Global Biogeochemical Cycles and
Biological Metabolism
I.
A.
B.
Biogeochemistry & Biogeochemical Cycles
Global cycles: nitrogen, water, carbon
Carbon cycle through time
II Biological Metabolism
II.
A.
B.
C.
Redox reactions: basis of metabolism
The metabolic pathways
Microbial Habits
I. What is Biogeochemistry?
Biogeochemistry = the study of how the cycling of
elements through the earth system (water, air, living
organisms soil and rock) is governed by physical,
organisms,
physical
chemical, geological and biological processes
hydrosphere
atmosphere
biosphere
pedosphere
lithosphere
Key Names
Vladimir Vernadsky (1863
(1863-1945):
1945) Russian scientist
known as the “father of biogeochemistry”, invented the
terms geosphere, biosphere, and “noosphere”
G. Evelyn Hutchinson (1903-1991): famous limnologist
(considered to be founder of limnology) (also studied
the question of how biological species coexist)
1
Global Change and the N-cycle
“The nitrogen dilemma is
not just thinking that
carbon is all that
matters. But also
thinking that global
warming is the only
environmental issue. The
weakening of biodiversbiodivers
ity, the pollution of
rivers... Smog. Acid rain.
Coasts. Forests. It’s all
nitrogen.”
- Peter Vitousek
Global Change and the N-cycle
Human alteration of N-cycle is LARGE
(> 100% in fixation relative to the
background rate of 90-140 Tg N/yr):
No place on
earth
unaffected
by this
(terrestrial)
80 to
90 Tg
20 Tg
40 Tg
Vitousek et al.,
1997
2
Atmospheric N2: 3.9 x 109
Reactive N (NOx, NH3)
Vegetation:
4,000
Soils:
100,000
Units:
Stocks (Tg N)
or Flows (Tg N/yr)
Atmospheric N2: 3.9 x 109
Huge but
inaccessible
Reactive N (NOx, NH3)
Vegetation:
4,000
Soils:
100,000
Units:
Stocks (Tg N)
or Flows (Tg N/yr)
3
Atmospheric N2: 3.9 x 109
Reactive N (NOx, NH3)
Vegetation:
4,000
Note big
difference in
N turnover
times in
terrestrial
vs. Marine
biota
Terrestrial:
4000/1200 =
3-4 yrs
Soils:
100,000
Marine:
300/8000=
2 weeks
Atmosphere:
p
3.9x109/~300
≈ 107 years!
Units:
Stocks (Tg N)
or Flows (Tg N/yr)
natural
N fixation
Atmospheric N2: 3.9 x 109
Reactive N (NOx, NH3)
Vegetation:
4,000
Soils:
100,000
Units:
Stocks (Tg N)
or Flows (Tg N/yr)
4
Atmospheric N2: 3.9 x 109
Human
N fixation
Reactive N (NOx, NH3)
Vegetation:
4,000
Soils:
100,000
Units:
Stocks (Tg N)
or Flows (Tg N/yr)
I. The Global water cycle
Atmosphere: 13,000
Freshwater available
for interaction with
terrestrial biosphere
is small fraction
Ice:
33 x 106
Lakes:
230,000
Vegetation:
10,000
Oceans:
1.350 x 109
Soil water:
120,000
groundwater:
15.3 x 106
In km3 (pools) and
km3/yr (fluxes)
5
I. The Global water cycle
71
1,000
Atmospheric supply to
Land (precipitation) is
greater than land return
to atmosphere
(evapotranspiration)
Ice:
33 x 106
Transpiration
Precip: 1
111,000
