3.3.

The Carbon Cycle

Introduction
-

The carbon cycle is the driving force behind other cycles (e.g., N, S and parts of
the P cycle)

The most important source of organic carbon in soil is plant residues

-

Up to 10% (DW) solubles, sugars, amino acids, amino sugars

Remainder is polymers:

- 2-5% protein
- 15-60% cellulose
- 10-30% hemicellulose
- 5-30% lignin
Most compounds are too large for microorganisms to take up

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Description of major classes of compounds

comprising plant residues
-

Carbohydrates
- sugars, starch, hemicellulose, cellulose
- Starch
- &(14) branched linkages of
amylose
- &(16) branched linkages of
amylopectin
-

Starch hydrolysing enzymes are

the amylases

Many microorganisms can

decompose starch

Description of major classes of compounds

comprising plant residues
-

Carbohydrates
- sugars, starch, hemicellulose, cellulose
- Cellulose
- Most abundant plant constituents
-

Some fungi have in cell walls

Often found together with lignin

and hemicellulose

Cell walls are long, interwoven,

interconnected strands of micro
fibrils, each made of smaller units
of long-chain cellulose molecules

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Description of major classes of compounds

comprising plant residues
-

Carbohydrates
- sugars, starch, hemicellulose, cellulose
- Cellulose
- Polymer composed of units of
glucose with (1-4) linkages
-

Many microorganisms can

metabolise cellulose

The multi-enzyme complex is

cellulase

Description of major classes of compounds

comprising plant residues
-

Carbohydrates
- sugars, starch, hemicellulose, cellulose
- Hemicellulose
- More heterogeneous than cellulose
-

Not polymers of single type of unit

They generally contain 2-4

monosaccharide units or uronic acid

Most is found in close physical

proximity to cellulose in primary and
secondary cell walls of higher plants

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Description of major classes of compounds

comprising plant residues
-

Phenolic polymer present in the cell

wall

It contains small amounts of nitrogen

Cereal straw contains 10-20% lignin

Fungi are primarily responsible for

lignin degradation:

Lignin

- Brown rot fungi (only degrade

polysaccharides associated with
lignin)
- Soft rot fungi (mainly after
polysaccharides)
- White rot fungi
-

Bacteria are not as important as fungi

Actinomycetes

Description of major classes of compounds

comprising plant residues
-

Phenolic polymer present in the cell

wall

It contains small amounts of nitrogen

Cereal straw contains 10-20% lignin

Fungi are primarily responsible for

lignin degradation:

Lignin

- Brown rot fungi (only degrade

polysaccharides associated with
lignin)
- Soft rot fungi (mainly after
polysaccharides)
- White rot fungi
-

Bacteria are not as important as fungi

Actinomycetes

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Description of major classes of compounds

comprising plant residues
-

Lignin

http://forest.mtu.edu/classes/fw5350/carbon_substrates/slide22.html

Description of major classes of compounds

comprising plant residues
-

Protein

Amino acids are the building blocks of proteins

The peptide bond is readily hydrolysed by proteases

Many plant and animal cells have lipids such as fats and
waxes

Lipids break down by lipases (esterases)

Fat and Oil

Other sources: manure, sewage sludge, compost

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Decomposition of Organic Detritus

Soil contains organic matter that is different in composition from plant residues
Plant residues do not degrade to only microbial cells and carbon dioxide
- Over the course of decomposition:
- C is loss as CO2
- Microbial biomass is formed
- Microbial biomass turns over as well as
does C in plant residues
- A fraction of C will become protected
through physical and chemical
mechanisms
- At the end of the growing season, ~ 33% of
the C from plant residues will remain in soil

Decomposition of Organic Detritus

Soil contains organic matter that is different in composition from plant residues
Plant residues do not degrade to only microbial cells and carbon dioxide
cmol+kg1
Daysof
incubation

Lignin
%

Hydroxyl
%

Carboxyl Cation
Content Exchange
Capacity

19.3

19.3

28

25

14

21.8

21.8

24

40

28.0

28.0

81

42

88

30.8

30.8

95

47

135

34.3

34.3

113

58

180

39.4

39.4

142

60

244

38.3

38.3

139

81

355

37.6

37.6

139

82

- Changes in properties of oat straw

during decomposition
- Lignin will decompose as well, but
slower than cellulose and
hemicellulose
- Lignin is NOT a recalcitrant fraction
of plant residues

Alexander
Alexander

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Soil Organic Matter and Thermodynamic Stability

