CHAPTER 4

Dissolved inorganic matter results from solution and weathering processes, either by the water body itself or by indirect inputs like surface drainage and hydrothermal sources. Inorganic particles are common in water which is erosive or which re-suspends sediments. Sand and other mineral grains are swept up by waves on marine and lake shores, and lowland rivers are characteristically turbid as they carry a heavy load of fine inorganic particles. In addition to resulting from erosion, inorganic particles also have biogenic origins. The siliceous frustules of diatoms and the shells of many kinds of invertebrates and protists all result from living organisms, as does coral sand eroded from reefs.

Organic molecules have been present in water as long as water has been present on the planet. In addition to their presence in bulk water, organic molecules adsorb to interfaces and are thus found in the surface film, over the substratum, and over the surface of particles.

The evolution of living organisms probably began when organic molecules became aligned on an aquatic substratum and began to replicate. Candidate substrata are clay particles, the surface of bubbles or the surface film of water bodies. Life is thought to have begun around marine hydrothermal vents but the air-water interface at the margins of ancient oceans was also suitable, especially where there was vigorous volcanic activity. Whatever the origins, we can be certain that life began in water.

A major step in the evolution of living organisms came with the development of single-celled organisms surrounded by a cell wall across which organic matter passed. This step was essential for the development of a changed environment inside the cell, with cell metabolism occurring in a regulated environment rather different to that of the surrounding water. The evolution of multicellularity then allowed the complex variety of life forms that we see today, where cells have become specialised into different functions so that each cell no longer had to perform all functions of a living organism.

Unicellular and multicellular marine organisms remain in an almost isotonic environment, i.e., their cell contents are not appreciably different in ionic concentration to the surrounding water. Fresh waters provide a contrast as this dilute medium sets up an osmotic gradient that causes cells to become flooded with water unless some measures are taken to prevent the influx. The diversity of freshwater life shows that this has been achieved successfully by many different types of organisms.

In considering aquatic organisms we must make reference to fossils. If we were to travel back tens and hundreds of millions of years we would recognise some familiar multicellular aquatic organisms but there would also be many that were unfamiliar. Some (e.g., several of those preserved as fossils in the Burgess Shales [4.1.]) are unlike contemporary animals and our view of the life forms in ancient oceans has been transformed by findings such as these. However, unicellular organisms were little different from those present today, an indication of the success of their mode of life. These unicells are vital for the functioning of all aquatic systems and they are found everywhere, even under extreme conditions.

Manufacturing essential nutrients from chemicals (chemosynthesis) and light (photosynthesis)

Some unicells lived and continue to live in aquatic environments like hot springs and hydrothermal vents that are rich in reduced compounds such as methane and hydrogen sulphide. They evolved mechanisms to manufacture vital materials for growth and metabolism from these reduced compounds, thus producing their own food by chemosynthesis [4.2.].

Other unicells developed pigments that harnessed light energy. This energy was used in the transformation of carbon dioxide and water into carbohydrate by the chemical process of photosynthesis [4.2.]. An important by-product of photosynthesis is oxygen and the gas escaped to the atmosphere to provide much of the oxygen on which much of life depends. Today, when there are worries about the amount of carbon dioxide in the atmosphere, photosynthesis by marine organisms represents a key sink for this gas and a possible means of controlling its quantity, especially if iron is present in the water [4.3.].

Gases and minerals dissolve in water but it is sometimes difficult to differentiate materials in solution from those forming extremely fine suspensions. For this reason, and to allow rapid processing of samples, it has become a convention to regard all matter passing through a filter of pore size 0.45 µm to be dissolved and everything retained to be particulate. Each fraction is further subdivided into that which is organic or inorganic, but I will concentrate on organic matter in this chapter. Thus, dissolved organic matter (DOM) passes through the filter and particulate organic matter (POM) does not.

DOM contains many colloidal particles (colloids are defined here as having a long axis between 1 nm and 1 µm), viruses and even small bacteria (a filter of pore size 0.2 µm being considered suitable for sterilisation of fluids). Particles, whether colloidal or of larger dimension, have coatings of DOM and other chemicals and these also need to be taken into account. Add to this the caution needed in looking at any filtration process (variation in pore size, adsorption on to the filter surface, effect of the filtration process on the state of the matter) and we can see that this operational division between dissolved and particulate matter is far from ideal.

