ECOLOGY

LECTURE 3
Biogeochemical cycles

All living things require energy in one form or another. At the cellular level,
energy is used in most metabolic pathways (usually in the form of ATP),
especially those responsible for building large molecules from smaller
compounds. Living organisms would not be able to assemble complex organic
molecules (proteins, lipids, nucleic acids, and carbohydrates) without a
constant energy input.

Photosynthetic and chemosynthetic organisms are autotrophs, which are organisms

capable of synthesizing their own food (more specifically, capable of using inorganic
carbon as a carbon source). Photosynthetic autotrophs (photoautotrophs) use
sunlight as an energy source, and chemosynthetic autotrophs (chemoautotrophs)
use inorganic molecules as an energy source. Autotrophs are critical for ecosystems
because they occupy the trophic level containing producers. Without these
organisms, energy would not be available to other living organisms, and life would
not be possible.

Energy flows directionally through ecosystems, entering as sunlight leaving as heat

during energy transformation between trophic levels. Rather than flowing through
an ecosystem, the matter that makes up organisms is conserved and recycled. The
six most common elements associated with organic molecules—carbon, nitrogen,
hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and
may exist for long periods in the atmosphere, on land, in water, or beneath Earth’s
surface. Geologic processes, such as weathering, erosion, water drainage, and the
subduction of the continental plates, all play a role in the cycling of elements on
Earth. Because geology and chemistry have major roles in the study of these
processes, the recycling of inorganic matter between living organisms and their
nonliving environment are called biogeochemical cycles. Biogeochemical cycles or
‘substance turnover pathways’ are the routes that substances travel and are recycled
through the Earth and its spheres.
The six aforementioned elements are used by organisms in a variety of ways.
Hydrogen and oxygen are found in water and organic molecules, both of which
are essential to life. Carbon is found in all organic molecules, whereas nitrogen is an
important component of nucleic acids and proteins. Phosphorus is used to make
nucleic acids and the phospholipids that comprise biological membranes. Lastly,
sulfur is critical to the three-dimensional shape of proteins.
Minerals cycle through the biosphere between the biotic and abiotic components
and from one organism to another.

The Water Cycle

The hydrosphere is the area of Earth where water movement and storage occurs: as
liquid water on the surface (rivers, lakes, oceans) and beneath the surface
(groundwater) or ice, (polar ice caps and glaciers), and as water vapor in the
atmosphere. The human body is about 60 percent water and human cells are more
than 70 percent water. Of the stores of water on Earth, 97.5 percent is salt water
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(see Figure 1 below). Of the remaining water, more than 99 percent is groundwater
or ice. Thus, less than one percent of freshwater is present in lakes and rivers. Many
organisms are dependent on this small percentage, a lack of which can have negative
effects on ecosystems. Humans, of course, have developed technologies to increase
water availability, such as digging wells to harvest groundwater, storing rainwater,
and using desalination to obtain drinkable water from the ocean. Although this
pursuit of drinkable water has been ongoing throughout human history, the supply
of fresh water continues to be a major issue in modern times.
The various processes that occur during the cycling of water are illustrated
in Figure 2 below. The processes include the following:

Figure 1. Only 2.5 percent of water on Earth is fresh water, and less than 1 percent
of fresh water is easily accessible to living things.

Water molecules are made of hydrogen and oxygen atoms. Hydrogen and oxygen
are nutrients that organisms need. Clearly there is no problem obtaining these
nutrients in aquatic ecosystems. However, they are sometimes in short supply in
terrestrial ecosystems. The cycling of water in nature involves both aquatic and
terrestrial ecosystems and the air above them. Let’s see how this occurs:

