Presentation to the course instructor

1. WOLLO UNIVERSITY
SCHOOL OF BIO-SCIENCE AND TECHNOLOGY
DEPARTMENT OF BIOLOGY
Agricultural Microbiology (BIOM6365)
Nutrients Biotransformation and Geochemical Cycling
By: Gedefaw Wubie
Ordered By: Dr. Mussa Adal
June, 2019
Dessie; Ethiopia
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2. Contents
• Biogeochemical Cycles
• Nitrogen Cycle
• Phosphorus cycle
• Sulfur cycle
• Carbon cycle
2

3. Biogeochemical Cycles
What is a Cycle?
• Cycle: Continuous movement or transfer of
something.
• Cycling in Ecosystems:
– All Matter (nutrients) continuously move between
organisms and regions.
– Energy continuously moves between organisms…
3

4. Biogeochemical Cycles
 Describe the flow of essential elements from the
environment through living organisms and back into the
environment.
4

5. Nitrogen cycle
• What is nitrogen?
 The largest single source of nitrogen is in
the atmosphere.
• Where is nitrogen found in the
environment?
 Nitrogen makes up 78% of our air!
 Nitrogen is required for the manufacture of
amino acids and nucleic acids)
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6. Forms of Nitrogen
• Urea  CO(NH2)2
• Ammonia  NH3 (gaseous)
• Ammonium  NH4
• Nitrate  NO3
• Nitrite  NO2
• Atmospheric Dinitrogen N2
• Organic N
• What happens to atmospheric nitrogen
(N2) in the nitrogen cycle?
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7. Atmospheric nitrogen is converted to ammonia or
nitrates.
Ammonia (NH3)
Nitrogen combines with
Hydrogen to make
Ammonia
Nitrates (NO3)
Nitrogen combines with
Oxygen to make
Nitrates
Atmospheric
Nitrogen (N2)
N
N
N
N

8. Why does atmospheric nitrogen need to be
converted???
It is one of nature’s great ironies…
 Nitrogen is an essential component of
DNA, RNA, and proteins—the
building blocks of life.
 Although the majority of the air we
breathe is nitrogen, most living
organisms are unable to use nitrogen
as it exists in the atmosphere!
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9.  How does atmospheric nitrogen get
changed into a form that can be used by
most living organisms?
 By traveling through one of the four
processes in the Nitrogen Cycle!
9
Nitrogen
Cycle

10. By traveling through one of the four
processes in the Nitrogen Cycle!
(1) Nitrogen Fixation
(3) Nitrification (2) Ammonification
(4) Denitrification
Nitroge
n Cycle

11. • The first process in the nitrogen cycle
is…
Nitrogen Fixation!
What is
“nitrogen fixation”
and
what does it mean
to say
nitrogen gets “fixed”?
11
Nitrogen
Cycle
(1) Nitrogen
Fixation

12. “Nitrogen Fixation” is the process that causes the strong two-atom nitrogen
molecules found in the atmosphere to break apart so they can combine with other
atoms.
Nitrogen gets “fixed” when it is combined with oxygen or
hydrogen.
N
N
N
N
N
Oxygen Hydrogen
Oxygen
Hydrogen
N

13. There are three ways that nitrogen gets
“fixed”!
(a) Atmospheric Fixation
(b) Industrial Fixation
(c) Biological Fixation
Bacteria

14. Atmospheric Fixation
(Only 5 to 8% of the Fixation
Process)
The enormous energy of lightning
breaks nitrogen molecules apart
and enables the nitrogen atoms to
combine with oxygen forming
nitrogen oxides (N2O).
Nitrogen oxides dissolve in rain,
forming nitrates.
Nitrates (NO3) are carried to the
ground with the rain.
Lightning “fixes” Nitrogen!
Nitrogen
combines
with Oxygen
Nitrogen oxides forms
Nitrogen oxides
dissolve in rain
and change to
nitrates
Plants use nitrates
to grow!
(NO3)
N
N O
(N2O)

15. Industrial Fixation
Under great pressure, at a
temperature of 600
degrees Celcius, and with
the use of a catalyst,
atmospheric nitrogen (N2)
and hydrogen are
combined to form
ammonia (NH3). Ammonia
can be used as a fertilizer.
Industrial Plant combines
nitrogen and hydrogen
Ammonia is formed
Ammonia is used a fertilizer in soil
(NH3)
N
N
H
N
H3

16. Biological Fixation
(where MOST nitrogen fixing is completed)
There are two types of “Nitrogen Fixing Bacteria”
Free Living Bacteria
(“fixes” 30% of N2) Symbiotic Relationship Bacteria
(“fixes” 70% of N2)

