Module 3: Ecosystems: What are they and how do they work?

Chris Merkord

Core Case Study: Tropical Rain Forests Are Disappearing

  • Cover only 7% of the earth’s surface, but can contain up to half of the world’s terrestrial plant and animal species

  • To date, human activities have destroyed or degraded more than half of the earth’s tropical rain forests

    • logging, crop development, cattle grazing, and encroaching civilization
  • Why should you be concerned about the disappearance of tropical rain forests?

Used with permission from Peel, M. C et al., (2007) University of Melbourne from Wikimedia Commons. Blue areas denote Tropical Rainforest coverage

Used with permission from Peel, M. C et al., (2007) University of Melbourne from Wikimedia Commons. Blue areas denote Tropical Rainforest coverage

Core Case Study: Tropical Rain Forests Are Disappearing

Effect 1 - Biodiversity Loss

  • Clearing these forests causes the extinction of many of their plant and animal species
  • Loss of key species in these forests can have a ripple effect that leads to the extinction of other species that they help support

Effect 2 - Climate Change

  • Warms the atmosphere and speeds up climate change.

  • Fewer plants using photosynthesis to remove human-generated emissions of carbon dioxide (CO2)

  • Resulting increased levels of CO2 in the atmosphere contributes to atmospheric warming and climate change,

Core Case Study: Tropical Rain Forests Are Disappearing

Effect 3 - System Change and Tipping Point

  • Large-scale losses of tropical rain forests can change regional weather pattern in ways that can prevent the forest from returning in cleared or degraded areas.

  • When this irreversible ecological tipping point is reached, the tropical rain forests in such areas become drier and less-diverse tropical grasslands

Earth’s Life-Support System Has Four Major Components

  • Earth’s life-support system has four spherical components that interact with each other.

  • Life is sustained by the cycling of nutrients and energy between and through these systems.

  • Atmosphere: composed of the troposphere and the stratosphere.

  • Hydrosphere: water at or near the earth’s surface (ice, water, and water vapor).

  • Geosphere: composed of a hot core, a thick, mostly rocky mantle, and a thin outer crust.

  • Biosphere: wherever life is found within the other three spheres.

Source: SciencePhoto.com

Source: SciencePhoto.com

Three Factors Sustain the Earth’s Life

  • The one-way flow of high-quality energy Solar energy principle of sustainability Greenhouse effect

  • The cycling of nutrients Chemical cycling principle of sustainability

  • Gravity

Greenhouse Earth. High-quality solar energy flows from the sun to the earth. It is degraded to lower-quality energy (mostly heat) as it interacts with the earth’s air, water, soil, and life forms, and eventually some of it returns to space.

Certain gases in the earth’s atmosphere retain enough of the sun’s incoming energy as heat to warm the planet in what is known as the greenhouse effect.

From Wikimedia Commons, a freely licensed media file repository

From Wikimedia Commons, a freely licensed media file repository

Ecology

Ecology

Ecology: how living organisms (biotic components) interact with one another and with the nonliving (physical and chemical) environment (abiotic component).

Levels of Biological Organization

Biotic component consists of nested levels of biological organization:

  • Organelles – specialized structures within cells that perform specific functions
  • Cells – the basic units of life
  • Tissues – groups of similar cells working together
  • Organs and organ systems – structures composed of multiple tissues with coordinated functions
  • Organisms – individual living entities
  • Populations – members of the same species living in the same area
  • Communities – all interacting populations of different species in an area
  • Ecosystems – communities plus the abiotic environment they interact with
  • Biosphere – the sum of all ecosystems on Earth

A sequence of images showing increasing levels of biological organization, from cellular organelles and cells, to tissues, organs, organisms, populations, ecosystems, and the biosphere.

Diagram illustrating levels of biological organization from organelles to the biosphere. Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Trophic Structure: Who Eats Whom in an Ecosystem

  • Ecologists describe the flow of energy and matter in ecosystems using trophic levels, which group organisms based on how they obtain nutrients and energy.

