Beneficial and harmful microorganisms, fermentation technology

1 Classification of microorganisms – bacteria, viruses, fungi, algae, protozoa, mycoplasma

Microorganisms are tiny living organisms that cannot be seen with the naked eye; a microscope is required to see them. They are found everywhere in nature—in soil, water, air, food, and the human body. Microorganisms are both our friends and our enemies—some are extremely beneficial, while others are harmful.

Six Major Types of Microorganisms

Viruses – the link between living and non-living

Viruses contain DNA or RNA protected within a protein capsid. Outside a living cell, they can exist as inactive, crystal-like virions—a non-living property. However, upon entering a living cell, they begin to grow and multiply, and also exhibit mutations—both living properties. Tobacco mosaic virus (TMV) in plants and influenza virus in humans are prime examples.

2 Structure and size of bacteria

Bacteria are the most numerous organisms on Earth—adapted to every environment, from snowy peaks to hot springs. They have no nuclear membrane—their DNA floats directly in the cytoplasm as a nucleoid. Under unfavorable conditions, they can remain dormant for years by forming a tough protective covering called an endospore.

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🖼️ Main shapes of bacteria – coccus, bacillus, spirillum and other shapes

Types of bacteria based on size

Nutritionally, bacteria are of two types: autotrophic (which make their own food through photosynthesis or chemosynthesis) and heterotrophic (which are parasites or saprophytes). Their growth and reproduction occur so rapidly by binary fission that under favorable conditions, one bacterium can multiply into millions in a matter of hours.

Special structure of the virus – bacteriophage

Bacteriophage is a special type of virus that infects only bacteria. Its structure is extremely complex and specialized—the head houses the genetic material, while the tail and foot fibers allow it to attach to the bacterial cell and inject its DNA into it.

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🖼️ Structure of a bacteriophage (T4 phage) – head, tail and leg fibres

3 Beneficial microorganisms — food production (curd, bread, idli-dosa)

We use microorganisms or their products in many food items every day like curd from milk, idli-dosa batter, bread, etc., which are mainly prepared by the process of fermentation – the detailed science of fermentation is explained in Topics 9-11 of this chapter.

Curd Formation

Main factors in curd formationLactobacillusThe other is lactic acid bacteria (LAB). They grow in milk and produce lactic acid, which causes the milk proteins to coagulate and turn into curd. Aged curd is added to fresh milk as a starter/inoculum. Consumption of curd increases vitamin B12 and helps prevent harmful pathogens in the intestines.

Fermentation of Idli-Dosa Batter

The lentil-rice batter is fermented by bacteria naturally present in the air, water, the vessel, and on the surface of the raw ingredients. During fermentation, carbon dioxide (CO₂) gas is produced, which makes the batter fluffy and light—this process is what makes idlis soft and spongy.

Bread Making

Baker's yeast - Saccharomyces cerevisiae(a type of fungus)—is used, which ferments sugars to produce CO₂ gas. This gas is trapped in the dough and causes it to swell, making the bread soft and spongy.

Other Traditional Fermented Foods

• Toddy – A traditional drink made from the fermentation of palm tree sap.
• Fermented fish, fermented soybeans and bamboo shoots – these improve taste, aroma and digestibility.
• Algae called Chlorella – used in soups, ice cream and nutritious foods.

4 Beneficial Microorganisms – Drug Manufacturing

Penicillin—the first antibiotic

'Anti' means against, 'biotic' means life—that is, antibiotics are substances that act against disease-causing microorganisms. The first antibiotic was penicillin, discovered by Alexander Fleming.Penicillium notatumIt was first developed into an effective drug by Ernest Chain and Howard Florey, earning the Nobel Prize in 1945 for their work.

Other important antibiotic-producing microorganisms

Modern Bioactive Molecules

5 Biological nitrogen fixation and biofertilizers

The atmosphere is rich in nitrogen gas (N₂) (about 78%), but plants cannot use it directly. Certain microorganisms convert atmospheric nitrogen into compounds useful to plants—this is called biological nitrogen fixation, which is the most natural way to reduce dependence on chemical fertilizers.

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Biological nitrogen fixation by root nodules in leguminous plants (Fabaceae)

Major nitrogen-fixing microorganisms

National Policy on Biofertilizers

The Government of India has launched several schemes to promote natural and organic farming – the National Mission on Natural Farming (NMNF, total budget ₹2,481 crore) and the National Mission on Natural Farming (NMNF) launched on 25 November 2024 – the National Mission on Natural Farming (NMNF) – launched on 25 November 2024. These schemes aim to encourage farmers to adopt chemical-free farming, in which biofertilizer microorganisms such as Rhizobium and Azotobacter play a central role.

6 Biocontrol/biopesticides – Bt, Trichoderma, Baculovirus

Biological control is a method that uses living organisms or microorganisms to control pests and pathogens instead of chemical pesticides. It is considered an environmentally friendly and sustainable agricultural practice—unlike chemical pesticides, they affect only the target pest, not beneficial insects or humans.

