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Chapter 14 - Biogeochemical Cycling
Objectives
• Be able to give an explanation of why biogeochemical cycles are important
• Be able to explain what the GAIA hypothesis is
• Be able to list three major biogeochemical changes between early and
modern earth
• Be able to define the term reservoir and give an example of a small easily
perturbed reservoir and a large stable reservoir
• Be able to list the three major plant polymers
• Be familiar with all parts of the carbon, nitrogen, and sulfur cycles
• Be able to draw each cycle and describe the microbial activities associated
with each leg of the cycles
• Be able to give an example of a microbe associated with each leg of the
cycle
Elemental Breakdown
Chemical composition
of an E. coli cell
% dry mass of an E. coli
cell
Major elements
Carbon
Oxygen
Hydrogen
Nitrogen
Sulfur
Phosphorus
50
20
8
14
1
3
Minor elements
Potassium
Calcium
Magnesium
Chlorine
Iron
2
0.05
0.05
0.05
0.2
Trace elements
Manganese
Molybdenum
Cobalt
Copper
Zinc
All trace elements
combined comprise 0.3%
of dry weight of cell
How has earth maintained conditions favorable for life? Compare
atmospheres and temperatures on Earth, Venus, and Mars.
Atmosphere and Temperatures found on Venus, Mars, and Earth
Gas
Venus
Mars
Earth
no life
Carbon dioxide
Nitrogen
Oxygen
Argon
Methane
96.5%
3.5%
Trace
70 ppm
0
95%
2.7%
0.13%
1.6%
0
98%
1.9%
0
0.1%
0
0.03%
79%
21%
1%
1.7ppm
459
-53
290  50
13
Surface temperature 0C
Earth
with life
Biogeochemical activities are:
unidirectional
on a geologic time scale
cyclical
on a contemporary scale
atmosphere
H 2O
O2
CO2
The concept of
a reservoir
lithosphere
hydrosphere
Turnover
rates
3 x 10 2 yr
2 x 10 3 yr
2 x 10 6 yr
Relative reservoir sizes: H2O > O2 >> CO2
To understand cycling of elements, the size and cycling activity level of the
reservoirs of the element must be defined. atmospheric CO2 is a relatively
small reservoir of carbon that is actively cycled. Such small, actively cycled
reservoirs are most subject to perturbation.
What reactions drive biogeochemical cycling?
Physical transformations
dissolution
precipitation
volatilization
fixation
Chemical transformations
biosynthesis
biodegradation
oxidoreductive-biotransformations
Driving force for biogeochemical cycles is sunlight
Energy Flow
<0.1%
Primary producers
100%
CO2
Decomposers
CO2 and minerals
The ability to photosynthesize allows
sunlight energy to be trapped and
stored. This is not an efficient process
although 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.
Grazers
15%
Predators
2%
Predators
0.3%
Net primary productivity of some natural and managed ecosystems
Description of ecosystem
Tundra
Desert
Temperate grassland
Temperate forest
Tropical rainforest
Cattail Swamp
Freshwater pond
Open ocean
Coastal seawater
Upwelling area
Coral reef
Corn field
Rice paddy
Sugarcane field
Net primary productivity
(g dry organic matter/m2/yr)
400
200
Up to 1,500
1,200 – 1,600
Up to 2,800
2,500
950 – 1,500
100
200
600
4,900
1,000 – 6,000
340 – 1,200
up to 9,400
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 N2 was present, it was not in a usable form for
microbes.
Aerobic
Anaerobic
Fossil fuels
Photosynthesis
CO2 + H2O
O2 + CH2O
Fermentation
CH2O
Alcohols, acids,
H2 + CO2
Respiration
Methanogenesis
CH4
Global Carbon Reservoirs
Carbon Reservoir
Atmosphere
CO2
Ocean
Biomass
Carbonates
Dissolved and
particulate organics
Land
Biota
Humus
Fossil fuel
Earth’s crust
Metric tons
carbon
Actively
cycled
6.7 x 1011
Yes
4.0 x 109
3.8 x 1013
2.1 x 1012
Yes
No
Yes
5.0 x 1011
1.2 x 1012
1.0 x 1013
1.2 x 1017
Yes
Yes
Yes
No
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 CO2 reservoir
beginning with industrialization. As a result, the level of CO2 in the
atmosphere has increased 28% in the past 150 years.