    Organisms fall into a small number of functional roles:

    • Producers: Capture energy (usually sunlight) and manufacture organic molecules from inorganic materials such as carbon dioxide, water, and nutrients.
    • Consumers: Obtain energy by eating producers, other consumers, or organic remains.
    • Detritivores: Consumers that feed on detritus—small fragments of dead organisms and organic waste.
    • Decomposers: Specialized consumers (primarily bacteria and fungi) that chemically break down organic matter into inorganic nutrients, returning them to the environment for reuse by producers.

    Together, these groups define how energy enters ecosystems and how nutrients are recycled through living and nonliving components.

Producers: The Entry Point of Energy into Ecosystems

Producers

  • organisms (plants, algae, and some bacteria)
  • manufacture the organic nutrients they need using energy and inorganic materials from their environment

Photosynthesis

  • Producers capture solar energy and use it

  • Convert carbon dioxide (CO₂) and water (H₂O) into carbohydrates such as glucose (C₆H₁₂O₆), which store chemical energy

  • Oxygen (O₂) released as a byproduct of this process accumulates in the atmosphere, making aerobic life possible for most organisms

Diagram of photosynthesis showing carbon dioxide and water entering a leaf, light energy driving the reaction, and glucose and oxygen being produced.

Photosynthesis converts carbon dioxide and water into glucose and oxygen using light energy. From Wikimedia Commons, a freely licensed media file repository

Consumers: Obtaining Energy from Other Organisms

Consumers

  • Cannot produce their own food
  • Obtain energy and nutrients by feeding on producers, other consumers, or the wastes and remains of organisms

Several major consumer types are commonly recognized:

  • Primary consumers (herbivores): Animals that feed primarily on plants or algae
  • Carnivores: Animals that obtain energy by feeding on the tissues of other animals

Diagram of an ecosystem showing a tree as a producer using sunlight, carbon dioxide, and water; a primary consumer and secondary consumer feeding on plant material; decomposers in the soil breaking down organic matter; and the cycling of water, nutrients, and gases between organisms and the environment.

An ecosystem diagram illustrating producers, consumers, and decomposers, and the movement of energy and matter among them, including sunlight, carbon dioxide, oxygen, water, and soil nutrients. From Wikimedia Commons, a freely licensed media file repository.

Decomposers: Recycling Matter in Ecosystems

Decomposers are consumers that obtain energy and nutrients by breaking down the wastes and remains of plants and animals.

They are a subset of heterotrophs and are primarily bacteria and fungi.

Through decomposition, these organisms convert organic matter into inorganic nutrients that are returned to the soil, water, and air, where they can be reused by producers.

Diagram of an ecosystem showing a tree as a producer using sunlight, carbon dioxide, and water; a primary consumer and secondary consumer feeding on plant material; decomposers in the soil breaking down organic matter; and the cycling of water, nutrients, and gases between organisms and the environment.

An ecosystem diagram illustrating producers, consumers, and decomposers, and the movement of energy and matter among them, including sunlight, carbon dioxide, oxygen, water, and soil nutrients. From Wikimedia Commons, a freely licensed media file repository.

Detritivores: Breaking Down Organic Matter

Detritivores obtain energy and nutrients by feeding directly on detritus—the wastes and dead bodies of other organisms.

By physically fragmenting organic material, detritivores help convert large, complex remains (such as fallen tree trunks) into simpler forms that can be further decomposed into inorganic nutrients usable by plants.

In natural ecosystems, wastes and dead organisms are not discarded; they function as resources that support nutrient cycling, consistent with the chemical cycling principle of sustainability.

Illustration showing a fallen tree trunk progressively broken down by detritivores such as beetles, ants, and termites, followed by fungi and mushrooms that complete decomposition and release nutrients into the soil.

Detritus feeders and decomposers acting on a fallen log over time, illustrating how insects, fungi, and other organisms break down dead wood and return nutrients to the soil.