The water cycle is driven by the Sun’s energy as it warms the oceans and other
surface waters. This leads to evaporation (liquid water to water vapor) of liquid
surface water and sublimation (ice to water vapor) of frozen water, thus moving
large amounts of water into the atmosphere as water vapor. Water vapour enters
the atmosphere through transpiration from vegetation. Transpiration is the loss of
water through pores in the leaves of plants. It also enters the atmosphere through
evaporation from bodies of water and the soil. In the cool upper atmosphere this
vapour condenses, forming clouds. Over time, this water vapor condenses into
clouds as liquid or frozen droplets and eventually leads to precipitation (rain, snow,
hail), which returns water to Earth’s surface. When this occurs, some of the water
falling on the ground runs along the surface of the ground to a stream, pond or other
body of water. This is called surface runoff. Some of the water also soaks into the
ground by a process called percolation. Some water percolates down to the bedrock.
Then it becomes ground water and gradually runs back to lakes and other bodies of
water. Some of the water in the soil moves up to the roots of plants by capillarity.
The roots absorb the water. This is how most plants get the hydrogen and oxygen
they need. Animals can obtain water by eating plants or by eating other animals. Of
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course, they can also obtain water by drinking it directly from a body of water. When
plants and animals die, they decompose. During the decomposition process, the
water present in their tissues is released into the environment.

Ecologists combine transpiration and evaporation into a single term that

describes water returned to the atmosphere: evapotranspiration. Water in the soil
that is not taken up by a plant and that does not evaporate is able to percolate into
the subsoil and bedrock where it forms groundwater.
Groundwater is a significant, subsurface reservoir of fresh water. It exists in
the pores between particles in dirt, sand, and gravel or in the fissures in rocks.
Groundwater can flow slowly through these pores and fissures and eventually finds
its way to a stream or lake where it becomes part of the surface water again. Many
streams flow not because they are replenished from rainwater directly but because
they receive a constant inflow from the groundwater below. Some groundwater is
found very deep in the bedrock and can persist there for millennia. Most groundwater
reservoirs, or aquifers, are the source of drinking or irrigation water drawn up
through wells. In many cases these aquifers are being depleted faster than they are
being replenished by water percolating down from above.
Rain and surface runoff are major ways in which minerals, including phosphorus
and sulfur, are cycled from land to water. The environmental effects of runoff will
be discussed later as these cycles are described.

Figure 2. Water from the land and oceans enters the atmosphere by evaporation or
sublimation, where it condenses into clouds and falls as rain or snow. Precipitated
water may enter freshwater bodies or infiltrate the soil. The cycle is complete when
surface or groundwater reenters the ocean. (credit: modification of work by John M.
Evans and Howard Perlman, USGS)
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KEY TERMS:

- evaporation: the process of changing water into vapor

- condensation: the process of changing vapor into water

- precipitation: any form of water that falls to the earth’s surface

- surface run-off water that moves along the earth’s surface, it is not absorbed

- percolation: draining or seeping of water into the earth

- capillarity: when water is moved towards the surface

- absorption: when plants take water from the gound

-transpiration: water leaving the pores from leaves on plants

- decomposition: breaking down organic matter, releases water to the

environment

- Aquifers are underground collections of water (These are what we tap into
for well water)

The Carbon Cycle

• Carbon is the main building block for all living things (It is 18% of your body
mass)

• Carbon is critical in fossil fuels (coal, natural gas, fuel)

• Diamonds and pencil lead (graphite) are pure Carbon

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• Increases in CO2 contribute to climate change

• Carbon is the second most abundant element in organisms, by mass.

• Its role in the structure of biomolecules is of primary importance.

Carbon compounds contain energy, and many of these compounds from dead plants
and algae have fossilized over millions of years and are known as fossil fuels. Since
the 1800s, the use of fossil fuels has accelerated. Since the beginning of the Industrial
Revolution the demand for Earth’s limited fossil fuel supplies has risen, causing the
amount of carbon dioxide in our atmosphere to drastically increase. This increase
in carbon dioxide is associated with climate change and is a major environmental
concern worldwide.
The carbon cycle is most easily studied as two interconnected subcycles: one
dealing with rapid carbon exchange among living organisms and the other dealing
with the long-term cycling of carbon through geologic processes. The entire carbon
cycle is shown in Figure 3 below.

