Ecosystems are systems, not sealed boxes

An ecosystem is a biological system that includes all the organisms in a defined area and the abiotic environment with which they interact. A pond, a rotting log, a coral reef or a grassland can count as an ecosystem, as long as we’re clear about where we draw the boundary.

A system is a set of interacting components that together behave as a whole. In an ecosystem, those components include organisms, air, water, soil, rock, light, dissolved ions and organic matter.

An open system is a system that allows both matter and energy to cross its boundary. Ecosystems fit this model: sunlight enters, heat leaves, organisms migrate, gases diffuse, water flows, minerals are washed in or out, and organic matter can move across the boundary.

A closed system is a system that allows energy to cross its boundary but does not allow matter to enter or leave. Perfectly closed ecosystems are rare in nature, but the idea helps separate two points students often mix up: energy can pass through systems, whereas matter can be retained and recycled.

This is the first big idea of the topic: ecosystems need a continuous energy input, but atoms of matter can be used again and again.

Sunlight usually starts the energy flow

In most ecosystems, sunlight is the original energy source. Photosynthesis is a metabolic process that uses light energy to synthesize carbon compounds from carbon dioxide. Plants, algae and cyanobacteria trap light energy, then store some of it as chemical energy in carbon compounds such as sugars.

A producer is an autotrophic organism that forms the first trophic level in a food chain by making carbon compounds available to other organisms. After producers have fixed energy into organic molecules, that chemical energy can move to the organisms that feed on them.

Sunlight that reaches the surface is not necessarily sunlight captured by producers. A desert may receive intense light but capture little of it because water limits plant growth. In a forest, less light may reach ground level because the canopy absorbs much of it, yet the ecosystem can still capture a great deal of energy overall because producer biomass is high.

In aquatic ecosystems, light penetration limits photosynthesis. Water absorbs and scatters light, while suspended particles or plankton make the water more turbid. Open ocean water may allow photosynthesis to roughly 200 m, whereas murky coastal water may have much shallower light penetration. Below the light zone, ecosystems cannot rely directly on photosynthesis in that location.

There are important exceptions. Some cave ecosystems receive organic matter washed in from outside, such as dead leaves carried by streams. Others, including isolated cave systems and deep-ocean ecosystems below light penetration, depend on chemical energy rather than sunlight. In these ecosystems, producers use energy released from inorganic chemical reactions.

Nature of science: useful generalizations

A scientific law is a general principle that describes a repeated pattern in nature and can be used to make predictions. A law does not, by itself, explain the mechanism; theories and models do that work.

Useful generalizations in science come from many observations, apply across a wide range of cases, stay simple enough to use, and make testable predictions. “Energy is conserved” is useful here: plants transform light energy into chemical energy, but they do not create energy. “Energy transformations are not perfectly efficient” matters just as much: some energy becomes dispersed as heat whenever energy is transferred or transformed.

So the guiding question is already taking shape: matter can cycle because atoms remain atoms, but energy becomes dispersed as heat and must be replaced, usually by sunlight.

Chemical energy passes when organisms feed

A food chain is a sequence of organisms where each organism feeds on the one before it in the sequence. It’s a deliberately simplified model: useful, but never the whole story.

In most food chains, the first organism is a producer. It has already converted light energy into chemical energy in its carbon compounds. When a herbivore eats the producer, some of that chemical energy moves into the consumer’s body. When a carnivore eats the herbivore, some passes on again.

A consumer is a heterotrophic organism that obtains organic matter by ingesting other organisms or parts of organisms. In food chains, primary consumers feed on producers, secondary consumers feed on primary consumers, and tertiary consumers feed on secondary consumers.

Food-chain arrows show the direction in which energy and biomass transfer. The detail matters: the arrow points from food to feeder, not from predator to prey. Read an arrow as “is eaten by” or “passes energy to”.

For example, a local version might be: grass → grasshopper → lizard → kestrel. Chemical energy in grass biomass passes to the grasshopper as it feeds, then to the lizard, then to the bird. At every step, much of the energy does not continue along the chain, so food chains are short.

