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Reanalysis of previously published data on trends in sedimentation rates over time in eight small lakes in the northern range shows variations associated with elevation and character of lake basin (kettle lakes or lakes in slide-deposit terrain) that must be taken into account in evaluating whether sedimentation rates have changed over time in response to increases in the elk herd. Total sedimentation rates and those of allogenic silica increased in most lakes between park establishment and the 1980s-1990s. Total organic sedimentation rates, and those of biogenic silica and phosphorus, increased during park history indicating eutrophication. Two species of diatoms characteristic of eutrophic conditions increased during park history in three of five lakes. Although more comprehensive research is needed on this question, an increase in the northern herd is the most probable hypothesis to explain the evidence from this preliminary study.

This chapter describes some approaches for understanding biodiversity-ecosystem function at larger spatial and at longer temporal scales. It first considers the importance of building a credible evidence base of biodiversity change effects on ecosystem functioning at seascape scales. It then explores the different aspects of biodiversity change, compositional and species richness, within contrasting bottom-up controlled and top-down controlled systems, namely, estuaries and coral reefs. The two systems are affected by eutrophication and overfishing.

This chapter examines changes in aquatic communities. Key threats to lake plant communities include shoreline development, heavy boat traffic, nutrient runoff, and consequent lake eutrophication and turbidity. Many invasive species capitalize on these conditions, forcing more elaborate efforts to control the excessive growth of invasive lake plants and algae. Lake plant communities also sometimes surprise scientists, as when a previously degraded community recovers beyond what we might expect.

Although current understanding of the sources, fate and impacts of many contaminants are now well-known and regulated by national and international bodies and conventions, a number remain problematic. Some are produced in very large quantities (e.g. nutrients, detergents, oil) and others are persistent in the environment (e.g. radioactivity and plastics). All are known threats that have either been ignored, took time to manifest, or have been challenging to manage. For most of these pollutants, regulations exist but changes in the nature (e.g. microplastics) or scale (e.g. increased use of fertilisers, increased livestock culture and sewage production, and changes in energy consumption as the global population grows) may mean existing regulation or management is in some way deficient. For others, (e.g. radioactivity, plastics and threats to biosecurity such as non-native invasive species introductions) the challenges associated with regulation and management are yet to be solved.

Seven regions are described in terms of their pollution history, other synergistic human pressures, the current challenges and management approaches. Although the timing and detailed impacts vary, primarily for historical reasons, between regions all show similar patterns of change. Sea regions exposed to centuries of human activity (North Sea, Black Sea, Mediterranean Sea and Chesapeake Bay) are considered, as are those for which pollution is more recent (Canadian LOMAs and Coral Sea), and those expected to experience intense pressure in the near future (Arctic Ocean). Nutrients from agriculture and sewage from growing human populations are ubiquitous and not easily managed in marine systems. Controls on industrial discharges have succeeded in halting, sometimes reversing, degradation in some regions (Black Sea, Mediterranean, North Sea, Chesapeake Bay). However, shipping, coastal development and offshore infrastructure continue to apply pressure. While most regions are subject to international agreements and management regimes the effectiveness varies.

The last chapter of Lakes and Ponds deals with how human activities affect the natural ecosystems and their function through eutrophication, contamination, acidification, brownification and increases in UV radiation, and how such anthropogenic disturbances may affect biodiversity and the ability of organisms to utilize a specific habitat. In addition, the chapter addresses novel environmental threats, such as global climate change and effects from our everyday chemicals, such as contraceptives, nanoparticles and antidepressant drugs. However, also possibilities and signs of improvement are discussed, providing hope for coming generations.

Marine organisms can experience conditions ranging from limiting supply of nitrogen in open ocean regions to toxicity of high concentrations of nitrogen associated with coastal eutrophication. Photoautotrophs show physiological acclimation to low N stress and relatively high tolerance to variable elemental stoichiometry. Symbioses and associations can help overcome low N supply in a range of ecosystems. Stress due to N limitation was once regarded as more ecologically relevant but increasing anthropogenic N loading is resulting in more common stress to photoautotrophs due to high N concentrations, especially for coastal benthic macrophytes. High N also affects competitive interactions between functional groups such as corals and macroalgae. Heterotrophs are less flexible stoichiometrically, and N supply and use is coupled more tightly with energy supply through catabolism of organic (food) molecules, releasing nitrogenous wastes. The responses of mixotrophic organisms to low or high N stress are poorly understood but N status can affect toxin production in harmful algal bloom species. In all groups, larval and recruiting life stages may be more sensitive to N stress, particularly high ammonium and nitrite toxicity. Identifying N stress increasingly uses molecular biological approaches but correct interpretation of such data requires a better understanding of the physiological effects of N stress on marine organisms.

