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Most (but by no means all) benthic species have larval stages which use the water column for dispersal. As indicated in the previous chapter, a key process affecting recruitment to sediment systems is the need to disperse larvae in order to colonize new areas, even to the extent of releasing larvae at spring tides when the tidal excursion will be greatest, thus effecting an even greater dispersal. Seasonal release of larvae is the norm: most species develop gametes in spring and spawn in late spring or early summer (see Rasmussen 1973 for an excellent data set of the times of planktonic larval occurrence and settlement by many important north-west European boreal benthic species). Some species, however, avoid the high competition for food at this time and release gametes in autumn and winter. Thus larvae of benthic organisms are a key and often dominating component of the spring–summer plankton and play important roles as food for planktonic species such as fish larvae. Conversely, a number of planktonic species have resting stages in sediments. The most important of these are undoubtedly the diatoms and many flagellates, and also certain calanoid copepods such as Acartia, which are of course key components of the phytoplankton and zooplankton respectively. Diatom cysts are often found, and there is increased interest in the survival and hatching processes of dinoflagellate cysts that lead to harmful algal blooms. Similarly, the seasonal occurrence of many zooplankton species results from hatching of resting stages in the sediment (see (see Smetacek (1995), Boero et al. (1996)Pati et al. (1999) and Boero and Bonsdorff (2008) for reviews). The implication of many important planktonic species having benthic resting phases is that by predating cysts, benthic species may be able to control abundances of planktonic species. In this context the meiofauna are important predators (Pati et al. 1999). It is now important to consider the scales of temporal variation in benthic assemblages. First, seasonal changes occur in benthic assemblages of soft sediments even in the depths of the deep sea (e.g. Hsü and Thiede 1992). In spring, as light levels and temperature increase, a plankton bloom occurs.

Given the discussion above regarding natural changes in the marine benthos, we should now consider the human-mediated (anthropogenic) changes and the response of benthic systems to human impacts. From the 1960s to the 1980s the general opinion seemed to be that pollution (considered in the next chapter) was the most important marine problem, but we now realize that habitat change and habitat loss are of greater concern: see, for example, the Quality Status Report 2000 (OSPAR 2000). One of the greatest effects on the integrity of the seabed and hence its biota is now known to be caused by bed trawling. This has now generated an enormous literature, and the reader is directed to Daans and Eleftheriou (2000) and Hollingworth (2000) for more details. We can take this information and summarize the overall ecosystem effects of fisheries in detailed flow diagrams (referred to as ‘horrendograms’!) to show the interlinked and complex nature of the impact—the effects trawling are included here, but see also those in McLusky and Elliott (2004) (e.g. Fig. 8.1). Historically, the effects of trawling on benthos caused concern as early as 1376 when a petition was made to the English parliament by fishermen concerned over the damage done to the seabed and fisheries by bottom trawling (De Groot 1984). This was despite the gear used by sailing vessels in those days being relatively light and towed at slow speeds and in shallow water only. When steam trawlers were developed in the early 1900s, everything changed. The weight and size of trawls increased and use of tickler chains (mounted on the bottom rope to disturb bottom-living fish upwards and into the trawl net) were of great concern, although studies done in the 1970s to allay the fears of fishermen did not find long-term effects on macrobenthos (Jones 1992). At the end of World War II the otter trawl was developed and its use became widespread. This and the beam trawl (see Fig. 8.4) were (and still are) the types of gear most widely used to fish the seabed.