Atmosphere: 13,000
Lakes:
230,000
Vegetation:
10,000
Soil water:
120,000
Oceans:
1.350 x 109
groundwater:
15.3 x 106
In km3 (pools) and
km3/yr (fluxes)
I. The Global water cycle
Atmosphere: 13,000
71
1,000
Opposite
i true
is
t
over
the ocean
(precip <
evapotranspiration)
Atmospheric supply to
Land (precipitation) is
greater than land return to
atmosphere
(evapotranspiration)
Ice:
33 x 106
Transpiration
Precip: 1
111,000
Precip: 385
5,000
Evaporation: 425
5,000
40,000
Lakes:
230,000
Vegetation:
10,000
Oceans:
1.350 x 109
Soil water:
120,000
groundwater:
15.3 x 106
In km3 (pools) and
km3/yr (fluxes)
6
I. The Global water cycle
Atmosphere: 13,000
71
1,000
Ice:
33 x 106
Plants power
water return to
atmosphere on
land
Transpiration
Ocean
water
powers
land
precip
Precip: 1
111,000
Precip: 385
5,000
Evaporation: 425
5,000
40,000
Lakes:
230,000
Vegetation:
10,000
Oceans:
1.350 x 109
Soil water:
120,000
groundwater:
15.3 x 106
Atmospheric
turnover
time:
13,000/
496,000
= 0.026 yrs
≈ 1 week
In km3 (pools) and
km3/yr (fluxes)
Facts about the global water cycle
496 x 103 km3
• Global precip: 385,000 (ocean) + 111,000 (land)
496 x 103 km3  510 x 106 km2 = 0
0.97
97 x 10-33 km
Earth surface area
≈ 1 meter of precip
(global average)
• Land area is 148 x 106 km2  111148 = 0.75 m
average land precip
– Comparison: Tucson gets 0.30
0 30 m
m,
–
tropical forests 2 or 3 m
7
Overview: The Modern Global carbon cycle (1990s)
Total FF.
FF
emissions
Total landuse change
emissions
Values in black are natural, values in red are anthropogenic
Note: 1990s values (IPCC 2007, Ch. 7)
8
What is residence time of C in atmosphere?
One estimate is from land+ocean flux: 120+70=190; 597/190 ≈ 3yrs
BUT: this is not an estimate of removal rate to ocean of excess CO2 (2.2).
Better: 597 / 2.2 = 270 years.
But in truth, for CO2, no single residence time.
Total FF.
FF
emissions
Total landuse change
emissions
Values in black are natural, values in red are anthropogenic
Note: 1990s values (IPCC 2007, Ch. 7)
Fun problem in global biogeochemistry:
How likely is it that in your next breath, you will inhale at
least one molecule of nitrogen (N2) that Julius Caesar
exhaled in his last breath?
(Julius Caesar, the famous Roman emperor, was
assassinated on March 15, 44 BC by a group of Roman
senators).
This requires some basic chemistry:
1 mole of air is 6.02 x 1023 molecules
At STP, 1 mole occupies ~22 liters.
Also helpful: whole atmosphere: 1.8 x 1020 moles of air
What is atmospheric mixing ratio of N2?
What is N2 mixing time in the atmosphere?
What is N2 residence time in the atmosphere?
9
First, the concentration, in the whole atmosphere, of
Caesar’s last-breath N2 molecules
Concentration 
# N 2 molecules in Caesar ' s last breath
# molecules in whole atmosphere
1 L of air in breath 