Food webs are better models of real communities

A community is all the populations of different species living and interacting in the same area. Real communities rarely fit into neat single chains: one animal may eat several foods, and the same prey may be eaten by several predators.

A food web is a model that represents multiple feeding relationships in a community by linking many food chains together. It’s still a model, so it leaves out details such as seasonal changes, age of organisms, parasites and exact quantities eaten, but it does show the web-like structure of feeding.

To construct one:

• identify the organisms in the community;
• find reliable evidence of what each organism feeds on;
• place producers near the bottom where possible;
• add consumers above them, grouping similar trophic positions where practical;
• draw arrows from food to feeder, showing the direction of energy and biomass transfer.

Local communities work well because the model then has real meaning. Invertebrates can be collected using a sweep net for flying insects or by using a beating stick and beating sheet under vegetation to dislodge small animals. Identification guides or reliable biodiversity databases can then help connect the organisms with their feeding habits. The biology starts when the names become interactions.

Do not force every organism into one tidy row. Omnivores and generalist predators may occupy different trophic levels in different food chains, so their position in a web is often approximate.

Dead organic matter is still energy-rich

A decomposer is an organism that gets energy and nutrients by breaking down dead organic matter and wastes. In most ecosystems, the main decomposers are bacteria and fungi.

Decomposers use chemical energy stored in carbon compounds from organic matter. That organic matter can be whole dead organisms, dead parts of organisms such as fallen leaves or shed skin, or faeces. Faeces still contain chemical energy because animals do not digest and absorb all the food they eat.

A saprotroph is a decomposer that digests dead organic matter externally by secreting enzymes and then absorbing the soluble products. Picture fungal hyphae: they grow through dead material, release digestive enzymes into it, and absorb sugars, amino acids and other small molecules.

A detritus feeder is an animal that ingests dead organic matter and digests it internally. Earthworms, woodlice and many insect larvae feed this way. Decomposers and detritus feeders are usually left out of simple grazing food chains, but in energy terms they matter a lot because they receive energy from material that did not pass to the next consumer.

Without decomposers, dead matter would build up, and chemical elements would stay locked in bodies, leaves, wood and faeces. I think of decomposers as the recycling department of the ecosystem — not glamorous, but absolutely non-negotiable.

Autotrophs build carbon compounds from inorganic materials

An autotroph synthesizes its own carbon compounds from simple inorganic substances, using an external energy source. Its carbon source is usually carbon dioxide, or hydrogen carbonate ions in water.

This does not mean “making food from soil”. Autotrophs take elements from simple inorganic sources: carbon dioxide or hydrogen carbonate for carbon, nitrate or ammonium for nitrogen, phosphate for phosphorus, and other mineral ions for other elements.

They need energy because carbon fixation and the anabolic reactions that build macromolecules are not energetically free. Carbon fixation is a metabolic process that converts inorganic carbon into organic carbon compounds. Anabolic reactions are metabolic reactions that build larger molecules from smaller molecules, increasing chemical complexity and usually requiring energy.

Fixed carbon is used to make sugars, amino acids, fatty acids, nucleotides and other compounds. Those smaller building blocks can then be joined into polysaccharides, proteins, lipids and nucleic acids. This is where producer biomass begins.

The external energy source may be light, as in plants and algae, or energy from chemical reactions, as in some bacteria and archaea.

Two routes into autotrophy

A photoautotroph is an autotroph that uses light as its external energy source to synthesize carbon compounds from inorganic substances. Plants, algae and cyanobacteria are photoautotrophs.

A chemoautotroph is an autotroph that uses energy released by inorganic chemical reactions to synthesize carbon compounds from inorganic substances. Many chemoautotrophs are prokaryotes.

The useful reactions are often oxidation reactions. An oxidation reaction is a chemical reaction in which a substance loses electrons. In living systems, oxidation can release energy, which can then be passed to electron carriers and used to make ATP or reduced coenzymes for carbon fixation.