17. Free Living Bacteria
Highly specialized bacteria live in the soil and have the ability to
combine atmospheric nitrogen with hydrogen to make ammonia
(NH3).
Free-living bacteria live in
soil and combine
atmospheric nitrogen with
hydrogen
Nitrogen changes into
ammonia
N
N
H
N H3
(NH3)
Bacteria

18. Symbiotic Relationship
Bacteria
Bacteria live in the roots
of legume family plants
and provide the plants
with ammonia (NH3) in
exchange for the plant’s
carbon and a protected
home.
Legume plants
Roots with nodules
where bacteria live
Nitrogen changes into
ammonia.
NH3
N
N

19. • Most atmospheric nitrogen (N2) is “fixed”
and changed to ammonia (NH3). Ammonia
is highly toxic to many organisms.
Can plants use ammonia?
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20. Very few plants can use ammonia (NH3)…
…but, fortunately the
second process
Ammonification can help!
(1) Nitrogen Fixation
(2) Ammonification

21. What is
ammonification?
Ammonification: Bacteria decomposers break down amino acids
from dead animals and wastes into nitrogen ammonium.
Bacteria decomposers break down amino acids into ammonium

22. Why is ammonification necessary?
Because plants cannot use the organic forms of
nitrogen that are in the soil as a result of:
(1) wastes (manure and sewage)
(2) compost and decomposing roots and leaves

23. How does ammonification occur?
Microorganisms convert the organic nitrogen to ammonium.
The ammonium is either taken up by the plants (only in a few
types of plants) or is absorbed into the soil particles.
Ammonium (NH4) in the soil is stored up to later be changed
into inorganic nitrogen, the kind of nitrogen that most plants
can use.
Ammonium (NH4) is
stored in soil.
Bacteria converts organic nitrogen to
ammonium (NH4)
Ammonium (NH4) is used by some
plants
Bacteria

24. What happens to ammonium (NH4) stored
in the soil???
It travels through the
third process
of the nitrogen cycle called Nitrification!
(1) Nitrogen Fixation
(2) Ammonification
(3) Nitrification

25. First we will quickly “run through” a general overview of the
Nitrification Process
Nitrifying bacteria in the ground first combine ammonia with oxygen
to form nitrites. Then another group of nitrifying bacteria convert
nitrites to nitrates which green plants can absorb and use!
Nitrifying bacteria in soil combine
ammonia with oxygen
Ammonia changes to nitrites
Nitrifying bacteria in soil convert
nitrites to nitrates
Plants absorb nitrates and
grow!
Ammonia
Nitrites Nitrates
(NH3) (NO3)
(NO2)

26. Nitrification is a biological process during which nitrifying
bacteria convert toxic ammonia to less harmful nitrate.
Nitrification aids in the decomposition of nitrogenous material
and thus in the recycling of nitrogen atoms since the
decontamination of organic nitrogen produces ammonia that is
subsequently oxidized to nitrate by nitrification.
There two bacterial species involved. Nitrosomonas sp.
 Bacteria oxidize ammonia into nitrite, while Nitrobacter
bacteria convert nitrite to nitrate, with both species utilizing the
energy released by the reactions.

27. Cont…
• Ammonia can be used by some plants.
• Most nitrogen taken up by plants is
converted by chemoautotrophic
bacteria from ammonia, which is
highly toxic to many organisms, first
into nitrite (NO2
-), and then into
nitrate (NO3
-).
• This process is called nitrification, and
these bacteria are known as nitrifying
bacteria.
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28. Nitrifiers such as Arthrobacter (heterotroph), Aspergilli’s
(heterotroph), and Nitrosomonas (autotroph) are delicate
organisms and extremely susceptible to a variety of inhibitors.
They are extremely slow growing, unlike many bacteria that
can double their numbers every hour or so.
In order to thrive, nitrifying bacteria need a relatively clean
environment with a steady supply of ammonia and oxygen.

29. Nitrification is a Two Step Process
First Step: Ammonium Oxidation
The microorganisms involved are called the ammonia oxidizers. Nitrosomonas is
the most extensively studied and usually the most numerous in soil. Nitrosospira is
an aquatic nitrifier.
•Nitrosomonas
•Nitrosospira
•Nitrosococcus
•Nitrosolobus
Ammonia-Oxidizing Bacteria:
These organisms are chemoautotrophs, growing with ammonia as the energy and
CO2 as the main carbon source.
 Species are distributed in a great variety of soils, oceans, brackish environments,
rivers, lakes, and sewage disposal systems.

