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Nutritional classification of microorganisms

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All living organisms need a source of carbon, energy and electrons to carry out their metabolic activities and bacteria have been classified based on the methods used to obtain these three important components. Carbon is one of the most important elements for living systems as it forms the backbone of all biological macromolecules. Microbes that obtain their carbon from carbon dioxide are termed autotrophs while those that rely on pre-made organic compounds in the environment are heterotrophs. Energy for carrying out cellular reactions comes either from the conversion of light energy or by the oxidation of chemicals. Phototrophic organisms utilize light as a source of energy, while chemotrophsobtain energy by the oxidation of either inorganic or organic compounds. For the cell to carry out many of its metabolic reactions a source of electrons is also necessary and again microbes can be classified by the methods they use to obtain them. Microbes that obtain their electrons from organic compounds are termed organotrophs while those that obtain electrons from inorganic compounds are called lithotrophs (literally rock eaters). By combining the above sets of terms it is possible to describe the nutritional modes of an organisms. For example a chemoorganotrophic heterotroph obtains its energy from chemicals, its electrons from organic compounds and its carbon from premade organic compounds. In many cases a single organic compound can serve all these roles. A second example is a photoautotrophic lithotroph that will obtain energy from the sun, carbon from CO2, and electrons from inorganic compounds. By combining these classification it is possible to categorize most prokaryotes into just four major groups as listed in Table 6-4. Table 6-4. Major nutritional types of prokaryotes. Nutritional Type Photoautotrophic lithotrophs Photoheterotrophic organotrophs Chemoautotrophic lithotrophs Chemoheterotrophic organotrophs Energy Source Light Light Chemicals (H2, NH3, H2S) Organic compounds Organic compounds Organic compounds Most bacteria, some archaea Carbon Source Electron Source CO2 Organic compounds CO2 Inorganic (H2O or H2S) Organic compounds Inorganic compounds Examples Cyanobacteria, some purple and green bacteria Some purple and green bacteria Bacteria and many archaea

This method of classifying microbes, while useful in understanding the nutritional modes of microorganisms, is an artificial construct. There are microorganisms capable of more than one mode of growth and they will in fact cross categories depending upon environmental conditions. For example Rhodobacter sphaeroides is capable of growth on CO2, light and obtaining electrons from H2S, thus growing as a photoautotrophic lithotroph. However, the microbe is also capable of growing aerobically in the dark with an organic compound as its carbon source. In this case living as a chemoheterotrophic organotroph. Some microbes are even capable of growth using several modes at once. Beggiatoa species are capable of chemolithoautotropic growth on reduced sulfur compounds and CO2. However, in the presence of limiting amounts of reduced sulfur compounds they will supplement their metabolism by utilizing acetate (an organic compound) at the same time! 1.

Examples of Nutritional Classifications

In this section we present some specific examples of microbes, their physiology and their habitats and relate this information to their nutritional classification. By examining examples of different types of microbes it will hopefully clarify what each type of nutritional category means. In addition this will begin to introduce you to the diversity of microbes living in the world. Later chapters will cover microbial diversity in much greater detail. Interestingly many of the most studied microorganisms are chemoheterotrophs. One may get the mistaken sense that this means that chemoheterotrophs are the most common microbes in the environment and this is probably pretty far from the truth. Autotrophy and photosynthesis are very common metabolic activities and dominate a

large number of habitats from the open ocean to deep in the earth. Here we present a representative of each of the four nutritional types to give you a sense of how these microorganisms differ in their metabolism. One example of a photoautotrophic lithotroph would be the cyanobacteria Oscillatoria. This microbe has a photosynthetic system that is similar to that used by photosynthetic eukaryotes. In other words it generates its energy from the sun and uses carbon dioxide as its source of carbon. Due to their simple nutritional requirements, a few salts and sunlight, they are found in many places including damp soil, dripping rocks, fresh and seawater and in hot springs. Under the microscope they form filaments that are 5 m wide and hundreds of m long. An example of a photoheterotrophic organotroph is the purple bacterium Rhodobacter sphaeroides. While this microbe is capable of growing photoautotrophically, it can also utilize simple carbon compounds as sources of electrons, yet still use light as its method of energy generation. These microbes are aquatic, often occurring in fresh water lakes in the zones several meters below the surface where light is still present, but oxygen is absent. In these anaerobic environments organic molecules are incompletely degraded to organic acids. R. sphaeroides has adapted its metabolism such that it can take advantage of these carbon sources when they are available. An example of a chemoautotropic lithotroph is the ammonia oxidizer Nitrosomonas europaea. This microbe is found in many different habitats including soil, sewage, fresh water, the walls of buildings and on monuments; basically anywhere that ammonia is available. It is especially common in urban settings where high levels of nitrogen compounds are present due to pollution. N. europaea converts ammonia into nitrous acid and in the process consumes oxygen. The energy generated from this process is used to convert carbon dioxide into cellular material. It has a competitive advantage in places that contain oxygen and ammonia, but not much organic carbon. This explains its ability to grow in unusual places such as on the surface of bricks and monuments. This activity can be damaging since the metabolic activity of these microbes lowers the pH and slowly dissolves the stone. A second example of this class is Ignicoccus islandicus. This microbes was isolated from a submarine, ocean vent containing high temperature and high sulfur and hydrogen concentrations. hydrogen gas serves as the source of energy and electrons, while carbon dioxide is the source of carbon. Deep sea ocean vent communities are intriguing ecosystems containing many unique micro- and macroorganisms. These communities and their environment are described in more detail in Chapter 24. There are a large number of chemoheterotrophic organotrophs and one example is Escherichia coli. Because of the notoriety of certain pathogenic E. coli strains, you may find it surprising that the vast majority of E. coli do not cause illness in humans, in fact they are common inhabitants of the intestines of many mammals. In the warm environment of the intestines they take advantage of the large amount of organic carbon compounds consumed by their host. These are degraded to generate energy and the same compounds are also used to synthesize cell material. Another example of a chemoheteroorganotroph is the brown rot fungus Gloeophyllum trabeum. This organism and its relatives are some of the major degraders of wood and its major polymer lignocellulose in terrestrial ecosystems. Wood serves as the source of energy, electrons and carbon for the fungus. This fungus and its relatives are essential for the efficient degradation of lignocellulose, a very recalcitrant polymer. G. trabeum uses a novel mechanism to attack the polymer by creating extracellular enzymes that produce hydroxide radicals (OH) that rapidly attack the polymer. A final example of a chemoheterotrophic organotroph is Thermotoga maritima. This bacterium grows on a number of sugars, alcohols and organic acids in environments where oxygen is absent. T. maritima has the highest optimal growth temperature of any bacteria (although several archaea grow at higher temperatures) with a growth optimum near 90C. It was originally isolated from heated ocean sediment near Volcana, Italy and has as its habitat areas of volcanic activity. Figure 6-2 A picture of the various microbes described above. Oscillatoria, R. sphaeroides, N. europaea,

Ignicoccus islandicus, E. coli, Gloeophyllum trabeum, Thermotoga maritime