While formal functional/physiological classification of bacteria is a useful foundation, it does not embrace the flexibility exhibited by many organisms. For example, we know that many soil bacteria that can grow readily on "standard" organic substrates can adapt and continue to metabolize under the harsh conditions of C starvation often found in soil. The physiological strategies and mechanisms used by the "facultative oligotrophs" are only partially characterized and include scavenging of gaseous forms of C, which diffuse through the soil pore network.

Perhaps the best known example of facultativeness relates to oxygen requirements. Facultative anaerobes metabolize most efficiently as aerobes. Indeed the denitrifying pseudomonads, which often colonize the rhizosphere as aerobic chemo-heterotrophs, may seldom experience low oxygen concentrations that induce the nitrate reductase enzyme system associated with denitrification. Many micro-aerophiles also often operate under well-aerated conditions but, as facultative micro-aerophiles, are physiologically adapted to life at the low oxygen concentrations sometimes experienced in wet soils, particularly in microsites such as water-saturated aggregates beyond a critical radius that prevents adequate diffusive resupply after removal by respiratory (roots, animals, and microorganisms) demand (Greenwood, 1975).

Another aspect of flexibility is the capacity to metabolize more than one substrate, often simultaneously (for example, through cometabolism, see Chaps. 9 and 17), which may be the norm rather than the exception. This is reflected in the diversity of catabolic enzymes, both intracellular and extracellular. Among the most versatile degraders in the soil are the pseudomonads. They can degrade the most complex aromatic structures through to the simplest sugars (Powlowsky and Shingler, 1994). Pseudomonas cepacia, for example, can metabolize more than 100 different C substrates (Palleroni, 1984).

Flexibility is also evident from the way soil microbial communities have adapted rapidly to degrade new substrates that have been introduced as contaminants in soil, such as organoxenobiotics that have been synthesized de novo by industry. The development of populations with appropriate catabolic genes is one of the greatest phenomena exhibited by the soil microbial community and is discussed further below.

biodegradation capacity CELLULOSE

Plant residues provide the major source of soil organic matter and their biodegradation is critical to ecosystem productivity. Because plants typically contain up to


FIGURE 5.9 The chemical structure of cellulose, which consists of (-1,4-linked glucose molecules.


FIGURE 5.9 The chemical structure of cellulose, which consists of (-1,4-linked glucose molecules.

60% cellulose (Paul and Clark, 1989), the decomposition of cellulose is a key activity of soil bacteria and it is vital to the energy flow through soils and to the cycling of N, P, and S (the decomposition of cellulose is generally accompanied by immobilization of these nutrient elements).

In simple terms, the decomposition of cellulose is a relatively specialized depolymerization exercise (involving a restricted number of saprophytes) followed by hydrolysis to the simple sugar glucose, which is rapidly used as an energy source by most heterotrophic soil microorganisms. The cellulose polymer occurs in plant residues in a semicrystalline state and consists of glucose units joined by (-1,4 linkages, with chains held together by hydrogen bonding (Fig. 5.9) (see Chap. 12 for further details).

The cellulase enzyme complex, which catalyzes cellulose decomposition, occurs in a large number of cellulolytic bacteria (e.g., species of Bacillus, Pseudomonas, Streptomyces, and Clostridium) and fungi and operates a two-stage process. The first involves "conditioning" by decrystalizing cellulose and the second involves extracellular depolymerization units, eventually forming double to single sugar units by the enzyme cellobiase. Although the half-lives and turnover times of cellulose and hemicellulose in soil are on the order of days and weeks, glucose metabolism after cellulose depolymerization is extremely rapid (in the order of hours to a day) (Killham, 1994).

The term hemicellulose describes various sugar (hexoses and pentoses) and uronic acid polymers that, like cellulose, are decomposed by a relatively specialized depolymerization process, followed by a much more rapid assimilation and oxidation of the simple monomer. Pectin, a polymer of galacturonic acid subunits, provides a good example of this, with specialist pectinolytic bacteria such as species of Arthrobacter and Streptomyces producing the extracellular pectin depolymerases (exo- and endo-) and then a much wider range of heterotrophic soil microorganisms using galacturonic acid oxidase to exploit the energy bound in the subunit itself (Killham, 1994).

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