Download iv. carbon transformations in soil

IV. CARBON TRANSFORMATIONS IN SOIL
Required Readings:
Raich, J.W. and G. Mora. 2005. Estimating root plus rhizosphere contributions to soil respiration
in annual croplands. Soil Sci. Soc. Am. J. 69:634–639.
Cheng, W., D.W. Johnson and S. Fu. 2003. Rhizosphere effects on decomposition: Controls of
plant species, phenology, and fertilization. Soil Sci. Soc. Am. J. 67:1418–1427.
Collins, H.P., R.L. Blevins, L.G. Bundy, D.R. Christenson, W.A. Dick, D.R. Muggins and E.A.
Paul. 1999. Soil carbon dynamics in corn-based agroecosystems: Results from carbon-13 natural
abundance. Soil Sci. Soc. Am. J. 63:584-591.
Suggested Readings:
Sjoblad, R. D. and J. M. Bollag. 1981. Oxidative coupling of aromatic compounds by enzymes
from soil microorganisms. p. 113-152. In E. A. Paul and J. N. Ladd (eds.), Soil Biochemistry,
Volume 5. Marcel Dekker, New York.
Dagley, S. 1967. The microbial metabolism of phenolics. p. 287-317. In A. D. McLaren and G.
H. Peterson (eds.), Soil Biochemistry. Marcel Dekker, New York.
Lal, R., J.M. Kimble, R.F. Follett and C.V. Cole. 1998. The Potential of U.S. Cropland to
Sequester Carbon and Mitigate the Greenhouse Effect. Ann Arbor Press, Chelsea, MI, USA.
The most important element in the biological realm is carbon for it is carbon upon which the
chemistry of all life forms is based. A discussion of the transformations of carbon at the soil level
is best introduced from the view of the global carbon cycle. The distribution of carbon in some of
the main compartments in which carbon exists is given in Table 4.1.
Table 4.1. Distribution of Carbon in Some of the Main Compartments
Involved in the Carbon Cycle
Compartment
Atmosphere
Soil organic matter
Marine humus
Land life forms
Ocean life forms
Dissolved carbonate-bicarbonate
in oceans
Coal and petroleum
Sediments
Amount of Carbon
(x 1012 kg)
700
2,500
3,000
480
50
3,840
1 x 104
6 x 107
The amount of carbon contained in the soil organic matter of terrestrial soils is approximately
three to four times the content of carbon contained in the atmosphere. The annual input of carbon
to the soil has been estimated as 110 x 1012 g/year or about 15% of the total atmospheric carbon
dioxide. However, an equivalent amount of carbon is returned to the atmosphere as a result of
decay processes that occur primarily in the soil. With the addition of such a large amount of
carbon to the soil each year, it is readily apparent that this major nutrient would quickly become
exhausted in the atmosphere if all biological activity in the soil were to abruptly cease.
The atmospheric concentration of carbon dioxide is traditionally given as 0.03%. Concern has
been expressed because the level of carbon dioxide in the atmosphere is increasing. Fuel
combustion is most often mentioned as the major source of the additional carbon dioxide in the
atmosphere. Fuel combustion comprises about one-half of one percent of the total carbon in the
atmosphere.
The carbon in the soil organic matter turns over approximately every 25 years. Of course, certain
fractions have much more rapid turnover rates and other fractions are far more resistant and
remain unaltered for hundreds, or even thousands, of years.
Sources of Carbon Added to Soil. The majority of carbon entering the soil is comprised of plant
residues. Microbial and animal cells account for only a minor fraction of the total input of carbon
to the soil. The plant residues that are introduced to the soil have chemical compositions that
vary with type, age, and portion of the plant. A comparison of the composition of plant tissue,
yeast cells, mammalian muscle, and insect exoskeleton material is given in Table 4.2.
Since plant residues are the major input of carbon to soil, the compounds that are added in the
greatest concentration are cellulose, hemicellulose, lignin, protein, nucleic acid, aliphatic acids,
starch, and lipids. Polysaccharides, such as cellulose, hemicellulose, starch, etc. are condensation
polymers of monosaccharides or sugar units linked after elimination of water. Protein molecules
are made up of amino acids linked together via the peptide bond. Nucleic acids are long-chain
molecules consisting of a ribose (RNA) or deoxyribose (DNA) sugar moiety, phosphate, and the
bases guanine, adenine, thymine, cytosine, and uracil (RNA). Lignin consists of units that
contain an aromatic ring and a three-carbon side chain and is formed by the random
polymerization of these units into a nonspecific chemical structure.
Table 4.2. Chemical Composition of Some Living Organisms and Tissue
Carbon Source
Yeast Cells
Plant Tissue
Mammalian
Muscle
Insect
Exoskeleton
----------------------------------------- % ---------------------------------------Mannan and glucan
Chitin
Cellulose
Lignin
Protein, nucleic acid
Amino acids
Aliphatic acids
Soluble sugars
Glycogen
Starch
Lipids
Mineral ash
28
?
24
1-2
?
0.5
18
?
9
17
?
