1

Biogeochemical cycles

www.icbm.de/pmbioMicrobial Ecology SS2009

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.

2

Earth‘s natural environment can be devided into:

Biosphere

Atmosphere

(air)

Hydrosphere

(ocean)Pedosphere

(land)

Lithosphere

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)

3

mean oxidation state

CO2 +IV Carbon dioxide

C4H6O5 +I Malic acid

C6H12O6 0 Glucose, Biomass, Acetate

C2H5OH -II Ethanol

CH4 -IV Methane

Re

du

ctio

n

Oxid

atio

n

Carbon

NO3- +V Nitrate

NO2- +III Nitrite

N2 0 Nitrogen

NH4+ -III Ammonium

R-NH2 -III Amines

Re

du

ctio

n

Oxid

atio

n

Nitrogen

SO42- +VI Sulfate

S2O32- +II Thiosulfate

So 0 Sulfur

H2S -II Sulfide

R-SH -II Sulfhydryl-group

Re

du

ctio

n

Oxid

atio

n

Sulfur

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

4

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

5

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

Re

du

ctio

n

Oxid

atio

n

Carbon

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

6

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

Carbon cycle

7

Carbon cycle within the biosphere

mean oxidation state

CO2 +IV Carbon dioxide

C4H6O5 +I Malic acid

C6H12O6 0 Glucose, Biomass, Acetate

C2H5OH -II Ethanol

CH4 -IV Methane

Re

du

ctio

n

Oxid

atio

n

Carbon

8

Overall processes

of anoxic decomposition

9

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 %)

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

Re

du

ctio

n

Oxid

atio

n

Oxidation state of nitrogen in all organic compounds is - III

10

11

12

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

Wurzelknöllchen:

Symbiosis of

plants with

nitrogen-fixing

bacteria

13

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

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

14

Sulfur cycle

S-assimilation:

- assimilatory sulfate reduction (endergonic process)

SO42- + 4 H2 + 2H+ H2S

2 ADP2 ATP

mean oxidation state

of sulfur

SO42- +VI sulfate

S2O32- +II thiosulfate

So 0 sulfur

H2S -II sulfide

R-SH -II sulfhydryl-group

Re

du

ctio

n

Oxid

atio

n

15

SO42-

HS-

oxic

anoxic

Aerobic sulfide oxidation

respiratory process (O2 oder NO3-)

(sulfur oxidising bacteria, SOB)

16

SO42-

HS-

oxic

anoxic

Aerobic sulfide oxidation

(incomplete sulfide oxidation) SOB

SoS2O32-

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

SO42-

HS-, FeS, FeS2

oxic

anoxic

Thiosulfate reduction

sulfur reduction,

anaerobic respiration

(SRB, sulfur reducers,

Iron reducers, thiosulfate reducers)

SoS2O32-

17

SO42-

HS-

oxic

anoxic

Anaerobic

sulfide oxidation,

Photosynthesis process

(Green and red sulfur bacteria)

So

S2O32-

SO42-

h·!

Phototrophic sulfur bacteria

in the hypolimnion of lake Dagow

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+

18

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

19

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.

20

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

21

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 absobed 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?