Microbial Nutrition

Nutrients are substances required for microbial growth since they are used in biosynthesis and energy production. To obtain energy and to construct new cellular components, organisms must have a supply of raw materials or nutrients. The nutritional requirements of microorganisms is as important as the environmental factors such as temperature, oxygen levels, and the osmotic concentration for the successful cultivation of microorganisms.

Common Nutrient Requirements

Analysis of microbial cell composition shows that over 95% of cell dry weight is made up of a few major elements: carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus, potassium, calcium, magnesium, and iron. These are called Macro elements or macro nutrients because they are required by microorganisms in relatively large amounts. Carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus, potassium (C, O, H, N, S, and P) are components of carbohydrates, lipids, proteins, and nucleic acids. The other four macro elements - potassium, calcium, magnesium, and iron - exist in the cell as cations and have a variety of roles.

For example, potassium (K⁺) is required for activity by a number of enzymes, including some of those involved in protein synthesis. Calcium (Ca²⁺), among other functions, contributes to the heat resistance of bacterial endospores. Magnesium (Mg²⁺) serves as a cofactor for many enzymes, complexes with ATP, and stabilizes ribosomes and cell membranes. Iron (Fe²⁺ and Fe³⁺) is a part of cytochromes and a cofactor for enzymes and electron-carrying proteins.

All organisms, including microorganisms, require several micronutrients or trace elements besides macro elements. The micronutrients—manganese, zinc, cobalt, molybdenum, nickel, and copper—are needed by most cells. However, cells require such small amounts that contaminants in water, glassware, and regular media components often are adequate for growth. Therefore, it is very difficult to demonstrate a micronutrient requirement. In nature, micronutrients are ubiquitous and probably do not usually limit growth. Micronutrients are normally a part of enzymes and cofactors, and they aid in the catalysis of reactions and maintenance of protein structure. For example, zinc (Zn²⁺) is present at the active site of some enzymes but is also involved in the association of regulatory and catalytic subunits in E. coli aspartate carbamoyl transferase. Manganese (Mn²⁺) aids many enzymes catalyzing the transfer of phosphate groups. Molybdenum (Mo²⁺) is required for nitrogen fixation, and cobalt (Co²⁺) is a component of vitamin B12.

Besides the common macro elements and trace elements, microorganisms may have particular requirements that reflect the special nature of their morphology or environment. Diatoms need silicic acid (H₄SiO₄) to construct their beautiful cell walls of silica [(SiO₂) n]. Although most bacteria do not require large amounts of sodium, many bacteria growing in saline lakes and oceans depend on the presence of high concentrations of sodium ion (Na⁺).

Microorganisms require a balanced mixture of nutrients. If an essential nutrient is in short supply, microbial growth will be limited regardless of the concentrations of other nutrients.

 

Requirements for Carbon, Hydrogen, and Oxygen

The requirements for carbon, hydrogen, and oxygen often are satisfied together. Carbon is needed for the skeleton or backbone of all organic molecules, and molecules serving as carbon sources normally also contribute both oxygen and hydrogen atoms. They are the source of all three elements. Because these organic nutrients are almost always reduced and have electrons that they can donate to other molecules, they also can serve as energy sources.

The more reduced organic molecules are, the higher their energy content (e.g., lipids have a higher energy content than carbohydrates). This is because, as we shall see later, electron transfers release energy when the electrons move from reduced donors with more negative reduction potentials to oxidized electron acceptors with more positive potentials. Thus carbon sources frequently also serve as energy sources, although they don’t have to.

One important carbon source that does not supply hydrogen or energy is carbon dioxide (CO₂). This is because CO₂ is oxidized and lacks hydrogen. Probably all microorganisms can fix CO₂—that is, reduce it and incorporate it into organic molecules.

However, by definition, only autotrophs can use CO₂ as their sole or principal source of carbon. Many microorganisms are autotrophic, and most of these carry out photosynthesis and use light as their energy source. Some autotrophs oxidize inorganic molecules and derive energy from electron transfers.

The reduction of CO₂ is a very energy-expensive process. Thus many microorganisms cannot use CO₂ as their sole carbon source but must rely on the presence of more reduced, complex molecules such as glucose for a supply of carbon. Organisms that use reduced, preformed organic molecules as carbon sources are heterotrophs (these preformed molecules normally come from other organisms). Most heterotrophs use reduced organic compounds as sources of both carbon and energy.

A most remarkable nutritional characteristic of microorganisms is their extraordinary flexibility with respect to carbon sources. Laboratory experiments indicate that there is no naturally occurring organic molecule that cannot be used by some microorganism. Actinomycetes will degrade amyl alcohol, paraffin, and even rubber. Some bacteria seem able to employ almost anything as a carbon source; for example, Burkholderia cepacia can use over 100 different carbon compounds. In contrast to these bacterial omnivores, some bacteria are exceedingly fastidious and catabolize only a few carbon compounds. Cultures of methylotrophic bacteria metabolize methane, methanol, carbon monoxide, formic acid, and related one-carbon molecules. Parasitic members of the genus Leptospira use only long-chain fatty acids as their major source of carbon and energy.

