Organisms, including humans, alter the physical nature of aquatic environments by their activities and these alterations are superimposed on changes that occur by natural geological and hydrological processes. We have seen that human activity affects trophic structure, and civil engineering construction work and developments often have major consequences in coastal regions, around impoundments, and at many other locations. Many living aquatic organisms also engineer the environment in which they live.

The shapes of continents and thus of marine coasts have changed considerably over geological time periods [7.1.]. These changes result from tectonic movements, volcanic activity and the action of ice. On shorter time scales, the erosion of shorelines occurs by wave action, while other coasts are sites of sedimentation. This pattern of erosion and sedimentation is also a feature of lakes and rivers and it is important to bear in mind that engineering by natural events is a continuous process.

Marine coasts are developed for leisure or industrial purposes. This entails the construction of docks and marinas, coastal defence embankments, seaside resorts, large chemical works and power stations that require cooling water, and many other forms of development [7.2., 7.3., 7.4.]. Much of the World's coastal environment remains natural, but evidence of engineering by humans is commonplace in industrialised countries. In some cases the natural coast has almost disappeared, yet coastal marine organisms readily colonise the newly built structures like piers, jetties and harbour walls.

Large, natural lakes sometimes have industrialised margins [7.5.] that are similar to those on marine coasts and some recent lakes result from human activities e.g., water-filled quarries and pits from which minerals have been extracted, fish ponds, and canals (which are linear lakes). Lined excavations and reservoirs are constructed [7.6.] to meet the developing need for fresh water and these are filled either by rainfall and runoff, by influent streams, by piped water, or from underground supplies. Colonisation of these newly formed lakes by living organisms is often rapid and the lakes develop with time an ecosystem characteristic of the underlying geology of the region.

Streams and rivers are among the water bodies most heavily affected by human engineering as they provide a constant flow of fresh water that is harnessed to provide drinking water, a source of hydroelectric power, and water for irrigation. To achieve these ends, streams and rivers are impounded and the barriers range from small sluices made of wood through to massive dams [7.7., 7.8.]. Whatever the type of barrier, the effect is to interrupt displacement of water downstream and form a lake upstream. These lakes provide the water needed for domestic and industrial supplies or for irrigation. They also form the head of water necessary to drive turbines. Weirs across rivers are also built for "run-of-river" hydroelectric power generation [7.9.], using the force of discharging water down the valley or down an adjacent channel containing a turbine.

Like other lakes, impoundments often stratify during the summer months and this has important consequences downstream. As we have seen, production of suspension-feeding collectors is high in lake outlets where release is from the surface waters with their constant warm temperature and good quality particulate food in summer. In contrast, release of water from deep within the lake brings cooler water to the river downstream and it is often rich in nutrients. If low in oxygen, the vigorous turbulence that is often a feature of outlets downstream from a deep release rapidly produces good oxygen tension. The abundance of nutrients present provides conditions that support the abundant growth of primary producers and the consumers that depend on them. It is analogous to conditions at overturn in natural lakes. Impoundments also act as giant sedimentation traps along rivers, with particles settling out from suspension. Benthic animals within the impoundment thus have a good supply of inorganic and organic matter, but the amounts sedimenting can sometimes be very high and may have a swamping effect.

Rivers drain the land and it is natural that they should flood during periods of very high rainfall [7.10.]. Floods generate wetlands that are often productive, and which receive inputs of mineral particles and organic matter when the river extends over its banks. Falling water levels after flooding also bring organic matter to the river with runoff from the flood plain. However, human settlement and agriculture can be affected by these floods and some rivers are canalised to optimise discharge [7.11.], sometimes with the addition of storm channels. This practice is often considered essential to protect human settlements but conditions in canalised rivers and storm channels are very different to those in natural river channels. Not only is the substratum rather uniform but the banks are often cleared of emergent vegetation and suspended material is swept to the sea as retention is minimised to allow rapid discharge. We are beginning to recognise that retaining nutrients within rivers is essential for their health and conservationists now seek to return canalised river channels to their natural condition.

