Vorlesung 752-4001-00 Mikrobiologie Topics

WS 04/05
Biochemische Diversität: C-Zyklus

1. Overview: Photosynthesis, mineralization and storage

J. Zeyer
Institute of Terrestrial Ecology 2. Energy turnover and biochemistry of photosynthesis
ETH Zurich
3. Energy turnover and biochemistry of mineralization
22. Nov. 2004
4. Storage of assimilated carbon (Humus, Oil, etc.)

5. Case study I: CO2 cycle and global climate

6. Case study II: Methane oxidation in the subsurface

7. Varia

The carbon cycle in nature

Photosynthesis, mineralization
and carbon storage

Photosynthesis
CO2 + H2O CH2O + O2
Mineralization

Stored carbon
(e.g. humus, fuel)
Brock, 10th edit., 2003, Chapt. 19

Photosynthesis and mineralization: Conceptual model to measure redox potential

impact on ecology

Green-
house Oxic
gas Ozone Electron
atmosphere flux
1.2 Volt

Photosynthesis
CO2 + H2O CH2O + O2
Mineralization

Food Fossil CO2 CH2O H2O O2

chains fuels
Lake and sea
sediments
 Biosynthesis and Mineralization of Biomass
Redox values of microbiologically important reactions

Storage
Redox pair E0‘ (Volt)
Biomass
CH2O CO2 Humus, Oil, Coal, etc.
CO2/formate -0.43
- 0.4
2H+/H2 -0.41
Ferredoxin ox/red -0.39
NAD+/NADH -0.32
Electron Carriers
S0/HS- -0.27 NAD, FAD, Ferredoxin, etc
CO2/CH4 -0.24

Redox potential (Volt)

Fumarate2-/succinate2- +0.033
Methanogens
Fe(OH)3 + HCO3-/FeCO3 +0.20 H2
NO2-/NO +0.36 CO2 CH4

Photosynthesis
NO3-/NO2- +0.43

Mineralization
Sulfate reducers
Fe3+/Fe2+ +0.77 H2
SO42- H2S
Mn4+/Mn2+ +0.798
O2/H2O +0.82 Iron reducers
NO/N2O +1.18
FeOOH Fe2+
N2O/N2 +1.36
Denitrifiers
!G0‘ = -nF * !E0‘ (F = Faraday constant, 96.48 kJ / Volt) NO3- N2
+ 0.8
!G‘ = !G0‘ + RT * ln ([Products]/[Substrates]) Aerobic microorganisms
O2 H2O

Aerobic and anaerobic photosynthesis

Topics
CO2 as electron acceptor
CO2 + 4H+ + 4e- CH2O + H2O

- 0.4

(cyclic electron flow coupled via

ATP with reverse electron flow)
Photosynthetic systems produces ATP and NAD(P)H)

Anaerobic Photosynthesis
Aerobic Photosynthesis (electron flow along two

1. Overview: Photosynthesis, mineralization and storage

2. Energy turnover and biochemistry of photosynthesis Photosystem I

P700 Photosystem
Redox potential (Volt)

+0.3V/-1.3V P870
+0.5V/-1.0V
3. Energy turnover and biochemistry of mineralization

4. Storage of assimilated carbon (Humus, Oil, etc.)

5. Case study I: CO2 cycle and global climate H2S as electron donor
Photosystem II 2H2S 4H+ + 4e- + 2S0
6. Case study II: Methane oxidation in the subsurface P680
+1.0V/-0.8V

7. Varia

H2O as electron donor

+ 0.8
2H2O 4H+ + 4e- + O2

Electron flow in Electron flow in

oxygenic anoxygenic
photosynthesis photosynthesis
(green plants, (anaerobic purple
cyanobacteria) bacteria)

Brock, 10th edit., 2003, Chapt. 17 Brock, 10th edit., 2003, Chapt. 17
 Topics Mineralization of organic C-compounds

Conditions
CH2O CO2
e- Aerobic
1. Overview: Photosynthesis, mineralization and storage O2 H2O