Figure 3. Carbon dioxide gas exists in the atmosphere and is dissolved in water.
Photosynthesis converts carbon dioxide gas to organic carbon, and respiration cycles
the organic carbon back into carbon dioxide gas. Long-term storage of organic
carbon occurs when matter from living organisms is buried deep underground and
becomes fossilized. Volcanic activity and, more recently, human emissions bring
this stored carbon back into the carbon cycle. (credit: modification of work by John
M. Evans and Howard Perlman, USGS)
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The Biological Carbon Cycle

Organisms are connected in many ways, even among different ecosystems. A good
example of this connection is the exchange of carbon between heterotrophs and
autotrophs by way of atmospheric carbon dioxide. Carbon dioxide (CO2) is the basic
building block that autotrophs use to build high-energy compounds such as glucose.
The energy harnessed from the Sun is used by these organisms to form the covalent
bonds that link carbon atoms together. These chemical bonds store this energy for
later use in the process of respiration. Most terrestrial autotrophs obtain their carbon
dioxide directly from the atmosphere, while marine autotrophs acquire it in the
dissolved form (bicarbonate, HCO3–).
Carbon is passed from producers to higher trophic levels through consumption.
For example, when a cow (primary consumer) eats grass (producer), it obtains some
of the organic molecules originally made by the plant’s photosynthesis. Those
organic compounds can then be passed to higher trophic levels, such as humans,
when we eat the cow. At each level, however, organisms are
performing respiration, a process in which organic molecules are broken down to
release energy. As these organic molecules are broken down, carbon is removed
from food molecules to form CO2, a gas that enters the atmosphere. Thus, CO2 is a
byproduct of respiration. Recall that CO2 is consumed by producers during
photosynthesis to make organic molecules. As these molecules are broken down
during respiration, the carbon once again enters the atmosphere as CO2. Carbon
exchange like this potentially connects all organisms on Earth. Think about this: the
carbon in your DNA was once part of plant; millions of years ago perhaps it was part
of dinosaur.

Carbon is present in the atmosphere as carbon dioxide. Water also contains

carbon dioxide as it can dissolve it. Producers (plants and algae) use it to perform
photosynthesis and make food. Now the carbon is in the producers. Herbivores eat
the plants and carnivores eat the herbivores. Now the carbon is in animals. Both
plants and animals respire. Their respiration returns carbon dioxide to the
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atmosphere. Decomposers break down dead plants and animals as well as animal
waste. This too returns carbon dioxide to the atmosphere or soil.

The Nitrogen Cycle

• Nitrogen is used in DNA, protein, and ATP (our body’s power molecule)

• It is a limiting nutrient meaning that it is the least available nutrient so the amount
of growth depends on how much you have

• It is a main ingredient in fertilizers

• It makes up 78% of the atmosphere

Certain species of bacteria are able to perform nitrogen fixation, the process of
converting nitrogen gas into ammonia (NH3), which spontaneously becomes
ammonium (NH4+). Ammonium is converted by bacteria into nitrites (NO 2−) and
then nitrates (NO3−). At this point, the nitrogen-containing molecules are used by
plants and other producers to make organic molecules such as DNA and proteins.
This nitrogen is now available to consumers.
The process of denitrification is when bacteria convert the nitrates into
nitrogen gas, thus allowing it to re-enter the atmosphere.
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Human activity can alter the nitrogen cycle by two primary means: the
combustion of fossil fuels, which releases different nitrogen oxides, and by the use
of artificial fertilizers (which contain nitrogen and phosphorus compounds) in
agriculture, which are then washed into lakes, streams, and rivers by surface runoff.
Atmospheric nitrogen (other than N2) is associated with several effects on Earth’s
ecosystems including the production of acid rain (as nitric acid, HNO 3) and
greenhouse gas effects (as nitrous oxide, N2O), potentially causing climate change.
A major effect from fertilizer runoff is saltwater and freshwater eutrophication, a
process whereby nutrient runoff causes the overgrowth of algae, the depletion of
oxygen, and death of aquatic fauna.
In marine ecosystems, nitrogen compounds created by bacteria, or through
decomposition, collects in ocean floor sediments. It can then be moved to land in
geologic time by uplift of Earth’s crust and thereby incorporated into terrestrial rock.
Although the movement of nitrogen from rock directly into living systems has been
traditionally seen as insignificant compared with nitrogen fixed from the
atmosphere, a recent study showed that this process may indeed be significant and
should be included in any study of the global nitrogen cycle.