Iron-oxidizing bacteria are the required example. They get energy by oxidizing iron(II) ions to iron(III) ions. That released energy helps generate ATP and reducing power, and these are then used to fix carbon dioxide into organic compounds. These bacteria can live in acidic, iron-rich environments where sunlight is not the energy source.

The key comparison is simple: photoautotrophs use light; chemoautotrophs use energy from oxidation of inorganic substances. Both are autotrophs, because both make their own carbon compounds from inorganic carbon.

Heterotrophs remodel other organisms’ carbon compounds

A heterotroph is an organism that obtains carbon compounds from other organisms and uses them to synthesize the carbon compounds it needs. Animals, fungi and many bacteria are heterotrophs.

That wording is tighter than simply saying “heterotrophs eat food”. What matters is the sequence: complex carbon compounds from another organism are digested, absorbed and then rebuilt. Proteins can be digested into amino acids, nucleic acids into nucleotides, and polysaccharides into monosaccharides. The heterotroph uses these smaller molecules to build its own proteins, nucleic acids, glycogen, lipids and other compounds.

Digestion is a process that breaks large insoluble molecules into smaller soluble molecules. It may happen internally, as in an animal gut or a food vacuole, or externally, as in saprotrophic fungi releasing enzymes onto dead matter.

Assimilation is the incorporation of absorbed substances into the tissues or cells of an organism. Absorption moves molecules into the body or cell; assimilation makes them part of the organism.

Large polymers usually need digestion before they can cross membranes. Internal and external digestion may look different, but both do the same job: turning another organism’s macromolecules into usable building blocks.

All organisms respire carbon compounds

Cell respiration is a metabolic process in which cells release energy from carbon compounds and transfer some of that energy to ATP. Autotrophs respire, and so do heterotrophs.

Students sometimes assume plants photosynthesize instead of respiring, so this is worth making clear. Plants photosynthesize in light, but their cells respire day and night. They need ATP for active transport, synthesis of macromolecules, movement of materials inside cells, cell division and many other processes.

During respiration, cells oxidize carbon compounds such as sugars and lipids. These carbon compounds lose electrons as they are converted into carbon dioxide and water. The energy released phosphorylates ADP to ATP.

An ATP molecule is a nucleotide-derived energy carrier that supplies energy to cellular processes when it is hydrolysed. Biological work depends on this energy transfer: chemical energy in respiratory substrates becomes a short-term cellular currency, then powers active transport, biosynthesis, movement and temperature regulation in some animals.

Students are not expected to learn photoheterotrophs here; keep the categories in this topic to autotrophs and heterotrophs.

Trophic level means feeding position

A trophic level is the feeding position an organism has in a food chain, based on how it gets energy and carbon compounds.

Use these terms carefully:

• A producer is an autotroph at the first trophic level that makes carbon compounds available to other organisms.
• A primary consumer is a consumer that feeds on producers.
• A secondary consumer is a consumer that feeds on primary consumers.
• A tertiary consumer is a consumer that feeds on secondary consumers.

Many organisms don’t fit into one tidy trophic level. An omnivorous bird may eat seeds, insects and small vertebrates, so it could be a primary consumer in one food chain, a secondary consumer in another, and possibly a tertiary consumer in a third. Classify the organism from the particular feeding relationship, not from its name alone.

Energy pyramids show transfer and loss

An energy pyramid is a bar-chart model showing the energy available to each trophic level per unit area per unit time. Draw it as stepped horizontal bars, not as a smooth triangle. Producers sit at the bottom, with primary consumers above them, followed by secondary consumers and tertiary consumers.

Use energy per area per time as the units, for example kJ m⁻² yr⁻¹. If you are building a pyramid from research data for a specific ecosystem, keep the same units for every trophic level, choose a scale that makes comparison possible, and make the bar widths proportional to the data when the figure is intended to be quantitative.

Energy pyramids almost always get narrower towards the top because energy is lost between trophic levels. That makes them useful for showing both energy transfer and energy loss in food chains.