Carbon source
Release by fossil-fuel combustion
Land clearing
Forest harvest and decay
metric tons carbon/yr
7 x 109
3 x 109
6 x 109
Forest regrowth
Net uptake by oceans
-4 x 109
-3 x 109
Annual flux
9 x 109
Natural and anthropogenic CO2 sources and sinks
Natural sources of CO2
• respiration
• ocean degassing
• terrestrial degassing
• wildfires
Natural sinks for CO2
• terrestrial
uptake by plants
uptake by soils
• oceanic
partitioning
biomass production
Anthropogenic sources of CO2
• fossil fuel combustion
• cement production
• land use changes
Anthropogenic sinks for CO2
• chemical production
• biological materials
CO2 is not the only problem!
Global Atmospheric Concentrations of Selected Greenhouse Gases
CO2
(ppm)
CH4
(ppm)
N2O
(ppm)
SF6
(ppt)
PFC
(ppt)
Preindustrial
278
0.700
0.275
0
0
1992
356
1.714
0.311
32
70
50-200
12
120
3,200
50,000
Atmospheric
Lifetime
(years)
CH4 is 22 times stronger as a greenhouse gas than CO2
Carbon cycling on the habitat scale
The term reservoir can be used on a global scale or on a smaller scale
such as a habitat.
How does carbon cycle within a habitat?
Macro vs. microorganisms
simple vs. simple to complex substrates
aerobic vs. aerobic/anaerobic redox conditions
What are the major carbon inputs into the environment?
plant materials (through photosynthesis)
cellulose
15 – 60%
hemicellulose
10-30%
lignin
5- 30%
protein/nucleic acids
2-15%
fungal cell walls/arthropods
chitin
Cellulose
Cellulose degradation begins
outside the cell with a set of three
exoenzymes:
Molecular weight
up to 1.8 x 106
Glucose subunits
 1 - 4 linked
n
Glucose
subunit
β-1,4- endoglucanse
β-1,4- exoglucanase
β-1,4- glucosidase
Cellulose
 1-4 exoglucanase
 1-4 endoglucanase
+
(shorter pieces)
Cellobiose
(can be transported into cell)
 1-4 glucosidase
(cellobiase)
Glucose
Transport across membrane
Aerobic
a
An
TCA cycle
o
er
bic
Fermentation
Hemicellulose
Molecular weight
~ 40,000
Galacturonic
acid
Methylated
galacturonic acid
Chitin
Amino linkage
Acetyl
group
n
For the more complex polymers such as lignin a variety of oxidizing
enzymes are used. A specific example is the combination of lignin
peroxidase and oxidase which produce H2O2 to aid in degradation of lignin.
Percentage remaining
Lignin due to its complexity is generally degraded much more slowly than
cellulose or hemicellulose.
Lignin
Wheat straw
Cellulose
0
100
Days
Hemicellulose
200
Lignin polymer
Extracellular enzymes
Lignin monomers (transported into the cell)
Other phenols and
various portions
of lignin molecules
Coniferyl
alcohol
Ferulic
acid
Lignin polymer
Extracellular enzymes
Lignin monomers (transported into the cell)
Other phenols and
various portions
of lignin molecules
Coniferyl
alcohol
Ferulic
acid
Caffeic acid
Vanillic acid
Conyferyl
aldehyde
Adjacent hydroxyl
groups allow ring
cleavage
Vanillin
-carboxy-cis, cismuconic acid
Protocatechuic
acid
+
Succinic
acid
Acetic
acid
 - oxyadipic acid
TCA
CO2 + H2O
Caffeic acid
Vanillic acid
Conyferyl
aldehyde
Adjacent hydroxyl
groups allow ring
cleavage
Vanillin
-carboxy-cis, cismuconic acid
Protocatechuic
acid
+
Succinic
acid
Acetic
acid
 - oxyadipic acid
TCA
CO2 + H2O
The most complex organic polymer found in the environment is humus.
