Biochemische Diversität: C-Zyklus

(1)

Vorlesung 752-4001-00 Mikrobiologie WS 04/05

Biochemische Diversität: C-Zyklus

J. Zeyer

Institute of Terrestrial Ecology ETH Zurich

22. Nov. 2004

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.) 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

Brock, 10^th edit., 2003, Chapt. 19

CO

₂

+ H

₂

O CH

₂

O + O

₂

Photosynthesis, mineralization

and carbon storage

Photosynthesis Mineralization

Stored carbon (e.g. humus, fuel)

CO

2

+ H

2

O CH

2

O + O

2

Photosynthesis and mineralization:

impact on ecology

Photosynthesis Mineralization

Green- house gas

Fossil fuels Lake and sea

sediments Food

chains

Ozone Oxic

atmosphere _{1.2 Volt}

CO2 CH2O H2O O2 Electron

flux Conceptual model to measure redox potential

(2)

Redox values of microbiologically important reactions

Redox pair E0‘ (Volt)

CO2/formate -0.43

2H⁺/H₂ -0.41

Ferredoxin ox/red -0.39

NAD⁺/NADH -0.32

S⁰/HS^- -0.27

CO₂/CH₄ -0.24

Fumarate^2-/succinate^2- +0.033 Fe(OH)3 + HCO3-/FeCO3 +0.20

NO2-/NO +0.36

NO₃^-/NO₂^- +0.43

Fe³⁺/Fe²⁺ +0.77

Mn⁴⁺/Mn²⁺ +0.798

O2/H2O +0.82

NO/N2O +1.18

N2O/N2 +1.36

!G‘ = !G⁰‘ + RT * ln ([Products]/[Substrates])

!G⁰‘ = -nF * !E0‘ (F = Faraday constant, 96.48 kJ / Volt)

Biosynthesis and Mineralization of Biomass

Electron Carriers NAD, FAD, Ferredoxin, etc

+ 0.8 - 0.4

Redox potential (Volt) Methanogens

CO2 CH4

Sulfate reducers SO42- H2S H2

H2

Iron reducers FeOOH Fe²⁺

Denitrifiers NO3- N2

Humus, Oil, Coal, etc.

Storage

Photosynthesis

Aerobic microorganisms O2 H2O

Biomass CH2O CO2

Mineralization

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.) 5. Case study I: CO₂ cycle and global climate 6. Case study II: Methane oxidation in the subsurface 7. Varia

Aerobic and anaerobic photosynthesis

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

H2O as electron donor 2H2O 4H⁺ + 4e^- + O2 + 0.8

- 0.4

Aerobic Photosynthesis (electron flow along two Photosynthetic systems produces ATP and NAD(P)H)

Photosystem I P700 +0.3V/-1.3V

Photosystem II P680 +1.0V/-0.8V

H2S as electron donor 2H2S 4H⁺ + 4e^- + 2S⁰

Anaerobic Photosynthesis (cyclic electron flow coupled via ATP with reverse electron flow) Photosystem P870 +0.5V/-1.0V

Redox potential (Volt)

Electron flow in oxygenic photosynthesis

(green plants, cyanobacteria)

Brock, 10^th edit., 2003, Chapt. 17 Brock, 10^th edit., 2003, Chapt. 17

Electron flow in anoxygenic photosynthesis

(anaerobic purple

bacteria)

(3)

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.) 5. Case study I: CO₂ cycle and global climate 6. Case study II: Methane oxidation in the subsurface 7. Varia

Mineralization of organic C-compounds

decreasing energy yield

CH2O CO2

O2 ^e H2O

-

CH2O CO2

Fe³⁺ ^e Fe²⁺

-

CH2O CO2

NO3- ^e N2

-

CH2O CO2

SO42- ^e H2S

-

CH2O CO2

CO2 CH4

e^-

Conditions Aerobic

Iron reducing

Denitrifying

Sulfate reducing

Methano- genic

anaerobic, anoxic

Citric Acid Cycle (CAC):

Carbon oxidation to CO

₂

and genera- tion of reducing equivalents

Brock, 10^th edit., 2003, Chapt. 5

Respiratory chain:

Electron transfer to oxygen and generation

of proton gradient

Brock, 10^th edit., 2003, Chapt. 5

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.)

5. Case study I: CO₂ cycle and global climate 6. Case study II: Methane oxidation in the subsurface 7. Varia

(4)

Source: SCIENCE 290(13), 291 - 296, 2000

Carbon pools in the major reservoirs on

earth

Soil C Soil respiration Turnover^a

Vegetation type (t ha ^-1) (t ha ^-1) (years)

Estimated Turnover Time of Soil Carbon Based on Mean Carbon Pools and Mean Soil Respirations Rates

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 5 x 10⁷ 32

a) Turnover time is estimated based on the assumption that 30 % of soil respiration is derived from root respiration.

