Box 410 Biopolymers

Cellulose

Cellulose is the most common plant polymer forming the structural fibres of many plants. Cellulose is constructed solely of glucose monomers (Fig. 1a), i.e. isolated or single units with consistent structure, in this case based on a carbon ring. The glucose monomers are linked by an ether bond (C-O-C; Fig. 1a). Thus, cellulose has a simple straight chain structure. Degradation of cellulose occurs stepwise. Initially the large polymer chain is cleaved into smaller units containing, for example, two or three glucose monomers (cellobiose and cellotriose, respectively Fig. 1b) by the action of cellulase enzymes. It is this depolymerization reaction that is the rate-limiting step in cellulose biodegradation. The smaller units are then further degraded to produce glucose monomers that are then completely mineralized (converted to their inorganic constituents, e.g. CO2 and H2O) under aerobic conditions (Fig. 1c) or fermented to ethanol and CO2 under anaerobic conditions.

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH

Cellulose

CH2OH

CH2OH

Cellulose

Cellulase

CH2OH

OH Glucose

Fig. 1 Steps in the aerobic degradation of cellulose.

OH Glucose

CH2OH

CH2OH

CH2OH Cellobiose

6CO2 + 6H2O

CH2OH Cellobiose

6CO2 + 6H2O

Fig. 1 Steps in the aerobic degradation of cellulose.

(continued)

Hemicelluloses

Hemicelluloses are the second most common class of plant polymer. Hemicellluloses are more complex than cellulose, being polymers of hexose sugars (six-atom ring, e.g. glucose, galactose, mannose), and pentose sugars (five-atom ring, e.g. ribose, xylose and arabinose) as well as uronic acids including glucuronic and galacturonic acid. An example of the degradation of a hemicellulose is that of pectin (Fig. 2), which is a polymer of galacturonic acid. Pectin is important in plant structure, being involved in plant cell wall formation. Decomposition of pectin occurs in three stages. Initially, pectin esterase enzymes attack esters (COOCH3) on side-chains (Fig. 2a) resulting in carboxylic acid (COOH) where esters were originally (Fig. 2b). The second stage of degradation is depolymerization to form glucuronic acid monomers (Fig. 2c). These monomers are then mineralized to CO2 and H2O.

Lignin

Lignin is the third most common plant polymer after cellulose and hemicelluloses. Lignin gives wood its toughness and structural rigidity. Lignin is formed from the metabolic processing of glucose (non-

COOCH3 O

cooch3

cooch3

OH COOCH3

Stage 1: Pectin esterases attack side-chains

COOCH3

OH COOCH3

Stage 1: Pectin esterases attack side-chains

COOCH3

COOH O

Galacturonic acid monomers

x n —^^ 5CO2 + 5H2O + energy Galacturonic acid oxidase

Stage 3: Mineralization of galacturonic acid monomers Fig. 2 Steps in the aerobic degradation of the hemicellulose pectin.

(continued on p. 102)

aromatic) that is converted into three basic aromatic (see Section 2.7) monomers, coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. These monomers react together and with their precursors to produce lignin. Thus, lignin is a tremendously complex polymer with a random structure (Fig. 3). Lignin has a condensed structure that is highly aromatic, making it the most resistant component of plant tissues to degradation. Only a few soil organisms are capable of degrading lignin. These organisms belong to a group of fungi known as white rot fungi or basidiomycetes. They produce powerful non-specific extracellular enzymes called peroxidases which, with the aid of H2O2, O2- and 1O2, cause the depolymerization of lignin. Carbon-carbon bonds and ether (C-O-C) bonds are cleaved initially resulting in the formation of monomeric phenols, aromatic acids and alcohols; these are, in turn, mineralized to CO2 and H2O.

h3co h3co

Fig. 3 Partial structure of lignin. After Killops and Killops (1993).

o y och

Fig. 3 Partial structure of lignin. After Killops and Killops (1993).

Table 4.6 Relative proportions of biopolymers in plant-derived soil organic matter.

Plant residues

Percentage in soils

Cellulose 50

Hemicelluloses 20

Lignin 15

Protein 5

carbohydrates and amino acids 5

Pectin 1

Waxes and pigments 1

electrons is harnessed in the production of adenosine triphosphate (ATP), the cell's energy-storing compound. Terminal electron acceptors (e.g. oxygen) are the final place the electrons arrive in the electron transport chain. Although oxygen is not the only electron acceptor, it is the most thermodynamically favoured

Table 4.7 Order of bacterial reactions during microbial respiration of organic matter based on energy yield. Modified from Berner (1980), reprinted by permission of Princeton University Press.