In natural environments complex populations of microorganisms often will metabolize even relatively indigestible human-made substances such as pesticides. Indigestible molecules sometimes are oxidized and degraded in the presence of a growth promoting nutrient that is metabolized at the same time, a process called co-metabolism. The products of this breakdown process can then be used as nutrients by other microorganisms.

Requirements for Nitrogen, Phosphorus, and Sulfur

To grow, a microorganism must be able to incorporate large quantities of nitrogen, phosphorus, and sulfur. Although these elements may be acquired from the same nutrients that supply carbon, microorganisms usually employ inorganic sources as well. Biochemical mechanisms for the incorporation of nitrogen, phosphorus, and sulfur.

Nitrogen is needed for the synthesis of amino acids, purines, pyrimidines, some carbohydrates and lipids, enzyme cofactors and other substances. Many microorganisms can use the nitrogen in amino acids, and ammonia often is directly incorporated through the action of such enzymes as glutamate dehydrogenase or glutamine synthetase and glutamate synthase. Most phototrophs and many nonphotosynthetic microorganisms reduce nitrate to ammonia and incorporate the ammonia in assimilatory nitrate reduction. A variety of bacteria (e.g., many cyanobacteria and the symbiotic bacterium Rhizobium) can reduce and assimilate atmospheric nitrogen using the nitrogenase system

Phosphorus is present in nucleic acids, phospholipids, nucleotides like ATP, several cofactors, some proteins, and other cell components. Almost all microorganisms use inorganic phosphate as their phosphorus source and incorporate it directly. Low phosphate levels actually limit microbial growth in many aquatic environments. Phosphate uptake by E. coli has been intensively studied. This bacterium can use both organic and inorganic phosphate. Some organophosphates such as hexose 6-phosphates can be taken up directly by transport proteins. Other organophosphates are often hydrolyzed in the periplasm by the enzyme alkaline phosphatase to produce inorganic phosphate, which then is transported across the plasma membrane. When inorganic phosphate is outside the bacterium, it crosse the outer membrane by the use of a porin protein channel and then phosphate-specific transport systems subsequently moves the phosphate across the plasma membrane.

Sulfur is needed for the synthesis of substances like the amino acids cysteine and methionine, some carbohydrates, biotin, and thiamine. Most microorganisms use sulfate as a source of sulfur and reduce it by assimilatory sulfate reduction (see section 10.4); a few require a reduced form of sulfur such as cysteine.

Growth Factors

Microorganisms often grow and reproduce when minerals and sources of energy, carbon, nitrogen, phosphorus, and sulfur are supplied. These organisms have the enzymes and pathways necessary to synthesize all cell components required for their wellbeing. Many microorganisms, on the other hand, lack one or more essential enzymes. Therefore, they cannot manufacture all indispensable constituents but must obtain them or their precursors from the environment.

Organic compounds required because they are essential cell components or precursors of such components and cannot be synthesized by the organism are called growth factors. There are three major classes of growth factors: (1) amino acids, (2) purines and pyrimidines, and (3) vitamins. Amino acids are needed for protein synthesis, purines and pyrimidines for nucleic acid synthesis. Vitamins are small organic molecules that usually make up all or part of enzyme cofactors, and only very small amounts sustain growth.

Some microorganisms require many vitamins; for example, Enterococcus faecalis needs eight different vitamins for growth. Other growth factors are also seen; heme (from hemoglobin or cytochromes) is required by Haemophilus influenzae, and some mycoplasmas need cholesterol.

Knowledge of the specific growth factor requirements of many microorganisms makes possible quantitative growth response assays for a variety of substances. For example, species from the bacterial genera Lactobacillus and Streptococcus can be used in microbiological assays of most vitamins and amino acids. Microbiological assays are specific, sensitive, and simple. They are used in the assay of substances like vitamin B12 and biotin.

Many microorganisms can synthesize large quantities of vitamins and this has led to their use in industry. Several water-soluble and fat-soluble vitamins like riboflavin (Clostridium, Candida, Ashbya, Eremothecium), coenzyme A (Brevibacterium), vitamin B12 (Streptomyces, Propionibacterium, Pseudomonas), vitamin C (Gluconobacter, Erwinia, Corynebacterium), -carotene (Dunaliella), and vitamin D (Saccharomyces) are produced partly or completely using industrial fermentations.

 

Nutritional Types of Microorganisms

In addition to the need for carbon, hydrogen, and oxygen, all organisms require sources of energy and electrons for growth to take place. Microorganisms can be grouped into nutritional classes based on how they satisfy all these requirements.

