The open ocean, coral reefs, rocky and sandy shores, and mangroves

One World Ocean, and the zones defined by light

Although we name five oceans - the Arctic, Atlantic, Pacific, Indian and Southern - there is only one body of water. The boundaries between them are drawn by continents and by lines of latitude, not by anything in the water, and the Southern Ocean runs unbroken around Antarctica and joins the Atlantic, Pacific and Indian. The syllabus calls this single connected body the World Ocean, and the connection matters: heat, dissolved gases, nutrients, pollutants, plankton and larvae travel between the named oceans, so what happens in one is felt in the others.

The zones of the open ocean are defined by light penetration, because light is what decides whether a plant or an algal symbiont can photosynthesise there. The epipelagic zone runs from the surface down to about 200 m. It is the photic zone: light is strong enough for photosynthesis, so the phytoplankton live here and this is where nearly all of the ocean's primary production happens. The mesopelagic zone, from about 200 m to 1000 m, is the twilight or dysphotic zone. There is still enough light for animals to see by, but not enough for net photosynthesis, so no plant can grow there; the animals that live in it either feed on what sinks from above or swim up to the surface at night to feed.

Below that there is no sunlight at all. The bathypelagic zone runs from about 1000 m to 4000 m and the abyssopelagic zone from about 4000 m to 6000 m. Both are aphotic: the only light is the blue-green glow of bioluminescence made by the animals themselves, the water is close to freezing, the pressure is enormous and the food supply is a thin rain of dead plankton, faecal pellets and carcasses falling from the sunlit water far above. Because there is no light there is no photosynthesis, so the deep ocean has no plant production at all and its food web is built on material imported from the surface.

The benthic zone is different from the other four: it is not a layer of water but the sea floor itself, running from the shore to the bottom of the deepest trench. Because it underlies every depth, its light level depends on how deep it is - a coral reef's floor is brilliantly lit, while the abyssal plain is permanently dark with only a few centimetres of oxygenated sediment on top.

Regions of the ocean are also classified by latitude as polar, temperate or tropical, which decides water temperature, the amount of seasonal light and whether production peaks once a year, twice a year or stays fairly constant. Polar water is cold and close to freezing, with months of complete darkness and a short explosive summer bloom; temperate water has clear seasons and two blooms in spring and autumn; tropical water is warm all year, strongly stratified, and nutrient-poor.

The ocean and the atmosphere: carbon sink, oxygen source, climate control

The ocean and the atmosphere are in constant exchange across the sea surface, and the syllabus asks for four consequences of that exchange. The first is the ocean as a carbon sink. Carbon dioxide dissolves from the air into the surface water, where it reacts to form bicarbonate and carbonate ions, and it is then taken up by phytoplankton during photosynthesis and built into the calcium carbonate shells and skeletons of corals, molluscs and coccolithophores. When those organisms die, some of the carbon in their shells and in the faecal pellets of the animals that eat them sinks into deep water, where it can stay out of contact with the atmosphere for centuries. The ocean therefore holds by far the largest store of carbon at the Earth's surface, and it has absorbed a large part of the carbon dioxide that humans have released by burning fossil fuels.

The second is the ocean as a source of oxygen. Photosynthesis by phytoplankton, seaweed and seagrasses in the epipelagic zone releases oxygen into the water, and some of it passes into the atmosphere across the surface. Marine phytoplankton are among the most important producers of atmospheric oxygen on the planet, which is easy to forget because they are invisible and drift with the current. The exchange works both ways, so the ocean is both a sink and a source depending on the gas, the temperature and the biology of the water.

The third is temperature buffering. Water has a very high specific heat capacity, which means it takes a great deal of energy to warm it and gives that heat back slowly as it cools. The ocean therefore absorbs solar energy in summer and in the tropics without its own temperature rising much, and releases heat in winter and at high latitudes, so coastlines have smaller temperature ranges than inland areas at the same latitude. This is why maritime climates are mild and continental climates are extreme, and why coastal towns rarely see the frost or the heat of the interior.

