Biogeochemical cycles.ppt by maria ashraf

Biogeochemical cycle

1. BIOGEOCHEMICAL CYCLES

2. Biogeochemical cycleor substance turnover or
cycling of substances is a pathway by which a
chemical substance moves through both the
biotic (biosphere) and abiotic (lithosphere,
atmosphere, and hydrosphere) components of
Earth.

3. Biogeochemical activities are:
unidirectional on a geologic time scale
cyclical on a contemporary scale
To understand cycling of elements, the size and cycling activity level of the reservoirs of
the element must be defined. atmospheric CO
2is a relatively small reservoir of carbon
that is actively cycled. Such small, actively cycled reservoirs are most subject to
perturbation. H2O
O2
CO2
Turnover
rates
3 x 10 yr
2 x 10 yr
2 x 10 yr
2
3
6
atmosphere
lithosphere
hydrosphere
Relative reservoir sizes: H2O > O2>> CO2
The concept of
a reservoir

4. Physical transformations
dissolution
precipitation
volatilization
fixation
Chemical transformations
biosynthesis
biodegradation
oxidoreductive-biotransformations
What reactions drive biogeochemical cycling?
Driving force for biogeochemical cycles is sunlightEnergy Flow
Primary producers
Grazers
Predators
Predators
D
e
c
o
m
p
o
s
e
r
s
C
O

a
n
d

m
in
e
r
a
ls
2
100%
15%
2%
0.3%
CO
2
<0.1%
The ability to photosynthesize allows
sunlight energy to be trapped and stored.
This is not an efficient processalthough
some environments are more productive
than others.Only 10-15% of the energy
trapped in each trophic level is passed on
to the next level.

5. The Carbon Cycle
The development of photosynthesis allowed microbes to tap into sunlight energy and
provided a mechanism for the first carbon cycle. At the same time the carbon cycle
evolved, the nitrogen cycle emerged because nitrogen was limiting for microbial growth.
Although N
2was present, it was not in a usable form for microbes.Aerobic Anaerobic
Fossil fuels
FermentationPhotosynthesis
Respiration
Methanogenesis
CO + H O
22 O + CH O
2 2 Alcohols, acids,
H + CO
22
CH
4
CH O
2

6. Carbon Reservoir Metric tons
carbon
Actively
cycled
Atmosphere
CO
2
Ocean
Biomass
Carbonates
Dissolved and
particulate organics
Land
Biota
Humus
Fossil fuel
Earth’s crust
6.7 x 10
11
4.0 x 10
9
3.8 x 10
13
2.1 x 10
12
5.0 x 10
11
1.2 x 10
12
1.0 x 10
13
1.2 x 10
17
Yes
Yes
No
Yes
Yes
Yes
Yes
No
Global Carbon Reservoirs

7. The carbon cycle is a good example of one that is undergoing a major perturbation
due to human activity.
Human activity has had a large impact on the atmospheric CO
2reservoir beginning with
industrialization. As a result, the level of CO
2in the atmosphere has increased 28% in
the past 150 years.
Carbon source metric tons carbon/yr
Release by fossil-fuel combustion 7 x 10
9
Land clearing 3 x 10
9
Forest harvest and decay 6 x 10
9
Forest regrowth -4 x 10
9
Net uptake by oceans -3 x 10
9
Annual flux 9 x 10
9

8. Natural sources of CO
2
•respiration
•ocean degassing
•terrestrial degassing
•wildfires
Anthropogenic sources of CO
2
•fossil fuel combustion
•cement production
•land use changes
Natural sinks for CO
2
•terrestrial
uptake by plants
uptake by soils
•oceanic
partitioning
biomass production
Anthropogenic sinks for CO
2
•chemical production
•biological materials
Natural and anthropogenic CO
2sources and sinks

9. The Nitrogen Cycle
N is cycled between: NH
4
+
(-3 oxidation state) and NO
3
-
(+5 oxidation state)

10. Nitrogen Reservoir Metric tons nitrogenActively cycled
Atmosphere
N
2
Ocean
Biomass
Soluble salts (NO
3, NO
2
-
, NH
4
+
)
Dissolved and particulate
organics
Dissolved N
2
Land
Biota
Organic matter
Earth’s crust
3.9 x 10
15
5.2 x 10
8
6.9 x 10
11
3.0 x 10
11
2.0 x 10
13
2.5 x 10
10
1.1 x 10
11
7.7 x 10
14
No
Yes
Yes
Yes
No
Yes
Slow
No
Global Nitrogen Reservoirs

11. Summary for nitrogen fixation:
energy intensive
inhibited by ammonia
occurs in aerobic and anaerobic environments
end-product is ammonia
nitrogenase is O
2sensitive
Fate of ammonia (NH
3) produced during nitrogen fixation
plant uptake
microbial uptake
adsorption to colloids (adds to CEC)
fixation within clay minerals
incorporation into humus
volatilization
nitrification
}
assimilation and mineralization