16-60
5-30
2-15
?
5-30
?
5-40
1-25
1-13
80
5
?
2-7
5
5
25-55
25-37
?
?
4-5
1
Soil is often the receptacle for organic waste products derived from agricultural and industrial
activities. Compared to the total amount of carbon input to soil as plant residue or litter, the
amount of carbon added as organic wastes is minimal. That does not eliminate, however, our
need to understand the chemistry of the compounds involved. Animal manures are generally
easily disposed of by spreading on the soil and offer benefit to producers of crops by supplying
essential plant nutrients and by improving the aggregation of the soil. A problem occurring with
increasing frequency, however, is that a very large amount of manure may be generated as a
result of a single farm operation, making it difficult to dispose of the manure within a reasonable
distance from its source. Sewage sludges (i.e. biosolids) may also be applied to soil with the
same benefits as that noted for manures. However, some sludges contain heavy metals and
undesirable organic compounds. Land application of these materials must be carefully controlled
because of the threat the metals and organic compounds may enter the food chain in
concentrations great enough to cause health problems. Other chemicals, such as agricultural
pesticides and industrial solvents, also enter the soil environment. Thus a large number of
compounds that vary in their chemical composition are continually being added to the soil.
Soil Organic Matter. The organic components in the soil, including the microbial biomass but
excluding the macrofauna and macroflora, constitutes the soil organic matter. An exact definition
of the chemical composition of the organic matter is often more difficult to define. Chemical
analyses of various kinds have found that soil organic matter is comprised of 10-20%
carbohydrates, 20% materials containing N, 10-20% aliphatic fatty acids and alkanes, and 4060% aromatic compounds. The composition of soil organic matter has been found to be
remarkedly similar from soil to soil over a broad range of climatic, topographic, and vegetative
variations.
A classical fractionation scheme based on extraction techniques divides the soil organic matter
into three distinct classes; (a) fulvic acid which is soluble in alkali and acid, (b) humic acid
which is soluble in alkali but insoluble in acid, and (c) humin which is insoluble in both alkali
and acid.
Fulvic acids are the most highly oxidized and the lowest molecular weight humic materials found
in soil. They are composed of a series of aromatic rings with a large number of side chains, e.g.
benzene carboxylic acids and phenolic acids. In addition, polysaccharide and low molecular
weight fatty acids are associated with the fulvic acid fraction. A flexible and open structure
allows binding of organic and inorganic compounds into void spaces, which are of varying
dimensions, within the fulvic acid molecules.
Humic acids are comprised of higher molecular weight materials and can form hydrogen bonds,
thus precipitating at low pH values. The building blocks of purified humic acids are both
nonpoly- and polyaromatic in structure and contain few carbohydrate residues.
Humin is only poorly defined and its solubility is attributed to the firmness of its binding to the
mineral part of the soil. A comparison of the elemental composition of fulvic acid, humic acid,
and humin is provided in Table 4.3.
Table 4.3. Elemental Composition of Organic Fractions from a Scottish Agricultural
Soil.
Elemental Analysis (%)
Fraction
Fulvic Acid
Humic Acid
Humin
Ash (%)
C
N
H
O
8.5
2.2
12.5
43.6
51.7
55.9
4.9
5.1
5.9
1.7
2.9
0.9
49.8
40.3
37.3
Organic matter in soil, because of its variation in composition, is used to different extents by soil
microorganisms, and is thus of varying ages. The “age” of the soil organic matter can be
obtained using carbon-dating methods. The ages of organic matter vary not only among soils but
also with the organic matter fractions (Table 4.4).
Table 4.4. Radiocarbon Age of Some Canadian Soils and Organic Matter Fractions
Soil
Organic Fraction
Melfort
Unfractionated
0-15 cm
15-25 cm
Oxbow
Unnamed
Radiocarbon Age
870
960
Fulvic Acid
Humic Acid
Humin
470
1,235
1,135
Unfractionated
0-8 cm
18-32 cm
20
1,340
Virgin Grassland
Cropped
420
1,960
Roles of Soil Organic Matter. Plants require only light and a suitable supply of inorganic
nutrients to grow. The presence of organic matter in soil, therefore, is not an absolute
requirement. However, most of the major agronomic crops are grown in soils where the physical
environment and the nutrition of the plants cannot be closely monitored or controlled. Soil
humus can play a dominant role in controlling these factors and it is generally true that soils that
contain a higher concentration of organic matter are a better media for plant growth than low
organic matter soils. The contribution of organic matter in maintaining a fertile soil are really
indirect and may be summarized as follows:
i.
Humic substances impart a dark brown color to the soil which facilitates warming and
hence plant growth.
ii.
Soil structure and stability are maintained by soil organic matter due to aggregation.
iii. Soil organic matter acts as a reservoir for plant nutrients.
iv. Rapid changes in pH are buffered by soil humus.
v.
Soil organic matter can form stable complexes with some metals and thus influence
their availability.
vi. Mineralization of organic matter provides a direct source of nitrogen, phosphorus and
sulfur.
vii. Soil organic matter interacts with commercial pesticides reducing their efficiency.
viii. The physiology of a plant may be affected directly by humic compounds which interact
with the root or which are taken up into the plant.