The fourth is global climate control. Surface currents and the slow thermohaline circulation carry warm water from the tropics towards the poles and cold water back along the deep sea floor, redistributing heat around the planet and shaping where rain falls. Evaporation from the warm surface supplies the water vapour that becomes rainfall, and the temperature of the sea surface controls how much of it evaporates. Change the circulation or the surface temperature and you change weather patterns thousands of kilometres inland, which is why the ocean is treated as part of the climate system rather than as a passive container of water.

• Carbon sink: carbon dioxide dissolves in surface water, is used by phytoplankton and locked into calcium carbonate shells; sinking debris carries it to deep water for centuries.
• Source of oxygen: photosynthesis by phytoplankton, seaweeds and seagrasses releases oxygen, some of which enters the atmosphere.
• Temperature buffering: water's high specific heat capacity means the ocean absorbs and releases heat slowly, so coastal climates are milder than inland ones at the same latitude.
• Global climate control: surface currents and the thermohaline circulation move heat from the tropics to the poles, and evaporation from the sea supplies water vapour for rainfall.
• Cold water dissolves more carbon dioxide than warm water, so a warming ocean takes up less of it - the sink weakens as the water warms.

Corals as animals, and the conditions a reef needs

A coral is an animal, not a plant and not a rock. Corals belong to the phylum Cnidaria, the same phylum as jellyfish and sea anemones, and the reef is built by colonies of tiny polyps. Each polyp is a hollow, sac-like animal with a ring of tentacles around a single opening, and each sits in a cup of calcium carbonate that it has secreted itself. The polyps are sessile - fixed in one place, unable to move - and they are joined to their neighbours so that a colony shares tissue and, in many species, a continuous skeleton. A reef is therefore the accumulated skeleton of thousands of generations of animals, with only the thin living layer on the outside alive.

The reason a tropical reef can exist in water that is almost devoid of nutrients is zooxanthellae, single-celled algae that live inside the tissues of the polyp. The partnership is a symbiosis, and because both partners benefit it is specifically a mutualism. This is why the word 'photosynthesis' appears in a topic about an animal: the polyp does not photosynthesise, its symbionts do.

The conditions required for reef formation follow directly from that partnership and from the polyp's own needs. Water must be warm, roughly 20 to 30 °C, which is why reefs are confined to the tropics and subtropics. It must be shallow, generally less than about 50 m and best above 20 m, because the zooxanthellae need light. It must be clear, because sediment and plankton in the water absorb light and because silt settles on the polyps and smothers them. It must be low in nutrients, because a nutrient-rich sea grows thick phytoplankton and filamentous algae that shade the coral and overgrow it - the clearest blue water is the best reef water. Salinity must be fully marine and stable, around 35, because corals cannot tolerate much dilution by fresh water, so reefs do not form off large river mouths. There must be hard substrate for the larvae to settle on, and moderate water movement to bring oxygen and plankton and to remove sediment without smashing the fragile branches.

The structure of a hard coral polyp and how it feeds

The syllabus limits the polyp to seven structures, and each one has a job you should be able to state in a phrase. The tentacles form a ring around the mouth and are the polyp's hands: they capture small animals from the water and push food towards the mouth. They are armed with nematocysts, which are stinging cells - each one contains a coiled thread with a barb and a dose of toxin that fires out on contact, paralysing or holding prey too small and too quick to be caught otherwise. The mouth is the only opening to the gut, so food goes in and waste comes out through the same hole.

Inside, the stomach (the gastrovascular cavity) digests the prey and distributes the nutrients around the colony, and it is also where the zooxanthellae live and where their products are released. The skeleton has three named parts. The calyx is the cup-shaped depression in the skeleton in which the polyp sits. The theca is the wall of that cup, the calcified side of the corallite that rises around the polyp and can be raised when the polyp retracts. The basal plate is the flat plate of calcium carbonate at the bottom of the cup, on which the polyp rests and with which it is cemented to the colony and the reef beneath.

