BharatNotes Why this chapter matters for UPSC: Microorganisms underpin multiple GS3 themes — biotechnology (GMOs, recombinant insulin, Bt crops), agriculture (biofertilizers, biopesticides), environment (bioremediation, biogas), and public health (AMR, vaccines, disease control). Antimicrobial resistance (AMR) is a recurring Mains topic.
PART 1 — Quick Reference Tables
Types of Microorganisms
| Type | Structure | Key Examples | UPSC Relevance |
|---|---|---|---|
| Bacteria | Prokaryote; single-celled | Lactobacillus, Rhizobium, E. coli, Bt | Biofertilizers, curd, biotech |
| Viruses | Not cells; protein coat + nucleic acid | COVID-19, Influenza, Dengue, Polio, HIV | Pandemic, vaccine policy |
| Fungi | Eukaryote; can be multicellular | Penicillium, Yeast, Aspergillus | Antibiotics, fermentation, aflatoxin |
| Protozoa | Single-celled eukaryote | Plasmodium, Entamoeba, Leishmania | Malaria, kala-azar (VL) |
| Algae | Photosynthetic; aquatic | Chlorella, Spirulina | Biofuel, superfood, N-fixation |
Common Diseases Caused by Microorganisms
| Disease | Causative Agent | Type | Mode of Spread |
|---|---|---|---|
| Tuberculosis (TB) | Mycobacterium tuberculosis | Bacterium | Airborne droplets |
| Cholera | Vibrio cholerae | Bacterium | Contaminated water/food |
| Malaria | Plasmodium spp. | Protozoan | Anopheles mosquito |
| Dengue | Dengue virus (DENV) | Virus | Aedes mosquito |
| COVID-19 | SARS-CoV-2 | Virus | Airborne/droplet |
| Kala-azar (VL) | Leishmania donovani | Protozoan | Sandfly bite |
| Amoebic dysentery | Entamoeba histolytica | Protozoan | Contaminated food/water |
| Botulism | Clostridium botulinum | Bacterium | Improperly canned food |
PART 2 — Detailed Notes
Bacteria — Useful and Harmful
Rhizobium: Nitrogen-fixing bacteria found in root nodules of leguminous plants (beans, peas, lentils, soybean). They convert atmospheric nitrogen (N₂) into ammonia (NH₃) usable by plants — a process called biological nitrogen fixation. This reduces the need for nitrogenous chemical fertilizers.
Free-living nitrogen fixers: Azotobacter (aerobic, in soil) and Azospirillum (in rhizosphere). These form the basis of biofertilizer formulations used in organic farming.
UPSC GS3 — Biofertilizers: Biofertilizers are preparations containing living microorganisms that promote plant growth by fixing nitrogen, solubilising phosphorus, or producing growth hormones.
- Rhizobium — for legume crops (pulse cultivation, soybean)
- Azotobacter / Azospirillum — for cereals, vegetables
- Blue-Green Algae (BGA) / Cyanobacteria — for paddy fields (e.g., Anabaena, Nostoc)
- Phosphate Solubilising Bacteria (PSB) — converts insoluble phosphate to plant-available form
Promoted under National Mission on Sustainable Agriculture (NMSA) and PKVY. Reduce chemical fertilizer dependence and improve soil health.
Microorganisms in Food Production
- Yeast (Saccharomyces cerevisiae): Fermentation — glucose → ethanol + CO₂; used in bread making (CO₂ causes dough to rise), beer, wine
- Lactobacillus: Converts lactose in milk to lactic acid → curd/yoghurt; also used in cheese, buttermilk, and fermented foods
- Leuconostoc mesenteroides: Involved in fermentation of idli and dosa batter (along with Lactobacillus)
- Aspergillus oryzae: Used in soy sauce and sake production
Pasteurisation (Louis Pasteur, 1864): Milk is heated to 72°C for 15 seconds, then rapidly cooled to below 5°C. This kills pathogenic bacteria (Salmonella, Listeria, E. coli O157) without completely sterilising the milk. Pasteurisation extends shelf life and makes milk safe for consumption. It is NOT the same as sterilisation (which kills all microorganisms). Ultra-High Temperature (UHT) treatment (135°C for 2–4 seconds) gives longer shelf life at room temperature.
Microorganisms in Medicine
- Penicillin: Discovered by Alexander Fleming in 1928 from Penicillium notatum fungus — first antibiotic; revolutionised medicine
- Streptomycin: Discovered by Selman Waksman from Streptomyces griseus — first antibiotic effective against TB
- Tetracycline, Erythromycin, Ampicillin — other important antibiotics from microorganisms
- Vaccines: Use killed/attenuated pathogens or their antigens to build immunity (Polio — Salk/Sabin vaccines; BCG for TB; DPT; COVID-19 vaccines: Covaxin, Covishield)
UPSC GS3 — Recombinant Insulin (Biotechnology): Insulin was traditionally extracted from pig/cattle pancreas — expensive and limited. In 1982, Eli Lilly (USA) produced the first recombinant human insulin by inserting the human insulin gene into Escherichia coli (E. coli) using recombinant DNA technology — the first commercially approved GMO product in medicine.