30. Second step: Nitrite Oxidation
• Microorganism involved: Nitrobacter
• These bacteria comprise a diverse group of rod, ellipsoidal,
spherical, and spiral-shaped cells.
• At least one strain of Nitrobacter has been described that can grow
by anaerobic respiration (denitrification).
• Nitrite-oxidizing bacteria are found in aerobic, but occasionally also
in anaerobic, environments where organic matter is mineralized.
• They are widely distributed in soils, fresh water, brackish water,
seawater, mud layers, sewage disposal systems, and inside stones of
historical buildings and rocks.
• They are also found inside corroded bricks and on concrete surfaces
such as in cooling towers and highway-automobile tunnels.
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31. How does nitrogen reenter the atmosphere in the
nitrogen cycle?
Through the fourth process called denitrification!
(1) Nitrogen Fixation
(2) Nitrification
(3) Ammonification
(4) Denitrification

32. What does denitrification do?
Denitrification converts nitrates (NO3) in the soil
to atmospheric nitrogen (N2) replenishing the
atmosphere.
Nitrates (NO3) in
Soil
Nitrogen in atmosphere (N2)

33. denitrification process
Denitrifying bacteria live deep in soil and in aquatic sediments
where conditions make it difficult for them to get oxygen. The
denitrifying bacteria use nitrates as an alternative to oxygen, leaving
free nitrogen gas as a byproduct. They close the nitrogen cycle!
Emissions from industrial combustion and gasoline engines create nitrous
oxides gas (N2O).
Volcano eruptions emit nitrous oxides gas (N2O).
Denitrifying bacteria live deep
in soil and use nitrates as an
alternative to oxygen making a
byproduct of nitrogen gas.
Nitrogen in atmosphere closes the
nitrogen cycle!
(NO3)
(N2)

34. (1) Nitrogen Fixation
(3) Nitrification (2) Ammonification
(4) Denitrification
Nitrogen
Cycle
Nitrates in Soil
Ammonia is converted to
nitrites and nitrates.
Organic nitrogen is converted
to ammonium.
(a)
(b)
(c)
N2
NH3
NO3
N2O

35. (1) _____________
(3) ____________ (2) _____________
(4) _____________
Nitrogen
Cycle
Nitrates in Soil
Ammonia is converted to
nitrites and nitrates.
Organic nitrogen is converted
to ammonium.
(a)
(b)
(c)
N2
NH3
NO3
N2O

37. Shortly:
Nitrogen cycle.
Nitrogen-fixing bacteria convert atmospheric nitrogen (N2)
into ammonia (NH3).
Ammonia or ammonium in converted to nitrate (NO3) by
nitrifying bacteria in the soil.
Plants assimilate nitrate, ammonia, or ammonium, producing
protein and nucleic acids in the process; then animals eat plant
proteins and produce animal proteins.
Ammonifying bacteria break down the nitrogen compounds
of dead organisms, releasing ammonia that can be reused.
 Nitrogen is returned to the atmosphere by denitrifying
bacteria, which convert nitrate to atmospheric nitrogen.

38. Reservoir – atmosphere (as N2); soil (as NH4
+ or
ammonium, NH3 or ammonia, N02
- or nitrite,
N03
- or nitrate
Assimilation – plants absorb nitrogen as either NH4
+ or as
N03
-, animals obtain nitrogen by eating plants
and other animals. The stages in the
assimilation of nitrogen are as follows:
Nitrogen Fixation: N2 to NH4
+ by nitrogen-fixing bacteria
(prokaryotes in the soil and root nodules), N2 to N03
- by
lightning and UV radiation.
Nitrification: NH4
+ to N02
- and N02
- to N03
- by various nitrifying
bacteria.
Release – Denitrifying bacteria convert N03
- back to N2
(denitrification); detrivorous bacteria convert organic
compounds back to NH4
+ (ammonification); animals
excrete NH4
+ (or NH3) urea, or uric acid.
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39. Summary of the nitrogen cycle
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40. The sulfur cycle
• The sulfur cycle contains both atmospheric and terrestrial processes.
Within the terrestrial portion, the cycle begins with
the weathering of rocks, releasing the stored sulfur.
• The sulfur then comes into contact with air where it is converted
into sulfate (SO4).
• The sulfate is taken up by plants and microorganisms and is
converted into organic forms; animals then consume these organic
forms through foods they eat, thereby moving the sulfur through the
food chain.
• As organisms die and decompose, some of the sulfur is again
released as a sulfate and some enters the tissues of microorganisms.
• There are also a variety of natural sources that emit sulfur directly
into the atmosphere, including volcanic eruptions, the breakdown of
organic matter in swamps and tidal flats, and the evaporation of
water.
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41. Cont…
• particles and tiny air borne droplets, sulfur also
acts as a regulator of global climate.
• Sulfur dioxide and sulfate aerosols
absorb ultraviolet radiation, creating cloud cover
that cools cities and may offset global warming
caused by the greenhouse effect.
• The actual amount of this offset is a question that
researchers are attempting to answer.
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42. Sulfur cycle
42

