land areas. We explain why nutrient transport by birds is important and how the characteristics of birds are especially effective for nutrient transport. In the case of seabirds, birds link distant ecosystems by transporting nutrients that otherwise would remain in a certain place, in ways that few other animals can. We present case studies that show the direct and indirect ecological effects of avian nutrient transport, and describe provisioning services provided by those ecological interactions. Globally, seabirds transfer an estimated 10,000 to 100,000 tons of phosphorus from sea to land annually, making up an extremely important supporting ecosystem service, due to humans' excessive use of phosphorus. Lastly, we discuss some negative effects of bird nutrient transport on people and environments, e.g. excessive nitrogen and phosphorus can pose threats to certain habitats, underlining the importance of assessing the costs and benefits of bird-mediated nutrient dynamics in human-dominated ecosystems. We must consider the diversity of ways in which humans value habitats and ecosystem services of birds, in order to find ways to balance the various ecological functions of birds.

Wetlands play important functions in ecosystems, mainly through the capture and transfer of energy involving plants, animals, and microorganisms. Wetland functions range from primary production to water budget, food chains, nutrient cycling, and duck production. These functions produce services that often give wetlands an economic value to individuals or to society or both. This chapter explores four functions of wetlands: primary production, food webs (secondary production), litter decomposition, and nutrient cycling. It also discusses the carbon cycle, nitrogen and sulfur cycling, nitrogen fixation, nitrification, ammonification, and phosphorus cycling.

The Procellariiformes — the order of oceanic tube-nosed seabirds that includes the albatrosses, petrels, and shearwaters — are an ancient group that has survived comparatively unchanged since the earliest Cenozoic. They exhibit comparatively low levels of extinction before the Late Quaternary; however, there is strong evidence that extensive species-level extinctions have occurred in the Holocene, and 56% of Holocene procellariiform species have lost populations. Recent extinctions in the group have been primarily driven by invasive mammal predation, as well as increasingly by direct fisheries mortality. There is growing recognition that a diverse range of terrestrial ecosystems are in fact supported by nutrients that originate from marine systems, with seabirds acting as a primary vector for nutrient transfer. Any disruption to these nutrient imports through seabird extinction may drastically affect ecosystems at both small and large scales, as has almost certainly already happened in regions such as New Zealand.

By definition, the water table of wetlands is near, at, or above the hydrosoil (sediment) surface. These changing hydrologic conditions are primary drivers of nutrient fluxes in the sediments and all aspects of plant biology: physiology, growth, and productivity. Because of the very nature of low elevational gradients within wetlands, there is a tendency for these regions of the whole ecosystem to retain organic matter either produced there by wetland plants or organic matter imported there from upland areas. The accumulated organic matter and associated nutrients promote two basic features of wetland ecosystems: an anoxic, reducing habitat of vigorously growing microbial communities on and within the sediments and organic debris, and very actively growing aquatic plants that are adapted to these growth conditions. This chapter discusses wetland ecosystem processes, focusing on periphyton as a critical metabolic component of aquatic ecosystems, nutrient retention and nutrient cycling in wetlands, modulation of periphyton by light availability, modulation of macrophytes and periphyton by mortality and losses, and potential effects of global climate change and related environmental conditions on ecosystem processes.

This chapter applies ecological theory to examine long-term soil dynamics. It develops ideas about soil recovery from disturbance as a means to guide future investigations of soil resilience as humanity's demands on soil increase over the coming decades. The discussions cover soil disturbance, resilience, and recovery; soil organic matter dynamics; and soil nutrient cycling.

This chapter examines recovery of carbon and nutrient stocks and hydrological functions in regenerating tropical forests. Rates of recovery depend on many factors including soil fertility, soil texture, rainfall and seasonality, frequency of burning, initial species colonization, temperature, and site productivity. Long-term accumulation of biomass and nutrients in forest vegetation ultimately leads to the recovery and retention of carbon and nutrients in the soil and in the entire forest ecosystem. As woody stems grow in height and diameter, basal area increases and woody tissue becomes the dominant component of stand-level biomass. Growth of regenerating forests may be limited by nutrient availability on highly weathered, nutrient poor soils and in areas where soil nutrient stock have been depleted. Colonization of roots by arbuscular mycorrhizae can be important for supporting rapid growth rates of pioneer species. Regrowth of forests can rapidly restore hydrological functions, such as evapotranspiration, infiltration, and stream flow.