This chapter gives a broad overview of freshwater algae in standing (lentic) and flowing (lotic) waters, with information on their morphological and taxonomic diversity. Algal communities are considered in relation to phytoplankton, substrate-attached and biofilm organisms. Methods are given for their collection, sample processing, enumeration, and biomass estimation in different aquatic situations. The relevance of these algae to human activities is considered particularly in relation to eutrophication of standing waters and the occurrence of harmful algal blooms. Control strategies to limit the growth of colonial blue-green algae are discussed within the context of an integrated management policy

This chapter discusses what happened around 1950 that led to the expansion of dead zones. For the Gulf of Mexico, there are many reasons to think the flow of the Mississippi River has changed since the days of Mark Twain, considering the construction of so many levees, dikes, floodways, spillways, weirs, and revetments. Rain-absorbing grasslands and forests have been replaced by asphalt, roof shingles, and other hydrophobic material that hasten rainwater to the Gulf. But the flow of the Mississippi has not changed enough to explain why the Gulf dead zone grew around 1950. As the chapter discusses, what did change was nutrients. It shows that concentrations doubled in the Mississippi River from the 1930s to the 1990s, which stimulated algal growth and production of organic material that eventually led to depletion of dissolved oxygen. In addition to creating dead zones, the increase in nutrients has stimulated harmful algal blooms, leading to fish kills and beach closings.

A group of sea otters laze at the edge of Elkhorn Slough. They float on their backs in the steel- gray water, paws folded against their chests, gazing at the small boat steered by ecologist Brent Hughes of the University of California–Santa Cruz. Hughes has documented a profound shift in the slough’s ecology, triggered by the otters. Sea otters were nearly driven to extinction by fur hunters in the 1800s, and were gone from Elkhorn Slough for a century. In 1984, when the first sea otters recolonized, Elkhorn Slough’s once bountiful eelgrass beds had dwindled to a few small, scattered patches. Now, more than thirty years after the sea otters’ return, expanding eelgrass beds grow lush beneath the water’s surface, the dense leaves sheltering juvenile fish and feeding an array of invertebrate grazers. The slough, on the central California coast, is one of the most severely polluted estuaries on the planet. Artificial fertilizer applied to 2.69 million acres of farmland in the neighboring Salinas Valley runs into its waters. The excess nutrient load causes eutrophication. It also fuels the growth of epiphytic algae that thrive on the surface of eelgrass leaves, blocking the sunlight the grass needs and smothering whole beds. The problem is common in estuaries around the globe, which receive heavy loads of nutrients from rivers draining polluted watersheds. Seagrass meadows filter contaminants from water and prevent coastal erosion in addition to acting as nurseries for fish and invertebrates. These crucial habitats are disappearing. The global distribution of seagrasses has decreased by 29 percent over the last 140 years, and 58 percent of the surviving seagrass meadows are in decline. Nutrient pollution of coastal waters had long been thought to be the main driver of this trend. But in Elkhorn Slough, the eelgrass has made a remarkable comeback even as pollution loads continued to climb. The mechanism of this welcome ecological shift was unknown until Hughes demonstrated that sea otters are the key. He began to put the pieces of the puzzle together when he went diving in Tomales Bay, an unpolluted estuary to the north. The eelgrass in Elkhorn Slough was lush and green despite intense pollution; in Tomales Bay, where there are no sea otters, the eelgrass was a dull brown, smothering under epiphytic algae.

So far, we have seen how sophisticated systems of agriculture had grown up in many different places and at various times in order to overcome problems associated with the decline of soil fertility arising from continuous exploitation. In Europe and elsewhere, it was clearly understood that manures and various materials such as potassium (or sodium) nitrate could rejuvenate the soil, and empirically probably little more could have been achieved in this direction. Nevertheless, the supply of the products capable of doing this was clearly limited. Only when the scientific basis of the action of fertilisers and manures had been fully understood could further advances be made, and this only happened with the scientific revolution, which began to flower in the sixteenth century and continues in bloom to this day. The empirical experience of centuries seems to have led to the supposition in Europe that the air was somehow involved in restoring the fertility of soils and in the facilitation of plant growth. However, the reason for this influence could not have been presented in modern terms. A lot of the discussion was centred about the mysterious substance nitre, which was then not simply the salt we recognise today. There are many instances of statements to the effect that nitre was absorbed from the air and even references in the older literature to aerial nitre. Solid nitre was, of course, very well-known in the form of saltpetre and was widely employed as a constituent of gunpowder. This kind of nitre could also be used as a fertiliser, though there was not enough of it around to “waste” by spreading it on the soil. Then, as is often true today, warfare was regarded as a more important use for such a resource. Nitre could be extracted from manures and from ashes, and, because it was a crystalline solid, it certainly was not the mysterious something that was present in the air. There was no understanding of the modern notions of elements and compounds. It would take a long time—two centuries—for a truly scientific approach to agricultural chemistry to be developed, but it is still worthwhile to enquire what exactly writers of treatises in the mid-seventeenth century really meant.