Soil organic matter is one of our most important natural resources. It supports a great diversity of
important biochemical reactions that are part of the overall carbon cycle. These reactions include
both the formation and decomposition of important natural organic compounds.
Oxidative Coupling. Synthesis of lignin in plant and humic acids in soils involves enzymemediated oxidative coupling reactions. Oxidative coupling is the process by which phenolics or
aromatic amines are linked together. The products formed contain C-C, C-O, C-N and N-N
bonds and impart stability to the materials after the reaction has been completed. In some cases,
these reactions are initial steps in the biodegradation of organic compounds. Although specificity
towards a substrate may be observed, the oxidative coupling reactions can involve many
different phenolics or aromatic amines. In addition to formation of lignin and humic acids,
oxidative coupling also is responsible for the incorporation into organic matter of many synthetic
(i.e. man-made) agricultural and industrial chemicals.
The initial step in the oxidative coupling reactions involves the production of an aryloxy radical
from phenol (Figure 4.1) or other related substrates.
Figure 4.1. Formation of aryloxy radicals from phenol.
Oxidative coupling enzymes are metal-containing enzymes that are designated as either
monophenol monooxygenases or peroxidases. Commonly included under the monophenol
monooxygenases are two distinct classes of enzymes commonly referred to as laccases or
tyrosinases, although the laccase designation is really an historical one.
Laccases and tyrosinases contain copper and require molecular oxygen, but no coenzyme, for
activity. Peroxidases possess an iron (ferric) porphyrin coenzyme and require hydrogen peroxide
(H2O2) for activity. As previously noted, the oxidative coupling reactions exhibit broad substrate
specificities.
Free radical formation is not generally considered associated with tyrosinase activity. Instead,
tyrosinase activity catalyze two types of reactions—cresolase activity refers to the ortho
hydroxylation of tyrosine and other monophenols to form o-diphenols (Figure 4.2). The
subsequent dehydrogenation of o-diphenols to form o-quinones is known as catecholase activity.
Both of these reactions are important in both the synthesis and degradation of organic molecules
in soil.
Figure 4.2. Cresolase (top) and chatecholase (bottom)
activity of tyrosinase.
Metabolism of Phenolics and Aromatic Amines. The degradation of ring structures is a common
reaction in soils and is required for the cycling of many carbon compounds introduced into the
soil plus the metabolism of natural humic compounds. In general, biological oxidations result in
the formation of water by the trrasfer of electrons or hydrogen atoms to oxygen. However, in
certain systems, oxygen is incorporated directly into the substrate molecule via the action of
enzymes called oxygenases. If one atom of oxygen is incorporated, the enzymes and reactions
involved are called monooxygenases. Monooxygenses introduce one or two hydroxyl groups to
the benzene ring of aromatic compounds to produce a phenol or in case of the introduction of
two hydroxyls, catechol is formed. The oxygen not introduced into the ring is reduced to water.
If both atoms of oxygen are incorporated, the enzymes and reactions are referred to as
dioxygenases and the benzene ring is broken.
The breaking of the benzene ring is a fundamental biochemical reaction of the carbon cycle.
Dioxygenases cleave the benzene ring in one of two ways. Ortho fission breaks the ring between
the two carbon atoms that contain the hydroxyl groups (Figure 4.3). Meta fission breaks the ring
between a carbon atom containing one hydroxyl group and a neighbor carbon atom that contains
a hydrogen atom.
Figure 4.3. Illustration of ortho and meta fission of a substituted catechol.
Once the ring is broken, metabolism does not cease, but continues to eventually form reaction
products that can enter the tricarboxylic acid cycle and produce useful energy or carbon
skeletons for cell synthesis. The reactions following ortho ring fission (from right to left) are
shown below (Figure 4.4).
Figure 4.4. Conversion of ring-fission projects of catechol into tricarboxylic acid cycle
intermediates.
Dioxygenases break the benzene ring almost exclusively via meta fission. The pathways that lead
from ring breakage to tricarboxylic cycle intermediates is illustrated by also using catechol as the
model compound (Figure 4.4).
Figure 4.4. General scheme for the degradation of catechols by meta fission and the conversion
of the ring structure to tricarboxylic acid cycle intermediates.
Theories of Humus Formation. But how does the carbon that enters the soil actually become
stabilized as soil organic matter (i.e. humus)? Several theories have been proposed to describe
the overall process of humus formation. The modified lignin theory proposes that humus is
basically lignin material that has been only slightly modified to form lignin-protein complexes.
These complexes are dark-colored and resistant to microbial attack. The polyphenol theory
describes a process by which all plant components, including lignin, are first broken down into
simple monomers. These monomers are then polymerized into high molecular weight, dark
colored complexes through a series of reactions including oxidative coupling reactions. Probably
both theories partially describe the overall process of humus formation in soil, but humus is one
of the most complex natural products found and its formation probably cannot be simply defined
by a single set of reactions.