Nutrition comes from two directions at once. By day the polyp lives on the products of its zooxanthellae: the algae photosynthesise inside the coral's tissues, using carbon dioxide and nutrients from the polyp's waste, and release sugars, glycerol and amino acids that can supply the great majority of the coral's energy. The polyp gives the algae a safe place inside its tissue, a supply of carbon dioxide and nitrogen and phosphorus from its waste, and a position in bright shallow water. By night many polyps extend their tentacles and feed as consumers, catching zooplankton and small animals with their nematocysts and digesting them in the stomach, which supplies the protein and phosphorus that the symbionts cannot provide in sufficient quantity. Corals also absorb some dissolved organic matter directly through the body surface. This is why a coral can survive a short period without feeding but not without light.

The four types of tropical coral reef

Reefs are classified by two things only: how far the reef is from the coast, and whether there is a lagoon between the reef and the land. Learn the four shapes as a progression, because they are usually described as stages of the same history - a reef growing up around a volcanic island as the island sinks or the sea level rises.

A fringing reef is attached directly to the shore, with no lagoon, and it is the commonest type on a tropical coast with a narrow shelf. A barrier reef lies further offshore and is separated from the land by a lagoon of shallow, sheltered water, often several kilometres wide and deep enough for boats; the Great Barrier Reef off Queensland is the largest example in the world. A patch reef is small and isolated, a mound of coral growing up from the floor of a lagoon or reef flat, with no connection to the shore and no lagoon of its own. An atoll is a ring of reef, often broken into channels, enclosing a central lagoon with no land inside it except low sand cays; atolls are found far out in the tropical ocean, classically on the submerged remains of a volcanic island, and the Maldives is built almost entirely of them. Note the lagoon question: fringing and patch reefs have none, barrier reefs and atolls do, and at an atoll the lagoon is in the middle of the reef, not between the reef and a continent.

Why reefs matter, how they erode, and what artificial reefs can do

The importance of coral reefs is easiest to remember as five headings from the syllabus. Biodiversity: although reefs cover a tiny fraction of the sea floor, they hold a very large share of marine species, because the complex three-dimensional skeleton provides an enormous number of niches, refuges and feeding surfaces. Food source: reef fish, crabs, lobsters, octopus, sea cucumbers and giant clams feed millions of people and support both local and commercial fisheries, and the reef is the nursery that stocks the surrounding sea. Coastal protection: the reef flat and the crest break wave energy offshore, so the shore behind it is sheltered from storms and the beach is not stripped away. Tourism: diving, snorkelling and glass-bottom boats bring income and employment to tropical countries, and they depend on a reef that is still alive and colourful. Medicines: reef organisms produce a wide range of chemical defences, and compounds derived from sponges, soft corals and other reef invertebrates have been investigated for and used in drugs, including antiviral and anticancer agents and painkillers.

Reef erosion means the loss of living coral and of reef structure, and the syllabus gives five causes. pH change - ocean acidification - lowers the concentration of carbonate ions in the water, so corals calcify more slowly and their skeletons begin to dissolve, which makes the whole reef framework weaker. Temperature change causes bleaching: above the coral's tolerance the polyp expels its zooxanthellae, so the colony turns white, loses most of its energy supply and starves if the heat lasts. Predation by the crown-of-thorns starfish, Acanthaster planci, which eats the living tissue and can strip a reef when its populations outbreak, and by parrotfish and other browsers, removes coral faster than it can regrow. Physical damage from tropical cyclones, boat anchors, divers, dragging fishing gear and destructive fishing breaks the branches and overturns the colonies. Sediment washed off cleared land or dumped from dredging settles on the polyps, blocks the light and forces the coral to spend energy cleaning itself, and the runoff carries nutrients that let algae overgrow the coral.

The effects run together: loss of live coral means loss of the three-dimensional structure, and with it the fish and invertebrates that depend on it, so biodiversity falls; the fishery and the tourism income fall with it; and because a dead reef no longer absorbs wave energy, the coast behind it erodes and storm damage on land increases. A bleached reef can recover if the water cools quickly and larvae arrive from elsewhere, but a reef that is repeatedly bleached, buried in silt or eaten by starfish shifts permanently to a covering of algae.