In some ecosystem energy diagrams, decomposers may be shown separately. They receive energy from dead organisms, dead parts and faeces from several trophic levels. Decomposers play an important role in energy transformations, but they are not usually treated as one step in a simple grazing food chain.

Why less energy reaches each next level

Less energy is available at each step in a food chain because only some of the energy in one trophic level is converted into biomass in the next.

There are three main causes.

First, consumption is incomplete. Consumers rarely eat every part of every organism in the trophic level below. Roots, bones, hair, shells, bark and dead uneaten bodies may go to decomposers or detritus feeders instead.

Second, digestion is incomplete. Some ingested material is not digested or absorbed, so it is egested as faeces. The chemical energy in faeces is still real energy, but it has left the grazing food chain and can support decomposers and detritus feeders instead.

Third, organisms use cell respiration. They oxidize carbon compounds to release energy for ATP production. The carbon dioxide and water produced by respiration cannot pass chemical energy to the next trophic level as food.

This does not happen because a gram of carnivore tissue contains less energy than a gram of herbivore tissue. Energy content per unit mass does not decrease as you move up trophic levels. What changes is the total biomass available at each higher level: there is less of it.

The often-quoted “10% transfer” is a rough rule of thumb, not a law. Transfer efficiency varies between ecosystems and food chains, but the pattern is consistent: much less energy is available at each successive trophic level.

Energy flows because heat cannot be recycled biologically

Autotrophs and heterotrophs both convert chemical energy into heat. During cell respiration, some of the energy released by oxidation of carbon compounds is transferred to ATP, but not all of it. Some passes straight into the surroundings as heat. Later, when ATP drives cellular processes such as muscle contraction, active transport or biosynthesis, more heat is produced.

This follows from the fact that energy transfers are not 100% efficient. Heat can warm bodies and surroundings, but organisms cannot collect that heat and rebuild it into chemical energy for a food chain. Over time, heat leaves the ecosystem, passes to the wider environment and ultimately escapes to space.

That is why energy cannot be recycled in ecosystems. It flows through them: sunlight or chemical energy enters, chemical energy moves through food chains and decomposer pathways, and heat leaves.

Combustion gives a practical estimate of the chemical energy stored in biomass. A known mass of dry biomass is burned, and the heat released warms a known mass of water. The calculation can be written as Eᵦ = (m𝓌cΔT) / mᵦ, where Eᵦ is energy content of biomass (J kg⁻¹), m𝓌 is mass of water heated (kg), c is the specific heat capacity of water (J kg⁻¹ K⁻¹), ΔT is the temperature rise of the water (K), and mᵦ is the mass of biomass burned (kg). In school experiments, the final answer is often converted to J g⁻¹ or kJ g⁻¹.

Simple calorimetry loses heat to the air and apparatus. Combustion may also be incomplete, so the method usually underestimates the true energy content.

Food chains are short because energy runs out

Large amounts of energy are lost between trophic levels, so an ecosystem can only support a limited number of levels. After just a few transfers, too little energy is still flowing to maintain another population of consumers.

At each successive stage, there are usually fewer organisms, smaller organisms, or less total biomass. The energy content per unit mass is not the issue here; the total amount of food biomass available is.

This is why apex predators often need large territories or have low population densities. They are not necessarily inefficient animals. They just live at the end of a chain where little total energy remains available.

Some food chains have only two stages, such as a large herbivore feeding on plants with little predation. Others may have four or five stages, especially in aquatic systems with small planktonic producers and consumers. Indefinite chains, though, do not occur.

Primary production is producer biomass gain

Biomass is the total mass of living or recently living organic material in a specified organism, trophic level or area. Here, biomass mostly matters as stored carbon compounds.

Production means carbon compounds build up in biomass through growth and reproduction. Biomass increases when organisms get larger, and when reproduction produces more growing organisms.

Autotrophs carry out Primary production when carbon compounds accumulate in their biomass. They fix carbon dioxide or hydrogen carbonate into organic molecules, then build these into plant, algal or bacterial biomass.