Usually, the nitrogen must be in the form of chemicals called nitrate. Then the
plant roots can absorb it. Lightning forms some nitrate by causing oxygen and
nitrogen in the atmosphere to join. Rhizobium bacteria can do the same thing. This
bacteria lives on the roots of plants called legumes such as beans, peas and alfalfa).
Many bacteria and blue-green algae also form nitrates. The changing of nitrogen to
nitrates is called nitrogen fixation. Plants use the nitrates that they absorb to make
plant proteins. Animals get the nitrogen that they need to make proteins by eating
plants or other animals. When plants and animals die, bacteria change their nitrogen
content to ammonia. The nitrogen in the urine and fecal matter of animals is also
changed to ammonia by bacteria. The pungent odour of outhouses, chicken pens,
hog yards, cat litter boxes and wet baby diapers is ample evidence of this fact.
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Ammonia, in turn, is converted to nitrites and then to nitrates by bacteria. This

process is called nitrification and completes the main part of the cycle. Many plants
are able to use ammonia directly. Therefore all of it does not have to be converted
to nitrate before plants absorb it. When people use synthetic fertilizers they add
nitrite or nitrate into the soil. This skips most of the nitrogen cycle and thus the
bacteria and microorganisms lose their food source. Plants and algae in the water
need nitrogen to grow. Some fish species depend on these plants for food.

The Phosphorus Cycle

• Phosphorus is used in DNA, phospholipids (like in our cell membrane) and ATP

• Phosphorus is a limiting nutrient for plants and in aquatic systems

• Is a main ingredient in fertilizer with Nitrogen

• It is NOT found in the atmosphere

Phosphorus is an essential nutrient for living processes. It is a major component of

nucleic acids and phospholipids, and, as calcium phosphate, it makes up the
supportive components of our bones. Phosphorus is often the limiting nutrient
(necessary for growth) in aquatic, particularly freshwater, ecosystems.
Phosphorus occurs in nature as the phosphate ion (PO43-). In addition to
phosphate runoff as a result of human activity, natural surface runoff occurs when it
is leached from phosphate-containing rock by weathering, thus sending phosphates
into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-
containing ocean sediments form primarily from the bodies of ocean organisms and
from their excretions. However, volcanic ash, aerosols, and mineral dust may also
be significant phosphate sources. This sediment then is moved to land over geologic
time by the uplifting of Earth’s surface. (Figure below)
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Phosphorus is also reciprocally exchanged between phosphate dissolved in the

ocean and marine organisms. The movement of phosphate from the ocean to the land
and through the soil is extremely slow, with the average phosphate ion having an
oceanic residence time between 20,000 and 100,000 years.

Figure 5. In nature, phosphorus exists as the phosphate ion (PO43-). Weathering of

rocks and volcanic activity releases phosphate into the soil, water, and air, where it
becomes available to terrestrial food webs. Phosphate enters the oceans in surface
runoff, groundwater flow, and river flow. Phosphate dissolved in ocean water cycles
into marine food webs. Some phosphate from the marine food webs falls to the ocean
floor, where it forms sediment. (credit: modification of work by John M. Evans and
Howard Perlman, USGS)
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Excess phosphorus and nitrogen that enter these ecosystems from fertilizer
runoff and from sewage cause excessive growth of algae. The subsequent death and
decay of these organisms depletes dissolved oxygen, which leads to the death of
aquatic organisms such as shellfish and fish. This process is responsible for dead
zones in lakes and at the mouths of many major rivers and for massive fish kills,
which often occur during the summer months (see Figure 6 below).

Figure 6. Dead zones occur when phosphorus and nitrogen from fertilizers cause
excessive growth of microorganisms, which depletes oxygen and kills fauna.
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Worldwide, large dead zones are found in coastal areas of high population density.
(credit: NASA Earth Observatory)

A dead zone is an area in lakes and oceans near the mouths of rivers where large
areas are periodically depleted of their normal flora and fauna. These zones are
caused by eutrophication coupled with other factors including oil spills, dumping
toxic chemicals, and other human activities. The number of dead zones has increased
for several years, and more than 400 of these zones were present as of 2008. One of
the worst dead zones is off the coast of the United States in the Gulf of Mexico:
fertilizer runoff from the Mississippi River basin created a dead zone of over
8,463 square miles. Phosphate and nitrate runoff from fertilizers also negatively
affect several lake and bay ecosystems including the Chesapeake Bay in the eastern
United States.