Seaweeds anchor to substrata and are found to depths of many metres, especially in tropical and sub-tropical waters with good light transmission. These algae attach using a holdfast and kelp forests are found in some regions [7.12.], the dense "stands" of algae often reducing the turbulence of wave action. The seaweeds of shallow rocky coasts have a more limited effect but they do provide shelter against waves, although they are often abraded in the process. Conditions on rocky coasts are quite dissimilar to those found in the coastal seagrass beds so typical of tropical and sub-tropical oceans. Here, wave action is much gentler and seagrasses create organically rich microhabitats by trapping POM and mineral grains from the tidal flow of water [7.13.]. Further organic matter is generated by the in situ decomposition of the seagrasses after death. Similar trapping of particles by plants occurs in tidal estuaries and coastal swamps, some of the particles originating from inputs of dead leaves from the emergent plants so characteristic of these habitats.

In fresh waters, marginal and rooted macrophytes engineer the habitat in a similar way to that described for estuarine and marine swamp plants. Rooted plants in rivers increase sedimentation dramatically as they reduce current velocity around their stems and promote conditions for sedimentation beneath and just downstream from each plant [7.14.]. As the sediment builds so does current velocity between plants and this has a scouring effect. In some rivers the growth of rooted aquatic plants is so great that it causes water to back up and flood adjacent meadows. This natural process causes sufficient concern for "weed cutting" to be undertaken in the river, plants being cut away to allow a clearer passage for the discharging water.

In addition to these facets of engineering, the growth of plants increases the amount of living substratum available for colonisation by micro-organisms. These coat submerged plants and form food for scrapers, the plants themselves also being eaten by shredders, although this is often after death and conditioning. The living plants are also a substratum for suspension-feeding collectors that depend on moving water to bring their food and these animals are often found attached to coastal seaweeds, mangroves, or to rooted plants within rivers.

Beaver (Castor canadensis) fell trees and branches that they use for food and to construct a dam across a stream or small river [7.15.]. The dam impounds water and creates a pond upstream, with consequent flooding of the river margins. Beaver live in lodges constructed from twigs and branches and they anchor potential food that they have felled into the sediments of the impoundment. Good insolation within the pond enhances the growth of aquatic plants, fertilised by sedimenting organic matter and the breakdown of submerged terrestrial vegetation. Clearing of trees for construction and food also causes many herbaceous plants to colonise the ground under the newly opened canopy adjacent to the pond. Beaver dams are analogous to impoundments made by humans in their effect on ecosystems. They interrupt the downstream movement of organic matter and also provide conditions that support the colonisation of suspension-feeding collectors at the outlet from the pond.

Among the most impressive structures engineered by animals are coral reefs that fringe land masses in the tropics [7.16.] or form atolls of small islands around extinct submarine volcanoes [7.17.]. Many reef-forming corals secrete a calcareous skeleton [7.18.] on which the polyps grow. In time the calcareous skeletons grow over each other to form coral limestone on which the most recent living polyps locate [7.19.] so that their symbiotic algae can photosynthesise. The calcium for the formation of the coral skeleton is extracted from sea water that is rich in calcium ions and massive concretions are found over thousands of years. Red coralline algae play a part in consolidating the reef as they also secrete calcium salts.

Hydrothermal vents are features of the deep submarine world and are formed largely by tectonic action. Pogonophorans secrete long tubes that are cemented to adjacent tubes to make a characteristic mass [7.20.]. This not only provides a secure base in which the worms live, but also alters the architecture around vents. It provides shelter and attachment sites for other animals and provides a substratum for micro-organisms.

Many aquatic animals have wonderfully detailed designs of body shape and feeding apparatus that show well the principles of elegant engineering. Indeed, evolution is a mechanism that selects for effective solutions to design problems. In addition, individual animals affect the engineering of the environment in which they live in a number of ways.

