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Ecology Class Notes - Biogeochemical Cycle (Nutrient cycle)

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 Botany – Ecology Notes

Biogeochemical cycle (Nutrient cycle):

You have already learnt that living organisms required several chemical
elements for their life processes.
There may be used as part of their structural component or as parts of enzymes
which influence various life processes unlike energy which flows
unidirectionally, nutrients are continuously exchanged between the organisms
and their physical environment.

(“Bio” - living, “Geo” – earth - rock, “Chemical” - element).

The cycling of the nutrients in the biosphere is called biogeochemical or
nutrient cycle.
It involves movement of nutrient elements through the various components of
an ecosystem.
There are more than 40 elements required for the various life processes by
plants and animals; that it’s proper growth and development.
Most important elements are C, H, O, P, K, N, S, Ca, Fe, Mg, B, Zn, Cl, Mo, Co, I
& Fe.
These elements are continuously cycling in the ecosystem through the
biogeochemical cycles and the planet earth has no input of these nutrients.
The nutrients (matter) from the dead remains of organisms are recovered and
made available to the producers by decomposers.
Thus the nutrients are never lost from the ecosystems.
Exchange of nutrients between organisms and their environment is one of the
essential aspects of an ecosystem.
All organisms require nutrients for their growth, development, maintenance
and reproduction.
Circulation of nutrients within the ecosystem or biosphere is known as
biogeochemical cycles and also called as ‘cycling of materials’.
There are 3 basic types, 1. Hydrologic or Water cycle, 2. Gaseous cycle (It
includes atmospheric Oxygen, Carbon and Nitrogen cycles) and
3. Sedimentary cycle – It includes the cycles of Phosphorus, Sulphur and
Calcium - Which are present as sediments of earth.

1. Hydrologic or Water cycle:

Earth is a watery planet of the solar system but a very small fraction of this is
available to animals and plants.
Water is not evenly distributed throughout the surface of the earth.
Major percentage of the total water on the earth is chemically bound to rocks
and does not cycle.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 1

 Botany – Ecology Notes

Out of the remaining, nearly 97.3% is in the oceans and 2.1% exists as polar ice
cubes.
Thus only 0.6% is present as fresh water in, the form of atmospheric water
vapors, ground and soil water.
The ice cubes and the water deep in the oceans form the reservoir.
Solar radiation and earth’s gravitational pull are the main driving forces of
water cycle.
Evaporation, condensation and precipitation are the main processes involved in
water cycle these processes alternate with each other.
Water from oceans, lakes, ponds, rivers, streams and soil surface evaporates by
sun’s heat energy.
Plants also transpiration huge amounts of water through their leaves.
Water remains in the vapour state in air and forms clouds, which float with the
wind.
Clouds meet with the cold air in the mountainous regions above the forests and
condense to form rain, which falls due to gravity.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 2

 Botany – Ecology Notes

2. Gaseous cycle:

2.1. Oxygen cycle:

The oxygen cycle is the biogeochemical transitions of oxygen atoms between
different oxidation states in ions, oxides, and molecules through redox reactions
(oxidation-reduction reaction) within and between the spheres/reservoirs of
the planet Earth.
The word oxygen in the literature typically refers to the most common oxygen
allotrope(element changeable form), elemental/diatomic oxygen (O2), as it is a
common product or reactant of many biogeochemical redox reactions within
the cycle.
Processes within the oxygen cycle are considered to be biological or geological
and are evaluated as either a source (O2 production) or sink (O2 consumption).

Reservoirs: Oxygen is one of the most abundant elements on Earth and

represents a large portion of each main reservoir.
By far the largest reservoir of Earth's oxygen is within the silicate and oxide
minerals of the crust and mantle (99.5% by weight).
The Earth's atmosphere, hydrosphere and biosphere together weigh less than
0.05% of the Earth's total mass.
Besides O2, additional oxygen atoms are present in various forms spread
throughout the surface reservoirs in the molecules of biomass, H2O, CO2,
HNO3, NO, NO2, CO, H2O2, O3, SO2, H2SO4, MgO, CaO, AlO, SiO2, and PO4.