Formation of humus is a two-stage process that involves the formation of
reactive monomers during the degradation of organic matter, followed by the
spontaneous polymerization of some of these monomers into the humus
molecule.
Ultimately, these large polymers are degraded and produce new cell
mass, CO2 (which returns to the atmosphere), and contribute to the
formation of a stable organic matter fraction, humus. Humus turns
over slowly, at a rate of 3 to 5% per year.
In addition to mineralization to CO2, a number of small carbon
molecules are formed largely as a result of anaerobic activities and in
some instances as a result of anthropogenic activity. These include:
Methane generation
The methanogens are a group of obligately anaerobic Archaea that can reduce
CO2 to methane (use CO2 as a terminal electron acceptor) both
chemoautotrophically or heterotrophically using small MW molecules such as
methanol or acetate.
4H2 + CO2
CH4 + 2H2O
G0 = -130.7 kJ
Although much methane is microbially produced, there are other sources as
well. What happens to the methane? This is of concern because methane is a
greenhouse gas 22 times more effective than CO2 in trapping heat.
Estimates of methane released into the atmosphere
Source
Biogenic
Ruminants
Termites
Paddy fields
Natural wetlands
Landfills
Oceans and lakes
Tundra
Abiogenic
Coal mining
Natural gas flaring and venting
Industrial and pipeline losses
Biomass burning
Methane hydrates
Volcanoes
Automobiles
Total
Total biogenic
Total abiogenic
Anthropogenic
Methane emission
(106 metric tons/year)
80 - 100 
25 - 150
70 - 120 
120 - 200
5 - 70 
1 - 20
1-5
10 - 35
10 - 35
15 - 45
10 - 40
2-4
0.5
0.5




349 - 820
302 - 665
48 - 155
81 - 86% of total
13 - 19% of total
190 – 405
54 - 49% of total
Methane utilization
In most environments, the methane produced is utilized by methanotrophic
microbes as a source of carbon and energy. The first enzyme in the
biodegradation pathway of methane is methane monooxygenase (MMO). This
enzyme is of interest because it can aid in the degradation of highly chlorinated
materials such as TCE (trichloroethylene). The oxidation of TCE does not provide
energy for the microbe, it is simply a result of nonspecific catalysis by the MMO
enzyme. This is also called cometabolism.
MMO
CH4 + O2
CH3OH
HCHO
methanol
formaldehyde
HCOOH
formic acid
CO2 + H2O
Carbon monoxide- a highly toxic molecule that is produced largely as a result
of fossil fuel burning and photochemical oxidation of methane in the
atmosphere. Despite the fact that this is a highly toxic molecule, some
microbes can utilize is as a source of energy.
CO2
CO
CO2
CO
CO
CO2
In summary, there is huge variety in the types of carbon-containing molecules found in
the environment. Similarly microbes have developed an equal variety in their metabolic
approaches to deriving carbon and energy from these compounds.
The Nitrogen Cycle
N is cycled between: NH4+ (-3 oxidation state) and NO3- (+5 oxidation state)
Global Nitrogen Reservoirs
Nitrogen Reservoir
Atmosphere
N2
Ocean
Biomass
Soluble salts (NO3, NO2-, NH4+)
Dissolved and particulate
organics
Dissolved N2
Land
Biota
Organic matter
Earth’s crust
Metric tons nitrogen
Actively cycled
3.9 x 1015
No
5.2 x 108
Yes
Yes
Yes
6.9 x 1011
3.0 x 1011
2.0 x 1013
No
2.5 x 1010
Yes
1.1 x 1011
Slow
7.7 x 1014
No
Nitrogen must be fixed before it can be incorporated into biomass.