Gross primary production is the total amount of carbon compounds produced by autotrophs through photosynthesis or chemosynthesis in a given area and time. Net primary production is the amount of producer biomass left after autotrophs have used some carbon compounds in respiration. That remaining portion is available for growth, reproduction and consumption by other organisms.

Primary production is measured as mass of carbon per unit area per unit time, usually g C m⁻² yr⁻¹. Biomes vary a lot in primary production because they differ in light, temperature, water availability, nutrient availability and length of growing season. Tropical forests can accumulate biomass rapidly; deserts and tundra generally accumulate biomass slowly.

This connects directly to rising carbon dioxide. If photosynthesis increases plant biomass, carbon has moved from an atmospheric or dissolved inorganic pool into an organic biomass pool.

Secondary production is heterotroph biomass gain

Secondary production is the accumulation of carbon compounds in biomass by heterotrophs. It happens when heterotrophs assimilate digested food molecules into their own tissues and use them to reproduce.

A caterpillar turning leaf amino acids into caterpillar proteins is secondary production. So is a fish converting prey molecules into muscle. A fungus absorbing products of external digestion and growing new hyphae counts as secondary production too.

In an ecosystem, secondary production is lower than primary production because heterotrophs lose biomass through respiration. Carbon compounds that could have been built into biomass are oxidized to carbon dioxide and water. That releases energy for ATP production, but it leaves less organic carbon retained in the body.

Production therefore usually declines from primary consumers to secondary consumers and beyond. The same idea explains why plant-based food production can feed more people per hectare than meat production: eating producers usually has fewer energy-loss steps than eating higher-level consumers.

Carbon cycle diagrams show pools and fluxes

A carbon pool is a store of carbon in a particular form or place. Examples include carbon dioxide in the atmosphere, dissolved carbon dioxide and hydrogen carbonate in water, biomass in producers, biomass in consumers, dead organic matter, peat and fossil fuels.

A flux is carbon moving from one pool to another. On carbon cycle diagrams, pools are usually drawn as boxes, with fluxes shown as labelled arrows.

You need to be able to show three biological fluxes: photosynthesis, feeding and respiration. Photosynthesis moves carbon from atmospheric or dissolved carbon dioxide into producer biomass. Feeding moves organic carbon from producers to consumers, and from consumers to other consumers. Respiration moves carbon from organisms back to carbon dioxide in air or water.

A good carbon cycle diagram isn’t an art competition. It’s a clear model. Label each pool with the form or location in which carbon is stored, and label each arrow with the process that moves the carbon. In terrestrial ecosystems, include atmospheric carbon dioxide. In aquatic ecosystems, include dissolved carbon dioxide and hydrogen carbonate ions as inorganic carbon pools.

Death, egestion and decomposition may also be included, as they show how carbon enters dead organic matter and returns to carbon dioxide through decomposer respiration.

Whether an ecosystem stores or releases carbon depends on the balance

A carbon sink is a system or pool that has a net uptake of carbon over a specified time. An ecosystem is a carbon sink when photosynthesis removes more carbon dioxide than respiration releases.

A carbon source is a system or pool that has a net release of carbon over a specified time. An ecosystem is a carbon source when respiration releases more carbon dioxide than photosynthesis removes.

That balance can shift with season, disturbance and time scale. A growing forest may act as a sink as biomass and soil carbon accumulate. During a fire, the same forest becomes a source because combustion releases carbon dioxide rapidly.

Decomposition matters. In most ecosystems, saprotrophs break down dead organic matter and respire, releasing carbon dioxide. Where conditions are waterlogged, acidic or anaerobic, decomposition can slow down, so peat can accumulate. Over long times, this sequestration removes carbon from the active cycle.

Sequestration is the long-term removal and storage of carbon from the active carbon cycle. Peat formation, soil carbon accumulation and fossil fuel formation are examples on very different time scales.

