Ecosystems are systems, not sealed boxes

An ecosystem is a biological system made up of all the organisms in a defined area, together with the abiotic environment they interact with. A pond, a rotting log, a coral reef and a grassland can all be treated as ecosystems, as long as we are clear about where the boundary is drawn.

A system is a set of interacting components that behave together 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 lets both matter and energy cross its boundary. Ecosystems are open systems: sunlight enters, heat leaves, organisms migrate, gases diffuse, water flows, minerals are washed in or out, and organic matter can be carried across the boundary.

A closed system is a system that lets energy cross its boundary but does not let matter enter or leave. Perfectly closed ecosystems are rare in nature, but the idea helps separate two things students often blur together: energy passes through systems, while matter can be retained and recycled.

Here’s 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 provides the first input of energy. Photosynthesis is a metabolic process that uses light energy to synthesize carbon compounds from carbon dioxide. Plants, algae and cyanobacteria trap light energy and 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 fix energy into organic molecules, organisms that feed on them can receive that chemical energy.

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

In aquatic ecosystems, photosynthesis depends on how far light penetrates. Water absorbs and scatters light, and 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 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 explain the mechanism by itself; theories and models do that.

Scientists build useful generalizations from many observations. They apply across a wide range of cases, stay simple enough to use, and make testable predictions. “Energy is conserved” works well 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.

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 in which each organism feeds on the previous organism 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. If a carnivore then 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 of transfer of energy and biomass. The direction 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 $\to$ grasshopper $\to$ lizard $\to$ 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, which is why 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 don’t line up as 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. Even so, it shows 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.

Don’t 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, bacteria and fungi do most of this work.

Decomposers use the chemical energy stored in carbon compounds from organic matter. That organic matter can be whole dead organisms, dead parts such as fallen leaves or shed skin, or faeces. Faeces still contain chemical energy because an animal does not digest and absorb all the food it eats.

A saprotroph is a decomposer that secretes enzymes to digest dead organic matter outside its body, then absorbs the soluble products. Fungal hyphae are a useful picture here: 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 eats dead organic matter and digests it inside its body. Earthworms, woodlice and many insect larvae do this. Simple grazing food chains don’t usually include decomposers and detritus feeders, but they matter energetically because they take in energy from material that never passed to the next consumer.

Without decomposers, dead matter would pile up. Chemical elements would stay locked in bodies, leaves, wood and faeces. That’s why 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 is an organism that makes its own carbon compounds from simple inorganic substances, using an external energy source. Its carbon usually comes from carbon dioxide, or from hydrogen carbonate ions in water.

This is not “making food from soil”. Autotrophs take the elements they need 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 used to build macromolecules do not happen for free, energetically. 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.

Once carbon has been fixed, autotrophs use it to make sugars, amino acids, fatty acids, nucleotides and other compounds. These smaller building blocks can then be joined to form polysaccharides, proteins, lipids and nucleic acids. Producer biomass starts here.

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 reactions that supply the energy 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 may be passed to electron carriers and then 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, which 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 straightforward: photoautotrophs use light; chemoautotrophs use energy from oxidation of inorganic substances. Both count as autotrophs because they 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 more precise than saying “heterotrophs eat food”. What matters is the reshaping of carbon compounds: complex carbon compounds from another organism are digested, absorbed and rebuilt. Proteins may be digested into amino acids, nucleic acids into nucleotides, and polysaccharides into monosaccharides. The heterotroph then uses these smaller molecules to build its own proteins, nucleic acids, glycogen, lipids and other compounds.

Digestion

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

Assimilation

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 have to be digested before they can cross membranes. So internal and external digestion may look different, but they serve the same basic purpose: 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.

This is a common trap: plants don’t photosynthesize instead of respiring. In light, plants photosynthesize, but their cells still respire all the time, day and night. They need ATP for active transport, synthesis of macromolecules, moving 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 released energy 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 occupies 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.

Plenty of organisms don’t fit into one tidy trophic level. An omnivorous bird may eat seeds, insects and small vertebrates, so it can 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 specific feeding relationship, not just from its name.

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 with stepped horizontal bars, not as a smooth triangle. Producers sit at the bottom, with primary consumers, secondary consumers and tertiary consumers above them.

Use energy per area per time as the units, for example $kJ\ m^{-2}\ yr^{-1}$. When you build a pyramid from research data for a specific ecosystem, keep the units the same for every trophic level, choose a scale that makes comparison possible, and make the bar widths proportional to the data if the figure is meant to be quantitative.

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

Some ecosystem energy diagrams show decomposers separately. They receive energy from dead organisms, dead parts and faeces from several trophic levels, so they matter 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 successive stage in a food chain because only some of the energy in one trophic level is converted into biomass in the next trophic level.

There are three main causes.

First, incomplete consumption. 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, incomplete digestion. 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, cell respiration. Organisms 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 is not because a gram of carnivore tissue contains less energy than a gram of herbivore tissue. Energy content per unit mass does not fall as you move up trophic levels. What changes is the total biomass available: there is less of it at each higher level.

The often-quoted “10% transfer” is only a rough rule of thumb, not a law. Transfer efficiency varies between ecosystems and food chains, but the pattern is dependable: 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, oxidation of carbon compounds releases energy, but not all of it is transferred to ATP. Some energy goes straight to the surroundings as heat. More heat is produced later, when ATP is used for cellular processes such as muscle contraction, active transport or biosynthesis.

