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Biogeochemical cycles
www.icbm.de/pmbio Microbial Ecology SS2010
Biogeochemistry
‚The study of the exchange of material between the living and
nonliving components of the biosphere. The biogeochemical
cycling of nutrients involves the physical transportation and its
chemical and biochemical transformation‘ (Jjemba 2004)
Reservoir: An amount of material, defined by certain biological, chemical or
physical characteistics (eg. CO2 in the atmosphere, S in rocks).
Flux: Amount of material that is transfered from one reservoir to another per
unit time.
Source and sink: Refer to the flux out of or into a reservoir
Turnover time: duration it will take to empty the reservoir in the absencce
of sources if the sink remains constant.
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Biogeochemistry
Earth‘s natural environment can be devided into:
Biosphere
Atmosphere
(air)
Hydrosphere
(ocean) Pedosphere
(land)
Lithosphere
3
Elements or compounds do not exist or
cycle individually but rather always
interact and overlap with other
geochemical cycles.
Most important cycles:
C, O, N, P, S (and Fe)
Simplified molecular composition of living material
The Redfield-ratio: C106:H263:O110:N16:P1:(S1)
mean oxidation state
CO2 +IV Carbon dioxide
C4H6O5 +I Malic acid
C6H12O6 0 Glucose, Biomass, Acetate
C2H5OH -II Ethanol
CH4 -IV Methane
Reduction
Oxid
ation
Carbon
NO3- +V Nitrate
NO2- +III Nitrite
N2 0 Nitrogen
NH4+ -III Ammonium
R-NH2 -III Amines
Reduction
Oxid
ation
Nitrogen
SO42- +VI Sulfate
S2O32- +II Thiosulfate
So 0 Sulfur
H2S -II Sulfide
R-SH -II Sulfhydryl-group
Reduction
Oxid
ation
Sulfur
4
Carbon cycle
The central nutrient cycle:
Determination of the amount of CO2 in the atmosphere, as well as rate of
microbial turnover of organic matter.
Includes all life and inorganic C reservoirs.
Organic carbon constitue a relatively small reservoir of carbon, most are
carbonate minerals
Microorganisms play important role in regulating the pools.
Particulate organic matter POM
Dissolved organic matter DOM
Particulate organic carbon POC
Dissolved organic carbon DOC
Carbon pools
Much of the carbon on Earth is tied up inorganically in the form of carbonates
(limestone and dolomite) about 1022g
Another great fraction is trapped as aged organic matter (Bitumen, coal, natural gas, petroleoum) about 1022g
Unaged dead material 1018g
Living biomass 1017g
Carbon on the atmosphere 1017g
Living systems depend on unaged, dead organic matter and atmospheric carbon
In order not to exhaust this carbon, it has to be recycled
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Carbon cycle
Photo- and chemo autotrophic organisms
e.g. Calvin-cycle, reverse TCA,
reductive AcetylCoA- cycle, 3-Hydroxypropionate Cycle
Primary production:
CO2 + 4 e- + 4 H+ <CH2O> + H2O
+IV 0
mean oxidation state
CO2 +IV Carbon dioxide
C4H6O5 +I Malic acid
C6H12O6 0 Glucose, Biomass, Acetate
C2H5OH -II Ethanol
CH4 -IV Methane
Reduction
Oxid
ation
Carbon
6
Photosynthetic Primary production
CO2 + H2O ! <CH2O> + O2
CO2 + H2O " <CH2O> + O2
Consumption (remineralisation)
The biggest syntrophic
relation of all living
creatures
Stochiometry
1:1:1:1
runs via
biological
loops...
Primary production = Consumption + deposition
Carbon cycle
Composition of plant litter
Sugar (15%) direct uptake and utilization by many organisms
Hemicellulose (15%) polysaccharide, decomposed by bacteria
and fungi
Cellulose (20%) large molecule, transformed by bacteria and
fungi into glucose
Lignin (40%) complex, insoluble, toxic, large molecule; degraded by fungi and actinomycetes to sugars, carboxilic
acids, ammino acids, degradation depends on oxygen.
Waxes (5%) and phenols (5%) are less abundant, minor role in
C cylce, hardly degradable = long turnover time
7
Carbon cycle
Carbon cycle within the biosphere
8
mean oxidation state
CO2 +IV Carbon dioxide
C4H6O5 +I Malic acid
C6H12O6 0 Glucose, Biomass, Acetate
C2H5OH -II Ethanol
CH4 -IV Methane
Reduction
Oxid
ation
Carbon
9
Overall processes
of anoxic decomposition
Nitrogen cycle
N # 10 % of dry biomass
As nitrogen represent a biolimiting element in
many environments it plays a central role in
controlling biological productivity.
Microbial reclycling of nitrogen is essential for life!
The Redfield-ratio: C106:H263:O110:N16:P1:(S1)
Nitrogen is the most abundant gas in the atmosphere (79 %)
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Nitrogen species
N-Assimilation:
- Nitrogen fixation (endergonic process)
N2 + 3 H2 + 2H+ 2 NH4+
- Ammonification
NO3- + 8 e- + 10 H+ NH4
+ + 3 H2O
mean oxidation state
of nitrogen
NO3- +V Nitrate
NO2- +III Nitrite
N2 0 Nitrogen
NH4+ -III Ammonium
R-NH2 -III Amines
Reduction
Oxid
ation
Oxidation state of nitrogen in all organic compounds is - III
11
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Examples of microorganisms from the nitrogen cycle
Pseudomonas denitrificans reduces nitrate to nitrogen (when no
oxygen is available) ! Denitrification, anaerobic respiration
Many Cyanobacteria (e.g. in heterocystes) and bacteria reduce
nitrogen to ammonia. Important symbiotic nitrogen fixing microbes
are Rhizobia who live in „Wurzelknöllchen“ of plants.