Atmosphere:
The Atmosphere is ~20.9% oxygen by volume which equates to a total of
roughly 34x1018 mol of oxygen.
Other oxygen containing molecules in the atmosphere include ozone (O3),
carbon dioxide (CO2), water vapor (H2O), and sulfur and nitrogen oxides (SO2,
NO, N2O, etc.).
Biosphere:
The Biosphere is 22% oxygen by volume present mainly as a component of
organic molecules (CxHxNxOx) and water molecules.
The Hydrosphere is 33% oxygen by volume present mainly as a component of
water molecules with dissolved molecules including free oxygen and carbonic
acids (HxCO3).
Lithosphere - is 46.6% oxygen by volume present mainly as silica minerals
(SiO2) and other oxide minerals.
Reservoir Dynamics:

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 3

 Botany – Ecology Notes

Free Oxygen (O2) from the atmosphere forms an equilibrium concentration by

gas exchange with the hydrosphere as a dissolved gas in aqueous solution
according to Henry's law.
According to this law, O2 saturates in water at 450µM at 0ºC and 270µM at
25ºC, but other dissolved solutes in seawater can reduce this saturation
concentration.
Oxygen concentrations in the hydrosphere can be influenced locally by the
presence or absence of turbulent mixing or local production or consumption of
O2 by biological metabolism.
Oxygen concentration in the soil and groundwater of the pedosphere(soil) is
determined by gas diffusion through soil pore space in air and rainwater and
can also be influenced locally by biological processes.
Oxygen is cycled between the biosphere and lithosphere within the context of
the calcium cycle, marine organisms in the biosphere create calcium carbonate
shell material (CaCO3) that is rich in oxygen.
When the organism dies, its shell is deposited on the shallow seafloor and
buried over time to create the limestone sedimentary rock of the lithosphere.
Weathering processes initiated by organisms can also free oxygen from the
lithosphere.
Plants and animals extract nutrient minerals from rocks and release oxygen in
the process.
Seasonal high latitude O2 level fluctuations of +/- 15 ppm in the northern
hemisphere(half circle world) have been observed and attributed to seasonal
cycles of primary production and respiration.
Human combustion of fossil fuels has been linked to a measured decrease of
around 1x1015 mol per year in O2 concentrations in recent decades.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 4

 Botany – Ecology Notes

Sources and sinks:

While there are many abiotic sources and sinks for O2, the presence of the
abundant concentration of free oxygen in modern Earth's atmosphere and
ocean is attributed to O2 production from the biological process of oxygenic
photosynthesis in combination with a biological sink known as the biological
pump and a geologic process of carbon burial involving plate tectonics.
Biology is the main driver of O2 flux on modern Earth, and the evolution of
oxygenic photosynthesis by bacteria, which is discussed as part of The Great
Oxygenation Event, is thought to be directly responsible for the conditions
permitting the development and existence of all complex eukaryotic
metabolism.
The main source of atmospheric free oxygen is photosynthesis, which produces
sugars and free oxygen from carbon dioxide and water:

2.2. Carbon cycle:

The circulation of carbon between organisms and environment is known as the
carbon cycle.
Carbon is an inevitable part of all biomolecules and is substantially impacted
by the change in global climate.
Cycling of carbon between organisms and atmosphere is a consequence of two
mutual processes of photosynthesis and respiration.
The releasing of carbon in the atmosphere increases due to burning of fossil
fuels, deforestation, forest fire, volcanic eruption and decomposition of dead
organic matters.
Atmospheric carbon dioxide is the source of all carbon in both living organisms
as well as in the fossils (used as fossil fuel).
It is highly soluble in water. Oceans also contain large quantities of dissolved
carbon dioxide and bicarbonates.
The carbon cycle (Fig) comprises the following processes:

Photosynthesis
Terrestrial and aquatic plants utilize CO2 for photosynthesis. Through this
process the inorganic form of carbon is converted into organic matter in the
presence of sunlight and chlorophyll.
The carbon dioxide is thus fixed and assimilated by plants. It is partly used by
them for their own life processes and the rest is stored as their biomass which is
available to the heterotrophs as food.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 5

 Botany – Ecology Notes

Respiration
Respiration is a metabolic process reverse of photosynthesis in which food is
oxidized to liberate energy (to perform the various life processes) and carbon
dioxide and water.
Thus the carbon dioxide of the atmosphere is recovered through this process.
Decomposition
After the death of the organisms the decomposers break down the remaining
dead organic matter and release the left over carbon back into the atmosphere.
Combustion (burning)
Fossil fuel such as crude oil, coal, natural gas or heavy oils on burning releases
carbon dioxide and carbon monoxide into the atmosphere.
Forests make a large amount of fossil fuel. Fossil fuel is product of complete or
partial decomposition of plants and animals as a result of exposure to heat and
pressure in the earth’s crust over millions of years.
Forests also act like carbon reservoirs as carbon fixed by them cycles very
slowly due to their long life.
They release CO2 by forest fires.