Many marine animals use calcium-rich sea water to construct shells or external coverings. These provide protection or a suitable shape for movement in water or over/through the substratum. Snail and bivalve shells are familiar to us from walks along the sea shore and the degree of strengthening they possess is often impressive. This protects the mollusc within against predators or erosive forces. When it occurs, sculpturing and extensions of the shell also provide a means of reflecting light and thus reduce the threat of overheating [7.21.]. Shells have a high density and accumulate into deposits that are eventually transformed into chalk and limestone rock after the molluscs die. Large snail and bivalve shells also form a substratum to which other animals attach, and shells form a substratum for the growth of biofilm that is food for scrapers.

Another major group of molluscs that have shells are the cephalopods [7.22.]. Several cephalopods have internal shells used for support and for resisting the antagonistic action of muscles, in addition to their role for protection. Through time the shelled cephalopods also have contributed their calcareous skeletons to the mass of shells that develops on the sea bed or in intertidal zones and one group of cephalopods, the ammonites, are among the most familiar fossils.

The skeletons and external coverings of many other marine organisms add to the banks of calcareous deposits. These deposits are usually much less common in fresh waters where animals are not as heavily strengthened and where calcium is often in much lower supply.

Many marine organisms make tubes in which they live and this engineering can alter the substratum markedly. Calcareous tubes are secreted by some tube-dwelling polychaetes, often forming white masses on the surface of rocks or on the shells of bivalves [7.23.]. Other polychaetes live within tubes of sand grains bound with mucus. The use of mucus in construction is widespread among marine animals, just as it is for feeding.

Freshwater animals also build structures and among the most impressive are the movable cases constructed by some larval caddisflies. These cases may be of small stones, green vegetation cut into equal lengths, small twigs of various lengths, and other forms [7.24.]. All are cemented with silk, a very powerful adhesive secreted by many insect larvae. Larval midges (Chironomidae) often occur in huge numbers in lakes and rivers and most of them build tubes from silk and detritus [7.25.]. If sediment from a pond is placed as a thin layer into a dish, midges transform it into tubes within 24 hours, something which often surprises the observer. This demonstrates engineering of the substratum in a very direct way and these larvae also clear organic matter from feeding territories around their tubes.

All aquatic animals engineer their environment by feeding activities. A shark attacking a large fish cuts it into ingestible pieces and all that remains are some fragments of fish and shark excreta, the rest being assimilated. Such a process is hardly likely to be significant in altering the particle composition of the water, but the activities of collectors certainly do have a significant effect. For example, midge larvae ingest detritus from the substratum, assimilate a small fraction of this and egest the rest in the form of faecal pellets. Pellets are bound by mucus that is ingested with the detritus and comes originally from the exudates of bacteria and small algae. The pellets thus remain as discrete aggregates until they are slowly conditioned and broken apart and, as we have seen, it is quite characteristic for the substratum to appear pelletised where there are high population densities of midge larvae.

Bivalves are among the most numerous suspension feeders of marine benthic zones and these animals draw particles into the mantle cavity on the respiratory current. Of the material trapped on the gills, some is ingested and subsequently egested as faecal pellets, and the remainder passes out with the exhalant current as pseudofaeces. Where bivalves are found in high population densities [7.26.], their processing rates of particles are impressive and significant changes in the particle size spectrum are likely to result. Suspension-feeding bivalves can alter the turbidity of water by their conversion of suspended particles to sedimenting faeces and pseudofaeces. Increased clarity of water then gives higher penetration of solar radiation into the water and a likely increase in plant growth.

The faecal pellets of suspension feeders are obviously much larger than their ingested constituents and this has an important consequence. In streams and rivers the large, compacted faecal pellets sediment to the substratum from the current more rapidly than do smaller particles. Similarly, the pellets produced by pelagic animals in lakes and oceans sink more rapidly than their constituent particles and some reach the substratum of profundal regions [7.27.]. Whatever the water body, pellets are food for benthic detritus feeders (predominantly deposit-feeding collectors and shredders) once they become sedimented to the substratum.