Microorganisms can be classified as either heterotrophs or autotrophs with respect to their preferred source of carbon. Autotrophs can use CO₂ as their sole or principal source of carbon. Heterotrophs use reduced, preformed organic molecules as carbon sources are (these preformed molecules normally come from other organisms).

There are only two sources of energy available to organisms: (1) light energy, and (2) the energy derived from oxidizing organic or inorganic molecules. Phototrophs use light as their energy source; chemotrophs obtain energy from the oxidation of chemical compounds (either organic or inorganic).

Microorganisms also have only two sources for electrons. Lithotrophs (i.e., “rock-eaters”) use reduced inorganic substances as their electron source, whereas organotrophs extract electrons from organic compounds.

 

 

 

Sources of Carbon, Energy, and Electrons
Carbon Sources
Autotrophs	CO2 sole or principal biosynthetic carbon source
Heterotrophs	Reduced, preformed, organic molecules from other organisms
Energy Sources
Phototrophs	Light
Chemotrophs	Oxidation of organic or inorganic compounds
Electron Sources
Lithotrophs	Reduced inorganic molecules
Organotrophs	Organic molecules

 

Despite the great metabolic diversity seen in microorganisms, most may be placed in one of four nutritional classes based on their primary sources of carbon, energy, and electrons. The large majority of microorganisms thus far studied are either photolithotrophic autotrophs or chemoorganotrophic heterotrophs.

Photolithotrophic autotrophs (often called photoautotrophs or photolithoautotrophs) use light energy and have CO₂ as their carbon source. Eukaryotic algae and cyanobacteria employ water as the electron donor and release oxygen. Purple and green sulfur bacteria cannot oxidize water but extract electrons from inorganic donors like hydrogen, hydrogen sulfide, and elemental sulfur. Chemoorganotrophic heterotrophs (often called chemoheterotrophs, chemoorganoheterotrophs, or even heterotrophs) use organic compounds as sources of energy, hydrogen, electrons, and carbon. Frequently the same organic nutrient will satisfy all these requirements. It should be noted that essentially all pathogenic microorganisms are chemoheterotrophs.

The other two nutritional classes have fewer microorganisms but often are very important ecologically. Some purple and green bacteria are photosynthetic and use organic matter as their electron donor and carbon source. These photoorganotrophic heterotrophs (photoorganoheterotrophs) are common inhabitants of polluted lakes and streams. Some of these bacteria also can grow as photoautotrophs with molecular hydrogen as an electron donor. The fourth group, the chemolithotrophic autotrophs (chemolithoautotrophs), oxidizes reduced inorganic compounds such as iron, nitrogen, or sulfur molecules to derive both energy and electrons for biosynthesis. Carbon dioxide is the carbon source. A few chemolithotrophs can derive their carbon from organic sources and thus are heterotrophic. Chemolithotrophs contribute greatly to the chemical transformations of elements (e.g., the conversion of ammonia to nitrate or sulfur to sulfate) that continually occur in the ecosystem.

 

 

Major Nutritional Types of Microorganisms -defined in terms of energy, electron, and carbon sources
Major Nutritional Types	Sources of Energy, Hydrogen/Electrons, and Carbon	Representative Microorganisms
Photolithotrophic autotrophy (Photolithoautotrophy)	Energy - Light energy Electrons- Water/ Inorganic compounds Carbon - CO2	Algae,   Cyanobacteria Purple and green sulfur bacteria
Photoorganotrophic heterotrophy (Photoorganoheterotrophy)	Energy - Light energy Electrons-Organic compounds Carbon-Organic compounds	Purple non-sulfur bacteria Green non-sulfur bacteria
Chemolithotrophic autotrophy (Chemolithoautotrophy)	Energy-Inorganic  compounds Electrons-Inorganic compounds Carbon - CO2	Sulfur-oxidizing bacteria Hydrogen bacteria Nitrifying bacteria  Iron-oxidizing bacteria
Chemoorganotrophic heterotrophy (Chemoorganoheterotrophy)	Energy–Organic  compounds Electrons-Organic compounds Carbon-Organic compounds	Protozoa, Fungi Most non-photosynthetic bacteria (including most pathogens)

 Although a particular species usually belongs in only one of the four nutritional classes, some show great metabolic flexibility and alter their metabolic patterns in response to environmental changes. For example, many purple nonsulfur bacteria  act as photoorganotrophic heterotrophs in the absence of oxygen but oxidize organic molecules and function chemotrophically at normal oxygen levels. When oxygen is low, photosynthesis and oxidative metabolism may function simultaneously. Another example is bacteria such as Beggiatoa that rely on inorganic energy sources and organic (or sometimes CO₂) carbon sources. These microbes are sometimes called mixotrophic because they combine chemolithoautotrophic and heterotrophic metabolic processes. This sort of flexibility seems complex and confusing, yet it gives its possessor a definite advantage if environmental conditions frequently change.

Reference

Prescott's Microbiology: Christopher J. Woolverton, Joanne Willey, and Linda Sherwood