An artificial reef is a structure placed on the seabed to act as a hard substrate on which reef organisms can settle. Purpose-built concrete modules and specially designed units are used, as are limestone boulders and cleaned ships and other structures, and coral fragments are sometimes attached to them. The benefits are that they provide hard surface where the bottom is otherwise sand or mud, they create structure for fish and invertebrates, they can stabilise sediment, they can support dive tourism and they can be placed to take pressure off a damaged natural reef. The limitations are equally examinable: they do not fix the cause of the erosion, so a coral transplanted onto a module in water that is too warm or too turbid will also bleach or suffocate; they can attract fish and concentrate fishing effort on them; some materials leach pollutants or break down; and a structure placed in the wrong place can simply be buried or swept away.

The rocky shore: zones, the tide, and the shift from abiotic to biotic control

A rocky shore is divided into zones by how long each one is out of the water during the tidal cycle. At the top, the splash zone is wetted only by spray and by the highest spring tides, so it is damp rather than submerged. The upper shore is covered only at high tide, and on a neap tide may hardly be covered at all. The middle shore is covered and uncovered twice a day by every tide. The lower shore is exposed only briefly at low water, and the subtidal zone below it is permanently submerged. The pattern is not a tidy ladder of equal bands - the exact heights depend on the tidal range and on how exposed the shore is to waves - but the order never changes.

The abiotic factors change across those zones during a single tidal cycle, which is the point most answers miss. On the upper shore, low tide means desiccation: the organism loses water to the air, and the longer the emersion the more it loses. It also means a large temperature range, because rock in the sun heats far above water temperature while at night it can fall close to freezing, and salinity swings, because water evaporating from a pool concentrates the salt while rain dilutes it. Wave action is strongest low on the shore and on an exposed headland, and it brings oxygen and food but also threatens to tear organisms off the rock. Light is at its maximum when the rock is exposed, which is a problem for algae that would dry out and an opportunity for the ones that can tolerate it. In pools cut off by the tide, oxygen falls overnight as respiration continues without photosynthesis, and pH swings with it.

The classic examinable pattern is that abiotic factors control the upper shore and biotic factors control the lower shore. High up, only the organisms that can survive drying, heating and dilution live there at all, and their upper limit is set by physical tolerance rather than by their neighbours - the barnacles on the top of the shore are not there because they prefer it but because nothing else can hold that ground against the physical stress. Lower down, conditions are mild and stable, and space becomes the limiting resource: competition for rock surface between barnacles, mussels, algae and sponges, and predation by dog whelks, starfish, crabs and shore birds, decide who actually occupies the space. A predator or a dominant competitor can therefore set the lower limit of a species, while its upper limit is set by desiccation - which is why removing a predator experimentally allows its prey to spread downwards, and why the same species sits higher on a sheltered shore than on an exposed one.

The adaptations follow from the stresses, and the syllabus wants them with named organisms. Against desiccation, the limpet Patella vulgata has a conical shell that sheds water, a large muscular foot that clamps it down to seal in a film of water, and a homing behaviour that returns it to the same scar in the rock before each low tide; barnacles such as Semibalanus balanoides close calcareous plates over the body and are cemented in place; the wrack Fucus vesiculosus has a thick, mucilage-coated frond that resists drying, lies flat to shade itself at low tide, and uses air bladders to stand up towards the light when submerged. Against wave action the same limpet's low profile and clamped foot reduce drag, mussels anchor with byssus threads, kelp attaches with a holdfast rather than roots, and anemones such as Actinia equina withdraw their tentacles and contract into damp crevices. Mobile animals behave their way out of trouble instead: periwinkles seal the shell with an operculum, and crabs and small fish move down the shore or into pools as the tide falls.

• Patella vulgata (limpet): conical shell, large muscular foot clamped to the rock, homing to a scar - seals in water and resists both drying and wave drag.
• Semibalanus balanoides (barnacle): cemented to the rock, plates close over the body to retain water; feeds by filtering with feathery cirri when submerged.
• Fucus vesiculosus (bladder wrack): leathery mucilage-covered frond that resists drying, air bladders for buoyancy, holdfast for attachment.
• Nucella lapillus (dog whelk): drills through barnacle and mussel shells with its radula and a softening secretion; tolerates exposure by retreating into crevices.
• Actinia equina (beadlet anemone): retracts its tentacles and contracts when exposed, lives in damp crevices and pools on the lower shore.
• Laminaria (kelp): holdfast instead of roots, flexible stipe, restricted to the lower shore and subtidal where it is rarely exposed.