Bacterial reaction

DG° (kJmol-1 of CH2O)

Aerobic respiration: important in all oxygenated Earth

surface environments

CH2O + O2 ^ CO2 + H2O

-475

Denitrification: most important in terrestrial and marine

environments impacted by anthropogenic inputs from

fertilizers

5CH2O + 4NO- ^ 2N2 + 4HCO-+ CO2 + 3H2O

-448

Manganese reduction: minor reaction important in some

marine sediments

CH2O + 3CO2 + H2O + 2MnO2 ^ 2Mn2+ + 4HCO3

-349

Iron reduction: can be significant in some soils and marine

sediments with high iron contents from contamination or

weathering flux (e.g. Amazon Delta)

CH2O + 7CO2 + 4Fe(OH)3 ^ 4Fe2+ + 8HCO- + 3H2O

-114

Sulphate reduction: major process in anaerobic marine

sediments, especially on continental shelves

2CH2O + SO42- ^ H2S + 2HCO-

-77

Methanogenesis: important process in freshwater wetlands,

waterlogged soils and in deeply buried low-sulphate marine

sediments

2CH2O ^ CH4 + CO2

-58

Note: Free energy value for organic matter (CH2O) is that of sucrose.

Note: Free energy value for organic matter (CH2O) is that of sucrose.

(Table 4.7), and is therefore utilized first by aerobic organisms. Once oxygen has been used up other electron acceptors are used in order of energy efficiency (Table 4.7), by nitrate, manganese, iron and sulphate reducers. This order of electron acceptor usage is common to most biotic Earth surface environments (see Sections 5.5 & 6.2.4), although the relative importance of each electron acceptor depends on its concentration in specific environments. Sulphate reduction, for example, is not a common process in most soils because sulphate is in low concentrations in most continental waters except in some coastal areas (see Section 5.5). Methanogenesis can, however, be an important microbial reaction in waterlogged soils, especially paddy fields and marshes.

Soil microorganisms (fungi, bacteria and actinomycetes) play a major role in the degradation of organic matter, ultimately releasing nutrient elements — about 98% nitrogen, 5-60% phosphorus and 10-80% sulphur to the soil nutrient pool—along with micronutrients such as boron and molybdenum, into the soil for reuse by plants and animals. The role of biotic soils as sources of N and CH4

to the atmosphere, and N and P to the hydrosphere is discussed in Sections 3.4.2 and 5.5.1 respectively.

The biosphere clearly influences rates of weathering reactions but there is debate as to how much. Some estimates suggest the presence of biotic soils enhance weathering rates by 100-1000 times over abiotic weathering rates. There is also interest in whether microbial participation in weathering is simply a coincidental byproduct of metabolism. Is it possible that the microbes get something for their trouble? If soil bacteria do gain something by colonizing specific mineral substrates then the likely controls are nutrient element availability, absence of toxic elements or capacity to help buffer microenvironmental pH, all parameters that contribute to the success or failure of a microbial population. Recent work shows that in some weathering systems specific silicate minerals are heavily colonized and broken down by bacteria, whereas other minerals are left untouched. The colonized minerals contain the nutrient elements phosphorus (P) and iron (Fe) (see Section 5.5.1), while the uncolonized minerals are typically aluminium-rich but lacking nutrient potential. If bacteria are widely proven to select beneficial minerals to weather, we will need to rethink the traditional view that mineral weathering is mainly controlled by relative instability, as shown for example in Fig. 4.14.

The debate surrounding weathering rates is important, since the consumption of CO2 by soil weathering reactions (Section 4.4.3) lowers atmospheric partial pressure of CO2 (pCO2). Some researchers argue that, prior to the evolution of vascular land plants some 400 million years ago, weathering rates may have been much lower, giving rise to a higher atmospheric pCO2 and enhanced greenhouse warming (see Section 7.2.4). Others, however, believe that thin soils, stabilized by primitive lichens and algae, covered the land surface billions of years before the evolution of vascular plants. These primitive biotic soils may have been quite effective in enhancing weathering rates, acting in a 'Gaian' way (see Section 1.3.3) by consuming atmospheric CO2 and lowering global temperatures. This cooling effect may have helped improve the habitability of the early Earth for other organisms.

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