- Soil organic matter ultimately
originates from photosynthesis
- Fresh organic matter is the most
reduced fraction in soil and hence
thermodynamically unstable
- As organic matter decomposes, it
acts as an electron pump supplying
electrons to more oxidised species
Macias and Camps Arbestain (2010)

Soil Organic Matter and Thermodynamic Stability

- The transformation of organic macromolecules
into CO2 requires that the chemical bonds of the
former be broken first
- This process requires an initial input of activation
energy
- If this energy investment is not made, no
reactions will take place

Madigan et al. (2012)

- + In soil, non-ideal conditions are common:

- Stabilisation mechanisms
- Adverse environmental conditions

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Protection of Organic Matter in Soil

Kleber et al. (2007)l

circumneutral
pH

Ca++

Al+++

polar

polar

nonpolar

Mg++
polar

Mineral
permanently charged/hydroxylated

Alexander

Ca++
Mg++

Al+++
low pH

Page 8

Protection of Organic Matter in Soil

(Conant et al., 2011)

Protection of Organic Matter in Soil

(Schmidt et al., 2011)

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Protection of Organic Matter in Soil

- Physical Protection

- Chemical Protection

- Selective preservation of recalcitrant compounds charcoal

- Other adverse environmental

conditions
Jastrow and Miller (1998)

Protection of Organic Matter in Soil

- Physical Protection

Jastrow and Miller (1998)

- Spatial inaccessibility of organic matter to decomposer organisms

- The spatial arrangement of soil particles is complex with a discontinuous
pattern of pore spaces of various sizes and shapes that are more or less
filled with water and/or air
- Biodegradation requires contact between the substrate and the microbial
cell in the case of small molecules, or between polymers and extracellular
enzymes.

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Protection of Organic Matter in Soil

- Physical Protection

Jastrow and Miller (1998)

- However such contacts are

infrequent in soil as both the
substrate and microorganisms
occupy a very small proportion of
the soil volume and are
heterogeneously distributed

Huang (2004)

Protection of Organic Matter in Soil

- Physical Protection

Jastrow and Miller (1998)

Organic substrates can be located in pores to which

microorganisms have no access because pore neck too
small or water pathway (for bacteria and protozoa) is
discontinuous
15% of soil porosity in a sandy soil and 52% in a clayey
soil is inaccessible to microorganisms because pore neck
< 0.2 m
At 0.1 bar, pores > 30 m are filled with air (53% in sandy
soil and 14% in clayey soil) limited diffusion of nutrients
and substrates
Chenu and Stotzky (2002)

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Protection of Organic Matter in Soil

- Chemical Protection

- Interaction of organic compounds with minerals and metal ions decreases

their rate of decomposition
- Long-term preservation is mainly due to interactions with minerals:
- With Fe and Al oxides, allophane
- With 2:1 clay minerals, e.g., vermiculite, smectite
- With 1:1 clay minerals, e.g. kaolinite
- The increased stability of organo-mineral associations against microbial
decomposition is mainly related to the greater amount of chemical energy
required for enzymatic cleavage of chemical bonds

Protection of Organic Matter in Soil

- Selective preservation of recalcitrant compounds charcoal

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Protection of Organic Matter in Soil

- Other adverse environmental

conditions

TOKOMARU

FOXTON

Page 13

EGMONT

Factors affecting decomposition

Aeration
Moisture
Temperature
Nutrient availability
Residue composition (C:N)
Osmotic potential (e.g., saline soils)

Jastrow and Miller (1998)

Aeration
- O2 status in a soil microenvironment is affected by
rate of diffusion of O2 to site of microorganisms

Paul and Clark (1989)

- Aerobes and anaerobes coexist in soils.

- Denitrification (an anaerobic process) occurs in well-drained soils
- Anoxic environments may exist at microsites in aerobic soils
caused by depletion of O2 around a high concentration of
available carbon or due to poor drainage

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Aeration

Madigan et al. (2012)

- The change from aerobic to anaerobic metabolism occurs as

O2 concentration lowers below 1%
- Water-saturated soil aggregates larger than 3 mm in radius
have no O2 in the centre

Classification of soil microorganisms based electron acceptors

Electron acceptors

Anoxic conditions

Oxic conditions

Use of NO3-, Fe+3, Mn+4, SO42-, organic compounds

Use of O2
Aerobes

ATPs

Facultative
anaerobe

ATPs

Page 15

Anaerobes

ATPs

Aeration
- Microbial communities in reducing environments,
e.g., flooded soils, differ in composition and activity
from those of aerobic sites.
- Why aerobes need O2?
- High enough redox potential for appropriate electron acceptors to be
present
- O2 is required by certain enzymes and growth factors
- Aerobes have detoxification mechanisms

- Why anaerobes cannot tolerate O2?