Cellular Respiration: Releasing Stored Chemical Energy

Producers, consumers, and decomposers all rely on cellular respiration to release the chemical energy stored in glucose and other organic compounds.

In most organisms, this occurs through aerobic respiration, which uses oxygen to convert glucose back into carbon dioxide and water, releasing energy that fuels growth, maintenance, and reproduction.

Diagram illustrating aerobic respiration with glucose and oxygen as inputs and carbon dioxide, water, and ATP energy as outputs.

Aerobic cellular respiration, showing glucose and oxygen being converted into carbon dioxide, water, and usable chemical energy. From Wikimedia Commons, a freely licensed media file repository.

Anaerobic Respiration: Energy without Oxygen

Some decomposers, including yeast and certain bacteria, obtain energy by breaking down glucose and other organic compounds in the absence of oxygen.

This process is known as anaerobic respiration, or fermentation.

Rather than producing carbon dioxide and water, anaerobic respiration generates a variety of end products, depending on the organism and pathway involved, including:

  • methane gas (CH₄)
  • ethyl alcohol (C₂H₆O)
  • acetic acid (C₂H₄O₂), the main component of vinegar
  • hydrogen sulfide (H₂S), a toxic gas with a characteristic rotten-egg odor

All organisms obtain energy through aerobic or anaerobic respiration, but only producers (plants, algae, and some bacteria) carry out photosynthesis.

Energy Flow and Nutrient Cycling Sustain Ecosystems

Ecosystems—and the biosphere as a whole—are sustained by two fundamental processes:

  • One-way energy flow: Energy enters ecosystems as sunlight, is captured by producers, transferred through trophic levels, and is ultimately lost as heat.
  • Nutrient cycling: Matter such as carbon, nitrogen, and water is continuously recycled between organisms and the physical environment.

Together, these processes reflect two core scientific principles of sustainability: energy flows through ecosystems, while nutrients cycle within them.

Diagram illustrating one-way energy flow from the sun through plants, herbivores, carnivores, and detritivores, with energy lost as heat during respiration and nutrients cycling back through the ecosystem.

Energy flow through an ecosystem showing sunlight captured by producers, transfer to herbivores and carnivores, losses through respiration as heat, and the role of detritivores in recycling matter. From Wikimedia Commons, a freely licensed media file repository.

Soil: The Foundation of Life on Land

Soil is a complex, living system composed of:

  • rock fragments and mineral particles
  • essential mineral nutrients
  • decaying organic matter
  • water, air, and a diverse community of organisms

Soil is one of Earth’s most important forms of natural capital.

Although it is technically renewable, soil forms extremely slowly, making the protection and renewal of topsoil critical for long-term sustainability.

Soil Profiles and Horizons

  • Soils store organic carbon, helping regulate Earth’s climate
  • Soil structure is organized into horizontal layers called horizons
  • A vertical cross-section of these layers is a soil profile
  • Major horizons in a mature soil:
    • O – organic layer (leaf litter)
    • A – topsoil
    • B – subsoil
    • C – weathered parent material

Diagram of a soil profile with labeled horizons, including organic litter at the surface, topsoil, subsoil, weathered parent material, and underlying bedrock.

Soil profile showing distinct horizons (O, A, B, C, and R) and illustrating how soil structure supports plant growth and nutrient storage. From Wikimedia Commons, a freely licensed media file repository.

Ecologically Active Soil Layers

  • Most plant roots and the majority of soil organic matter are concentrated in:
    • the O horizon (leaf litter)
    • the A horizon (topsoil)
  • These layers support dense communities of: bacteria, fungi, earthworms, insects and other soil invertebrates
  • Through feeding and decomposition, soil organisms:
    • break down complex organic compounds
    • produce humus, a stable mixture of partially decomposed plant and animal material
      • Improves soil structure, nutrient availability, and water retention, supporting plant growth and ecosystem productivity.

