Learning Objectives

Define ecosystem

Describe how organisms acquire energy and nutrients through trophic levels in a food web

Explain the role of autotrophs, heterotrophs, and decomposers in the food web

Describe the biogeochemical cycles of water, carbon, nitrogen, phosphorus, and sulfur

Discuss the impact of human-made disruptions of a biogeochemical cycle

Discuss how contamination through human-made processes can be toxic to living organisms

Demonstrate graphing skills

Trophic Levels and Food Webs

An ecosystem is a community of interactions between and among living organisms and non-living organisms. In ecosystems, nutrients and energy flow continuously from producers (for example, plants) to consumers (for example, herbivores) and decomposers (for example, mushrooms and bacteria). Chemical elements such as water, carbon, nitrogen, sulfur, and phosphorus are cycled through the abiotic (nonliving) and living (biotic) components of ecosystems. Abiotic components include sunlight, temperature, soil, water, pH (availability of H+ ions), and nutrients. All energy that powers ecosystems comes from the Sun.1 Ninety-nine percent (99%) of the solar energy that reaches Earth is reflected back into space; that is, 99% of solar energy is not captured, stored for use, or converted for productive use as an energy source.2

Energy flow involves building up biomass such as the growth of plant leaves or the change in stature of animals as they mature; the predation of these leaves and animals; and decomposition of the dead plants and animals by fungi and bacteria. Plants, animals, bacteria, and fungi occupy distinct positions in the food chain or food web. When thinking of an ecosystem from the perspective of the flow of energy between trophic levels along a food chain, the order of energy (and nutritive) flow can be regarded as:


Autotrophs that make their own food and build up the biomass for their own bodies

Primary/secondary/tertiary consumers

Heterotrophs take in producers as food (energy sources) and digest (break down) the food

into small molecules that can be used as energy as well as to build biomass


They consume dead plants and animals and aid in breaking down tissues to chemical elements that can be used by living organisms; includes bacteria and fungi—called saprophytes—as well as scavengers like flies, beetles and detritivores like earthworms

The food chain is a simplified representation of energy flow between trophic levels in an ecosystem. A food web is a more accurate representation because energy and nutrients can flow in non-linear ways in an ecosystem. An example of nonlinear flow is that heterotrophs consume fungi (a decomposer).

Food Web

Energy Flow

Heterotroph (Consumer)

Autotroph (Producer)

Abiotic components and decomposed nutrients


Biogeochemical Cycles in Ecosystems

In living systems, energy flow can be considered as part of a nutrition cycle. The ‘food web’ and the tiered system of primary, secondary and tertiary trophic levels largely reflect the flow of nutrients. Keep in mind that the nutrients needed by you and all living organisms range widely from very simple chemical elements like hydrogen and nitrogen to complex molecules like carbohydrates.

The food web can be viewed as a cycle of nutrients that includes living as well as nonliving entities in an ecosystem. There are several different cycles that provide plants and animals with the nutrients—and energy—necessary for normal growth and function. The nutrient cycles are based on fundamental elements which serve as the building blocks for more complex biological structures such as the cellulose for plant leaves or the amino acids for proteins.

These cycles are biogeochemical cycles which is a term that underscores the interdependence of living (“bio-“) and non-living (“-geochemical”) entities of ecosystems. Five key cycles of chemical elements (in addition to the water cycle) are necessary to sustain living organisms and healthy ecosystems: Oxygen, carbon, nitrogen, sulfur, and phosphorus. These element cycles occur naturally as two different types of biogeochemical cycles: (1) Atmospheric or oceanic and (2) soils, rocks and minerals. You are likely familiar with the percentage of certain elements in the atmosphere: Nitrogen at 78%, Oxygen at 21% and Carbon Dioxide at 0.03%. Subtle shifts in the percentage representations of the chemical elements and molecules in the atmosphere, water, or land can shift the balance for supporting life and healthy ecosystems.

Example Biogeochemical Cycle: The Nitrogen Cycle

Nitrogen is a macronutrient which means that living organisms need to take in large quantities of nitrogen for growth and health. Two other elements are also essential nutrients that will be found, along with nitrogen, in most plant fertilizers: Potassium (K) and phosphorus (P). These elements can be retrieved after breakdown of organic matter from dead animals and their waste products. Intriguingly, the amount of human-made nitrogen now surpasses the amount that occurs in nature, clearly shifting the balance of the biogeochemical cycle for nitrogen.3

Nitrogen is incorporated into many tissues and biological products in living systems. These include DNA, RNA, and proteins (enzymes). The nitrogen cycle requires that elemental nitrogen is available for organisms to assimilate as a necessary component of biomass such as the proteins needed to build muscle. To this end, decomposers such as bacteria and fungi (mushrooms) are critical for breaking down dead tissue and waste products into elemental forms and also helping to convert the breakdown constituents into forms usable by plants and fungi. (Keep in mind that fungi and bacteria must also rely on their own breakdown products for their own nutrition and growth.)