This process is called nitrogen fixation.
Biological inputs of nitrogen from N2 fixation
land - 135 million metric tons/yr (microbial)
marine - 40 million metric tons/yr (microbial)
The enzyme that catalyzes
nitrogen fixation is nitrogenase.
fertilizers - 30 million metric tons/yr (anthropogenic)
Rates of Nitrogen Fixation
N2 fixing system
Rhizobium-legume
Anabaena-Azolla
Cyanobacteria-moss
Rhizosphere assoc.
Free-living
Nitrogen fixation
(kg N/hectare/yr)
200-300
100-120
30-40
2-25
1-2
1-2 kg N/hec/yr
2- 25 kg/N/hec/yr
Examples of free-living bacteria:
Azotobacter
- aerobic
Beijerinckia
- aerobic, likes acidic soils
Azospirillum
- facultative
Clostridia
- anaerobic
Free-living bacteria must also protect nitrogenase from O2
complex is membrane associated
slime production
high levels of respiration
conformation change in nitrogenase when O2 is present
Summary for nitrogen fixation:
energy intensive
end-product is ammonia
inhibited by ammonia
occurs in aerobic and anaerobic environments
nitrogenase is O2 sensitive
Fate of ammonia (NH3) produced during nitrogen fixation
plant uptake
microbial uptake
}
assimilation and mineralization
adsorption to colloids (adds to CEC)
fixation within clay minerals
incorporation into humus
volatilization
nitrification
Ammonia assimilation and ammonification
NH3 is assimilated by cells into:
proteins
cell wall constituents
nucleic acids
Release of assimilated NH3 is called ammonification. This process can
occur intracellularly or extracellularly
proteases
chitinases
nucleases
ureases
A
-
-
At high N concentrations
NH+
3
=O
+
glutamate
dehydrogenase
H 2O
-
NAD
NADH
+
NH 3
 - ketoglutarate
glutamate
B
NH+
3
-
ADP + Pi
=O
ATP
+
NH3
glutamine
synthetase
NH2
glutamine
 - ketoglutarate
At low N concentrations
Ferredoxin
-
2e
glutamatesynthase
(GOGAT)
glutamate
2H+
NH+
3
Transamination
glutamate
Summary for ammonia assimilation and ammonification
Assimilation and ammonification cycles ammonia between its organic
and inorganic forms
Assimilation predominates at C:N ratios > 20
Ammonification predominates at C:N ratios < 20
Fate of ammonia (NH3) produced during nitrogen fixation
plant uptake
microbial uptake
adsorption to colloids (adds to CEC)
fixation within clay minerals
incorporation into humus
volatilization
nitrification
Nitrification - Chemoautotrophic aerobic process
NH4
+
Nitrosomonas
NO2
Nitrosomonas:
34 moles NH4+ to fix 1 mole CO2
-
Nitrobacter
NO3-
Nitrobacter:
100 moles NH4+ to fix 1 mole CO2
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.
Summary for nitrification
Nitrification is an chemoautotrophic, aerobic process
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 in managed systems can result in nitrate leaching and
groundwater contamination
What is the fate of NO3- following nitrification?
plant uptake
biological uptake (assimilatory nitrate
}
reduction)
microbial uptake
accumulation (disturbed vs. managed)
fixation within clay minerals
leaching (groundwater contamination)
dissimilatory nitrate reduction
• nitrate ammonification
• denitrification
Assimilatory nitrate reduction
many plants prefer nitrate which is reduced in the plant prior to use however,
nitrogen in fertilizer is added as ammonia or urea.