Diagram of a soil profile with labeled horizons, including organic litter at the surface, topsoil, subsoil, weathered parent material, and underlying bedrock.

Soil profile showing distinct horizons (O, A, B, C, and R) and illustrating how soil structure supports plant growth and nutrient storage. From Wikimedia Commons, a freely licensed media file repository.

Soil Is the Foundation of Life on Land

  • In a fertile soil, these two layers teem with bacteria, fungi, earthworms, and numerous small insects, all interacting by feeding on and decomposing one another.

  • Break down soil’s complex organic compounds into a mixture of the partially decomposed plant and animal remains, called [humus]{.keyword}

Energy

Energy Flow in Ecosystems: The Big Picture

  • Energy enters ecosystems as sunlight.
  • Producers convert solar energy into chemical energy through photosynthesis.
  • Energy moves upward through trophic levels as organisms consume one another.
  • Energy flow is one-way — it does not cycle.

Source: mrgscience.com

Source: mrgscience.com

Energy Transfer Between Trophic Levels

  • Energy stored in organic molecules passes from:
    • Producers → Primary consumers → Secondary consumers → Tertiary consumers
  • At each transfer, organisms use most of the energy for:
    • metabolism
    • movement
    • growth
    • reproduction
  • Only a small fraction (about 10%) of energy becomes biomass available to the next level.

Source: mrgscience.com

Source: mrgscience.com

The Energy Pyramid

  • Energy availability decreases at higher trophic levels.
  • With each transfer, much energy is lost as heat through respiration.
  • Because energy diminishes at each step:
    • Food chains are short.
    • Top predators are few in number.
  • This pattern is represented by an energy pyramid.

Source: mrgscience.com

Source: mrgscience.com

Food Chains: Linear Energy Pathways

  • A food chain shows a single pathway of energy flow.
  • Example:
    • Grass → Rabbit → Fox
  • Food chains are simplified representations of feeding relationships.

Example food chain. Source: brittanica.com

Example food chain. Source: brittanica.com

Food Webs: Real Ecosystem Complexity

  • In natural ecosystems:
    • Most consumers eat more than one species.
    • Most organisms are eaten by multiple predators.
  • These interconnected feeding relationships form a food web.
  • Food webs more accurately represent how energy moves through ecosystems.

Example food web Source: brittanica.com

Example food web Source: brittanica.com

Matter / Nutrients

From Energy Flow to Nutrient Cycling

Energy and matter behave differently in ecosystems:

  • Energy flows:
    • Enters as sunlight
    • Moves through trophic levels
    • Is lost as heat
    • Does not get recycled
  • Nutrients cycle:
    • Atoms (C, N, P, H₂O) are reused
    • Move between organisms and the physical environment
    • Are conserved and continuously recycled

Energy flows through ecosystems.
Matter cycles within them.

Primary Productivity

Gross Primary Productivity (GPP)

  • Total rate at which producers capture solar energy through photosynthesis
  • Represents total carbon fixed into organic molecules

Net Primary Productivity (NPP)

  • Energy remaining after producers use some for respiration

    \[\text{NPP} = \text{GPP} - \text{Respiration by producers}\]

  • Represents biomass available to consumers

Source: sciencesauceonline.com

Source: sciencesauceonline.com

Ecosystem Productivity

Net Ecosystem Productivity (NEP)

  • Net carbon accumulation in an ecosystem
  • \[\text{NEP} = \text{GPP} - \text{Total ecosystem respiration}\] (includes respiration by producers, consumers, and decomposers)
  • Indicates whether an ecosystem is a carbon sink (positive NEP) or carbon source (negative NEP)

Net Primary Productivity Varies Among Ecosystems

  • Net primary productivity (NPP) differs dramatically across terrestrial and aquatic ecosystems.

  • Ecosystems with warm temperatures, ample sunlight, and sufficient water (e.g., tropical rainforests, swamps, marshes, coral reefs) tend to have high NPP.