2.3. Nitrogen cycle:

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted
into multiple chemical forms as it circulates among atmosphere, terrestrial, and
marine ecosystems.
The conversion of nitrogen can be carried out through both biological and
physical processes.
The majority of Earth's atmosphere (78%) is atmosphere nitrogen, making it the
largest source of nitrogen.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 6

 Botany – Ecology Notes

However, atmospheric nitrogen has limited availability for biological use,

leading to a scarcity of usable nitrogen in many types of ecosystems.
The nitrogen cycle is of particular interest to ecologists because nitrogen
availability can affect the rate of key ecosystem processes, including primary
production and decomposition.
Human activities such as fossil fuel burning, use of artificial nitrogen fertilizers,
and release of nitrogen in wastewater have dramatically altered the global
nitrogen cycle.
Human modification of global nitrogen cycle can negatively affect the natural
environment system and also human health.

Nitrogen is present in the environment in a wide variety of chemical forms

including organic nitrogen, ammonium (NH+4), nitrite (NO−2), nitrate (NO−3),
nitrous oxide (N2O), nitric oxide (NO) or inorganic nitrogen gas (N2).
Organic nitrogen may be in the form of a living organism, humus or in the
intermediate products of organic matter decomposition.
The process in the nitrogen cycle is to transform nitrogen from one form to
another.
Many of those processes are carried out by microbes, either in their effort to
harvest energy or to accumulate nitrogen in a form needed for their growth.
For example, the nitrogenous wastes in animal urine are broken down by
nitrifying bacteria in the soil to be used by plants.
Nitrogen cycle consists of the following steps: fixation, ammonification,
nitrification, denitrification and sedimentation.

1. Nitrogen fixation: Conversion of free nitrogen of atmosphere into the

biologically acceptable form or nitrogenous compounds is referred to as
nitrogen fixation. This process is of two types:
(a) Physicochemical or non-biological nitrogen fixation
(b) Biological nitrogen fixation.
In physicochemical process of nitrogen fixation, atmospheric nitrogen combines
with oxygen (as ozone) during lightning or electrical discharges in the clouds
and produces different nitrogen oxides :

N2, + 2(O) Electric = 2NO

2NO + 2 (O) Discharge = 2NO2,

2NO2 + (O) = N2 O5

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 7

 Botany – Ecology Notes

The nitrogen oxides get dissolved in rain water and on reaching earth surface
they react with mineral compounds to form nitrates and other nitrogenous
compounds :

N2O5 + H2O = 2HNO3

2HNO3 + CaCO2 = Ca(NO3) + CO2 + H2O

During combustion of various types, some nitrogenous compounds are formed

which are washed down along with rain water.
At high pressure and temperature, nitrogen and hydrogen react to form
ammonia (industrial nitrogen fixation).

2. Biological nitrogen fixation: is carried out by certain Prokaryotes.

Some blue-green algae fix significant amounts of nitrogen in the oceans, lakes
and soils.
Symbiotic bacteria (Rhizobium) inhabiting the root nodules of legumes and also
the species of alder, buckbrush and a number of other non-leguminous genera
and symbiotic blue-green algae (species of Nostoc, Anabaena, etc.) found in free
state or in the thalli of Anthoceros, Salvenia, Azolla, coralloid roots of Cycas fix
atmospheric nitrogen.
The relation is mutualistic because the microbes use energy from the plants to
fix nitrogen that is made available to the host plants and other plants of the
community.
Certain free living nitrogen fixing bacteria, such as Azotobacter, Clostridium,
Beijerinckia, Derxia, Rhdospirillium also fix free nitrogen of atmosphere in the
soil.
Frankia, an actinomycetous fungus found in the roots of Alnus, Percia, Casuarina,
etc. also fixes nitrogen.
Nitrogen fixing organisms combine the gaseous nitrogen of atmosphere with
hydrogen obtained from respiratory pathway to form ammonia which then
reacts with organic acids to form aminoacids.
Biological nitrogen fixation is the major source of fixed nitrogen upto 140-700
mg/m2/year as against 35mg/m2/year by electrical discharge and
photochemical fixation.