Just as whole water is analysed for chemical components, e.g., amino acids, carbon, nitrogen, etc., so is the filtrate after water has been passed through a 0.45 µm pore-size filter. This brings a new series of acronyms: DOC is dissolved organic carbon; DIN dissolved inorganic nitrogen, etc. Each study will have its own requirements but the commonest unit used in analysing this fraction is dissolved organic carbon.

A classification of organic matter used in running water biology is shown in Table 4.1. The change in dimensions of particles along streams and rivers has been a major topic of interest in these habitats and this classification was devised to allow changes to be monitored. In some studies, UPOM is used as a discrete category, FPOM being re-classified as being of diameter < 1 mm but > 50 µm. Care is thus needed when comparing data to make sure how categories are being defined.

Category	Diameter
Coarse Particulate Organic Matter (CPOM)	> 1 mm
Fine Particulate Organic Matter (FPOM)	< 1mm but > 0.45 µm
Ultrafine Particulate Organic Matter (UPOM)	< 50 µm but > 0.45 µm

In addition to discrete particles there are always some aggregates, and aggregates can dominate in some water samples. So how are these classified? Usually, aggregates are considered as particles having dimensions of length, width and area just like discrete particles, so the significance of aggregates is easily overlooked. To complicate matters, aggregates can be loosely associated and readily broken apart (often during filtration), or can be held together by very strong forces so that they resemble discrete particles.

Sometimes the components of aggregates are identified, so they may be described as consisting of diatom frustules or identifiable animal remains. More often they are described as being amorphous, consisting of various unidentifiable fragments of organic and inorganic matter bound in an organic matrix. This matrix consists of polysaccharides.

Another feature of particles is that they can have coatings of materials adsorbed on them. Whether a particle is discrete or in the form of an aggregate, there are areas on the surface that are charged and these act as binding sites for chemicals in the water. Other particles also become adsorbed and some of these already have their own adsorbed coatings.

Organic matter comes into water from aerial or terrestrial sources (e.g., as falling leaves, in rain, as drainage, etc.) or is generated from within the system (e.g. by photosynthesis and chemosynthesis). Inputs from outside the system are termed allochthonous; autochthonous inputs are generated within the system. The importance of the two types of input will vary with the location of the water body. For example, streams draining through woodlands have large allochthonous inputs, while large lakes and oceans have large autochthonous inputs.

In addition to the organic matter contributed by dead bodies, almost all living animals also produce egesta. Ingested food is digested and the remains, together with the waste products of metabolism, are passed out as faeces and urine. The organic composition of faeces varies with the efficiency with which dietary constituents are assimilated and the rate at which faecal matter is produced also varies with food quality. Animals with lower quality diets, like many detritivores, feed almost continuously and produce large amounts of faecal material. In contrast, carnivores have the most nutritious diet and many eat and defecate irregularly as food is often retained within the gut to allow efficient digestion.

Micro-organisms, plants and animals produce secretions from within the body and these are exuded through the body wall. There are many kinds of exudates but the commonest are those consisting largely of polysaccharides in combination with proteins. Often called mucosubstances these are complex polymers that hydrate on exposure to water, often dramatically so: a small amount of exuded polymer becomes a large amount of mucosubstance . These exudates are used for attachment, as shunts for excess carbon within cells, as a means of protection, for defence [4.4.], and for many other purposes. The term exopolymer is used to describe these secretions throughout this book.

Reproduction of organisms generates living organic particles. The first unicellular organisms divided by splitting genetic material and subsequently the cell, a method of reproduction that continues in contemporary single-celled organisms [4.5.]. With multicellularity came the evolution of special reproductive cells, with male and female gametes fusing to form a zygote. Many aquatic animals, from the primitive to the highly evolved, use external fertilisation and shed gametes into the water. Other organisms use internal fertilisation with cell fusion occurring within the body of the animal, followed by release of the zygote. The offspring at birth may be little developed or at an advanced stage of development. Shed gametes, zygotes and more developed offspring add to the numbers of organic particles in water, often in pulses when reproduction occurs at certain times of year.