- Oxygenated environments are toxic to them: e.g. H2O2
- Need low redox potential for their enzymatic activities

Aeration
- Population of anaerobic bacteria in
the upper few cm of soil can be as
10 times their numbers than at
greater depths
- aerobic bacteria produce these
anoxic environment by consuming
the O2 stored in microsites
- Roots contribute as well

Paul and Clark (1989)

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Moisture effects
Decomposition has similar shape of moisture
response as does net primary production (NPP)
Declines at extremely low and high moisture

Less sensitive to low moisture than is NPP (no litter

accumulation in deserts)
More sensitive to high moisture than is NPP (SOM
accumulation in waterlogged soils)

Generally, microbial activity in soil is optimal at -0.1 bar and decreases as soil
becomes waterlogged or more droughty
Fungi are generally more tolerant to water stress than are bacteria
Waterpressure

Microorganisms

(bar)
15

Rhizobium,Nitrosomonas

100

Clostridium,Mucor

250

Micrococcus,Penicillium

650

Xeromyces,Saccharomyces

Paul and Clark (1989) from Harris (1981)

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Moisture effects

Temperature
Microbes as a group can live
between 0-70 C
Some exceptions (many
Archaeobacteria):
in presence of high salt content
(e.g., artic brine lakes)
because freezing point is
lowered
In thermal vents at 100 C
where water under pressure
does not boil

Page 18

Temperature
Within certain range of temperatures, most microbial
processes increase in rate with temperature

Paul and Clark (1989)

Temperature
Growth temperature (C)
Type oforganisms

Minimum

Optimum

Maximum

Cryophilic

0.50

015

1520

Mesophilic

1020

2040

4045

Thermophilic

2545

4560

6080

Page 19

Moisture and Temperature

Van Camp(2004)

Moisture and Temperature

Page 20

Other environmental effects

pH
Certain groups of organisms vary in acid tolerance

Bacteria neutral to slightly alkaline

Nitrifiers are sensitive to low pH
Exception are few acidophilic bacteria (e.g. Thiobacillus)
Most fungi prefer acid environment
Most cyanobacteria prefer pH > 7
Actinomycetes generally do not tolerate low pH

Microbes also modify soil pH

Other environmental effects

Soil texture
Protection of SOM by clay minerals
Aggregate structure (anaerobic micro-sites)
Sorption of cells on soil particles

Essential nutrients may be limited

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Substrate quality:
3.

Toxicity
Phenolics evolved to protect plants from herbivores and pathogens
also affect decomposers
Importance of this effect is uncertain

4.

Nutrient concentrations
Nutrients are essential to support microbial growth

Soil Organic Matter Properties

Physical Role

Binding soil particles to form aggregates

Helps reduce erosion
Helps reduce compaction
Increasing water stable aggregates
Increasing water holding capacity
Improves tilth

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Soil Organic Matter Properties

Chemical Role

Source and sink for nutrients

SOM retains cations (CEC)
Buffers pH
MO active in nutrient recycling
Filters contaminants

Soil Organic Matter Properties

Biological Role
Nutrient cycling
Source of C and of electrons to microbes
Source of nutrients to microbes and plants
May inactivate some organic pesticides
But also may enhance degradation of pesticide
residues

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Measurement of SOM
Loss on ignition
Chemical oxidation
Elemental analysers

Expression of SOM
Usually on a dry weight basis
%OC or %OM w/w
SOM usually 58% organic carbon
organic matter : organic carbon
100:58
1.724

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NZ soils usually up to 10% organic C

= 17% organic matter
Arable
Pasture
Peat

3.5% organic C, 6% OM
4.9% organic C, 8.4% OM
46% organic C, 79% OM

The amount of organic matter in a soil

and the stability of soil structure are
fundamental properties which influence
the chemical, physical and biological
environment in the soil they define soil
quality

Page 25

Soil Quality
Accept, hold and release nutrients and other
chemical constituents
Accept, hold and release water to plants. Streams
and groundwater
Promote and sustain root growth
Maintain suitable soil biotic habitat
Respond to management
Resist degradation (e.g. erosion)

Page 26