12. NH
3 is assimilatedby cells into:
proteins
cell wall constituents
nucleic acids
Ammonia assimilation and ammonification
Release of assimilated NH
3is called ammonification. This process can occur
intracellularly or extracellularly
proteases
chitinases
nucleases
ureases

13. Summary for ammonia assimilation and ammonification
Assimilation and ammonification cycles ammonia between its organic and inorganic
forms
Fate of ammonia (NH
3) produced during nitrogen fixation
plant uptake
microbial uptake
adsorption to colloids
fixation within clay minerals
incorporation into humus
volatilization
nitrification

14. Nitrification-Chemoautotrophic aerobic process
Nitrosomonas Nitrobacter
NH
4
+
NO
2
-
NO
3
-
Nitrosomonas:
34 moles NH
4
+
to fix 1 mole CO
2
Nitrobacter:
100 moles NH
4
+
to fix 1 mole CO
2
Summary for nitrification
Nitrification is an chemoautotrophic, aerobic process
Nitrification in managed systems can result in nitrate leaching and groundwater
contamination
Nitrification is sensitive to a variety of chemical inhibitors and is inhibited at low pH.
(There are a variety of nitrification inhibitors on the market)
Nitrification is important in areas that are high in ammonia (septic tanks, landfills,
feedlots, dairy operations, overfertilization of crops). The nitrate formed is highly mobile
(does not sorb to soil). As a result, nitrate contamination of groundwater is common.
Nitrate contamination can result in methemoglobenemia (blue baby syndrome) and it
has been suggested (not proven) that high nitrate consumption may be linked to stomach
cancer.

15. What is the fate of NO
3
-
following nitrification?
accumulation (disturbed vs. managed)
fixation within clay minerals
leaching (groundwater contamination)
dissimilatory nitrate reduction
•nitrate ammonification
•denitrification
plant uptake
microbial uptake
biological uptake (assimilatory nitrate
reduction)}
Assimilatory nitrate reduction
many plantsprefer nitrate which is reduced in the plant prior to use however, nitrogen in
fertilizer is added as ammonia or urea.
assimilatory nitrate reduction is inhibited by ammonium
nitrate is more mobile than ammonium leading to leaching loss
microorganismsprefer ammonia since uptake of nitrate requires a reduction step

16. Dissimilatory nitrate reduction
Dissimilatory reduction of nitrate to ammonia (DNRA)
use of nitrate as a TEA
(anaerobic process) –less energy produced
inhibited by oxygen
not inhibited by ammonium
found in a limited number of
carbon richenvironments
stagnant water
sewage plants
some sediments
Denitrification
use of nitrate as a TEA
(anaerobic process) –more energy produced
many heterotrophic bacteria are denitrifiers
produces a mix of N
2 and N
2O
inhibited by oxygen
not inhibited by ammonium

17. NO
3
-
NO
3
-
NO
2
-
NO
2
-
NO NO
2 N
2
N
2NO
2
NONO
2
-
Cytoplasm
Periplasm
Inner
membrane
Outer
membrane
Outside cell
nitrate
reductase
nitrite reductase
nitric oxide
reductase
nitrous oxide
reductase Denitrification requires a set of 4 enzymes:
nitrate reductase
nitrite reductase
High [NO
3
-
] favors N
2production
Low [NO
3
-
] favors N
2O production
nitric oxide
reductase
nitrous oxide
reductase

18. Denitrification
NO, N
2O deplete the ozone layer
Reaction of N
2O with ozone
O
2+ UV light O + O
O + O
2 O
3(ozone generation)
N
2O + UV light N
2 + O
*
N
2O + O
*
2NO (nitric oxide)
NO + O
3 NO
2+ O
2 (ozone depletion)
NO
2+ O
*
NO + O
2
returns fixed N to atmosphere:
get formation of NO, N
2O
NO
3 NO N
2O N
2

19. Summary for nitrate reduction
Nitrate assimilated must be reduced to ammonia for use.
Oxygen does not inhibit this process
Nitrate assimilation is inhibited by ammonia
1. Assimilatory nitrate reduction
2. Dissimilatory nitrate reduction to ammonia (DNRA)
Anaerobic respiration using nitrate as TEA
Inhibited by oxygen
Limited to a small number of carbon-rich, TEA poor environments
Fermentative bacteria predominate
3. Dissimilatory nitrate reduction (denitrification)
Anaerobic respiration using nitrate as TEA
Inhibited by oxygen
Produces a mix of N
2and N
2O
Many heterotrophs denitrify

20. Sulfur Cycle
10th most abundant element
average concentration = 520 ppm
oxidation states range from +6 (sulfate) to -2 (sulfide)