A widely accepted definition of marine pollution is“the introduction by man, directly or indirectly, of substances or energy into the marine environment (including estuaries) resulting in such deleterious effects as harm to living resources, hazards to human health, hindrance to marine activities including fishing, impairment of the quality for use of seawater, and reduction of amenities”.(Wells et al. 2002).This differs from contamination since it results in biological damage, whether to the natural or human system, whereas contamination can be regarded merely as the introduction of substances by human activities (McLusky and Elliott 2004). Furthermore, pollution and pollutants can refer to biological and physical materials as well as chemicals (Gray 1992, Elliott 2003). In the case of the benthos, there is an extensive literature indicating that every type of pollutant has an effect on the benthos and so it is not surprising that the benthos is the mainstay of any monitoring and investigative programme. Pollution can affect organisms living in sediments by physical variables associated with the pollution source, such as increased sedimentation of particles, which leads to smothering of the fauna. In such cases the effect can in fact be regarded as a disturbing factor if the effects lead to mortality of individuals (Gray 1992). Alternatively, pollution can affect the fauna by toxicity where increased concentrations of contaminants lead to biochemical and physiological effects and ensuing mortality if certain thresholds for adaptation are exceeded. Here, however, we first treat the effects of the most widespread form of pollution affecting the marine environment— increased organic matter in sediments. Excess organic matter enters the marine environment principally as sewage, although it can also include waste from paper pulp mills or changed river run-off, for example. Excess organic matter causes physical effects such as smothering and also leads to reduced oxygen concentrations in the water column or pore-water in sediments. Sewage discharged into confined bodies of water frequently leads to the well-known symptoms termed eutrophication, resulting, in the most extreme cases, in a total lack of oxygen and the presence of hydrogen sulfide in the sediment, with a corresponding absence of fauna (e.g. de Jonge and Elliott 2001).

The benthos does not, of course, live in isolation from other parts of the ecosystem. Here we consider the roles that the benthos plays in the system and how the complex interactions that are found can be modelled using ecosystem models. First, we examine methods that allow us to establish food webs based not only on examining each species in the field and in laboratory feeding studies, but also using stable isotopes of carbon and nitrogen to ascertain the likely feeding mode of a species. It is relatively easy to determine the mode of feeding of some benthic organisms (see for example the excellent review of Fauchald and Jumars 1979, although this is now slightly dated and requires revision). Polychaetes have characteristic feeding structures, so one can determine from their morphology whether they are filter feeders, deposit feeders, or predators. Bivalves show similar morphological characteristics and it is easy to determine whether they are deposit or filter feeders. Some polychaetes have large jaws, e.g. the nereids, and one might assume that they are predators. Yet when Nereis vexillosa was studied in detail (Woodin 1977), it was found that it attached pieces of algae to its tube, which grew and were used for food, so-called ´gardening´. Nereids also are able to filter feed by creating a mucous bag and pumping water through their burrows, which filters the water; the mucous bag is then consumed. More recently, studies have shown varied and possibly opportunistic feeding by different benthic species; for example Christensen et al. (2000) showed how the suspension- and deposit-feeding abilities of nereids influenced sediment nutrient fluxes. These studies show that it is perhaps not so straightforward as once thought to interpret feeding mode simply from morphological features. The definition of functional groups and feeding guilds is increasingly used to help explain and interpret ecological functioning (e.g. Elliott et al. 2007 discuss the rationale behind functional groups). The eminent and immensely experienced benthic biologist Tom Pearson (2001) shows in detail that while the concept of functional groups gives us a greater understanding of the benthos, the idea is criticized by some as we do not have sufficient information about feeding types and modes of life of many benthic species.

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.

Our next major question is, how can we characterize the sediment as a habitat for biota? Marine sediments range from coarse gravels in areas subjected to much wave and current action, to muds typical of low-energy estuarine areas and to fine silts and clays in deep-sea sediments. The settling velocity of those particles and the ability of any particle to be re-suspended, moved, and redeposited depends on the prevailing hydrographic regime (e.g. see Open University 2002). The latter will in turn influence the transport of a species´ dispersal stages, especially larvae which will then be allowed to settle following metamorphosis under the appropriate hydrographic conditions (defined as hydrographic concentration). Hence the presence of fine sediments will indicate the depositing/accreting areas which may also be suitable for passively settling organisms. Clearly the particle size is of major importance in characterizing sediments, although sediments can also be categorized by their origin (fluvial, biogenic, cosmogenic, etc.) and their material (quartz, carbonates, clays, etc.) (Open University 2002). On a typical sandy beach the coarsest particles lie at the top of the beach and grade down to the finest sediments at the waterline. The top of the beach is dry and there is much windblown sand, since coarse sands drain rapidly, whereas at the lower end of the beach the sediments are wet, with frequent standing pools. Coarse sediment is found at the top of the shore because as the waves break on the beach the heaviest particles sediment out first. Finer particles remain in suspension longer and are carried seaward on the wave backwash. Beaches change their slope over the seasons, being steeper in winter and shallower in summer. A greater degree of wave energy will produce steeper beaches, as particles are pushed up the beach and so may be stored there, whereas gentle waves produce shallow, sloping beaches. Waves hitting the shore obliquely will create sediment movement as longshore drift. Subtidally, waves are important in distributing and affecting sediments down to depths of 100 m, but the effect decreases exponentially with depth and so the dominant subtidal influences on sediment transport are currents.