2. Energy turnover and biochemistry of photosynthesis CH2O CO2 Iron

decreasing energy yield

e-
Fe3+ Fe2+ reducing
3. Energy turnover and biochemistry of mineralization

anaerobic, anoxic
4. Storage of assimilated carbon (Humus, Oil, etc.) CH2O CO2
e- Denitrifying
NO3- N2
5. Case study I: CO2 cycle and global climate
CH2O CO2 Sulfate
e-
6. Case study II: Methane oxidation in the subsurface SO42- H2S reducing

7. Varia
CH2O CO2 Methano-
e-
CO2 CH4 genic

Citric Acid Cycle

(CAC):
Carbon oxidation
to CO2 and genera-
tion of reducing
equivalents

Brock, 10th edit., 2003,

Chapt. 5

Topics

Respiratory chain:
Electron transfer to
oxygen and generation 1. Overview: Photosynthesis, mineralization and storage
of proton gradient
2. Energy turnover and biochemistry of photosynthesis

3. Energy turnover and biochemistry of mineralization

4. Storage of assimilated carbon (Humus, Oil, etc.)

5. Case study I: CO2 cycle and global climate

6. Case study II: Methane oxidation in the subsurface

7. Varia

Brock, 10th edit., 2003,

Chapt. 5
 Estimated Turnover Time of Soil Carbon Based on
Carbon pools Mean Carbon Pools and Mean Soil Respirations Rates
in the major
Soil C Soil respiration Turnovera
reservoirs on Vegetation type (t ha -1) (t ha -1) (years)
earth
Tundra 204 0.6 490
Boreal forests 206 3.2 91
Temperate grasslands 189 4.4 61
Temperate forests 134 6.6 29
Woodlands 69 7.1 14
Cultivated lands 79 5.4 21
Desert scrub 58 2.2 37
Tropical grasslands 42 6.3 10
Tropical lowland forests 287 10.9 38
Swamps and marshes 723 2.0 520
Global total 15 x 108 5x 107 32

a) Turnover time is estimated based on the assumption that

30 % of soil respiration is derived from root respiration.

Source: SCIENCE
Source: Soil Microbiology and Biochemistry, 2nd ed.,
290(13), 291 - 296, 2000 by E.A. Paul and F.E. Clark, Academic Press, 1996

Topics

1. Overview: Photosynthesis, mineralization and storage

2. Energy turnover and biochemistry of photosynthesis

3. Energy turnover and biochemistry of mineralization

4. Storage of assimilated carbon (Humus, Oil, etc.)

Science, Vol. 303,
353 - 356, 2004 5. Case study I: CO2 cycle and global climate

6. Case study II: Methane oxidation in the subsurface

7. Varia

Global atmospheric
concentration of
three well mixed
greenhouse gases

EOS 84(46),
2003
 Satellite data help predict terrestrial carbon sinks
Potter et al., EOS Vol. 84(46), 2003
Topics
__________________________________________

MODIS: Moderate Resolution Imaging Spectroradiometer

Sensor aboard NASA’s TERRA and AQUA satellites
1. Overview: Photosynthesis, mineralization and storage
Balance: Net primary production (NPP)
- Soil microbial CO2 fluxes
_____________________________ 2. Energy turnover and biochemistry of photosynthesis
Net ecosystem production (NEP)
============================
3. Energy turnover and biochemistry of mineralization
Observations 2001: Above average temp. was associated with positive NEP
Heavy rainfall was associated with negative NEP 4. Storage of assimilated carbon (Humus, Oil, etc.)
Terrestrial NPP for the globe:
Around 50 Pg C / year 5. Case study I: CO2 cycle and global climate
(Trend: increasing!)
6. Case study II: Methane oxidation in the subsurface
Seasonal patterns:
Very pronounced for 30o – 60o North
In summer positive NEP 7. Varia
In winter negative NEP

Literature: Potter et al.