Bacillus thuringiensis (Bt)

Bt meansBacillus thuringiensisBt is a bacterium used to control insects such as butterfly caterpillars. Its dried spores are mixed with water and sprayed on crops – when the larvae eat them, a specific toxin is produced in their digestive tract that kills only the target insect, leaving others unharmed. By directly transferring the gene for this Bt toxin into plants, insect-resistant plants such as Bt-cotton have been developed, which is widely used against the bollworm pest in cotton cultivation.

Trichoderma

It is a free-living fungus found in the ecosystem around plant roots and acts as an effective biocontrol agent against many plant pathogens.

Baculoviruses

These are viruses that specifically infect insects and arthropods. Of these, nucleopolyhedrosis virus (NPV) is particularly useful in biological control—it is a narrow-spectrum insecticide, meaning it affects only the target insect and is completely safe for plants, mammals, birds, fish, and beneficial insects.

7 Harmful microorganisms – human diseases, food poisoning, plant diseases

There is another side to microorganisms – some cause diseases in humans, animals and plants, contaminate food, and destroy valuable materials (cloth, paper, wood, leather).

major human disease-causing bacteria

Food Poisoning

Some bacteria secrete toxins into food and cause food poisoning—e.g.Staphylococcus, Salmonella typhimuriumAndClostridium botulinum(Which causes the very serious poisoning called botulism.) Fungi such as Mucor, yeast, and Aspergillus also play an important role in food spoilage.

Plant Pathogens

Bacteria that reduce soil fertility – Denitrification

While bacteria like Rhizobium fix nitrogen, some bacteria—such as Bacillus denitrificans and Thiobacillus denitrificans—reduce soil fertility by converting soil nitrate back into free nitrogen/ammonia. This is called denitrification—the other, opposite side of the biological nitrogen cycle.

8 Economic importance of fungi and algae

Economic importance of fungi

Economic importance of algae

Cyanobacteria – both advantages and disadvantages

Cyanobacteria (blue-green algae) like Nostoc and Anabaena are extremely useful for nitrogen fixation (detailed in Topic 5), but when they multiply excessively in ponds and lakes, they cause a 'Water Bloom/Algal Bloom' – a condition in which there is a severe depletion of oxygen in the water, foul smell spreads, and mass mortality of fish and other aquatic organisms can occur. Some cyanobacteria (such as Microcystis) also release toxins that can be fatal to animals.

9 Introduction to Fermentation – Definition, Process, Louis Pasteur

The story mentioned at the beginning of this chapter—Louis Pasteur's discovery in a French winery—is considered the formal beginning of the science of fermentation (Zymology). Pasteur was the first to scientifically prove that fermentation occurs through the biological action of microorganisms, not through some mysterious chemical process. His famous statement, "Fermentation is life without oxygen," is still quoted today.

Definition of Fermentation

Fermentation is an anaerobic biochemical process in which microorganisms (such as yeast and bacteria) convert carbohydrates such as sugars or starches into alcohols, acids, or gases in the absence of oxygen. The general equation can be understood as follows:

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🖼️ Respiration vs. Fermentation in Yeast Cells — Differences in the Presence and Absence of Oxygen

The Fermentation Process – Three Steps

• Anaerobic Conditions — Fermentation is a process that occurs in the absence of oxygen; cells use it as an alternative metabolic pathway to produce energy.
• Glucose breakdown (glycolysis) — Glucose is broken down into simpler molecules, releasing energy stored as ATP. NAD⁺ is regenerated from NADH during fermentation — this is essential for continued glycolysis.
• Final product formation—different products are formed depending on the type of fermentation (ethanol, lactic acid, hydrogen gas, or other acids)—detailed in the next two topics.

10 Types of Fermentation Part 1 – Alcoholic and Lactic Acid Fermentation

Alcoholic Fermentation

In this, sugar (glucose, fructose or sucrose) is decomposed by yeast or some bacteria under anaerobic conditions to form ethanol and carbon dioxide.

Major microorganisms are yeasts.Saccharomyces cerevisiaeIn beer production, it converts the sugars in malted barley into ethanol and CO₂, with the CO₂ producing foam and the alcohol providing flavor. In wine production, the natural sugars in grapes are fermented, with temperature and time control producing different wines. Large-scale production of bioethanol from corn, sugarcane, or cellulosic biomass follows this principle (details in Topic 13).

Lactic Acid Fermentation

In this, pyruvate is converted into lactic acid by the enzyme lactate dehydrogenase, and NAD⁺ is regenerated from NADH. This process is found in muscles and bacteria such as Lactobacillus.