The significance of the engineering of particles by suspension-feeding collectors has long been recognised in lakes and the sea but its importance in flowing waters is less well known. However, without the egestion of pellets by suspension feeders, much more fine POM and DOM would be carried downstream and the role of suspension feeders in retaining organic matter within streams and rivers is now becoming recognised.

The water industry is responsible for providing drinking water and for the treatment and disposal of wastes that contain pollutants. All purification processes depend on living organisms, either directly or indirectly.

Sources of drinking water contain DOM and POM that include bacteria, algae and animals, and much of this organic matter must be removed before drinking water is passed for supply. In developed countries, rigorous testing of water quality for levels of pesticides and pathogens ensure that drinking water is safe to consume and strict regulations are enforced. In developing countries, water treatment is more often on a local scale and analysis of quality is less common. However, water used for drinking and cooking is considerably cleaner after treatment than is the source water.

Water entering a treatment works is cleared of much POM using screens, followed by microstrainers or carbon filters. After this pre-treatment, small POM and DOM are removed by one of two processes: coagulation or slow sand filtration. Coagulating agents are positively charged and neutralise negative charges on organic matter to promote the formation of particles, a process that continues by flocculation and binding by exopolymers. Resulting flocs are usually removed by rapid sand filters, accumulating organic-rich residues which are then easily removed after back-washing.

Slow sand filters are common worldwide and provide a low-technology approach to water treatment [7.28.]. The basic filter is formed of a bed of sand through which water passes to a drainage channel and thence to a storage reservoir. In large slow sand filter works there are many beds, e.g., there may be more than 20, each of area c. 300 m², with a basal layer of drainage bricks, a layer of cobbles above that, and then a thick layer of sand on the top. Most sand filters are open to the atmosphere but others are covered or built underground, and the efficiency of the filters is improved if a layer of activated charcoal is included within the sand. Water may enter a slow sand filter with little pre-treatment, but modern industrial-scale works use ozonation to oxidise organic compounds and promote the development of flocs.

Newly constructed sand filter beds are inefficient in removing DOM and are run to waste until a microbial biofilm develops over the sand grains and the biotic community forms within the matrix of the bed. Protists, nematodes and oligochaete worms are the commonest organisms found in the community, which resembles that found in the sandy margins of natural bodies of fresh water. The microbial biofilm adsorbs DOM and colloids that are broken down by bacterial exoenzymes. Protists and invertebrates then remove bacteria from the water and from biofilms, and keep interstitial spaces open by grazing the accumulating biofilm. Organic matter in the water is thus converted to microbial and animal biomass and to CO₂.

The sand - water interface has a special significance in filtration. Particles that pass pre-treatment, or those generated within the water in beds, are trapped by the pores between sand grains and an organic-rich layer ("schmutzdecke") develops rapidly. This layer contains many bacteria, bacterial exopolymer, algae, and accumulated exopolymer from planktonic algae. Materials in the water column are trapped into the schmutzdecke by filtration, impaction, or adsorption as water passes slowly into the filter. The water in sand filter beds often supports a rich planktonic community that provides a means of converting organic matter to CO₂, just as occurs within the sand. The excreta, exudates, and bodies of planktonic organisms are added to the schmutzdecke and algal production is often high on the surface of the sand. There is thus abundant organic matter and high light intensity in open beds, but covering beds minimises algal growth. This is considered to be preferable.

The accumulated schmutzdecke of sand filter beds must be removed from time to time and beds are drained for cleaning. The interval between cleaning varies with organic loading and is sometimes only a few weeks. Close examination of the schmutzdecke after cleaning reveals not only unicellular and filamentous algae but also large numbers of oligochaete worms and chironomid midge larvae. Both types of invertebrate ingest organic matter and pelletise it, this being very distinct in midge larvae that also build their characteristic tubes. It is probable that the activity of these invertebrates is an integral part of filtration and their engineering serves to keep channels through the schmutzdecke open, as well as providing mucus-rich faecal pellets and silk tubes that are highly adsorptive, especially of some pesticides.