EOS 84(46), 2003

Major microbial activities in soil Rough estimates of CH4 released into

involving gaseous species the atmosphere (units: 1012 g/year)

Total 350 - 820

Mineralization CH2O + O2 -> CO2 Biogenic (81 - 86% of total) 302 - 665
Ruminants 80 - 100
Denitrification NO3- -> N2 (N2O) Termites 25 - 150
Paddy fields 70 - 120
Nitrification NH4+ + O2 -> NO3- (N2O) Natural wetlands 120 - 200 Microbial
Landfills 5 - 70 oxidation
Methanogenesis CO2 + H2 -> CH4 Oceans and lakes 1 - 20 reduces
Tundra 1 - 5 flux!
CH3COOH -> CH4 + CO2 Abiogenic (14 - 19% of total) 48 - 155
Coal mining 10 - 35
Natural gas flaring and venting 10 - 30
Methane oxidation CH4 + O2 -> CO2 Industrial and pipeline losses 15 - 45
Source: Biomass burning 10 - 40
Brock‘s
Biology of Methane hydrates 2 - 4
Microor- Volcanoes 0.5
ganisms Automobiles 0.5

Experimental approaches to determine Basic concept of a gas push-pull test (GPPT)

metabolism and fluxes of trace gases in soil (PPT successfully applied in groundwater!)

Eddy Injection of
well defined Extract and Typical result
Ratio conc. extr. / conc. Inject.

corre-
gas mixture analyze gas
lation FACE
(i.e. O2, CH4, composition
Air Entrap- experi-
ment Ar, Ne)
Exchange of ments
trace gases boxes Air
Tracer
CH4, N2O, CO2 gas

Analysis Methane
of conc. Methane (inhibited,
Soil profiles Soil sterile)
Laboratory (active)
studies with
soil samples Time (h)
Capillary fringe

Groundwater Groundwater
 Gas Profiles in Soil above a Contaminated Aquifer
Fate of methane in vadose zone above
oil contaminated aquifer (field site Studen)
CH4 [ µL/L ]
O2 x 10 [ mL/L ]
Atmosphere
0 10 20 30
O2 Concentration (%) 0
O2
0 5 10 15 20 25
0.0

Rhizosphere Low activity (1 Test)

Depth [ m ]
-0.5

-1.0 -1

Depth (m)
CH4 O2
Vadose Methane oxidation -1.5
zone
-2.0
2 O2 + CH4 --> CO2 + 2 H2O
-2.5
Methane oxidation
-2
-3.0

-3.5 Groundwater
CO2 + 4 H2 --> CH4 + 2 H2O
High activity (2 Tests, +/- inhibitor)
-4.0

Groundwater Methanogenesis Organic pollutant 0 5 10 15 20 25 30

(e.g. petroleum -3
hydrocarbons) CH4 Concentration (ppm)

Field GPPT : Results (ES&T 2005, in press)

! 13C values of important carbon reservoirs
Gas Ext / Gas Inj Ne
1
Low activity Ar
0.8 k= 0.68 h-1 ± 0.05 CH4
Biogenic CH4
0.6 !13C (CH4) = - 24.3 Injected CH4 : !13C = - 46.5 ‰
0.4 CH4 turnover ! Less negative Thermogenic CH4

0.2 Petroleum hydrocarbons

0
Biomass
0 1 2 3

1 1 Terrestrial carbonates
High activity Inhibited
0.8 0.8 Marine carbonates
k= 2.19 h-1 ± 0.26 k= -0.07 h-1 ± 0.04
0.6 0.6 CO2 of atmospere
!13C (CH4) = - 3.6 !13C (CH4) = - 44.4
0.4 0.4

0.2 10 0 - 10 - 20 - 30 - 40 - 50 - 60 - 70 - 80 - 90
0.2

0 0 ! 13C (%)
0 1 2 3 0 1 2 3

Extracted / Injected Volume

Biochemical pathways of methane Topics

( !13C values in !13C notation)

Atmosphere 1. Overview: Photosynthesis, mineralization and storage

2. Energy turnover and biochemistry of photosynthesis

Petroleum Acetate
CH4
hydrocarbons (- 40‰ to 3. Energy turnover and biochemistry of mineralization
(-28‰) - 110‰
4. Storage of assimilated carbon (Humus, Oil, etc.)

Dissolved inor- CO2 CO2 CO2 5. Case study I: CO2 cycle and global climate
ganic carbon (-16‰) (-4‰) (-15‰)
(DIC) (-14‰) Methanogenic Methanotrophic
microorganisms microorganisms 6. Case study II: Methane oxidation in the subsurface
(production (consumption
of methane) of methane)
Calcium carbo- 7. Varia
nate (CaCO3)
(ca. 0‰)

Measurement of !13C in methane:

Rolf Siegwolf, PSI