This chapter discusses the attributes of deciduous forest herbs that significantly contribute to ecosystem-level nutrient dynamics. It attempts to distinguish among characteristics that are unique to some or all herbaceous species. It compares nutrient content and seasonal patterns of nutrient accumulation among groups of deciduous forest herbs and with overstory species. It considers site quality (nutrient availability) as a determinant of herbaceous nutrient accumulation and discusses patterns of internal cycling (retranslocation) and decomposition of ephemeral materials. Finally, the chapter offers a fresh outlook on the influence of herbaceous populations on ecosystem-level nutrient cycling. In particular, it discusses the idea that spring ephemerals function to retard nutrient loss during spring runoff with regard to its potential use and limitations in understanding the complex nature of deciduous forest ecosystems.

This chapter begins with an account of the biodiversity and ecosystem functioning synthetic framework, the theory in which ecologists have formulated a range of hypotheses about the relationship between structure and function in ecosystems. This theory is now enriched by genomic analyses of microbial communities and screening of key genes that determine the rates of nutrient cycles. Various genomics platforms for community screening are discussed, including phylochips targeting 16S rRNA genes and geochips targeting genes with crucial roles in nutrient cycles. A detailed account is given of key genes in the nitrogen cycle (nitrogen fixation, ammonification, ammonia oxidation, nitrification, denitrification, anaerobic ammonia oxidation); the carbon cycle (anoxygenic and oxygenic photosynthesis, carbon fixation, methanotrophy, methanogenesis); the sulphur cycle (sulphate reduction, sulphur oxidation); and those of phosphorus, iron, calcium, and silicium. For each nutrient cycle, indicator genes are described that are used in microarray-based community screens and environmental DNA sequencing. Analysis of prokaryotic diversity in the environment has revealed a staggering diversity and has shown that the vast majority of species has remained unknown to date. Metagenomic surveys have revealed many surprises, e.g., the presence of proteorhodopsin genes in marine Gammaproteobacteria; the presence of ammonia monooxygenase genes in Archaea; many new clades of Acidobacteria in soil; and several new clades of RuBisco genes in the ocean. The assembly of microbial genomes from metagenomic libraries has also shed new light on the functioning of simple communities in extreme environments.

This chapter deals with the ecology of Tropical East Asia from the perspective of water, energy, and matter flows through ecosystems, particularly forests. Data from the network of eddy flux covariance towers is revealing general patterns in gross primary production, ecosystem respiration, and net ecosystem production, and exchange. There is also new information on the patterns of net primary production and biomass within the region. In contrast, our understanding of the role of soil nutrients in tropical forest ecology still relies mostly on work done in the Neotropics, with just enough data from Asia to suggest that the major patterns may be pantropical. Nitrogen and phosphorus have received most attention regionally, followed by calcium, potassium, and magnesium, and there has been very little study of the role of micronutrients and potentially toxic concentrations of aluminium, manganese, and hydrogen ions. Animal nutrition has also been neglected.

This chapter explores the role of animal behaviour as a critical link between human activity and ecosystem processes. It explores the impacts of behavioural trait changes on ecosystems, and describes how these effects are often the result of changes in traits related to consumption and nutrient cycling. It enumerates two mechanisms of rapid behavioural trait change that shape ecosystem processes: phenotypic plasticity and contemporary evolution, and considers their effects. It proposes a framework to integrate the ecosystem effects of plasticity and evolution using a reaction norm approach to parse the contributions of plasticity, evolution, and the evolution of plasticity to ecosystem change. It also suggests using the framework to predict the effects of human-driven trait change on ecosystems.