When aquatic plants and animals die, their bodies are invaded by micro-organisms to begin the process of decomposition. As breakdown progresses, material from within cells leaches out into the water.

Dissolved organic matter also leaches from inputs to aquatic systems from the air or surrounding land. Soluble chemicals leach rapidly on contact with water, as we readily demonstrate when making tea from dried tea leaves. Terrestrial, or emergent, perennial plants often have mechanisms that conserve valuable materials in storage areas like stems or roots, leaves then being shed annually in deciduous species. When shed leaves enter aquatic systems they contain a high proportion of refractory plant strengthening materials such as lignin and cellulose. The amount of DOM that leaches out is correspondingly small but different species leach to different degrees, often reflecting the toughness of the leaf. Inputs of wood contain similarly large amounts of strengthening compounds.

The microbial colonisation and subsequent breakdown of particulate organic matter is termed conditioning. In fresh waters, the initial agents of breakdown of organic particles are fungi and bacteria, the former being relatively rare in the sea. Many fungi invaded fresh waters from the land where they are essential for the breakdown of leaf litter and wood. They have evolved powerful exoenzymes (enzymes that are produced by the fungi to work externally) that digest plant cell walls and thus promote more rapid breakdown than could be achieved by bacteria alone. Aquatic fungi have the same role in attacking plant detritus. Bacteria, which are abundant in all water bodies, attach to all newly-exposed surfaces and also attack them with exoenzymes, eventually causing the matrix of tissues to disintegrate. In fresh waters bacteria thus exploit the new surfaces exposed by fungal attack, but bacteria alone are the dominant agents of breakdown in the sea.

Whether in fresh or marine waters the result of leaching and conditioning are inputs of DOM and POM, with the latter being reduced in particle size with time as fragmentation proceeds. The breakdown of organic matter occurs throughout the water column but the sites of highest significance are those where organic matter accumulates. These can be on a large scale (e.g. areas of deposition or settlement on mud flats, lowland rivers, lake beds) or on a smaller scale (e.g. leaf packs on the upstream side of stones in streams, strand lines on beaches, carcasses on the deep ocean bed). Sites of high microbial activity also occur within the water column. For example, some thermally-stratified oceans have a characteristic oxygen minimum around the thermocline where sinking particles are decelerated as they encounter denser cold water. The particles are usually colonised by large numbers of aerobic bacteria that use up some of the available oxygen.

Most decomposition in the water column is by aerobic micro-organisms, but some stratified lakes develop such low oxygen tensions near the substratum during summer that anaerobes are the only organisms able to survive. Anaerobic metabolism is also characteristic within sediments having a constant deposition of more particles. The reducing conditions within such sediments result in slow breakdown and the development of organically-rich strata that eventually produce beds of fossil fuels.

Many water bodies contain huge numbers of bacteria [4.6.]. For example, some organically-enriched lakes may contain > 10 million bacteria ml^-1, and coastal mud > 40 million bacteria cm^-2 (multiplication by volume, or area, gives an impression of the total numbers present in a habitat). However, direct counts do not give any impression of bacterial activity: cells may be dormant, or undergoing explosive growth, depending on conditions. Some bacteria are tolerant of extreme temperatures (hot or cold), high chemical concentrations, high or low pH, high barometric pressure, and many other physico-chemical factors. It is this tolerance of a wide range of conditions by different taxa and their powers of reproduction which have made bacteria so successful. Their extremely short generation time and ancient lineage has allowed selection for types that seem able to exploit any aquatic environment, even the most apparently hostile to living organisms.

Most bacteria are heterotrophs, i.e., they are dependent on outside sources of energy for metabolism and cannot manufacture their own food. Most of the carbon dioxide released from the surface of a water body results from microbial metabolism and this reflects their importance in the functioning of aquatic systems.

Planktonic bacteria are carried by water currents, and most are covered by flagella that allow them to move chemotactically towards sources of nutrients. However, many aquatic bacteria, both planktonic and benthic, remain firmly attached to surfaces. As we saw earlier, attachment between bacteria, or by bacteria on to a substratum, is achieved by secretion of exopolymer from the bacterial cells. These exudates take various forms, e.g., fibrils, blebs or sheets. In addition to ensuring attachment, the exopolymer provides a means of conserving exoenzymes and for acquiring adsorbed organic matter. The secretions of many bacteria combine to form biofilms.