  • Deserts, tundra, and open ocean regions generally have low NPP per unit area.

  • Although the open ocean has low NPP per square meter, its enormous area makes it a major contributor to global primary production.

  • Only energy stored as NPP (not GPP) is available to support consumers and higher trophic levels.

Bar chart comparing net primary productivity of different terrestrial and aquatic ecosystems, showing highest values in swamps, marshes, and tropical rainforests, and lowest values in deserts and open ocean.

Net primary productivity (g C/m²/year) across major terrestrial and aquatic ecosystems, illustrating large variation in biomass production per unit area. Source. Ap Environmental https://mhsapes.weebly.co-m/18-reading.html

What Happens to Matter in Ecosystems?

Energy flows.
Matter cycles.

  • Nutrients (C, N, P, H₂O) move repeatedly between:
    • atmosphere
    • hydrosphere
    • geosphere
    • biosphere
  • These pathways are called biogeochemical cycles.

Biogeochemical cycles are driven by:

  • Solar energy

  • Gravity

  • Biological processes

Human activities now alter these cycles at global scales.

The Water Cycle: Movement of Water Through Earth Systems

The hydrologic cycle moves water continuously among the atmosphere, land, and oceans.

Key processes

  • Evaporation – Solar energy converts liquid water to vapor.
  • Transpiration – Plants release water vapor to the atmosphere.
  • Condensation – Water vapor cools and forms clouds.
  • Precipitation – Water returns to Earth as rain, snow, or ice.
  • Runoff and infiltration – Water flows over land or enters soil.
  • Groundwater storage and discharge – Water is stored in aquifers and slowly returns to surface waters.

Although water is continuously recycled, only a small fraction is accessible freshwater; most is in oceans, ice, or deep underground.

Human Impacts on the Water Cycle

Human activities alter both the quantity and movement of water:

  • Freshwater withdrawal faster than natural recharge
  • Urbanization that reduces infiltration and increases runoff
  • Deforestation that lowers transpiration
  • Wetland drainage that disrupts natural water storage and filtration

Changes to the water cycle affect water availability, water quality, and ecosystem stability.

The Carbon Cycle: Movement of Carbon Through Earth Systems

Carbon cycles among the atmosphere, biosphere, oceans, and geosphere.

Major biological processes

  • Photosynthesis – Producers remove CO₂ from the atmosphere and convert it into organic carbon.
  • Respiration – Producers, consumers, and decomposers return CO₂ to the atmosphere.
  • Decomposition – Breaks down organic matter, releasing carbon back to air or soil.
  • Long-term storage – Carbon can be stored in oceans, soils, sediments, and fossil fuels.

Atmospheric CO₂ is a greenhouse gas and plays a central role in regulating Earth’s climate.

Human Impacts on the Carbon Cycle

Human activities are increasing atmospheric CO₂ by:

  • Burning fossil fuels faster than they form
  • Deforestation, reducing carbon uptake by plants

These changes shift the balance of the carbon cycle and contribute to climate change.

The Nitrogen Cycle: Transformations Driven by Microbes

Nitrogen is essential for proteins and DNA, but most organisms cannot use atmospheric nitrogen (N₂) directly.

Key processes

  • Nitrogen fixation – Specialized bacteria convert N₂ into ammonia (NH₄⁺).
  • Nitrification – Bacteria convert:
    • NH₄⁺ → NO₂⁻ → NO₃⁻
  • Assimilation – Plants take up NH₄⁺ or NO₃⁻ and incorporate nitrogen into organic molecules.
  • Consumption – Animals obtain nitrogen by eating plants or other animals.
  • Decomposition and denitrification – Decomposers return nitrogen to the soil, and some bacteria convert it back to N₂ gas.

Microorganisms drive most nitrogen transformations.