43. Chemical reaction involved
• The chemical processes help produce hydrogen In the
atmosphere.
• When the sulfur and the water in the atmosphere mix they
make sulfuric acid which is put into the rain and put onto the
earth surface
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44. Organic Reservoirs
• Soil
• Plants
 We are tying to come up with cleaner ways
to run factories so we put less sulfur into the
atmosphere thus reducing the sulfuric acid in
the rain which makes it better for the plants
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45. 45

46. Phosphorus Cycle
46

47. Uses of phosphorus
• key component of molecules that store energy
• ATP
• DNA and lipids ( fat and oil)
• Used to cell growth in the plant and animal
• Insufficient P results decreased crop yield.
• Phosphorus moves in a cycle through rocks, water, soil and sediments and
organisms.
• Over time, rain and weathering cause rocks to release phosphate ions and
other minerals. This inorganic phosphate is then distributed in soils and
water.
• Plants uptake the inorganic P, when they die it turns to the soil.
• most of our phosphorus is locked up in sediments and rocks.
• Due to this reason there is no sufficient P in the plant or in the soil.
• The availability of phosphorus in soil to plants depends of several
reversible pathways: Bacteria, ph and adsorption or using phosphate
solublizing fertilizers
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48. cont….
Reservoir – erosion transfers phosphorus to water and soil;
sediments and rocks that accumulate on ocean
floors return to the surface as a result of uplifting
by geological processes
Assimilation – plants absorb inorganic PO4
3- (phosphate) from
soils; animals obtain organic phosphorus when
they plants and other animals
Release – plants and animals release phosphorus when they
decompose; animals excrete phosphorus in their
waste products
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49. Carbon cycle
C is:
An element
The basis of life of earth
Found in rocks, oceans, atmosphere
carbon is required for building organic compounds
Common Compounds:
• Carbon Dioxide (CO2)
• Glucose (C6H12O6)
• Methane (CH4)
• Carbon Monoxide (CO)
49

50. Cont…
1. Reservoir – atmosphere (as CO2), fossil fuels (oil, coal),
durable organic materials (for example: cellulose).
2. Assimilation – plants use CO2 in photosynthesis; animals
consume plants.
3. Release – plants and animals release CO2 through respiration
and decomposition; CO2 is released as wood and
fossil fuels are burned.
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51. Fossil fuels
Examples Coal, Gas and Oil
Source:
Old, compressed, heated remains of organisms
Store HUGE quantities of carbon inside the earth (until dug up).
Release HUGE quantities of carbon dioxide when burned.
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52. Cont…
 The same carbon atoms are used repeatedly on earth. They
cycle between the earth and the atmosphere.
52

53. Carbonates
• Bicarbonate: (HCO3)
– Used as a buffer in organisms + water systems
• Calcium Carbonate: (CaCO3)
– Compound formed from the shell-remains of aquatic
organisms
– Found underground and in water systems
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54. Plant uses carbon dioxide
 Plants pull carbon dioxide from the atmosphere and use it to
make food –— photosynthesis.
 The carbon becomes part of the plant (stored food).
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55. Animal eat plants
• When organisms eat plants, they take in the
carbon and some of it becomes part of their
own bodies.
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56. Plants and animal die
• When plants and animals die, most of their bodies are
decomposed and carbon atoms are returned to the atmosphere.
• Some are not decomposed fully and end up in deposits
underground (oil, coal, etc.).
56

57. Carbon slowly returns to the
atmosphere
• Carbon in rocks and underground deposits is
released very slowly into the atmosphere.
• This process takes many years.
57

58. Carbon Cycle Diagram
Carbon in Atmosphere
Plants use
carbon to make
food
Animals eat
plants and
take in carbon
Plants and
animals die
Decomposers
break down dead
things, releasing
carbon to
atmosphere and
soil
Bodies not
decomposed —
after many
years, become
part of oil or coal
deposits
Fossil fuels are
burned; carbon
is returned to
atmosphere
Carbon slowly
released from
these substances
returns to
atmosphere

59. Carbon in the ocean
• Additional carbon is stored in the ocean.
• Many animals pull carbon from water to use in shells, etc.
• Animals die and carbon substances are deposited at the bottom
of the ocean.
• Oceans contain earth’s largest store of carbon.
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60. The carbon cycle
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61. 61

62. The human impacts
• Fossil fuels release carbon stores very slowly
• Burning anything releases more carbon into atmosphere —
especially fossil fuels
• Increased carbon dioxide in atmosphere increases global
warming
• Fewer plants mean less CO2 removed from atmosphere
• Burn less, especially fossil fuels
• Promote plant life, especially trees
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