The need to mitigate anthropogenic carbon emissions and to understand the impacts of the pervasive enrichment of natural systems with nitrogen and other nutrients has brought a new urgency to studies of ecosystem ecology. This chapter deals with the ecology of Tropical East Asia from the perspective of energy and matter flows through ecosystems, particularly forests. The availability of data from a network of eddy flux covariance towers is revealing general patterns in gross primary production, ecosystem respiration, net ecosystem production, and net ecosystem exchange. There is also new information on the patterns of net primary production and biomass within the region. In contrast, our understanding of the role of soil nutrients in tropical forest ecology still relies on work done in the Neotropics, with just enough data from Asia to suggest that the major patterns may be pantropical. Animal nutrition has been neglected, although there has been considerable speculation.

This chapter examines how nutrients, light, and temperature vary within and among different types of peatlands. It first explains the importance of nutrient cycling in the growth and metabolism of peatland plants, with particular emphasis on nitrogen, potassium, and phosphorus. It then considers nutrient effects on species composition, nutrient controls and limitations in peatlands, nutrient balance and retention, and how nutrients are affected by peatland drainage for forestry. It also describes the role of light in photosynthesis and its impact on vegetation before concluding with a discussion of temperature and other climatic factors that drive the growth rates of peatland plants, rates of peat accumulation and decomposition, and peatland distribution in a global context.

This chapter examines changes in nutrient availability in Watershed 7 (WS 7) immediately following and for 22 years after harvest. Researchers measured several indices of nutrient availability and nutrient cycling rates including total soil C and N, soil extractable cations, extractable NO₃ and NH₄, net soil N transformations, soil solution NO₃ concentrations, and nutrient fluxes in slash throughfall. Responses to cutting were measured against both pretreatment soil conditions and by comparison with data collected from an adjacent reference watershed. It is shown that changes of nutrient inputs, due to the input of logging residue, and changes in throughfall resulted in increased total C and N and extractable cation pools in surface soils. These increases were not long-lived, although slash residue remained on site. On the other hand, soil-extractable N and potential rates of N mineralization and nitrification remained elevated for more than 20 years after harvest. Changes in vegetation following harvesting have resulted in increased rates of N cycling. This continued rate of N cycling is evident not only in the soil N processes but also in continued stream export of NO₃-N.

Secondary forests cover approximately one third of the 0.5 million km2 of the Brazilian Amazon that have been cleared for agriculture (Houghton et al. 2000, Fearnside and Guimarães 1996). These forests counteract many of the deleterious impacts of forest conversion to agriculture and cattle pasture. They absorb carbon from the atmosphere, they reestablish hydrological functions performed by mature forests, and they reduce the flammability of agricultural landscapes. Secondary forests transfer nutrients from the soil to living biomass, thereby reducing the potential losses of nutrients from the land through leaching and erosion. They also allow the expansion of native plant and animal populations from mature forest remnants back into agricultural landscapes. The study of forest recovery has focused on aboveground processes, primarily biomass accumulation. The few studies that have examined the recovery of belowground functions in Amazon secondary forests have been restricted to the upper meter or less of soil (e.g. Buschbacher et al. 1988). A review of our knowledge of secondary forest recovery is needed that incorporates accumulating evidence that approximately half of the region’s forests rely upon root systems extending to depths of several meters to maintain evapotranspiration during prolonged seasonal drought (Nepstad et al. 1994, Jipp et al. 1998, Nepstad et al. 1999a, Hodnett et al. 1997; see also Richter and Markewitz 1995). This discovery demands a conceptual shift in our approach to forest recovery on abandoned land. Are secondary forests capable of regrowing deep root systems, thereby recovering hydrologic functions and fire resistance of the mature forest? At what rate does this recovery take place? How does this ability to tap a large soil volume change our thinking about the role that nutrient shortages play in restricting secondary forest recovery? In this chapter, we begin to address these questions with the goal of furthering a mechanistic understanding of forest recovery on abandoned Amazonian lands. Our analysis focuses on three measures of secondary forest development: biomass accumulation, nutrient accumulation, and hydrological recovery. We choose biomass accumulation, because it is the best integrative measure of secondary forest development, it is the basis for estimates of carbon sequestration by secondary forests, and it is the most frequently measured secondary forest parameter.