This chapter describes how phosphorus is used in biological molecules, structures, and physiology. It illustrates the role of phosphorus as a limiting nutrient for the production and growth for organisms and ecosystems. It also explains how phosphorus cycles in natural and agricultural ecosystems cause aquatic eutrophication of downstream surface waters.

The geography of natural water resources in the Mediterranean basin cannot simply be reduced to the study of water inputs, water distribution, and the pattern of runoff-generating precipitation determined by climate and relief—although these are, of course, fundamental controls (Margat 1992; Benblidia et al. 1996). Any consideration of basin-wide water resources also needs to consider a range of territorially determined factors affecting water resources. These include: (1) the nature of surface and underground flows, which depends on river basin and hydrogeological characteristics; (2) the natural storage capacity of lakes and aquifers and their role in regulating flows, and any losses from these stores which reduce the resulting flows; (3) the existence of favourable conditions for water management and exploitation such as suitable sites for dam construction and the productivity of aquifers, as these factors dictate accessibility to water resources and the production costs; (4) the natural quality of the water, its vulnerability to pollution and its capacity for self-purification; (5) any constraints imposed for reasons of environmental conservation, which may effectively exclude a proportion of water reserves from the category of exploitable resources. It is important to appreciate that each of these factors influences the assessment of water resources in a given area and each factor has its own geography (Margat 1997; Margat and Vallée 1999a). In spite of the broad similarities in climate and landscape between the different parts of the Mediterranean basin, there are considerable variations between regions that impact upon the availability of water resources. Many of the factors affecting water resources cited above are subject to a similar degree of variation (Grenon and Batisse 1989; Chapter 8) and these are discussed in turn below. Marking the transition between the temperate climate of Europe and the aridity of North Africa and the Near East, the Mediterranean climate contains wide variation, and this is reflected in a highly uneven distribution of rainfall (Benblidia et al. 1996; Margat and Vallée 1999a; Chapter 3). For example, moving from one extreme to another, average annual rainfall ranges from more than 3,000 mm in parts of the Dinaric Alps to less than 50 mm in Libya.

Throughout the previous chapters, we have focused on our understanding of the benthic system, its processes, structure, and functioning but, hopefully, we have also shown some of the changes to the system as the result of human activities. It is now relevant to look at the way in which management relies on and uses benthic data and information, the way in which benthic information and data are put into a wider context, and the way we manage marine sediments. Although examples in this chapter are mainly taken from European initiatives, the same examples exist in other regions. In all countries, there are many agencies and bodies involved directly or directly in the science and management of marine sediments—some carry out marine benthic studies and/or the monitoring, some require others to carry out the monitoring, and others use the benthic research and monitoring information. Throughout this book we have indicated many of the numerical techniques at our disposal for analysing benthic data, for linking them to the environmental variables, and for using them in understanding the functioning of the marine system, not least in relation to human activities. Indeed, Elliott (1996) suggested that there were approximately 26 groups of techniques for analysing the benthos and Gray (2000) describes recent methods and the progress made recently in analysing benthic data—by now we have added even more techniques. We have indicated here how some of the techniques have been adapted from other fields of ecology, such as terrestrial systems and even, in some cases, from other fields altogether; for example the main diversity index used, Shannon–Wiener H',was obtained from information and systems analysis. Figure 11.1 indicates how many of those methods link together in order to obtain a large amount of information from the benthos—it is axiomatic that no single technique gives a large amount of information and many of them rely on several techniques being used together. Figure 11.1 indicates how we start with community structural and primary variables (abundance, biomass, etc.) and move on from these into univariate and derived community variables as well as graphical techniques for community structure.

