Microbial growth substrates
The substrates are nutrients required for growth, metabolism and activity of microbial cells. Microbes, especially bacteria can grow on variable growth substrates and hence possess versatile metabolic activities. Nutritional versatility makes bacteria adaptable to different types of habitats and environments. That is why they are cultured in laboratory; a particular strain of the genus can be cultured on various nutrient media. Depending upon growth and energy substrate requirement, bacteria are classified as organotrophs and lithotrophs. Organotrophs grow on organic compounds and lithotrophs need inorganic substrates for growth. They can be chemotrophic (chemical compounds) or phototrophic (light energy) depending upon their source of energy. All microorganisms require carbon as substrate for building up cell components; autotrophic microbes use carbon dioxide as sole source of carbon while as heterotrophs require organic compounds as carbon source. Obligate parasites like viruses and rickettsias fulfill their carbon and energy requirement by growing and living in host tissue. Taking into consideration, the type of nutrition of particular species, bacteria are cultured on laboratory conventional nutrient media. These media are composed of known concentrations of essential growth elements like carbon, nitrogen, phosphorus, potassium in utilizable form; trace elements like salts of Fe, Mg, Mn, Mo, Cu, Ni, B, Co, Ca dissolved in water. Nutrient medium is sometimes supplied with growth factors like amino acids and vitamins B1, B6, B12, K, C, biotin, niacin, riboflavin and pantothenic acid. Conventional media are also called as defined media as their composition is known. Bacteria can also be cultured on chemically undefined media; such media contain substrates whose chemical composition is unknown. Such substrates are added as source of protein, carbohydrates, vitamins and fatty acids. They are generally derived from plant or animal tissues and routinely used in microbiology laboratories for growing the heterotrophic microorganisms. Some chemically undefined substrates are extracts of beef, yeast, meat, malt, corn meal, soil, leaf, root or seed; rumen fluid, blood serum, whole blood, casein hydrolysate and peptone.
Microbes produce adaptive enzymes in response to the presence of substrates; therefore many bacteria are able to utilize substances that are not usually preferred by other organisms. Metabolic versatility is hence the function of enzymes; hydrolases especially, which confer an extraordinary ability to grow on unusual substrates. These substrates are wastes from kitchen, agriculture, heavy industries, dairy, poultry, food processing, paint and varnish, paper and pulp, fish market, vegetable market, waste treatment or compositing units and least but not the last from hydroelectric and nuclear power stations. To name some, carbon monoxide and other toxic environmental pollutants, lignin, cellulose, lignocelluloses, pectin, spent wash, molasses, Corn steep liquor, sewage, sludge, human and animal excreta, night soil, organic solvents, waste vegetable oils, petroleum byproducts, raw milk and whey are unusual substrates used by bacteria for the growth.
Substrates in natural environment:
Among natural growth environments, soil is enriched habitat favoring the growth of diverse group of microorganisms. Soil and rhizosphere regions are plentiful with substrates such as root exudates consisting of sugars, amino acids, vitamins, fatty acids; humus, lignin, cellulose, pectin, compost derivatives, organic matter from dead remains of plants, animals or microbes, inorganic salts and minerals. Water bodies contain organic matter, trace elements, metal salts and pollutants received from different sources. Substrate composition of water is always dynamic and changes during flow and rainy season. Marine aquatic system consists of higher concentration of various salts and is also subjected to fluctuations in substrate composition. Air does not contain any growth substrate but moisture and dust in air harbor many forms of microbes including their spores. Microbial cells or spores can remain suspended in air in the form of droplet nuclei or aerosols for longer time.
Substrate related phenomena:
1. Diauxie growth- When two substrates are provided in the growth medium, microbes are known to consume the substrates sequentially. The cells will first consume the 'preferred substrate' over less preferred substrate. The second substrate will be consumed only when the first preferred one is completely utilized. Microbial cells thus are not greedy but very wise and patient! This sequential utilization of two substrates in growth medium was first time observed by Scientist Monod who called it 'Diauxie' (2 growth phases in Greek) phenomenon.
2. Extracellular digestion- Some substrates are macromolecules (cellulose) or highly charged molecules (DNA) and cannot pass cell membrane. To utilize such substrates, microbes degrade them outside the cell with the help of hydrolytic enzymes. This extracellular digestion breaks down larger molecules into smaller which can enter into cell to be metabolized endogenously. In Bacillus spp. starch, pectin and RNA are digested to glucose, galacturonic acid, and ribonucleocides by production of enzymes amylase, pectinase and ribonuclease respectively.
3. Substrates in limiting and excess quantity- Nutrient substrate limitation or excess is a kind of stress condition that microbes always encounter in natural environment. However, limiting or starvation conditions are more prevalent. Excess nutrients generally do not promote increased growth response as one might expect but instead they can be toxic and deleterious for survival. Excess amount of particular nutrient may also lead to scarcity of other nutrient/s. Microbes have adapted themselves to survive under substrate limiting conditions by one or other means. The most common strategy is reduced endogenous metabolism but it is not applicable for requirement of trace elements. Normally essential trace elements Fe, Ni, Cu, Mo and Zn are always present in limiting amount in particular niche which is necessary for proper metabolic functioning of microbe. In complex microbial community such as in soil, there is always competition to acquire these metal ions and microbes have developed sequestration systems (siderophores) to chelate these ions for growth. Increase in concentration of even one of the metal ions is highly toxic for growth and hence the survival of microorganisms. When nutrients are in excess, some microbes store them in cytoplasm as inclusions in polymeric forms such as PHB, glucan or polyphosphate granules. They are utilized during nutrient stress conditions. Some microbes like soil actinomycetes may transform into physiologically inactive state like spores to sustain unfavorable nutrient and environmental conditions.
Substrate utilization for purpose:
Microbial ability to grow on unusual substrates has been exploited for the production of secondary metabolites like antibiotics, vitamins and biosurfactants, enzymes, amino acids and SCP. They are also used for production of compost feed and fertilizer mixture. Microbe's potential to use different conventional and unconventional substrates is being used in industrial-domestic waste treatment, recycling processes, sewage treatment and biogas generation, in bioremediation and oil spill cleanup strategies. It seems that microbial substrate utilization is not limited to growth but it is very productive, meant for scavenging deadly and dirty and also the best substitute for environmental cleanup.
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