The sandy shore: an unstable, porous substrate with low biodiversity

A sandy shore is an ecosystem built on a substrate that will not hold still. The substrate is unstable and shifting: waves and currents move the sand with every tide, so anything that cemented itself to the surface would be scoured away or buried. It is also porous, so water drains through it quickly, and that single property explains most of the biology. Coarse sand has large particles and large pore spaces, so it is highly permeable - water passes through fast, draining the beach at low tide and pulling oxygen down into the sediment, but also drying the surface layers. Fine sand and silt have small pore spaces and are much less permeable: water is held, the sediment stays waterlogged, and oxygen is used up by bacteria faster than it can be replaced, so the layer below the surface becomes anoxic. This is exactly what the practical investigation of particle size and permeability shows, and it is why the animals of fine sand live close to the surface or keep a connection to it, while those of coarse sand can live deeper.

Biodiversity is relatively low for several reasons that work together. There is no hard surface for attachment, so the whole community of seaweeds, barnacles, mussels and anemones that dominates a rocky shore is missing. The surface is abrasive and mobile, so delicate organisms are damaged. Water drains away at low tide, so the surface dries and heats and cools far more than rock does, and the variation in temperature and salinity through the tidal cycle is greater than on a rocky shore. Oxygen is limited below the surface in fine sediment, and food is thin, because the sand itself contains little organic matter compared with the silt of an estuary. Only organisms with a way of burrowing, or of moving with the water, can live there - and because so few species can do it, the ones that can are often present in very large numbers. Low species diversity therefore does not mean low biomass: a sandy beach can hold a great many lugworms and cockles of very few species.

Biodiversity is relatively low for reasons that work together. There is no hard surface for attachment, so the seaweeds, barnacles, mussels and anemones of a rocky shore are absent; the surface is abrasive and mobile, so delicate organisms are damaged; water drains away at low tide, so the surface dries, heats and cools and varies more in temperature and salinity than rock does; and below the surface of fine sediment oxygen is used up faster than it is replaced. Food is also thin, because sand holds little organic matter compared with estuarine silt. Only organisms that can burrow, or that keep a connection to the surface, can live there - and because so few species can, the ones that can are often present in very large numbers, so low diversity does not mean low biomass.

The adapted organisms are therefore all burrowers or rapid movers. The lugworm Arenicola marina lives in a permanent mucus-lined U-shaped burrow, swallows sand and passes the digested remains out as a coiled cast, and extends a muscular, eversible proboscis to the surface to feed, so it is protected from abrasion and drying and irrigates its own burrow. The cockle Cerastoderma edule pulls itself down with a muscular foot and keeps short siphons at the surface to filter feed. Razor shells such as Ensis have a smooth, streamlined shell and a powerful foot for rapid vertical burrowing, with long siphons that stay in contact with the surface. Burrowing amphipods and isopods swim in the swash and dig into wet sand between tides, and the heart urchin Echinocardium cordatum lives deep in the sand, kept in contact with the surface by a funnel and moved by its spines.

• Unstable, shifting substrate: sand moves with every tide, scouring or burying anything attached at the surface.
• Porous: water drains through quickly at low tide, so the surface dries and the sediment drains and refills with each tidal cycle.
• Particle size controls permeability: coarse sand drains fast and holds oxygen; fine sand and silt drain slowly, stay waterlogged and become anoxic below the surface.
• No hard substrate: seaweeds, barnacles and mussels cannot attach, so an entire group of organisms is absent.
• Arenicola marina (lugworm): mucus-lined U-shaped burrow, eversible proboscis for surface feeding, sediment swallowed; casts mark its position.
• Cerastoderma edule (cockle): muscular foot to burrow, short siphons to draw water in while buried, ribbed shell resists crushing.
• Ensis (razor shell): smooth narrow shell and powerful foot for rapid vertical burrowing, long siphons kept at the surface.
• Echinocardium cordatum (heart urchin): lives deep in the sand, in contact with the surface through a funnel, moved by its spines.