Combustion moves stored carbon quickly to the atmosphere

Combustion is a chemical reaction in which a substance burns in oxygen, releasing energy and producing oxides such as carbon dioxide. When biomass, peat, coal, oil or natural gas burn, the carbon stored in them is oxidized to carbon dioxide and released to the atmosphere.

These carbon stores did not all form in the same way, or over the same timescale. Biomass may have formed recently through photosynthesis. Peat mostly forms where dead plant material decomposes incompletely in waterlogged, acidic, low-oxygen conditions. Coal formed mainly from ancient plant material that was buried and altered over geological time. Oil and natural gas formed from buried organic matter subjected to heat and pressure and then trapped in rocks.

Comparison of major carbon stores and how combustion transfers their carbon to atmospheric carbon dioxide.

Lightning strikes can start combustion naturally, especially during drought when vegetation is dry. Natural fires have always been part of some ecosystems. The major recent change is the rate: human activity has greatly increased combustion of fossil fuels and biomass, especially since industrialization.

Burning fossil fuels matters because it releases carbon that had been sequestered for millions of years. Peat burning is significant too, since peat can store carbon accumulated over thousands of years and release it in a much shorter time when drained or burned.

One direct consequence of rising carbon dioxide is that more combustion adds carbon dioxide to the atmosphere faster than natural sinks can remove it. Indirect consequences are developed in climate change, but the carbon-cycle link starts here.

Reading the Keeling Curve

The Keeling Curve is a long-term record of atmospheric carbon dioxide concentration. It began at Mauna Loa Observatory and shows seasonal fluctuations sitting on top of a long-term increase.

There are two features to analyse.

Start with the annual fluctuation. Carbon dioxide concentration rises during part of the year, then falls during another part. The main cause is the seasonal imbalance between photosynthesis and respiration on land. During the northern hemisphere growing season, land plants remove large amounts of carbon dioxide by photosynthesis, so atmospheric concentration falls. In autumn and winter, photosynthesis decreases while respiration and decomposition continue, so concentration rises again. The northern hemisphere gives the stronger seasonal signal because it has more land vegetation than the southern hemisphere.

The second feature is the long-term trend. The annual fall does not fully cancel the annual rise, so the baseline increases over decades. Combustion of fossil fuels is the main cause, with land-use change such as deforestation also contributing. Photosynthesis and ocean uptake remove some carbon dioxide, but they don’t remove enough to balance human emissions.

Remote monitoring stations are useful because they avoid strong local pollution signals from cities and industry. Using multiple stations also matters, since carbon dioxide mixing, hemispheric differences, vegetation patterns and local conditions can change the size and timing of fluctuations.

Database work can test explanations for differences among monitoring stations. For example, students can compare the size of the annual carbon dioxide fluctuation with nearby land mass, forest cover, latitude or seasonal temperature. That is good ecological data use: propose a relationship, gather comparable data, and look for a pattern instead of relying on one graph alone.

Autotrophs and heterotrophs depend on each other at huge scale

Aerobic respiration is cell respiration that uses oxygen as the final electron acceptor, so cells can produce ATP efficiently from carbon compounds. It depends on atmospheric oxygen.

Photosynthesis maintains atmospheric oxygen. In oxygenic photosynthesis, water is split and oxygen is released. Without photosynthetic organisms, oxygen would not stay available in the atmosphere at the concentration aerobic organisms need.

So heterotrophs depend on photosynthesizing autotrophs for oxygen. That dependence is bigger than a food chain; it’s a global atmospheric link.

It also runs the other way. Photosynthesis requires carbon dioxide. Respiration by autotrophs, heterotrophs and decomposers releases carbon dioxide back to the atmosphere or water. If carbon dioxide becomes limiting, photosynthesis can slow down.

The yearly fluxes are enormous. Terrestrial ecosystems fix and release huge quantities of carbon each year through photosynthesis and respiration. Even when the two fluxes are nearly balanced, the size of the exchange shows a major interaction between autotrophs and heterotrophs.

Energy transformation makes these biological processes possible: light energy drives photosynthesis, chemical energy in carbon compounds drives respiration, and ATP from respiration powers cellular work.