Source: Soil Microbiology and Biochemistry, 2nd ed., by E.A. Paul and F.E. Clark, Academic Press, 1996

Science, Vol. 303, 353 - 356, 2004

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.) 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

(5)

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

MODIS: Moderate Resolution Imaging Spectroradiometer Sensor aboard NASA’s TERRA and AQUA satellites Balance: Net primary production (NPP)

- Soil microbial CO2 fluxes _____________________________

Net ecosystem production (NEP)

============================

Observations 2001: Above average temp. was associated with positive NEP Heavy rainfall was associated with negative NEP Terrestrial NPP for the globe:

Around 50 Pg C / year (Trend: increasing!) Seasonal patterns:

Very pronounced for 30^o – 60^o North In summer positive NEP In winter negative NEP Literature: Potter et al.

EOS 84(46), 2003

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.) 5. Case study I: CO₂ cycle and global climate 6. Case study II: Methane oxidation in the subsurface 7. Varia

Major microbial activities in soil involving gaseous species

Mineralization CH₂O + O₂ -> CO₂ Denitrification NO₃^- -> N₂ (N₂O) Nitrification NH₄⁺ + O₂ -> NO₃^- (N₂O) Methanogenesis CO₂ + H₂ -> CH₄

CH₃COOH -> CH₄ + CO₂

Methane oxidation CH₄ + O₂ -> CO₂

Rough estimates of CH

₄

released into the atmosphere (units: 10

¹²

g/year)

Total 350 - 820

Biogenic (81 - 86% of total) 302 - 665

Ruminants 80 - 100

Termites 25 - 150

Paddy fields 70 - 120

Natural wetlands 120 - 200

Landfills 5 - 70

Oceans and lakes 1 - 20

Tundra 1 - 5

Abiogenic (14 - 19% of total) 48 - 155

Coal mining 10 - 35

Natural gas flaring and venting 10 - 30 Industrial and pipeline losses 15 - 45

Biomass burning 10 - 40

Methane hydrates 2 - 4

Volcanoes 0.5

Automobiles 0.5

Source:

Brock‘s Biology of Microor- ganisms

Microbial oxidation reduces flux!

Experimental approaches to determine metabolism and fluxes of trace gases in soil

Capillary fringe Groundwater Soil Air

Exchange of trace gases CH₄, N₂O, CO₂

Entrap- ment boxes

Eddy corre-

lation FACE

experi- ments

Analysis of conc.

profiles Laboratory

studies with

soil samples Time (h)

Ratio conc. extr. / conc. Inject. Typical result

Basic concept of a gas push-pull test (GPPT) (PPT successfully applied in groundwater!)

Groundwater Soil Air

Injection of well defined gas mixture (i.e. O₂, CH₄, Ar, Ne)

Extract and analyze gas composition

Methane (inhibited, sterile) Tracer

gas

Methane (active)

(6)

Fate of methane in vadose zone above oil contaminated aquifer (field site Studen)

Vadose zone

Atmosphere

Rhizosphere

Groundwater Methanogenesis Organic pollutant (e.g. petroleum hydrocarbons) O2

Methane oxidation 2 O2 + CH4 --> CO2 + 2 H2O

CO2 + 4 H2 --> CH4 + 2 H2O

0 5 10 15 20 25

-4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0

0 5 10 15 20 25 30

Methane oxidation

Groundwater

CH4 Concentration (ppm)

Depth (m)

O2 Concentration (%)

CH4 O2

CH

₄

[ µL/L ] O

₂

x 10 [ mL/L ]

-3 -2 -1 0

0 10 20 30

Depth [ m ]

Gas Profiles in Soil above a Contaminated Aquifer

High activity (2 Tests, +/- inhibitor) Low activity (1 Test)

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

Extracted / Injected Volume

Ne Ar CH

₄

0 0.2 0.4 0.6 0.8 1

0 1 2 3

High activity k= 2.19 h^-1 ± 0.26 0

0.2 0.4 0.6 0.8 1

0 1 2 3

Low activity Gas _Ext/ Gas _Inj

k= 0.68 h^-1 ± 0.05

0 0.2 0.4 0.6 0.8 1

0 1 2 3

Inhibited k= -0.07 h^-1 ± 0.04

!¹³C (CH4) = - 24.3 Injected CH4 : !¹³C = - 46.5 ‰ CH4 turnover ! Less negative

!¹³C (CH4) = - 44.4

!¹³C (CH4) = - 3.6

! ¹³C values of important carbon reservoirs

Biogenic CH4

Thermogenic CH4 Petroleum hydrocarbons Biomass

Terrestrial carbonates Marine carbonates

CO2 of atmospere

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

10

! ¹³C (%)

Biochemical pathways of methane ( !

¹³

C values in !

¹³

C notation)

Petroleum hydrocarbons (-28‰)

Dissolved inor- ganic carbon (DIC) (-14‰)

Calcium carbo- nate (CaCO3) (ca. 0‰)

Acetate

CO2 (-16‰)

CO2 (-4‰) Methanogenic microorganisms

(production of methane)

CH4 (- 40‰ to - 110‰

Atmosphere

CO2 (-15‰) Methanotrophic microorganisms (consumption

of methane)

Measurement of !¹³C in methane:

Rolf Siegwolf, PSI

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.) 5. Case study I: CO₂ cycle and global climate 6. Case study II: Methane oxidation in the subsurface 7. Varia