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

That is why energy cannot be recycled in ecosystems. It passes through: 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

In school experiments, the final answer is often converted to $J\ g^{-1}$ or $kJ\ g^{-1}$.

This simple calorimetry usually underestimates the true energy content because heat is lost to the air and apparatus, and combustion may be incomplete.

Food chains are short because energy runs out

Large amounts of energy are lost between trophic levels, so an ecosystem can support only a limited number of levels. After a few transfers, too little energy remains flowing through the chain to maintain another consumer population.

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

This is why apex predators often need large territories or exist at low population densities. They are not necessarily inefficient animals; they 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 have four or five stages, especially in aquatic systems with small planktonic producers and consumers. Indefinite chains 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 mainly matters as stored carbon compounds.

Production means carbon compounds accumulate in biomass through growth and reproduction. Biomass increases when organisms grow larger, and when reproduction adds more growing organisms.

Primary production is the accumulation of carbon compounds in biomass by autotrophs. Autotrophs do this by fixing carbon dioxide or hydrogen carbonate into organic molecules, then using these molecules to build 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 production 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 $g\ \text{C}\ \text{m}^{-2}\ \text{yr}^{-1}$. Biomes vary greatly in primary production because light, temperature, water availability, nutrient availability and length of growing season are not the same everywhere. Tropical forests can accumulate biomass rapidly; deserts and tundra generally accumulate biomass slowly.

This connects directly to rising carbon dioxide: when 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 take digested food molecules and build them into their own tissues, or use them to reproduce.

When a caterpillar turns leaf amino acids into caterpillar proteins, that 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.

Secondary production is lower than primary production in an ecosystem because heterotrophs lose biomass through respiration. Carbon compounds that might have become biomass are oxidized to carbon dioxide and water, releasing energy for ATP production and leaving less organic carbon in the body.

That is why production usually declines from primary consumers to secondary consumers and beyond. It also 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 usually appear as boxes, with labelled arrows showing the fluxes.

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 is not an art competition. It’s a clear model. Label each pool with what carbon is stored in, and label each arrow with the process that moves the carbon. For terrestrial ecosystems, include atmospheric carbon dioxide. For aquatic ecosystems, include dissolved carbon dioxide and hydrogen carbonate ions as inorganic carbon pools.

You can also show death, egestion and decomposition, since these explain 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 works as 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 works as a carbon source when respiration releases more carbon dioxide than photosynthesis removes.

That balance is not fixed. It can shift with season, disturbance and time scale. A growing forest can be a sink while 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, allowing peat to 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.

The age and formation of these carbon stores are not the same. 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.

Combustion can happen naturally after lightning strikes, especially during drought when vegetation is dry. Natural fires have always been part of some ecosystems. What has changed recently is the rate: human activity has greatly increased the 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 also significant, 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 this: 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, begun at Mauna Loa Observatory, with 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. In the northern hemisphere growing season, land plants photosynthesise and remove large amounts of carbon dioxide, so atmospheric concentration falls. In autumn and winter, photosynthesis decreases while respiration and decomposition continue, so concentration rises again. The northern hemisphere controls most of this seasonal signal because it has more land vegetation than the southern hemisphere.

Now look at the long-term trend. The annual fall does not fully cancel the annual rise, so the baseline climbs 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 help 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 annual carbon dioxide fluctuation size 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 rather than 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. That makes efficient ATP production from carbon compounds possible, and 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 in the atmosphere at the concentration aerobic organisms need.

So heterotrophs rely on photosynthesizing autotrophs for oxygen. It’s more than a food-chain link; it’s a global dependence on the atmosphere.

The dependence runs the other way too. 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. The two fluxes may be nearly balanced, but the size of the exchange still shows a major interaction between autotrophs and heterotrophs.

This gives a clear example of energy transformation making biological processes possible: light energy drives photosynthesis, chemical energy in carbon compounds drives respiration, and ATP from respiration powers cellular work.

Matter cycles because atoms are conserved

A chemical element is a pure substance made of only one type of atom. Living organisms need many elements, including carbon, hydrogen, oxygen, nitrogen and phosphorus, as well as smaller amounts of elements such as sulfur, calcium, potassium, sodium, magnesium and iron.

A nutrient cycle is the set of processes that moves a required chemical element between organisms and the abiotic environment. Here, nutrient means an element organisms need, not just “food”.

Ecosystems recycle all elements used by living organisms, not only carbon. Organisms take atoms from the abiotic environment, build them into body tissues, pass them on through feeding relationships, and eventually return them to the abiotic environment. The atoms don’t get used up.

Autotrophs get elements mostly as inorganic nutrients from air, water or soil. Heterotrophs get many elements in organic molecules in food, though they may also take in inorganic ions such as sodium, potassium and calcium.

Decomposers matter because they break down dead organisms, dead parts and faeces, releasing elements back into forms that can be used again. For example, nitrogen in proteins can return to the environment in simpler nitrogen-containing compounds. You do not need the detailed nitrogen cycle here; you do need the principle that decomposers unlock elements from organic matter.

That is the guiding contrast. Matter can be recycled because chemical elements remain as atoms and can move between pools. Energy cannot be recycled because each transfer disperses some energy as heat, so ecosystems need a continuing energy input.