India produces recombinant insulin domestically (BIOCON, Bengaluru-based, is among world's largest insulin manufacturers). This is a landmark example of how genetic engineering benefits human health.
Microorganisms in Agriculture — Bt and Biopesticides
Bacillus thuringiensis (Bt): A soil bacterium that produces crystal proteins (Cry proteins) toxic to specific insect larvae (caterpillars, bollworms, mosquito larvae) but harmless to humans, mammals, birds, and most beneficial insects. Used as:
- Biopesticide (spray): Applied to crops as microbial pesticide — organic farming alternative
- Bt crops (GMO): Bt toxin genes (Cry1Ac, Cry2Ab) inserted into crop plants so the plant itself produces the toxin — Bt cotton approved in India in 2002 (first GM food/fibre crop in India). Also Bt brinjal (approved 2010, approval suspended same year due to political opposition; Bangladesh commercialised Bt brinjal in 2014).
Microorganisms in Environment
- Decomposers: Bacteria and fungi break down dead organic matter → release nutrients back into soil (carbon cycling, nitrogen cycling)
- Biogas production: Anaerobic bacteria (methanogenic archaea) decompose organic waste → methane (CH₄) + CO₂; used for cooking and electricity; GOBARDHAN (Galvanizing Organic Bio-Agro Resources Dhan) scheme promotes biogas and CBG (Compressed Biogas) from cattle dung and agricultural waste. [Additional] Status (mid-2025): 108 CBG plants commissioned, 970+ community biogas plants functional under SBM-G; SATAT scheme (Sustainable Alternative Towards Affordable Transportation) targets 15 million tonnes/year CBG.
- Bioremediation: Using microorganisms to clean up environmental pollutants — oil spills (Pseudomonas), heavy metals, industrial effluent (sewage treatment plants use aerobic/anaerobic bacteria)
Harmful Microorganisms — Food Spoilage
- Aflatoxin: Produced by Aspergillus flavus and Aspergillus parasiticus on stored groundnuts, maize, and spices — carcinogenic (cause liver cancer); major food safety concern in tropical countries including India
- Botulism: Clostridium botulinum toxin in improperly canned/sealed foods — causes severe neurotoxic illness; most potent biological toxin known
- Food preservation methods: Pasteurisation, canning, salting, drying, pickling (acid medium), refrigeration, vacuum packing, chemical preservatives (sodium benzoate), irradiation (gamma rays)
Antimicrobial Resistance (AMR)
UPSC GS3 — AMR: A Critical Global Threat: Antimicrobial resistance (AMR) occurs when microorganisms evolve mechanisms to survive antibiotic treatment. Causes: overuse and misuse of antibiotics in humans and livestock; incomplete treatment courses; antibiotics in animal feed for growth promotion.
India's AMR burden:
- India is one of the world's largest consumers of antibiotics (both human and veterinary)
- NDM-1 (New Delhi Metallo-beta-lactamase 1): A resistance enzyme discovered in bacteria isolated from a patient in India in 2009–2010; makes bacteria resistant to nearly all antibiotics including carbapenems (last-resort drugs). The name "New Delhi" caused diplomatic controversy.
- ESKAPE pathogens (Enterococcus, Staphylococcus aureus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter) — most resistant organisms of clinical concern
India's response:
- National Action Plan on AMR (NAP-AMR) 2017–2021: Five-year plan covering surveillance, stewardship, infection prevention, R&D, and international cooperation
- Prescription-only policy for antibiotics (Schedule H and H1 under Drugs Rules)
- Restricting use of colistin (last-resort antibiotic) in poultry feed — banned in 2019
WHO: Declared AMR one of the top 10 global public health threats. Global deaths attributable to AMR: ~1.27 million directly per year (The Lancet, 2022 study).
[Additional] 2a. mRNA Vaccine Technology — Beyond COVID-19
The chapter mentions Covaxin and Covishield but does not explain vaccine platform types — a distinction that has appeared in UPSC GS3 (Science & Technology) questions and is critical for understanding future vaccine development.