One of the most fruitful aspects of ecological research is the search for common patterns in the bewildering variability of nature. Given current concerns about global warming, climate change, and habitat degradation, the determination and protection of biodiversity has become paramount. There are essentially three ways of describing an assemblage of organisms, and each of these gives more information on the patterns and interrelationships. First, we have the classical taxonomic method of identifying all species in the assemblage, to the highest taxonomic separation possible (usually to species) and then counting the abundance and weighing the biomass of each taxon. Secondly, we can determine the size and/or biomass spectra of all organisms in the assemblage irrespective of their identities, on the basis that organisms of different sizes or body weights play a different role in the ecosystem. Thirdly, we can determine the role that each organism can play in the system, again irrespective of its name, and define these as ecological groups or guilds—hence separating those feeding in different ways or those building tubes from their free-living associates (e.g. see Elliott et al. 2007 for a discussion of the guild concept). There are many methods of analysing assemblage data; for example Elliott (1994) identified over 25 groups of techniques for macrobenthic analysis (these are mentioned throughout this book and summarized in Chapter 11). Using these methods, when considering assemblages of marine organisms living in sediment, we can ask if there are any ‘rules’ that can be applied to patterns of abundance, size, and biomass distributions and how data on species distributions can be organized. Here, we first treat abundance, then size and biomass spectra, and finally how species assemblages can be assessed. Another way of describing assemblages is to examine the number of species and how abundance is distributed among species, although these are aspects of species diversity which will be addressed in the next chapter. In any sample of a biological community, whether marine, terrestrial, or freshwater, the immediately observable pattern is that most species are rare, represented by one or a few individuals, and only a few species are very common, represented by many individuals.

In the previous chapter we covered ways of describing samples of benthos, but specifically did not include diversity. We can talk of primary community variables, such as abundance (A), species richness (S) and biomass (B), and derived variables from these such as true diversity indices, evenness indices, and ratios indicating the relationship between species richness and abundance (A/S, the abundance ratio or the average abundance per species) and between biomass and abundance (B/A, the biomass ratio or the mean biomass per individual). Diversity is not just simply about the number of species found in a sample or area, but also uses data on the abundances of individuals among the species and the way those abundances are distributed among the species within the assemblage. There are many ways of describing diversity. Here we give a summary of the most important ones and reference sources of recent literature on the subject (see also the data analysis summary in Chapter 11). In the following section we consider simple indices (univariate) as measures of diversity; multivariate methods of analysing patterns will be covered in Chapter 7 on the effects of disturbance. The simplest way to measure diversity is the number of species found in a sample, called the species richness (S or SR). Yet diversity is not just about numbers of species; it is also concerned with the distribution of numbers of individuals per species. For example, if one assemblage has 50 individuals of each of 2 species A and B whereas another assemblage has 99 individuals of species A and 1 individual of species B, then both have the same species richness but the first assemblage is the more diverse. Thus a measure of diversity (an index) must take into account not only the number of species, but also the number of individuals per species. To distinguish this from species richness, the combination of individuals per species and number of species is called heterogeneity diversity. In fact there are a large number of diversity indices, and we do not propose to consider them all here (Magurran 2004 gives an excellent and detailed account and others are mentioned in the summary in Chapter 11).