microorganisms prefer ammonia since uptake of nitrate requires a reduction
step
assimilatory nitrate reduction is inhibited by ammonium
nitrate is more mobile than ammonium leading to leaching loss
Dissimilatory nitrate reduction
Dissimilatory reduction of nitrate to ammonia (DNRA)
use of nitrate as a TEA
(anaerobic process) – less energy produced
% N2 (Denitrification)
0
20
40
60
80
Rumen
Digested sludge
inhibited by oxygen
found in a limited number of
carbon rich environments
stagnant water
sewage plants
some sediments
Denitrification
C/e- acceptor
(relative scale)
not inhibited by ammonium
100
use of nitrate as a TEA
(anaerobic process) – more energy produced
many heterotrophic bacteria are denitrifiers
produces a mix of N2 and N2O
inhibited by oxygen
not inhibited by ammonium
100
Estuarine sediments
Lake sediments
Soil + C
Soil
80
60
40
20
+
% NH4 (Dissimilatory reduction)
0
Denitrification requires a set of 4 enzymes:
Outside cell
NO3
-
NO2-
NO
N2O
N2
Outer
membrane
NO
2
nitrite
nitritereductase
reductase
NO
N2O
nitrous oxide
reductase
Periplasm
Inner
membrane
nitrate
reductase
nitrate reductase
Cytoplasm
NO3
-
nitricoxide
oxide
nitric
reductase
reductase
NO2
-
High [NO3-] favors N2 production
Low [NO3-] favors N2O production
N2
nitrous oxide
reductase
Denitrification
returns fixed N to atmosphere:
NO3
NO
get formation of NO, N2O
NO, N2O deplete the ozone layer
Reaction of N2O with ozone
O2 + UV light
O+ O
O + O2
O3 (ozone generation)
N2O + UV light
N 2 O + O*
NO + O3
NO2 + O*
N2 + O*
2NO (nitric oxide)
NO2 + O2 (ozone depletion)
NO + O2
N 2O
N2
Summary for nitrate reduction
1. Assimilatory nitrate reduction
Nitrate assimilated must be reduced to ammonia for use.
Nitrate assimilation is inhibited by ammonia
Oxygen does not inhibit this process
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 N2 and N2O
Many heterotrophs denitrify
10th most abundant element
Sulfur Cycle
average concentration = 520 ppm
oxidation states range from +6 (sulfate) to -2 (sulfide)
Global Sulfur Reservoirs
Sulfur Reservoir
Atmosphere
SO2/H2S
Ocean
Biomass
Soluble inorganic ions
(primarily SO42- )
Land
Biota
Organic matter
Earth’s crust
Metric tons sulfur
Actively cycled
1.4 x 106
Yes
1.5 x 108
Yes
1.2 x 1015
Slow
8.5 x 109
1.6 x 1010
1.8 x 1016
Yes
Yes
No
1. Assimilatory sulfate reduction
The form of sulfur utilized by microbes is reduced sulfur. However, sulfide (S2-)
is toxic to cells. Therefore sulfur is taken up as sulfate (SO42-), 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 SO42- to S2-)
SO42- + ATP
APS
+
Ppi
adenosine phosphosulfate
APS + ATP
PAPS
+
3’ – phosphoadenosine – 5-phosphosulfate
PAPS + 2eSO32- + 6H+ + 6eS2- + serine
SO32- + PAP
S2cysteine + H2O
ADP
Sulfur Mineralization
terrestrial environments
SH – CH2- CH - COOH + H2O
NH2
OH – CH2- CH – COOH + H2S
cysteine
NH2
serine
marine environments
algae
dimethylsulfoniopropionate
Dimethylsulfide (DMS)
At a C:S ratio < 200:1, sulfur mineralization is favored
At a C:S ratio > 400:1, sulfur assimilation is favored
Both the H2S and the DMS generated during sulfur mineralization are volatile
and therefore significant amounts are released to the atmosphere. Here they
are photooxidized to sulfate.