Bacterial biofilms [4.7.] are found wherever there are aggregations of bacteria and these may be in the water column, at the air-water interface, or over and within the substratum. The benthic biofilms covering the substratum have complex structures and should not be conceptualised as a laminated sheet. Benthic biofilms are strongly three-dimensional, with some towers and troughs and a complex series of channels running through them. They play an important role as energy transducers. As well as covering surfaces, biofilms also fill interstitial spaces between mineral grains and are thus an important agent in promoting the local stability of sediments.

Almost all water bodies have an air-water interface, with the exception of those covered permanently by ice or those present within a substratum. The interface is strong, as seen when floating pins on the surface of water in children's magic shows. Any close examination of the surface of a water body in dead calm conditions reveals that many dust particles and even living organisms are on the surface, apparently not wetted.

On the aquatic side of the air-water interface there is an accumulation of hydrophobic materials in the surface microlayers [4.8.]. We do not know how the surface microlayers are structured, as they are so difficult to examine in situ. There may be a layering based on hydrophobicity, with lipids and the surface and a protein-polysaccharide layer below, or all hydrophobic materials may be formed into a gel matrix. We do know that the surface microlayers are highly dynamic. Incoming solar energy heats the surface film, promoting the evaporation of volatile compounds. Solar energy also causes photolytic changes in chemicals gathering under the surface, splitting large molecules into smaller ones, some of which are labile. UV light also has a damaging effect on living cells and this makes the surface microlayers a stressful place to live, despite high temperatures and the enrichment of organic matter. Metabolising the surface microlayer material are bacteria and a community of consumers, all of which are very numerous here compared to their numbers in the bulk water. The clean surface of materials falling through the water surface also collects a coating of microlayer organic matter. Some of this may remain attached and the matter that detaches is released back to the water column and may return back to the water surface.

The air-water interface, surface microlayers and their associated microbiota are called collectively the surface film and they play a very important role in the metabolism of aquatic systems. Two principal factors contribute to their importance: surface films cover much of the surface of the planet and all sunlight entering water bodies does so across the surface film. Of course, the film is easily disrupted by water movements, but the return of calm conditions allows the surface microlayers to become re-established. The dynamic nature of the surface film involves a complex interaction of physical (disruptive) and chemical (hydrophobic) forces.

Each bubble in surf or white water has a covering of surface film and thus hydrophobic matter. It is this hydrophobic matter that is flocculated into the spume that remains when bubbles burst after winds die down, or circulating currents cease. The materials that promote flocculation are largely biogenic exopolymers. Flocculation occurs wherever bubbles occur so this process is not confined to the surface film as bubbles are produced by organisms, from sediments, and from the escape of volcanic gases.

There is evidence that bubbles are sites of enhanced microbial metabolism and therefore of the transformation of organic matter. The reasons are complex but physico-chemical mechanisms such as flocculation and folding of hydrophobic molecules at the gas-water interface play an important part, as does the enrichment of heterotrophs on the surface of bubbles.

Wherever there is contact between particles of whatever size, charges promote attraction or repulsion. Where the charges are attractant, the effect will be the aggregation of the two particles to form a new, larger particle. Aggregates may have a very short duration or remain intact for long periods, but aggregation and dis-aggregation of organic matter occurs constantly. Longevity is promoted by the strength of attachment between components and these may be by chemical bonding (coagulation), the use of adhesive bridges of exopolymer (flocculation), or by a mixture of both. In addition to collision of particles caused by water movement, aggregates form from the coatings of bubbles after implosion as the gas goes into solution, or as the bubble bursts at the surface, causing compression of the coating materials. Aggregation of DOM into particles is also promoted by marked changes in salinity (as occur in estuaries), high concentrations of divalent cations (as in calcium-rich waters) and by turbulence, both at the surface and within the water column.

Among the most impressive aggregates seen in aquatic systems are those termed "marine snow" [4.9., 4.10.]. Flocculation of organic matter, especially exopolymer, produces small aggregates that give an initial appearance of submarine snowflakes and these combine to form larger aggregates. It is possible for marine snow aggregates to exceed 20 cm in diameter and they support an abundant community of bacteria, protists, algae and animals. They are effectively small islands of pronounced biological activity within the bulk water.