The mangrove forest: a tidal forest on muddy tropical coasts

A mangrove forest is a tidal ecosystem in the littoral zone of some tropical and subtropical coasts, dominated by salt-tolerant trees and shrubs growing in muddy sediment that is flooded and drained by every tide. It is not a single species but a community: the trees, the algae on their roots and in the mud, the crabs, snails, shrimps and fish that live among the roots, the birds that nest in the canopy and the plankton and juvenile fish in the creeks. The different tree species occupy different levels of the shore - species of Rhizophora, with their arching prop roots, usually nearest the water, and Avicennia species, with vertical pneumatophores pushing up through the mud, further back - so the forest is zoned by how much flooding and how little oxygen each species can tolerate.

The conditions required for a mangrove forest are a combination of climate and coast. The climate must be tropical or subtropical and frost-free, with water warm enough for the trees to grow all year, because mangroves cannot survive frost. The coast must be sheltered from strong wave action - estuaries, lagoons, deltas and leeward shores - because the seedlings cannot establish where waves scour the mud, and their roots cannot resist heavy surf. The sediment must be fine and muddy, so that it holds water and nutrients and the roots can penetrate it, and that mud is usually waterlogged and low in oxygen. There must be regular tidal flooding by salt water, to which the trees are adapted, together with a supply of fresh water and sediment from the land. Take away the shelter, the mud or the tidal water and the forest cannot form.

Rhizophora mangle, the red mangrove, shows three adaptations that the syllabus names. Its prop roots grow out from the trunk and lower branches and arch down into the mud, forming a tripod that braces the tree in a soft, unstable substrate where an ordinary root plate could not hold it upright; their surfaces carry lenticels, so oxygen from the air can be taken in and supplied to the roots, which is essential because the waterlogged mud contains very little. Salt exclusion happens at the root: the root membranes act as a filter that keeps most sodium and chloride ions out, so the tree can take up water from saline soil, and the small amount of salt that does get through is stored in older leaves that are then shed. Reproduction is viviparous: the seed germinates while it is still attached to the parent tree and grows into a long, cigar-shaped propagule, which eventually drops, floats, survives for weeks in salt water and then roots where it strands in the mud.

The ecological importance of the forest comes from the physical structure of the roots. They form a nursery: the tangle of roots and the muddy water beneath them provide refuge from larger predators, so juvenile fish, prawns, crabs and molluscs grow there before moving out to the reef or the open sea, which is why mangrove loss shows up as a fall in catches elsewhere. The roots also trap sediment: they slow the water moving through the forest, so particles settle out and are held, which stabilises the coastline and builds it up instead of letting it erode. In doing so the forest keeps sediment off the reefs and seagrass beds offshore, because sediment that would otherwise be carried out and smother corals or shade seagrasses is intercepted and held in the mangrove mud.

Its value to people runs along the same lines. The forest is coastal protection, because the roots and trunks absorb the energy of waves and storm surges and hold the shoreline together, which matters most where low-lying land behind it is densely populated. It is a food source, because the fish, prawns, crabs and molluscs reared among the roots are caught by coastal communities, and it supplies timber for construction and poles and fuel in the form of firewood and charcoal. It supports tourism, from boat trips and boardwalks to birdwatching, and it adds biodiversity that the surrounding mudflat or cleared pond does not have.

The threats are equally specific. Temperature change warms the water and raises sea level, so the trees are stressed and the shore they occupy may be drowned faster than they can move inland. Over-harvesting for timber and fuel removes the trees faster than they regenerate. Storm damage from cyclones strips canopy and breaks trunks, and a forest already weakened by other pressures recovers slowly. Change in coastal land use is the biggest of all: clearance for aquaculture ponds, agriculture, urban development, ports and tourist resorts removes the forest outright, and once the roots are gone the sediment that was held is released, the coast erodes and the silt is carried out towards the reef.