2. Nitrogen assimilation: Inorganic nitrogen in the form of nitrates, nitrites and

ammonia is absorbed by the green plants and converted into nitrogenous
organic compounds.
Nitrates are first converted into ammonia which combines with organic acids to
form aminoacids.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 8

 Botany – Ecology Notes

Aminoacids are used in the synthesis of proteins, enzymes, chlorophylls,

nucleic acids, etc.
Animals derive their nitrogen requirement from the plant proteins.
Plant proteins are not directly utilized by the animals. They ale first broken
down into amino acids during digestion and then the amino acids are absorbed
and manipulated into animal proteins, nucleic acids, etc.

3. Ammonification: The dead organic remains of plants and animals and

excreta of animals are acted upon by a number of microorganisms especially
actinomycetes and bacilli (Bacillus ramosus, B. vulgaris, B. mesenterilus).
These organisms utilize organic compounds in their metabolism and release
ammonia.

4. Nitrification: Certain bacteria, such as Nitrosomonas, Nitrococcus, Nitrosogloea

and Nitrospira in oceans and soils convert ammonia into nitrites and then
nitrites into nitrates.
These bacteria primarily use the energy of dead organic matter in their
metabolism.
2NH4+ + 2O2 = NO2- + 2H2O + energy
Conversion of nitrites to nitrates is brought about by several microbes like
Penicillium species, Nitrobacter, Nitrocystis etc.
Nitrocystis oceanus is the common marine autotroph which performs
nitrification for obtaining energy.
2NO2- + 2O2 = NO3- + energy
Some nitrates are also made available through weathering of nitrate containing
rocks.

5. Denitrification. Ammonia and nitrates are converted into free nitrogen by

certain microbes.
This process is referred to as denitrification. Thiobacillus denitrificans,
Micrococcus denitrificans, Pseudomonas aeruginosa are the common examples of
denitrifying bacteria.
2NO-3 ----- 2NO-2 ----- 2NO ----- N2O ------N2

6. Sedimentation: Nitrates of the soil are washed down to the sea or leached
deep into the earth along with percolating water.
Nitrates thus lost from the soil surface are locked up in the rocks, this is
sedimentation of nitrogen.
Nitrogen of rock is released only when the rocks are exposed and weathered.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 9

 Botany – Ecology Notes

Thus a large part of nitrogen is fixed up and stored in plants, animals, and
microbes.
Nitrogen leaves the living system in the same amount is taken in from the
atmosphere and the input and outflow of nitrogen are balanced in the
ecosystem.
The overall nitrogen cycle in nature is presented in Figure.

3. Sedimentary cycles:
Mineral elements required by living organisms are obtained initially from
inorganic sources.
Available forms occur as salts dissolved in soil water.
Mineral cycles essentially consist of two phases : (i) the salt solution phase, and
(ii) rock phase.
Mineral salts come directly from earth crust by weathering.
Soluble salts then enter the water cycle.
By movement of water minerals move from the soil to streams, lakes and
ultimately to sea where they remain permanently.

Other salts return to the earth's crust (outside) through sedimentation.

They become incorporated into sediments or rock beds and after weathering of
rocks they again enter the cycle.
Plants and some animals take minerals in the form of mineral solution from
their habitats.
After the death of living organisms the nutrients return to the soil and water
through the action of decomposers (bacteria and fungi) and transformers.
Green plants at one end and decomposers at the other play very important role
in circulation of nutrients.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 10

 Botany – Ecology Notes

3.1.Phosphorus cycle:
Already we know that plants and animals obtain phosphorus from the
environment.
Phosphorus is a component of nucleic acid, found in the biomolecules like
DNA, RNA, ATP, NADP and phospholipid molecules of living organisms.
Phosphorus is not abundant in the biosphere, whereas a bulk quantity of
phosphorus is present in rock deposits, marine sediments and guano (excrete
materials from seabirds used as manure for plant).
It is released from these deposits by weathering process.

After that, it circulates in lithosphere as well as hydrosphere.