Lakes and rivers also contain flocs that have a similar method of origin as marine snow. In lakes with low nutrient levels these are relatively easy to see. The "lake snow" flocs are found within the surface waters and they also accumulate near the thermocline of stratified lakes where currents and turbulence result in their formation, and the change in water density promotes their retention. In rivers, the analogues of marine snow ("river snow") are likely to be limited in size by the disruptive effect of turbulence generated by the flowing water. They are formed and broken apart rapidly, and their role in the biology of flowing waters may have been underestimated by this transience. Disruption of flocs also occurs during sampling and filtration so it is necessary to study them in situ.

In some aquatic habitats there are large quantities of exopolymer. For example, corals secrete mucus as a by-product of metabolism from their symbiotic algal cells and this prevents the sessile corals from becoming clogged with sedimenting particles, also serving as a shield against desiccation should the corals become exposed to air. The exopolymer forms into mucus sheets that then break into strings as they are carried by the ebb and flow of water over the reef. The mucus begins to adsorb particles and DOM and the strings break up eventually into small aggregates laden with other organic matter.

Algae in blooms also produce copious quantities of exopolymer and this forms into strings and ropes which adsorb organic matter and become colonised rapidly by bacteria. These aggregates contain gases produced by the metabolising bacteria and this gives the flocs buoyancy. Sometimes the flocs are carried to the sea surface and form a skin of decaying organic matter that becomes washed ashore in masses. On beaches used by the public these masses are certainly unsightly.

Faecal pellets are another important type of aggregate in all aquatic systems. The pellets of many animals remain discrete for days or weeks, especially where they are bound tightly together. Some animals secrete a membrane around the gut contents and faecal pellets are wrapped in this membrane. In most animals there is no external binding of pellets and they are held together in some other way, usually by exopolymer. This may be secreted by the gut in higher animals but exopolymer is often ingested, or exuded from ingested organisms on passage through the gut. As many hindguts feature a region where matter is compressed before egestion (to extract nutrients in solution) there is thus a mechanism that causes compaction of the constituents and increases further the binding of component particles with exopolymer in the production of faecal pellets.

Colloidal organic matter is abundant in all water bodies and forms 30-50% of all DOC in sea water. Many of these tiny particles consist of long-chain, refractory polymers that result from the breakdown of organic matter or from exudates. In environments where conditions for breakdown are poor, some are so refractory that they may remain little changed for thousands of years. However, they act as sites for adsorption of other organic and inorganic matter. Their abundance and small size results in a huge total surface area for attachment. Colloids may thus have a life extending from seconds through to thousands of years and the movement of materials on to their surface is likely to be dynamic. As adsorption of matter from heavy metal ions to labile organic molecules occurs, the significance of colloids in the functioning of aquatic systems is only just becoming appreciated.

Recently, the aggregation of polymers to form particles has received critical re-assessment. Using polymer gel theory, it has been possible to show that the transition of material from solution to particulate form (i.e. > 0.45 µm in diameter) passes through a colloidal phase where the constituents form readily into polymer gels. The resultant aggregates are likely to be more degradable than their components, just as marine and lake snow flocs provide sites of high biological activity.

However, the formation of colloids into polymer gels presents aquatic scientists with a problem. During filtration of natural water, gels are disrupted and aggregation also occurs within the filtrate so that the significance of these materials, and the dynamics of their change in form, has been little considered. This is yet another problem in using filters to delimit fractions of organic matter and mirrors the problem in using filtration for the study of flocs, as mentioned above.

When exopolymer is exuded from organisms it is in various forms, from fibrils through to mucous masses. Particles of colloidal size have been given the acronym CEPs (colloidal exopolymer particles) while flake-like particles of varying size, formed by the aggregation of CEPs, are referred to as TEPs (transparent exopolymer particles) [4.11.]. As their name suggests, the latter are often very thin and light readily passes through them. Both CEPs and TEPs bind aggregates and are again part of a dynamic system of aggregate formation and break-up.