Vaccine Platform Types — How Different Vaccines Work:
| Platform | Mechanism | COVID-19 Example | India Example |
|---|---|---|---|
| Inactivated/killed | Killed whole pathogen injected; immune system responds | Covaxin (Bharat Biotech + ICMR) — inactivated SARS-CoV-2 | Salk polio vaccine, rabies vaccine |
| Viral vector | Harmless virus carries the antigen gene into cells | Covishield (AstraZeneca/SII) — chimpanzee adenovirus vector | — |
| Protein subunit | Just the antigen protein; no nucleic acid | Corbevax (Biological E, Hyderabad) — spike protein receptor-binding domain | Hepatitis B vaccine |
| mRNA | Synthetic mRNA instructs host cells to produce antigen; host immune system responds; mRNA degrades quickly; no DNA alteration | Pfizer-BioNTech (Comirnaty), Moderna — first mRNA vaccines globally approved | Gemcovac-19 (Gennova Biopharmaceuticals, Pune) — India's first mRNA COVID vaccine; DCGI approved June 2022 |
Why mRNA vaccines are significant:
- No live pathogen needed → no risk of infection from the vaccine itself
- Scalable and programmable → can be rapidly redesigned for new variants or pathogens; took only ~11 months from genome sequencing to first approved mRNA COVID vaccine
- Applications beyond COVID-19: mRNA vaccines for influenza, HIV, RSV, cancer (personalised tumour neoantigens) are in clinical trials; the platform is broadly applicable
India's mRNA capability:
- Gemcovac-19 (Gennova Biopharmaceuticals, Pune): India's first indigenously developed mRNA COVID vaccine; self-amplifying mRNA platform; DCGI approved June 2022 — India became one of the first countries to develop a domestic mRNA vaccine
- CSIR-CCMB (Hyderabad): Also developed an indigenous mRNA vaccine candidate (AIC-CCMB, 2022) demonstrating India's emerging mRNA manufacturing capacity
[Additional] 2b. One Health Framework — Human, Animal, and Environmental Health Are One
The chapter covers AMR extensively but misses the policy framework that addresses it at its root — One Health — which recognises that 60%+ of infectious diseases in humans originate in animals, and that antimicrobial use in livestock directly drives resistance in human medicine.
[Additional] One Health — GS3 (Public Health / Biotechnology / AMR):
What is One Health? One Health is an integrated approach recognising that the health of humans, animals (domestic and wildlife), and the environment are interconnected and interdependent. Disease and antimicrobial resistance cannot be tackled in human health alone — they require simultaneous action across all three domains.
Why it matters for AMR:
- ~80% of antimicrobials globally are used in livestock and aquaculture (for growth promotion and disease prevention) — far more than in human medicine
- Resistant bacteria in animal guts → enter human food chain through meat, milk, eggs → or contaminate soil and water → spread resistant genes to human pathogens
- This is the exact mechanism behind why AMR spreads globally despite antibiotic restrictions in human medicine
Global governance: Managed jointly by the Quadripartite Alliance:
- WHO (World Health Organization)
- FAO (Food and Agriculture Organization)
- UNEP (UN Environment Programme)
- WOAH (World Organisation for Animal Health — formerly OIE)
India's National One Health Mission (NOHM):
- Approved by Cabinet; anchor institution: National Institute of One Health, Nagpur (under ICMR)
- Budget: ₹383.83 crore approved
- Covers: Zoonotic disease surveillance, AMR monitoring across human-animal-environment, pandemic preparedness
- India's NAP-AMR 2025–2029 (second five-year plan, superseding 2017-2021) explicitly adopts the One Health framework — covering human health, veterinary practice, agriculture/aquaculture, and environmental water/soil surveillance
Key UPSC connections:
- Zoonotic diseases (origin in animals, spread to humans): COVID-19, Nipah, HPAI (H5N1 bird flu), monkeypox, rabies, anthrax, brucellosis — all require One Health responses
- India's colistin ban in poultry (2019) was a One Health measure — protecting a last-resort human antibiotic from overuse in livestock
- India's ban on growth-promoter antibiotic use in animal feed (2017 amendment to Drugs and Cosmetics Act) — One Health in practice
Exam Strategy
Prelims traps:
- Smallpox was eradicated globally in 1980 (WHO declaration) — the only human disease eradicated so far; polio is near-eradicated but not yet officially declared
- Penicillin was discovered in 1928 by Alexander Fleming from the fungus Penicillium — not a bacterium
- Pasteurisation destroys pathogens but does NOT sterilise — UHT processing is closer to sterilisation
- Bt cotton was first approved in India in 2002 — not 2001 or 2003
- NDM-1 makes bacteria resistant — it is a resistance enzyme, not a bacterium itself
- Biofertilizers contain living microorganisms — not dead or chemical
Mains angles:
- India's AMR crisis: causes, consequences, National Action Plan
- Biotechnology in agriculture: Bt crops, GMO debate, biosafety regulations
- Bioremediation as environmental solution
Practice Questions
Prelims:
With reference to Bacillus thuringiensis (Bt), which of the following statements is/are correct?
- Bt toxin proteins are toxic to all insects including beneficial ones
- Bt cotton was the first genetically modified crop approved for cultivation in India
Select the correct answer:
(a) 1 only
(b) 2 only
(c) Both 1 and 2
(d) Neither 1 nor 2
- Bt toxin proteins are toxic to all insects including beneficial ones
Which of the following is correctly matched?
(a) Pasteurisation — kills all microorganisms in milk
(b) Rhizobium — free-living nitrogen-fixing bacterium in soil
(c) Penicillin — antibiotic derived from a fungus
(d) NDM-1 — a virus causing drug-resistant infections
Mains:
Antimicrobial resistance (AMR) is emerging as a silent pandemic. Examine the factors driving AMR in India and critically evaluate the National Action Plan on AMR. (CSE Mains 2022, GS Paper 3, 15 marks)
What is bioremediation? Discuss its applications in addressing environmental pollution in India with suitable examples. (CSE Mains 2020, GS Paper 3, 10 marks)