The producers absorb phosphorus in the form of phosphate ions, and then it is
transferred to each trophic level of food chain through food.
Again death of the organisms and degradation by the action of decomposers,
the phosphorus is released back into the lithosphere and hydrosphere to
maintain phosphorus cycle.

Phosphorus along with many other mineral elements reaches the Oceans and
settles down as sediment.
A good proportion of phosphorus leaches down to deep layers of soil.
In this way, major proportion of phosphate becomes lost to this cycle by
physical processes, such as sedimentation and leaching.
Biological processes such as formation of teeth and bones also keep phosphorus
locked up for some time.

3.2 Sulphur Cycle.

Sulphur cycle links soil, water and air.

Sulphur occurs in the soil and rocks as sulphides (FeS, ZnS, etc.) and crystalline
sulphates,

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 11

 Botany – Ecology Notes

In the atmosphere sulphur occurs in the form of SO2 and H2S. SO2 gas is formed
during combustion of fossil fuels or as a result of decomposition.
H2S or hydrogen sulphide gas is released to the atmosphere from water logged
soils, continental layer, lakes and springs.
The organic and inorganic sulphur and SO2 are formed through oxidation of
H2S in the atmosphere.
A small amount of sulphur occurs in dissolved state in rain water and through
rains it reaches earth surface.
Except a few organisms which need organic form of sulphur as amino acids
and cystein, most of the organisms take sulphur as inorganic sulphates.
Most of the biologically incorporated sulphur is produced in the soil from
aerobic breakdown of proteins by bacteria and fungi.
Under an aerobic condition, however, sulphur may be reduced directly to
sulphides, including H2S.

2H2S + O2 Baggiatoa spp 2S + 2H2CO

2S + 2H2O + 3O2 Thiobacillus 2H2SO4
Thio-oxidation

Green and purple photosynthetic bacteria use hydrogen of H2S as the oxygen
acceptor in reducing carbon dioxide.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 12

 Botany – Ecology Notes

Green bacteria are able to oxidise sulphide to elemental sulphur whereas the
purple bacteria can carry oxidation to sulphate stage.
In the ecosystems, sulphur is transferred from autotrophs to animals, then to
decomposers and finally it returns to environment through the decay of dead
organic remains (Figure).
Sedimentary aspect sulphur cycling involves precipitation of sulphur in
presence of iron anaerobic conditions.
Sulphides of iron copper, zinc, cadmium, cobalt are insoluble in neutral and
alkaline water and consequently sulphur is bound to limit the amount of these
elements.
Thus, sulphur cycle affords an excellent example of interaction and complex
biochemical regulation between the different mineral cycles.

The study of biogeochemical cycles in the ecosystem makes it clear that the
abiotic components of ecosystem are transformed into biotic structures through
metabolic processes and locked up in the biomass for some time depending
upon the return rate.
In lower plants with soft tissues the return rate is quicker than in higher plants
and animals.
The materials held up in the biomass are released to the environment by
decomposing activities.

The nutrient cycle is not a close circuit within an ecosystem.

The nutrients are continuously being imported as well as carried out of the
ecosystem.
Appreciable quantities of plant nutrients are brought to ecosystem by rain and
snow.
Small quantity of nutrients is carried to the forest by rains.
The gain of nutrients to the ecosystem from precipitation (rainfall),extraneous
material and mineral weather conditions is balance by losses.
Water draining away from forest carries with it more mineral matter than
supplied through precipitation.
Considerable quantities of nutrients in the forest are locked up in the trees and
the humus layer.
When trees and vegetation are removed, sufficient amounts of nutrient are
removed.
Intensive forestry and agriculture on some soils may reduce the nutrient
reserves to such an extent that soils become unfertile.
Ecosystem can remain productive only if the nutrients withdrawn are balanced
by an inflow or replacement.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 13

 Botany – Ecology Notes

QUESTIONS
What is ecosystem? What are the various components of ecosystem.
What are the major ecosystems of the world? Describe forest and pond
ecosystems in detail.
What is meant by energy flow in an ecosystem? What are the laws of
thermodynamics?
Write short notes on the following: Producers, Food chain and Food web,
Ecological pyramids, Hydrologic cycle, Nitrogen cycle, Productivity, Ecological
niches.
Describe various Biogeochemical cycles occurring in nature.

Dr. Abdul Hameed, Dept. of Botany, GAC, KGI 14

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