Clearly, sand filters owe much to their microbiological, protist and invertebrate communities for efficient functioning. Other methods for purifying drinking water appear more chemical than biological, but they require the by-products of biological activity. Chemicals are used to induce coagulation, the binding of aggregates by chemical charge. Once formed, the coagulated masses are held together by the adhesive qualities of exopolymer to form flocs which can be relatively easily removed, water that has been cleaned then being passed to the domestic water supply. Ozonation is often used to remove humic materials and thus colour from water, also serving to remove toxic compounds. Ozone bubbled into water entering a works produces masses of floc, just as occurs when any natural water containing exopolymer is vigorously aerated.

The development of townships meant that disposal of waste products presented problems. In small communities, effluent was, and still is discharged directly into rivers and is thus carried away. Large-scale effluent discharge creates many threats to both human and environmental health and there are also aesthetic concerns with this form of pollution. For this reason, sewage works were constructed and these use either trickling filters or the activated sludge process [7.29.]. Both are engineered to encourage biological processing.

Whatever the process used, the first stage of sewage treatment is the screening of large particles after which the influent is allowed to settle. Many particles sediment and the water, rich in FPOM and DOM, is passed for treatment. In trickling filter works the water is expelled through rotating pipes on to beds of clinker or porous synthetic material and the water then begins a long passage over and through the substratum [7.30.], which is coated in microbial biofilm. Organic matter is subsequently transformed to CO₂ and microbial tissue by the micro-organisms and the whole package forms the diet of protists, oligochaetes, nematodes and several kinds of insect larvae which live within the filter. The biological community of trickling filters is thus strikingly similar in function to the sand filter community described above. In the activated sludge process [7.31.] the water from settling tanks is passed into large tanks which are circulated either by rotors, upwelling fountains, or by aeration. Microbial floc from an earlier treatment is added to the water and the turbulence and bubbling of organically-enriched water encourages growth of bacteria and further floc formation, just as in natural environments. Copious quantities of exopolymer are produced and there is a high adsorption of DOM and colloids on to exopolymer produced by the burgeoning microbial population. Organic matter is again converted to CO₂. There are parallels here to the use of floc in treating drinking water, and also parallels to the development of thick exopolymer strings by phytoplankton in natural waters receiving excess nutrients.

Whatever the process, water is much cleaner after passage through a sewage works. Cleaned water is discharged to rivers, estuaries or the sea where the small levels of organic matter remaining are utilised rapidly by aquatic communities. Primary sludge from the settling tanks, and the sludge resulting from secondary treatment, must be removed and these are transported out to sea from some plants. Dumping of sludge has created major eutrophication problems in the past, so dumping sites are now monitored more carefully. In addition to dumping, sludge is burned and may be used to fuel power stations generating electricity, or applied to the land to give a "green" method of disposal if the amount of toxic effluent is low.

We are looking increasingly for natural solutions to the treatment of effluent, especially where there is insufficient demand, or capital, for the construction of industrial methods. Septic tanks [7.32.] are one of the earliest methods of sewage treatment and use a near-natural approach, with organic matter being decomposed anaerobically to produce gases like hydrogen sulphide and methane. This replicates the anaerobic breakdown of organic matter within marine, estuarine and freshwater sediments. From time to time, solids from tanks are pumped into tankers and taken to sewage works for disposal. The technology of septic tanks has been developed in some countries to encourage development of the anaerobic microbial community in digesters, the gaseous by-products being used as a fuel.

Perhaps the most natural way of treating effluent is to run screened water into wetlands [7.33.]. These habitats are inundated from time to time and they have emergent plants that grow well on the by-products of decomposition. Wetlands take up DOM and also trap POM effectively, so that water draining from a treatment wetland is of much higher quality than that which is entering. The process is almost entirely dependent on the resident biological community of micro-organisms, microscopic plants, emergent macrophytes, protists, invertebrates and vertebrates. There are problems of scale as it is unlikely that there are sufficient areas of wetland to enable this process to be operated near conurbations. However, it is effective and is capitalising on a completely natural ecosystem by enhancing its annual primary and secondary production.

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