Viruses are classified within DOM as they range in size from 25 - 300 nm but little work has been conducted on viruses in water, even though their role is likely to be significant. Most attention has focused on human viral pathogens that end up in water but aquatic organisms are also attacked by indigenous viruses. Virus diseases of aquatic organisms must occur widely and some population crashes of algae result from viral infection - a kind of algal influenza. Bacteriophages can also cause dramatic decreases in numbers of bacteria.

As viruses and algal cells have co-existed for very long periods of time, resistance to infection must have evolved. This results not only from immunological processes but also by indirect means. For example, the exopolymer exuded by algal cells is colonised by bacteria that utilise both the exopolymer and the adsorbed DOM that covers it. In so doing they disable viruses that infect the algae so there is almost a symbiotic relationship.

Much more needs to be found out about viruses in water. Some population crashes, or changes in the viability of organisms, may result from viral diseases and complex mechanisms to prevent viral attack are likely to be discovered.

As the majority of particles are more dense than water they sink through the water column. Sedimentation occurs in all water bodies, although currents and turbulence have a profound effect on the pattern of sedimentation, causing re-suspension of previously sedimented particles and prevention of the sedimentation of others. As we have seen, the sinking of particles is also affected by the change in the density of water across the thermocline.

Sediment traps record particle flux and these show that there is a general downward displacement of particles in oceans and lakes. This is compensated by an upward movement of hydrophobic, low-density organic matter and this upward flux can be over 50% of the values recorded in the downward flux of particles. The downward flux of organic matter is important, as its eventual fate is the ocean or lake bed [4.12.]. Clearly, particles in oceans have a long way to travel vertically and a lower percentage of material reaches the bed than in lakes, the amount also varying with local conditions of productivity. In oceans, the long transit time of sinking particles allows a succession of colonising heterotrophic organisms, many of them being adapted to the barometric pressure at the depth where they are found most abundantly. All these organisms are involved with the conditioning of the organic matter, so its composition changes during flux.

There are several mechanisms that decrease the rate at which dead organic particles sink through the water column (we will consider living particles later) and some that increase the rate of sinking. Sinking rate is related to size for any given density, the larger the particle the greater its sinking rate (see Chapter 8). Large particles have a small surface area to volume ratio and thus have a high mass but relatively low frictional resistance over their surface. Small particles show the reverse, with low mass and much higher friction over their surface. This relationship holds for solid particles of the same material but materials often vary in density and denser particles have a higher gravitational pull upon them.

Aggregates are often porous and water flow through the channels in porous particles creates large frictional resistance, so that sinking is slower. Large flocs like marine and lake snow are therefore slow to sediment and serve to maintain organic matter in the surface waters for longer time periods. As we have seen, inclusion of gas bubbles can maintain neutral buoyancy, or even cause aggregates to float to the water surface. Nevertheless flocculated material is a feature of the ocean bed, especially some time after surface storms. These flocs must form high in the water column as they often contain algal detritus.

Faecal pellets are common aggregates in the surface waters of oceans and lakes, especially those from the frequently abundant crustacean zooplankton [4.13.]. The diet of these animals varies from species to species and through time, but all feed on small living or dead particles. After digestion, waste products and unchanged food are excreted as compacted faecal pellets that sink away from the animals. As these pellets have a membranous coating there is unlikely to be much diffusion of the components but DOM is likely to leach rapidly from pellets, just as it does from pellets produced by benthic animals.

Faecal pellets produced by zooplankton are of lower nutrient value than the foods that surround the animals, at least until conditioning allows colonisation of the pellets by large numbers of bacteria. The leaching of DOM across membranes coating pellets provides nutrients for attaching bacteria and this has led some crustaceans to use a novel feeding strategy. These zooplankters cut away membrane colonised by bacteria and the fragments of membrane are ingested to give a high quality diet, something which also causes the contents of the pellets to become diffuse and thus sink more slowly. This is likely to further prompt colonisation and conditioning and results in the conservation of nutrients within the photic zone.

