Sources of Carbon, Energy and Electrons
Carbon provides the backbone of all organic molecules. How an organism acquires carbon and energy is used as the basis for the classification of its nutritional type. Autotrophs utilize radiant or chemical energy to build carbon-based organic molecules, while heterotrophs obtain energy by breaking the carbon-carbon bonds in already existing carbon compounds.
Photoautotrophs utilize radiant energy from sunlight both to produce ATP and to biosynthesize organic molecules such as carbohydrates for energy storage.
Photoheterotrophs gain carbon from pre-existing organic molecules and use radiant energy to drive the process of catabolism.
Chemoautotrophs harvest energy from inorganic sources such as hydrogen, sulfur and nitrogen These organisms are also called lithotrophs.
Chemoheterotrophic organisms harvest energy by oxidizing organic compounds These organisms are also called organotrophs.
Molecular oxygen (O2), oxygen bound in water and organic compounds are generally non-toxic to living things. However, some forms of oxygen-containing compounds are excellent oxidizing agents that can kill or inhibit cells.
Singlet oxygen (1O2) - generally produced during aerobic respiration and by the reactions between molecular oxygen and light.
Superoxide free radicals (O2-) - produced during aerobic respiration and sometimes by anaerobes, these molecules are very strong oxidizing agents that must be degraded before damage can be done to the cell. Aerobic organisms produce enzymes called superoxide dismutases that chemically convert superoxide to hydrogen peroxide (H2O2). Obligate anaerobes do not produce these enzymes so they are poisoned in the presence of oxygen.
Peroxide ions (O22-) - contained in hydrogen peroxide and are degraded by peroxidase enzymes such as catalase. The catalase test involves placing a sample of microbe into a drop of hydrogen peroxide. If the microbe produces catalase, the sample will vigorously bubble as the hydrogen peroxide is reduced to water and molecular oxygen. Most cluster-forming cocci in the family Micrococciaceae such as Staphylococcus epidermidis, S. aureus and Micrococcus produce catalase, while chain-forming cocci such as Streptococcus and Enterococcus do not.
Hydroxyl radicals (OH-) - formed as the result of exposure of water to inonizing radiation such as gamma or X-radiation, or the incomplete reduction of hydrogen peroxide. Though these are most highly reactive molecules, they do not accumulate in aerobes due to the activity of enzymes such as superoxide dismutase and peroxidase.
Aerobes are organisms that require oxygen in some form as a final electron and hydrogen acceptor during chemiosmosis/electron transport. Obligate aerobes such as Bacillus subtilis, Staphylococcus epidermidis and Pseudomonas aeruginosa must have a supply of molecular oxygen, while microaerophiles such as Neisseria gonorrheae, N. sicca, N. meningitidis and Helicobacter pylori require oxygen in some other inorganic form like carbon dioxide.
Aerotolerant organisms such as the Lactobacillus acidophilus and other lactobacilli do not utilize oxygen, but have enzymes necessary to detoxify poisonous forms of oxygen.
Facultative anaerobes do not use oxygen, bu do have the enzymes necessary to cope with free radicals such as superoxide and peroxides.
Obligate anaerobes such as Clostridium botulinum, C. tetani and C. perfringens do not utilize oxygen in any form.
Nitrogen is a limiting resource that makes up about 14% of the dry biomass of any organism. It is a key component of amino acids and nucleic acids. Though roughly 79% of the gaseous atmosphere is composed of nitrogen gas (N2), few organisms can utilize it in this form. Some, however, such as Rhizobium can reduce nitrogen to a more usuable form such as ammonia (NH4+) that is usable through a process called nitrogen fixation. These organisms often form symbiotic relationships with plants.
Other Chemical Requirements