11 Types of Fermentation Part 2 – Acetic, Butyric and Mixed Acid Fermentation

Acetic Acid Fermentation

It is a two-step process—first, ethanol is formed from sugar, then, with the help of acetic acid bacteria (AAB), the ethanol is oxidized to form acetic acid. Note that, unlike the fermentation we studied earlier, this requires the presence of oxygen.

Its most prominent commercial use is in the manufacture of vinegar, which is used for food preservation and flavoring. Kombucha—a fermented tea beverage—contains SCOBY (Symbiotic Culture of Bacteria and Yeast), which develops its distinctive sour taste from the formation of acetic acid during secondary fermentation.

Butyric Acid Fermentation

In this, carbohydrates are broken down by butyric acid bacteria under anaerobic conditions to form butyric acid, CO₂, and hydrogen (H₂). This fermentation plays an important role in the digestive system of ruminants and is also responsible for the development of the distinctive odor and flavor of butter and cheese.

Mixed Acid Fermentation

In this Escherichia coliAs the bacteria convert pyruvate into various acids and gases—lactic, acetic, succinic, and formic acids—they also produce ethanol, hydrogen, and CO₂. This microorganism is important in both ecology and industrial microbiology—it is also used in the production of industrial solvents (such as acetone).

12 Fermentation in dairy and bakery industries

The greatest daily use of fermentation technology is in the dairy and bakery industries, where safe and tasty products are produced on a large scale using precise species of microorganisms and under controlled conditions.

Fermentation in the dairy industry

Fermentation in the bakery industry

Yeast in bread makingSaccharomyces cerevisiaeIt ferments the sugars in flour to produce ethanol and CO₂. Tiny bubbles of CO₂ gas are trapped in the dough and cause it to rise (called proofing), making the bread light, fluffy, and spongy after baking. This same yeast is also used in the beer and wine industries (see Topic 10)—showing how a single microorganism underpins so many diverse industries.

13 Industrial Applications – Bioethanol and Factors Affecting Fermentation

Bioethanol — India's Green Energy Revolution

Large-scale production of bioethanol from sugarcane, maize, and cellulosic biomass through fermentation is today a focus of India's energy policy. The E20 (20% ethanol blending in petrol) target under India's Ethanol Blending Programme (EBP), originally set for 2030, was extended to 2025-26—and achieved ahead of schedule. E20 fuel has been made mandatory in all states and union territories across the country from April 1, 2026.

This achievement demonstrates that fermentation technology is no longer limited to food – it has also become a fundamental pillar of India's energy security and carbon emission reduction strategy.

Other industrial applications

• Industrial solvent production – Production of solvents like ethanol, acetone by bacteria like E. coli (mixed acid fermentation).
• Bioplastic production – using butyric acid from agricultural waste to manufacture biodegradable plastics – important for green chemistry and sustainable development.
• Waste Management and Biogas – Under anaerobic conditions, methanogenic bacteria such as Methanobacterium decompose organic matter to produce methane (CH₄) gas, which is the basis of biogas production.

Major factors affecting the fermentation process

14 Dairy Industry and Bio-Fertilizer Schemes of Rajasthan

Rajasthan is not only India's largest state by geographical area, but also among the country's leading milk producers—this directly connects to the dairy-fermentation topics of this chapter (12).

Rajasthan – second in the country in milk production

India is the world's largest milk producer and consumer—total production in 2024-25 was estimated at approximately 248-250 million tonnes. State-wise, Uttar Pradesh (38.8 million tonnes) ranks first, followed by Rajasthan (36.7 million tonnes)—and Rajasthan also ranks second in the country in per capita milk availability.

Rajasthan Cooperative Dairy Federation (RCDF) and Saras Brand

The Rajasthan Cooperative Dairy Federation (RCDF) is the backbone of the state's dairy industry, with the brand 'Saras' a household name in Rajasthan. Its processing plants in Jaipur, Bikaner, and Alwar together process over 2 million liters of milk per day, with new units planned for Udaipur and Kota by 2026. The state government has approved financial assistance of ₹1,500 crore to transform Saras from a regional to a national brand. RCDF's cooperative network currently comprises over 15,000 milk cooperatives, connecting approximately 800,000 milk producers.

Biofertilizer and Soil Health Schemes in Rajasthan

• Soil Health Card Scheme — This national scheme was launched on February 19, 2015, in Suratgarh, Rajasthan, a proud moment in the state's agricultural history. By July 2025, more than 250 million soil health cards had been distributed nationwide.
• Govardhan Organic Fertilizer Scheme – To promote the use of organic fertilizers in the state; under this scheme, 50,000 permanent vermicompost units are being constructed across Rajasthan to enable farmers to produce organic fertilizers locally, reducing costs and improving soil fertility.
• Special recommendations for the sandy soils of Rajasthan – compost addition, green manuring, minimum tillage and use of biofertilizers like rhizobacteria and mycorrhizae – to increase beneficial microbial activity and reduce dependence on chemical fertilizers.