Sulfide oxidation (nonbiological)
H2S and DMS are photooxidized to SO42- in the atmosphere
SO42- + water
H2SO4 (sulfuric acid)
acid rain – pH < 5.6
fossil fuel burning releases SO2
H2SO3 (sulfurous acid)
Normal biological production = 1 kg SO4/ha/yr
Rural production = 10 kg SO4/ha/yr
Urban production = 100 kg SO4/ha/yr
Aerobic sulfur oxidation
H2S not released to the atmosphere acts as substrate for sulfur-oxidizers.
Under aerobic conditions:
H2S + 1/2O2
S0 + H20
G = -50.1 kcal/mol
Chemolithotrophic bacteria
Beggiatoa
Thioplaca
Thiothrix
Thermothrix
Thiobacillus
What unusual community is based on the
chemoautrophic sulfur oxiders?
What is the conundrum for these organisms?
Depth (mm)
2.0
O2
Air
Beggiatoa
2.4
Beggiatoa
2.8
Mineral medium
with 0.2% agar
H2S
3.2
0
0.32
0.64
0.96
1.28
Dissolved O2 (mg/l)
1.6
Mineral medium
with 1.5% agar
1 - 8 mM Na2S
Most of these microbes deposit S0 as granules inside the cell. They
can further oxidize S0 but this is not preferred. However, there are
some sulfur oxidizers most notably Thiobacillus thiooxidans that are
acidophilic and prefer to oxidize S0 to SO42-.
Acidophilic sulfur-oxidizers:
Acidothiobacillus - obligate aerobes
acid intolerant spp.
H2S + 1/2O2
S0 + H2O
acid tolerant spp.
S0 + 3/2O2
+ H2 O
H2SO4
G = -149.8 kcal/mol
All sulfur oxidizers are aerobic with the exception of:
Acidothiobacillus denitrificans - uses nitrate as TEA
4NO3- + 3S0
3SO42- + 2N2
Under anaerobic conditions, H2S is utilized by photosynthetic bacteria:
Phototrophic oxidation
anaerobic photoautotrophic process:
CO2 + H2S
C(H2O) + S0
Anaerobic photosynthesis
CO2 + H2O
C(H2O) + O2
Aerobic photosynthesis
Chromatium
Ectorhodospirillum
Chlorobium
Green and purple sulfur bacteria
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
anaerobic
1. respiratory S0 reduction
2. dissimilatory SO42- reduction
heterotrophic
limited number of electron donors (substrates)
lactic acid
pyruvic acid
H2
small MW alcohols
Example of a heterotrophic sulfate reducer:
Desulfuromonas acetoxidans CH3COOH + 2H2O + 4S0
2CO2 + 2H2S
Examples of autotrophic sulfate reducers:
Desulfovibrio
H2 + SO42-
Desulfotomaculum
H2S + 2H2O- + 2OH-
Summary - Sulfate Reduction:
•
inhibited by oxygen
•
can result in gaseous losses to atmosphere
•
produces H2S which can result in anaerobic corrosion of steel and iron
set in sulfate-containing soils
Winogradsky column – great illustration of sulfur cycling
Set up:
Soil is mixed with 1 g CaCO3, 1 g CaSO4, and
shredded paper (cellulose). Soil is added to a
column and saturated with water. A soil-water
slurry is poured on top of this layer to the
desired thickness.
Column is incubated under lights or in a
window.
Population development
Initial conditions – aerobic, but O2 is used up quickly – aerobic
chemoheterotrophs
Second population – anaerobic, chemoheterotrophs ferment cellulose to
low molecular weight fatty acids and alcohols
Third population – anaerobic, chemoheterotrophs respire the low
molecular weight fatty acids and alcohols using SO4 as the TEA.
SO4
H2S (black) + CO2
Sulfate reducers
Fourth population – anaerobic, photoautotrophs photosynthesize using
H2S and CO2.
CO2 + H2S
S0
+ C(H2O)
Green and purple sulfur
bacteria
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