21. Sulfur Reservoir Metric tons sulfurActively cycled
Atmosphere
SO
2/H
2S
Ocean
Biomass
Soluble inorganic ions
(primarily SO
4
2-
)
Land
Biota
Organic matter
Earth’s crust
1.4 x 10
6
1.5 x 10
8
1.2 x 10
15
8.5 x 10
9
1.6 x 10
10
1.8 x 10
16
Yes
Yes
Slow
Yes
Yes
No
Global Sulfur Reservoirs

22. 1. Assimilatory sulfate reduction
The form of sulfur utilized by microbes is reduced sulfur. However, sulfide (S
2-
) is toxic
to cells. Therefore sulfur is taken up as sulfate (SO
4
2-
), and in a complex series of
reactions the sulfate is reduced to sulfide which is then immediately incorporated into
the amino acid serine to form cysteine.
Sulfur makes up approx. 1% of the dry weight of a cell. It is important for synthesis of
proteins (cysteine and methionine) and co-enzymes.
Assimilatory sulfate reduction (requires a reduction of SO
4
2-
to S
2-
)
SO
4
2-
+ ATP APS + Ppi
adenosine phosphosulfate
APS + ATP PAPS + ADP
3’ –phosphoadenosine –5-phosphosulfate
PAPS + 2e
-
SO
3
2-
+ PAP
SO
3
2-
+ 6H
+
+ 6e
-
S
2-
S
2-
+ serine cysteine + H
2O

23. Sulfur Mineralization
SH –CH
2-CH -COOH + H
2O
NH
2
OH –CH
2-CH –COOH + H
2S
NH
2
terrestrial environments
cysteine serine
marine environments
algae dimethylsulfoniopropionateDimethylsulfide (DMS)
At a C:S ratio < 200:1, sulfur mineralization is favored
At a C:S ratio > 400:1, sulfur assimilation is favored

24. Sulfide oxidation (nonbiological)
H
2S and DMS are photooxidized to SO
4
2-
in the atmosphere
Normal biological production = 1 kg SO
4/ha/yr
Rural production = 10 kg SO
4/ha/yr
Urban production = 100 kg SO
4/ha/yr
acid rain –pH < 5.6
Both the H
2S and the DMS generated during sulfur mineralization are volatile and therefore
significant amounts are released to the atmosphere. Here they are photooxidized to sulfate.
SO
4
2-
+ water H
2SO
4(sulfuric acid)
fossil fuel burning releases SO
2 H
2SO
3 (sulfurous acid)

25. Aerobic sulfur oxidation
H
2S + 1/2O
2 S
0
+ H
20 G = -50.1 kcal/mol
Chemolithotrophic bacteria
Beggiatoa
Thioplaca
Thiothrix
Thermothrix
Thiobacillus
H
2S not released to the atmosphere acts as substrate for sulfur-oxidizers.
Under aerobic conditions:
What unusual community is based on the
chemoautrophic sulfur oxiders?

26. Acidothiobacillus-obligate aerobes
acid intolerant spp.
Acidophilic sulfur-oxidizers:
H
2S + 1/2O
2 S
0
+ H
2O
acid tolerant spp.
S
0
+ 3/2O
2+ H
2O H
2SO
4
G = -149.8 kcal/mol
All sulfur oxidizers are aerobic with the exception of:
Acidothiobacillus denitrificans -uses nitrate as TEA
4NO
3-
+ 3S
0
3SO
4
2-
+ 2N
2

27. Phototrophic oxidation
anaerobic photoautotrophic process:
Chromatium
Ectorhodospirillum
Chlorobium
Under anaerobic conditions, H
2S is utilized by photosynthetic bacteria:
CO
2+ H
2S C(H
2O) + S
0
Anaerobic photosynthesis
CO
2+ H
2O C(H
2O) + O
2
Aerobic photosynthesis
Green and purple sulfur bacteria

28. Summary -Consequences of Sulfur Oxidation
•Solubilization and leaching of minerals, e.g., (phosphorus) due to decreased pH
•Acid mine drainage
•Acid rain
Dissimilatory sulfate reduction and sulfur respiration
Heterotrophic reduction of sulfur
1. respiratory S
0
reduction
2. dissimilatory SO
4
2-
reduction
anaerobic
heterotrophic
limited number of electron donors (substrates)
lactic acid
pyruvic acid
H
2
small MW alcohols

29. Desulfuromonas acetoxidansCH
3COOH + 2H
2O + 4S
0
2CO
2+ 2H
2S
Desulfovibrio
Desulfotomaculum
H
2+ SO
4
2-
H
2S + 2H
2O
-
+ 2OH
-
Example of a heterotrophic sulfate reducer:
Examples of autotrophic sulfate reducers:
Summary -Sulfate Reduction:
•inhibited by oxygen
•can result in gaseous losses to atmosphere
•produces H
2S which can result in anaerobic corrosion of steel and iron set in
sulfate-containing soils

30. Hydrologic (Water) Cycle

31. Phosphorus Cycle