The Sulfur Cycle

Sulfur is an essential element for the molecules of living things. As part of the amino
acid cysteine, it is involved in the formation of proteins. As shown in Figure 7 below,
sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found
in the form of sulfur dioxide (SO2), which enters the atmosphere in three ways: first,
from the decomposition of organic molecules; second, from volcanic activity and
geothermal vents; and, third, from the burning of fossil fuels by humans.

Figure 7. Sulfur dioxide from the atmosphere becomes available to terrestrial and
marine ecosystems when it is dissolved in precipitation as weak sulfuric acid or
when it falls directly to Earth as fallout. Weathering of rocks also makes sulfates
available to terrestrial ecosystems. Decomposition of living organisms returns
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sulfates to the ocean, soil, and atmosphere. (credit: modification of work by John M.
Evans and Howard Perlman, USGS)

On land, sulfur is deposited in four major ways: precipitation, direct fallout from
the atmosphere, rock weathering, and geothermal vents. Atmospheric sulfur is found
in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere, sulfur
is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly
from the atmosphere in a process called fallout. Also, as sulfur-containing rocks
weather, sulfur is released into the soil. These rocks originate from ocean sediments
that are moved to land by the geologic uplifting of ocean sediments. Terrestrial
ecosystems can then make use of these soil sulfates (SO42-), which enter the food
web by being taken up by plant roots. When these plants decompose and die, sulfur
is released back into the atmosphere as hydrogen sulfide (H2S) gas.
Sulfur enters the ocean in runoff from land, from atmospheric fallout, and from
underwater geothermal vents. Some ecosystems rely on chemoautotrophs using
sulfur as a biological energy source. This sulfur then supports marine ecosystems in
the form of sulfates.
Human activities have played a major role in altering the balance of the global
sulfur cycle. The burning of large quantities of fossil fuels, especially from coal,
releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls
through this gas, it creates the phenomenon known as acid rain, which damages the
natural environment by lowering the pH of lakes, thus killing many of the resident
plants and animals. Acid rain is corrosive rain caused by rainwater falling to the
ground through sulfur dioxide gas, turning it into weak sulfuric acid, which causes
damage to aquatic ecosystems. Acid rain also affects the man-made environment
through the chemical degradation of buildings. For example, many marble
monuments, such as the Lincoln Memorial in Washington, DC, have suffered
significant damage from acid rain over the years. These examples show the wide-
ranging effects of human activities on our environment and the challenges that
remain for our future.

Oxygen Cycle

Oxygen is another nutrient which is important to all living things. Note that the
carbon and oxygen cycles are independent but very closely related. Oxygen is
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present in our atmosphere in the form of ozone, water vapour, pure oxygen and
carbon dioxide. Plants and algae perform photosynthesis which removes carbon
dioxide and adds oxygen to the atmosphere. Animals perform cellular respiration
which removes oxygen from the atmosphere and adds carbon dioxide. When plants
and animals die, decomposers uses oxygen to break down organic material and
release carbon dioxide. Also, water dissolves oxygen and the aquatic life use this
oxygen for photosynthesis and cellular respiration. Fish need oxygen in the water to
perform cellular respiration.

Oxygen is one of the most abundant elements on earth. About 21% of our air is
composed of oxygen. It is also an atom in the molecule of water (H 2O). Oxide
compounds, such as CO2 also contain oxygen.

As we are aware oxygen is absolutely essential for all living organisms to survive.
It is the main component in respiration. It is also the element that allows and assists
combustion of any kind. Through photosynthesis, the replenishment of oxygen in
the atmosphere is done, where oxygen is one of the by-products. In fact,
photosynthesis and respiration are interdependent mechanisms that perform a unique
and amazing balancing.