Substrate Utilization

The degradative and overall enzyme profile of a soil bacterium determines the range of substrates it can use, although other factors (e.g., substrate availability, competition, environmental factors), considered in subsequent sections, also determine which substrates are being used at any given time. This concept of enzymatic profile applies to both chemoheterotrophs and chemoautotrophs. Table 5.3 highlights just some of the enzymes controlling both intracellular and extracellular use of substrates. The size of many of the substrates (e.g., lignin, cellulose) ensures that most depolymerization is extracellular, with only the final use of the simple building blocks being intracellular. Table 5.3 is by necessity a simplification as, in a number of cases, there is a suite of enzymes, rather than a single enzyme operating on the substrate in question. The enzymes listed in Table 5.3 can be classified as oxi-doreductases (e.g., glucose oxidase, ammonia monooxygenase, hydroxylamine oxidoreductase, nitrite oxidoreductase, methane monooxygenase), transferases (e.g., amino transferases), hydrolases (e.g., protease, urease, amylase, ligninase,

TABLE 5.3 Selected Examples of Enzymes and Associated Bacteria Involved in Organic Substrate Utilization

Degradative enzymes used for organic substrate utilization

Cellulase (cellulose ^ glucose subunits)

Glucose oxidase (glucose ^ CO2) Protease (protein ^ amino acids)

Deaminase/amino transferase; amino acid decarboxylase (removal of amino and carboxyl groups to liberate NH3 and CO2 from amino acids)

Urease (urea ^ ammonia + carbon dioxide) Amylase and glucosidase (starch ^ glucose) Ligninase (lignin ^ aromatic subunits)

Pectinase (pectin ^ galacturonic acid subunits)

Phosphatase (phosphate esters ^ phosphate)

Sulfatase (sulfate esters ^ sulfate) Invertase (sucrose ^ fructose + glucose)

Chitinase (chitin ^ amino sugar subunits) Amino acid decarboxylase

Distribution of enzymes/examples of soil bacteria with ecologically significant activity of these enzymes

Species of Bacillus, Cellulomonas, and Pseudomonas

Ubiquitous enzyme among soil bacteria

Widespread among soil prokaryotes but species of Pseudomonas and Flavobacterium are strongly proteolytic

More common enzymes than proteases, although major differences in rates between amino acids

About 50% of heterotrophic soil bacteria are ureolytic

Species of Bacillus, Pseudomonas, and Chromobacterium

While lignin degradation is primarily the domain of the white rot fungi, species of Arthrobacter, Flavobacterium, and Pseudomonas are sometimes involved

Species of Arthrobacter, Pseudomonas, and Bacillus (some species possess all of the pectinase enzymes—polygalacturonase, pectate lyase, pectin lyase, and pectin esterase); many plant pathogens possess pectinase to assist in plant host penetration

About 30% of heterotrophic soil bacteria possess phosphatase enzymes

Many fewer possess sulfatase

Particularly active in saprotrophic soil bacteria, such as species of Acinetobacter, and Bacillus

The actinobacteria Streptomyces and Nocardia

Both aromatic and nonaromatic amino acid decarboxylases are found in a wide range of soil bacteria synthesizing amino acids pectinase, phosphatase, sulfatase, invertase, chitinase), and lyases (e.g., amino acid decarboxylase).

Some of the enzymes highlighted in Table 5.4 are constitutive, while others are inducible. A more comprehensive yet highly accessible account of soil enzymes can be found in the review by Burns and Dick (2002).

TABLE 5.4 Selected Examples of Enzymes, Functional Genes, and Associated Soil Bacteria Involved in Autotrophic Oxidation of Substrates

Ammonia monooxygenase, amoA

Nitrosomonas, Nitrosospira, Nitrosococcus

(ammonia ^ hydroxylamine)

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