As in oceans and lakes, there is flux of particles in streams and rivers but this time it is largely horizontal, with vertical flux occurring as particles are transported downstream. More direct vertical movements of particles occur in rivers of high order and these commonly have beds that consist largely of fine, sedimented particles. As rivers are erosive of their beds and banks, there are many mineral particles in transport along much of the length of rivers and these can colour the water white, yellow or red, depending on underlying rock strata. They may be deposited on the flood plain after periods of high flow, deposited on the bed, or carried to a lake or the sea. Similar high mineral particle loads are found where there is wave action and runoff from surrounding land to lakes and oceans. These particles then sink wherever conditions are suitable for sedimentation.

A change in the composition of organic matter of rivers occurs from the low order headwaters to large, high order rivers. Streams and rivers are largely dependent on inputs of organic matter from outside the system, not surprising as they drain over and through soil profiles. Where the low order streams drain wooded watersheds there is a large influx of leaves and woody debris, so CPOM often dominates the organic matter biomass. It is retained by formation of snags, leaf packs, by attachment to the substratum, and by feeding of animals. Leaching and conditioning occur in situ and much of the resulting FPOM is carried downstream together with some of the CPOM. In high order rivers the dominant organic particles are FPOM and colloids and there will be a slow sedimentation to the substratum.

The often-turbulent nature of streams and rivers ensures that organic matter is mixed through the water column. However, current velocity may only be rapid at the surface of rivers of high order, and slow enough to allow sinking of particles through deeper water. Even slow current speed over the substratum is sufficient to sweep up some sedimented particles that are then carried as bedload, a general feature of rivers.

The organic matter that sinks through the thermocline in stratified lakes undergoes decomposition and conditioning in the hypolimnion. Only when the thermocline breaks down does the whole water column become mixed, with the resultant mixing of nutrients. This is the explanation for spring plankton blooms as algae grow well on nutrients that are released when summer stratification breaks down in the autumn of the previous year. After the initial bloom, the numbers of algae are reduced by feeding zooplankton, virus attack, and the depletion of nutrients in what is now the epilimnion of the newly stratified lake.

Similar conditions pertain in temperate oceans where stratification occurs but tropical oceans are usually permanently stratified, with a deep photic zone. Here, nutrients are in short supply as there is constant movement of materials across the thermocline to deep water, and the lack of vertical mixing prevents nutrients coming to the surface. The deep photic zone provides conditions ideal for photosynthesis but blooming of algae does not occur because nutrients are depleted permanently. Consequently, the water remains clear and the thermocline maintained at a deeper level than in other oceanic waters.

There are areas with high nutrient levels in tropical oceans. Coastal regions have organic inputs from outside (e.g., mangrove leaves) and within the water (e.g., seagrass beds). Coral reefs have self-sustaining nutrient circulation, there being little movement of organic matter to the surrounding sea and it is thus not lost across the thermocline. Where deep-sea currents come to the surface in upwellings, they bring organically-rich water and the mixing of nutrients through the water column. This is of great significance in some tropical oceans where upwellings reach the surface having been deflected by continental slopes. The enrichment of the surface waters brings high productivity as nutrients provide the energy base for algae and the organisms that benefit from algal growth.

Several regions of aquatic systems can be identified as sites of sedimentation: ocean and lake beds; high order rivers; mud flats not subject to vigorous wave action; etc. Deposition also occurs on a small scale: between stones, or behind rooted macrophytes, in the substratum of a river; in depressions, or fissures, in the substratum of shores; around wrecks, or other debris.

Particles that become sedimented on to a substratum are often re-suspended. In streams and rivers, floods will cause a flushing of material downstream and changes in the patterns of the bed cause particles constantly to be re-located. Over the ocean bed there is often a noticeable "benthic turbidity zone" where deposited particles are picked up by the constant currents that occur here and we are familiar with the movement of deposited particles on shores. All can be termed transport in bedload and this constant movement is a characteristic of particles in water. However, many particles become sedimented permanently and eventually amalgamate to form mineral, and organically-rich, strata. Materials that are resistant to breakdown (e.g., bones, shells and exoskeletal material) sometimes become fossilised and the tissues of organisms are also preserved when conditions are poor for microbial activity (e.g. in acidic, humic water, and in certain anaerobic sediments). Over long time periods the deposition of biogenic minerals in oceans has resulted in chalk and limestone strata and the abundance and thickness of these rocks are impressive reflections of earlier biological productivity.