1.8 10
20
3 N 2  1 mol air 
23

 6  10 molecules / mol
4 air  22 L air 


mols air / atmosphere 6  10 molecules / mol
23


 2  1022
Next, the average number you inhale per breath =
Concentration (molecules Caesar ' s N 2 / molecules air )   # molecules inhaled 


1 mol air 
23
 2 1022  1 L 
 6  10 molecules / mol 
22 L air 






 


 2 1022  2.7  1022  5.4  5
So on average you inhale 5 molecules of Caesar’s-breath N2 in every
breath!
II. What is Biological Metabolism?
Metabolism, simplified
oxygenic photosynthesis
H2O + CO2  CH2O + O2
Carbon in
atmospheric
CO2
Aerobic Respiration
Reduced Carbon
in organic matter
(plant biomass & energy
supply)
M
More
generally:
ll
autotrophy
e-donor + CO2  CH2O + e-acceptor
heterotrophy
10
Life is catalyzed Redox Reactions
• “Master variables” in soil & water chemistry: H+ and e• Control the direction, rate and endproducts of many
reactions.
• Electron transfer reactions near earth’s surface are
driven largely by C cycling:
• Photosynthesis: CO2(g) + H2O(l)  CH2O(s) + O2(g)
• Respiration:
CH2O(s) + O2(g)  CO2(g) + H2O(l)
• Both are full, balanced redox reactions.
Oxidation-Reduction Reactions
• A redox reaction involves the transfer of one
or more electrons (e-) from one species to
another.
h
Reduced
Oxidized
+
Species A Species B
Oxidized
Reduced
+
Species A
Species B
e-
e-
• The reaction proceeds in either direction,
depending on magnitude and sign of Gr
(change in Gibbs free energy = energy stored or released)
11
Some Redox Definitions
• Oxidation: The loss of e• Reduction: The g
gain of e• Oxidized Species:
– Oxidizing agent or “oxidant” in the reaction.
– Atom or compound that oxidizes the other atom or
compound.
– The electron acceptor.
– Is itself reduced (gains an e-) in the process.
• Reduced Species:
– R
Reducing
d i agentt or ““reductant”
d t t”
– Atom or compound that reduces the other atom or
compound.
– The electron donor.
– Is itself oxidized (loses an e-) in the process.
The full redox reaction:
Reduced
Oxidized
+
Species
p
A Species
p
B
Oxidized
Reduced
+
Species
p
A
Species
p
B
e-
e-
contains two half reactions, where each
pertains to a given element that undergoes
oxidation or reduction:
Red A  Ox A + m H+ (aq) + e-(aq)
Ox B + m H+ (aq) + e-(aq)  Red B
12
Thermodynamics of Redox
• The e-'s represent a common currency
f examining
for
i i conditions
diti
of
f
thermodynamic spontaneity and
equilibrium when comparing reactions.
• The thermodynamic spontaneity of the
reaction
react
on iss determ
determined
ned by the potent
potential
al
for e to be transferred in one direction
or another.
Half-Cell Conventions
• Half-Reaction: The elemental reaction used to
describe a redox reaction. Normally written as a
reduction:
• 0.25 O2 (g) + e- (aq) + H+ (aq)  0.5 H2O (l)
•
log K = 20.8
• Eh0 = standard half-cell potential (electromotive
force) [V] = 0.059*log K
• Describes the spontaneity of the reaction as written
(tendency of reaction to occur, driving force) under
standard state conditions of reactants and products.
• Measure of affinity of an electron acceptor for
electrons under standard conditions.
13
Standard Hydrogen Electrode
H2 = 1 atm
Platinum
electrode
½H2(g)  H+ + eaH+ = 1
Eh0 = 0.000 V
Log K = 0.0
• Thus given free energy of formation for
compounds
d  Eh0
• ΔG0r < 0 (Eh0 > 0): reduction has greater
tendency to occur than does the
reduction of H+ (aq) to H2 (g) (under
standard conditions).
14
Overall redox reaction in soil is sum of
two half-reactions
MnO2(s) + 4H+(aq) + 2e-  Mn2+ (aq) +2H2O (l); log K = 41.6
• is a reduction half-reaction.
• This reaction must be combined (coupled)
with another half-reaction that is inverted to
represent an oxidation half-reaction.
• No free electrons appear in balanced full
redox reactions.
reactions
• For example, the reduction of Mn(IV) to Mn
(II) could be coupled with the oxidation of
nitrite to nitrate (see next slide)
Summing two half reactions
MnO2(s) + 4 H+ + 2 e-  Mn2+ +2 H2O
log K = 41.6
41 6
2 x (0.5 NO2- + 0.5 H2O  0.5 NO3- + H+ + e-)
log K = -28.4
---------------------------------------------------------------------MnO2(s) + 2 H+ + NO2-  Mn2+ + NO3- + H2O
log K = 13.2
Will this reaction proceed under standard
conditions?
15
Terminal Electron Accepting Processes
• TEAPs refers to the fact that in natural
aqueous systems,
systems the availability of O2
to act as a terminal electron acceptor in
respiration is limited by its availability.
• Other oxidizing agents are used as O2
becomes depleted.
• The
Th order
d of
f use of
f these
th
alternative
lt
ti
TEAPs is the same as that of their
energetic yield.
Sequence of
TEAP iis
TEAPs
consistent with
the decrease in
energy yield per
mole of organic
g
matter
oxidized.
16
Falkowski et
al. (2008)
17
The change in Gibbs free energy G
(and Eh) can be calculated for all pairs
of redox reactions, giving theoretical
thermodynamic energy yields
yields.
Reactions that run “downhill” (release
energy) offer opportunities to power
metabolism, and hence, a possible
h bit for
habit
f life.
lif
Falkowski et al. (2008)
18