Bacteria use two mechanisms to support biogeochemical cycles. They use enzymes to break down dead tissue and waste products as well as to convert nitrogen compounds to a form that can be assimilated by plants and fungi. The enzymatic process converts nitrogen gas (N2) into nitrate (NO3−) and ammonium (NH4+), which permits plants and fungi to take up the nitrogen and use it to build proteins and nucleic acids. Plants and fungi cannot use nitrogen gas directly; nitrogen can only be used by living organisms in a non-gaseous or “fixed” form such as nitrates, nitrites, and ammonium.4

Nitrogen has been excessively extracted from naturally occurring sources such as saltpeter deposits in Chile, and many of these naturally-occurring sources of nitrogen have been depleted.5 Ammonia (NH4+) and nitrates (NO3−) are excessively produced through the coal and fertilizer industries. Nitrates are known to pollute drinking water, streams, and rivers as well as cause excessive growth of algae (eutrophication, which deprives other animals of access to dissolved oxygen in bodies of water, resulting in the death of these animals).

Human Impact on Biogeochemical Cycles

Humans have the impressive ability to transform the landscape and the environment—an ability that has had overall harmful consequences for living systems on Earth. Many human-made processes disrupt the balance of biogeochemical cycles and shift the natural proportions of essential elements like nitrogen and carbon dioxide (CO2) in the atmosphere, water and soil. Excess circulating carbon in the atmosphere as a result of human use of fossilized carbon-based dead organisms as a source of energy has shifted the carbon cycle balance in such a way that all the carbon in the atmosphere cannot be cycled in a balanced manner. Instead, excess carbon is being generated and goes into natural residential locations like the atmosphere and ocean at unnatural levels. The consequences of excess carbon in the form of carbon dioxide (CO2) has had disruptive consequences on Earth’s climate.

Carbon, nitrogen, and many other nutrients must be taken up by plants, animals, and fungi through air (such as plants take in CO2), oceans (such as plants that take in elemental nutrients and are symbiotic with heterotrophic corals), or from soil (such as fungi uptake nitrogen after it decomposes organic matter). The availability of these essential nutrients can be compromised due to human-made conditions that change the properties of soil (pH, salinity, constituent ions, heavy metals, etc.) and the atmosphere (acid rain, particulate matter, carbon dioxide concentration, etc.).

Several chemical elements are needed in only small quantities: These are referred to as micronutrients. Micronutrients can be toxic if they are consumed at high concentrations. In fact, many micronutrients are heavy metals. If you take a look at the label on a bottle of multivitamins, you will see many of these heavy metal micronutrients listed. These include iron (Fe), copper (Cu), and zinc (Zn). These nutritive heavy metals should be distinguished from toxic heavy metals such as mercury (Hg) and lead (Pb) because these latter metals have no role in the health and well-being of living systems.

Orientation to the Model System: Fungi (Mushrooms), Bioavailability of Nutrients and Human Impact

Fungi, or mushrooms, like all living organisms, grow and thrive best under a circumscribed range of environmental conditions. As decomposers, fungi play a pivotal role in cycling nutrients through the biogeochemical cycles. Many fungi co-exist symbiotically at the roots of plants to support nutrient cycling. If decomposers did not break down organic matter from dead plants and animals, life could not exist because essential elements like carbon and nitrogen would not be available for producers (plants) to take up at the autotrophic level of the food chain.

The soil quality needed to support living organisms like plants and fungi is dependent on the balance of many factors: Rain, pH, acid rain, concentration of heavy metals, aluminum, ammonium, sulfur, irrigation, salinity, and more. Soil quality is also impacted by the presence of decomposers (detritivores, scavengers, bacteria and fungi). Bacteria and fungi thrive under environmental conditions similar to those for other living organisms. Soils need to be within an optimal pH range to support the bioavailability (available to be taken in by living organisms) of chemical elements such as nitrogen and chloride.6 Decomposers grow optimally in soil with neutral pH.7 Soils high in salt concentrations (salinity) can only support certain living organisms,8 which means that biodiversity is compromised if there are significant changes in the salinity of soil.

Soil quality can be remediated to some degree by using decomposers. In the case of heavy metals, for example, certain fungi and plants take up these metals from contaminated and polluted soils. Incorporating metals into biomass is a natural process because many metals are micronutrients such as copper (Cu), zinc (Zn), iron (Fe), calcium (Ca) and potassium (K). In living systems, these micronutrient metals function with enzymes to carry out specific biological processes.9 (Bacteria is also used in remediation and can enzymatically transform toxic metals.)

In taking up these metals, plants and fungi accumulate (bioaccumulate and bioconcentrate) the metals, effectively removing much of these metals from underlying soil. The use of plants, fungi, and bacteria to aid in the removal of human-made soil contaminants is called bioremediation—a process that is being used at many of the 300,000 hazardous waste sites throughout the United States.10 Because bioaccumulation is a naturally occurring process, certain agricultural crops are also very efficient bioaccumulators/bioconcentrators of heavy metals, which is a major concern for agricultural farms located near any of the 300,000 hazardous waste sites or near waste incinerators (see below). Another popular remediation solution for hazardous wastes is incineration which involves burning three million tons of hazardous wastes every year—a number that is only 2% of the actual amount of hazardous wastes generated each year. Incineration transforms some heavy metals into air-borne particles, which, unfortunately, can eventually settle onto soil and into sediment, and then require another round of remediation.

In this set of laboratory exercises, you will grow mushrooms under various conditions as outlined below.

Procedure I Overview

Mushroom Yield ‐ Effect of Nitrate Concentration Level

Procedure II Overview

Mushroom Yield ‐ Effect of Heavy Metal Concentration Level

Procedure III Overview

Mushroom Yield ‐ pH Dependence


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