day 3 4 soil carbon decomposition

3.3. The Carbon Cycle

- 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

Introduction

- Most compounds are too large for microorganisms to take up

Carbohydrates- sugars, starch, hemicellulose, cellulose

Description of major classes of compounds comprising plant residues

- Starch - &(14) branched linkages of amylose

- &(16) branched linkages of amylopectin

- Starch hydrolysing enzymes are the amylases

- Many microorganisms can decompose starch

- 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

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

- 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

Lignin


- 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:

- 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

- Lignin


- 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:

- 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

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


- Lignin

- 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

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+kg1Daysof

incubationLignin%

Hydroxyl%

CarboxylContent

CationExchangeCapacity

0 19.3 19.3 28 25

14 21.8 21.8 24 6

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

Soil Organic Matter and Thermodynamic Stability

Macias and Camps Arbestain (2010)

- 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

Soil Organic Matter and Thermodynamic Stability

Madigan et al. (2012)

- 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

- + In soil, non-ideal conditions are common:- Stabilisation mechanisms- Adverse environmental conditions

Protection of Organic Matter in Soil

Alexander

Kleber et al. (2007)l

Min

eral

perm

anen

tly c

harg

ed/h

ydro

xyla

ted

pol

arpol

ar

non

pol

ar

Ca++

Mg++

Al+++

pol

ar

Al+++

low pH

Ca++

Mg++

circum-neutral pH


(Conant et al., 2011)


(Schmidt et al., 2011)


Jastrow and Miller (1998)

- Physical Protection

- Chemical Protection

- Other adverse environmental conditions

- Selective preservation of recalcitrant compounds charcoal




- 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.




- 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)




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)


- 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


- Selective preservation of recalcitrant compounds charcoal


- Other adverse environmental conditions

TOKOMARU EGMONTFOXTON

Factors affecting decomposition

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


Aeration- O2 status in a soil microenvironment is affected by

rate of diffusion of O2 to site of microorganisms

- 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

Paul and Clark (1989)

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

Aeration

Classification of soil microorganisms based electron acceptors

AnaerobesAerobes

Electron acceptors

Anoxic conditionsOxic conditions

ATPs ATPs

Use of O2 Use of NO3-, Fe+3, Mn+4, SO42-, organic compounds

Facultative anaerobe

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

- 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

Aeration


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,Nitrosomonas100 Clostridium,Mucor250 Micrococcus,Penicillium650 Xeromyces,Saccharomyces

Paul and Clark (1989) from Harris (1981)

Moisture effects

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

Temperature

Temperature

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


Temperature

Type oforganisms Minimum Optimum MaximumCryophilic 0.50 015 1520

Mesophilic 1020 2040 4045

Thermophilic 2545 4560 6080

Growth temperature (C)

Moisture and Temperature

Van Camp(2004)

Moisture and Temperature

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

Substrate quality:

3. ToxicityPhenolics evolved to protect plants from herbivores and pathogensalso affect decomposers Importance of this effect is uncertain

4. Nutrient concentrationsNutrients are essential to support microbial growth

Soil Organic Matter Properties

Binding soil particles to form aggregates Helps reduce erosion Helps reduce compaction Increasing water stable aggregates Increasing water holding capacity Improves tilth

Physical Role


Chemical Role Source and sink for nutrients SOM retains cations (CEC) Buffers pH MO active in nutrient recycling Filters contaminants


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

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 carbonorganic matter : organic carbon

100:581.724

NZ soils usually up to 10% organic C= 17% organic matter

Arable 3.5% organic C, 6% OM Pasture 4.9% organic C, 8.4% OM Peat 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

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)

day 3 4 soil carbon decomposition

Documents

lignin fungi

plant residues lignin

plant residues starch

plant residues cellulose

plant residues hemicellulose

lignin soft rot fungi

brown rot fungi

plant residues amino