Anabaena
with
heterocyst
Nitrosomonas oxidizes ammonia to nitrite (first step catalysed via
Oxygenase with O2 as electron acceptor) ! chemolithotrophic
process
Nitrococcus oxidises nitrite to nitrate (O2 as electron acceptor) !
chemolithotrophic process
13
Wurzelknöllchen:
Symbiosis of
plants with
nitrogen-fixing bacteria
S-cycle
S # 1 % of dry mass
Dissimilatoric processes are more important than assimilatoric processes
many reactions only catalysed by prokaryotes
sulfate (SO42-) most oxidised form (marine: 28 mM)
'sulfide' (H2S) most reduced form (toxic)
Sulfur (S), sulfite (SO32-), thiosulfate (S2O3
2-) and
tetrathionate (S4O62-) important intermediates
Reduced S-compounds serve also as electron
donators for anoxygenic phototrophic bacteria
14
H-S-H, H-S-
-S-S-S-S-
S-S-S
S S
S-S-S
O-
O=S
O-
O
-O-S-O-
O
O O
-O-S-S-S-O-
O O
O O
-O-S-S-S-S-O-
O O
"sulfide"
poly sulfide
S8-sulfur sulfate thiosulfate sulfite
trithionate tetrathionate
Important sulfur compounds
O
-O-S-S-
O
15
Sulfur cycle
S-assimilation:
- assimilatory sulfate reduction (endergonic process)
SO42- + 4 H2 + 2H+ H2S
2 ADP 2 ATP
mean oxidation state
of sulfur
SO42- +VI sulfate
S2O32- +II thiosulfate
So 0 sulfur
H2S -II sulfide
R-SH -II sulfhydryl-group
Reduction
Oxid
ation
16
SO42-
HS-
oxic
anoxic
Aerobic sulfide oxidation
respiratory process (O2 oder NO3-)
(sulfur oxidising bacteria, SOB)
SO42-
HS-
oxic
anoxic
Aerobic sulfide oxidation
(incomplete sulfide oxidation) SOB
So S2O32-
Thiomagerita namibiensis,
A sulfur oxidising bacterium
with intra cellular sulfur dropplets
Achromatium oxaliferum,
A sulfur oxidising bacterium
with intra cellular sulfur dropplets and Calcium carbonate crystals
17
SO42-
HS-, FeS, FeS2
oxic
anoxic
Thiosulfate reduction
sulfur reduction,
anaerobic respiration
(SRB, sulfur reducers,
Iron reducers, thiosulfate reducers)
So S2O32-
SO42-
HS-
oxic
anoxic
Anaerobic
sulfide oxidation,
Photosynthesis process
(Green and red sulfur bacteria)
So S2O3
2-
SO42-
h!"
Phototrophic sulfur bacteria
in the hypolimnion of lake Dagow
18
SO42-
HS-
oxic
anoxic
So
S2O32-
Thiosulfate- and sulfur disproportionation
“Anaerobic fermentation”
SRB
S2O32- + H2O SO4
2- + HS- + H+
4 So + 4 H2O SO42- + 3HS- + 5H+
19
Examples of microbes from the sulfur cycle
Desulfovibrio desulfuricans reduces sulfate to sulfide !
Desulfurication, anaerobic respiration
Thiobacillus oxidises sulfide and other reduced sulfur compounds to sulfate
(O2 as electron acceptor) and reduces CO2 ! chemolithoautotrophic process
Pyrobaculum reduces sulfur to sulfide (with peptides as electron donator) at
>100 °C ! Hyperthermophilic sulfur reducing Archaeon, anaerobic respiration (?)
Chlorobium oxidises sulfide (via sulfur) in the light to sulfate and
uses die reduction equivalents for the reduction of CO2 !
anoxygenic photosynthesis, photolithoautotrophic process
Sample from lake Dagow with
anoxygenic phototrophic bacteria
20
Iron- and manganese-cycle
Fe3+
Mn4+
Fe2+
Mn2+
Iron- and
manganese
reduction
Iron oxidation
Geobacter sp.
Shewanella sp.
Manganese oxidation
Arthrobacter sp.,
Bacillus sp.
Acidophilic iron oxidiser Acidithiobacillus ferrooxidans
Leptospirillum ferroxidans
Neutrophilic iron oxidiser Gallionella ferruginea
Leptothrix discophora
„iron stems“
Gallionella ferruginea
schematic
illustration
grown on Mn2+
brown: MnO2-precipitates
Leptothrix sp.
21
22
P-cycle
Phosphate does not run through redox cycles as the
other elements mentioned before.
However, the availability of phosphat is dependant on the
redox state. Phosphate precipitates with oxidised iron as
hardly soluble FePO4
Precipitation of
phosphate
in a waste-water
treatment plant
If FePO4 gets into anoxic conditions, Fe3+ is reduced to
Fe2+ and it becomes soluble and is released again
23
The greenhouse effect
Solar radiation (mainly short wavelength):
30% returned to outerspace by reflection 51% absorbed by ocean and land
19% absorbed by atmospheric gases
Atmospheric gases retain a significant fraction of solar radiation
Emission of this energy (as heat) warms up our atmosphere = steady-state temperature is determined by gas content
Once gases had absorbed radiation, steady-state would be established at an elevated temperature
71% of infrared light emitted from Earth is absorbed by one of the
atmospheric gases:
Atmosphere temperature rise if infrared-absorbing gases increase, including methane and nitrous oxide
Connection of atmospheric
and marine carbon cycle
Why does the marine carbon cylce play such an
important role in regulating global climate?