Human Impacts on the Nitrogen Cycle

Humans have greatly accelerated nitrogen movement through ecosystems by:

  • Industrial fertilizer production (fixing atmospheric N₂ at large scales)
  • Fossil fuel combustion, releasing nitrogen oxides (NOₓ)
  • Agricultural runoff, increasing nitrate in waterways

Consequences include:

  • Eutrophication and algal blooms
  • Oxygen depletion in aquatic systems
  • Acid rain formation

Acid Rain

Acid rain forms when sulfur dioxide (SO₂) and nitrogen oxides (NOₓ) are released into the atmosphere and react with water vapor to form sulfuric and nitric acids.

These acids return to Earth through precipitation (rain, snow, sleet, or dry deposition).

Impacts include:

  • Increased soil acidity
  • Leaching of essential nutrients
  • Altered chemistry of lakes and streams
  • Harm to aquatic organisms and forests

Algal Blooms and Eutrophication

  • An algal bloom is a rapid increase in algae, usually triggered by excess nutrients (especially nitrogen and phosphorus).

  • When blooms die and decompose: - Oxygen is depleted - Fish and other aquatic organisms may die - Ecosystem structure is disrupted

  • Regulation of nutrient pollution in some regions has reduced the frequency and severity of blooms, but they remain a widespread issue.

The Phosphorus Cycle: A Sedimentary Cycle

Phosphorus is an essential nutrient for DNA, ATP, and cell membranes.

Unlike carbon and nitrogen, phosphorus: - Does not have a major atmospheric phase - Cycles primarily through rocks, soils, water, and living organisms

Key processes

  • Weathering releases phosphate (PO₄³⁻) from rocks.
  • Plant uptake incorporates phosphorus into organic molecules.
  • Consumption and decomposition return phosphorus to soils and sediments.
  • Some phosphorus is transported to oceans and can become buried in marine sediments, removing it from short-term cycling.

Human Impacts on the Phosphorus Cycle

Humans accelerate phosphorus movement by:

  • Mining phosphate rock to produce fertilizers
  • Deforestation, which reduces phosphorus retained in topsoil
  • Agricultural runoff and soil erosion, which carry phosphorus into waterways

Excess phosphorus in aquatic systems contributes to: - Eutrophication - Algal blooms - Oxygen depletion

Ecosystem Final Thoughts

How Do Scientists Study Ecosystems?

Ecologists use multiple complementary approaches:

  1. Field research

    • Direct observation and measurement
    • Long-term monitoring
    • Tagging and tracking organisms
    • Remote sensing (satellites, drones)
  2. Controlled experiments

    • Manipulate variables in field or lab settings
    • Test specific causal hypotheses
  3. Modeling

    • Mathematical and computational models

    • Used when systems are too large, slow, or complex to manipulate directly

Laboratory Experiments and Models: Strengths and Limits

Laboratory systems may include:

  • Culture tubes
  • Aquaria
  • Greenhouses
  • Environmental chambers

Example of aquaria experimental setup. Credit: ELI IMADALI/AMERICAN-STATESMAN

Example of aquaria experimental setup. Credit: ELI IMADALI/AMERICAN-STATESMAN

Advantages

  • High control over variables
  • Replicable
  • Cost-effective
  • Faster results

Limitations

  • May oversimplify real ecosystems
  • Hard to capture full ecological complexity

Why Ecosystem Monitoring Matters

Understanding ecosystem health requires:

  • Long-term baseline data
  • Global assessments
  • Integration across climate, biodiversity, and nutrient cycles

Scientific monitoring helps us:

  • Detect ecosystem degradation
  • Develop management strategies
  • Identify ecological tipping points
  • Avoid crossing planetary boundaries

Ecosystems: Key Takeaways

  • Energy flows through ecosystems.
  • Matter cycles within ecosystems.
  • Producers, consumers, and decomposers structure energy flow and nutrient cycling.
  • Human activities now alter ecosystem processes at local and global scales.

Ecosystem sustainability depends on maintaining both energy flow and nutrient cycling.