The soil must provide a favorable physical environment for the growth of vines—their roots and beneficial soil organisms. Some of the important properties con­tributing to this condition are infiltration rate, soil strength, available water ca­pacity, drainage, and aeration. Ideally, the infiltration rate IR should be >50 mm/hr, allowing water to enter the soil without ponding on the surface, which is predisposed to runoff and erosion. The range of infiltration rates for soils of different texture and structural condi­tion is shown in table 7.1. Typically, the soil aggregates should have a high de­gree of water stability so that when the soil is subjected to pressure from wheeled traffic or heavy rain, the aggregates do not collapse, nor do the clays deflocculate. Some of the problems associated with the collapse of wet aggregates and clay de-flocculation, and the formation of hard surface crusts when dry, are discussed in section 3.2.3. Pans that develop at depth in the soil profile, as a result of remolding of wet aggregates under wheel or cultivation pressure, can be barriers to root growth. Soil strength is synonymous with consistence, which is the resistance by the soil to deformation when subjected to a compressive shear force (box 2.2). Soil strength depends on the soil matrix potential m and bulk density BD, as illustrated in fig­ure 7.1. In situ soil strength is best measured using a penetrometer, as discussed in box 7.1. The soil strength at a ψm of −10 kPa (FC ) should be <2 MPa for easy root penetration and should not exceed 3 MPa at –1500 kPa (PWP). As shown in figure 7.1, when ψm is between −10 and −100 kPa, the soil strength increases with BD. The BD of vineyard soils can increase, particularly in the inter-row areas because of compaction by machinery, such as tractors, spray equip­ment, and harvesters. Typically, compaction occurs at depths between 20 and 25 cm and is more severe in sandy soils than in clay loams and clays (except when the clays are sodic; see section 7.2.3). Figure 7.2 shows the marked difference in soil compaction, measured by penetration resistance, under a wheel track and un­der a vine row on a sandy soil in a vineyard.

One of the truisms of sampling design is that the design depends on the objectives. Too often objectives are not defined properly, with the result that the data collected cannot be used to answer the questions posed. A good example is that of a monitoring programme that aims to detect changes in an assemblage of benthic organisms caused by eutrophication but where the magnitude of change was not specified in the objectives, with the result that the monitoring programme was so loosely designed that insufficient samples were taken. A posteriori analyses of the results may show that the monitoring would take 10 years to detect a 10% change in the faunal composition. You may think that this is an unrealistic and hypothetical example, but our experience shows that far too often results such as this are the norm. We return to the types of monitoring in Chapter 11, but for now let us start with perhaps the simplest case: we wish to survey an area of coastal soft sediment simply to find out what is there (i.e. to map the habitats and prepare for a more detailed quantitative study of the benthic assemblages). Up to the last couple of decades, sampling subtidally below diveable depths was usually done blind. One had to resort to charts, perhaps prepared in the nineteenth century, which have depths and descriptions of sediments made from soundings done with handlines with candlewax in a hollowed-out part of the lead weight that touched sediment particles, enabling the sediment type to be crudely mapped. Since the 1980s huge technological advances have been made in mapping sediments. Two types of instrumentation have been developed: depth sounders of various types and remote-operated vehicles (ROVs). With sounders, accurate maps of the contours of the seabed can be produced and then indications of the hardness and roughness superimposed on the depth and good three-dimensional images produced with modern software. Sophisticated multibeam echosounders have been used to map the whole continental shelves of many countries. Now that the satellite-based differential global positioning system (DGPS) is generally available with an accuracy to a few metres, mapping of subtidal sediments has become much easier and more accurate.

Now that we have discussed how assemblages of marine soft sediments are structured, we need to consider functional aspects. There are a few main interrelationships that need to be discussed here— inter- and intraspecific competition, feeding and predator–prey interactions, the production of biomass, and the production and delivery of recruiting stages. Other functional aspects, such as the effects of pathogens and parasites and the benefits of association (mutualism, parasitism, symbiosis, etc.) are of less importance in the present discussion. By function we mean the rate processes (i.e. those involving time) that either affect (extrinsic processes) or are inside (intrinsic processes and responses) the organisms that live in sediments. Hence these include primary and secondary production and processes that are mitigated by the organisms that live in sediments, such as nutrient and contaminant fluxes into and out of the sediment. We begin with the historical development of the field since such aspects are often overlooked in these days of electronic searches for references. Functional studies of ecosystems really began with Lindeman´s classic paper (1942) on trophic dynamics. Rather than regarding food merely as particulate matter, Lindeman expressed it in terms of the energy it contained, thereby enabling comparisons to be made between different systems. For example, 1 g of the bivalve Ensis is not equivalent in food value to 1 g of the planktonic copepod Calanus, so the two animals cannot be compared in terms of weight, but they can be compared in terms of the energy units that each gram dry weight contains. The energy unit originally used was the calorie, but this has now been superseded by the joule (J), 1 calorie being equivalent to 4.2 joules. Ensis contains 14 654 J g-1 dry wt and Calanus 30 982 J g-1 dry wt. The basic trophic system is well understood and can be summarized as we showed earlier in Fig. I.8 which gives the links between various trophic levels and the role of competition, organic matter transport, and resource partitioning. In systems fuelled by photosynthesis (so excluding the chemosynthetic deep-sea vent systems), the primary source of energy for any community is sunlight, which is fixed and stored in plant material, which thus constitutes the first trophic level in the ecosystem.