Unit 5: Water, Environmental and Medical Microbiology

1. Brief Account of Microorganisms in Water

Aquatic environments (oceans, lakes, rivers) are teeming with microorganisms (bacteria, archaea, algae, protozoa, viruses). They form the base of the aquatic food web (e.g., photosynthetic algae and cyanobacteria). Most are harmless, but water can also be a major transmission route for disease.

Water-borne diseases are caused by pathogenic microbes transmitted through contaminated water. Examples include:

• Bacterial: Cholera (Vibrio cholerae), Typhoid fever (Salmonella typhi), Dysentery (Shigella).
• Viral: Hepatitis A, Polio.
• Protozoan: Giardiasis (Giardia lamblia), Amoebiasis (Entamoeba histolytica).

Water quality testing is crucial to ensure drinking water is safe (see section 4).

2. Waste Water Treatment Systems

The goal of wastewater (sewage) treatment is to remove pollutants and kill pathogens before the water is released back into the environment (like a river).

The process is typically divided into three stages:

1. Primary Treatment (Physical)

• Goal: To remove large solid materials.
• Process: Wastewater flows through screens (to remove trash) and then into a primary clarifier (settling tank).
• Result: Solid materials (sludge) settle to the bottom, while fats and oils float and are skimmed off. This removes about 30-40% of the pollutants.

2. Secondary Treatment (Biological)

• Goal: To use microbes to digest the dissolved organic matter.
• Process: This is an aerobic process. The liquid from primary treatment is sent to:
  • Activated Sludge System: The water is pumped into a large aeration tank and mixed with a microbe-rich "activated sludge." Air is bubbled through, and the aerobic microbes consume the organic matter. The water then goes to a secondary clarifier to let the microbes settle out.
  • Trickling Filter: The water is sprayed over a bed of rocks or plastic coated in a biofilm of microbes. As the water trickles down, the microbes consume the organic matter.
• Result: This removes about 90-95% of the organic pollutants (BOD).

3. Tertiary Treatment (Chemical/Physical)

• Goal: To "polish" the water, remove specific pollutants, and disinfect it.
• Process:
  • Nutrient Removal: Specific microbial processes (like denitrification) can remove nitrogen and phosphorus to prevent eutrophication.
  • Filtration: Sand filters remove any remaining suspended particles.
  • Disinfection: Kills remaining pathogens. This is most commonly done with chlorine, but UV light or ozone can also be used.

3. Determination of BOD and COD

BOD and COD are the two most important measurements used to determine the level of pollution in water.

BOD (Biochemical Oxygen Demand)

• Definition: The amount of dissolved oxygen (DO) required by aerobic microbes to decompose the biodegradable organic matter in a water sample.
• How it's measured: 1. A water sample is taken, and its initial DO level is measured. 2. The sample is sealed in a bottle and incubated in the dark at 20°C for 5 days. 3. After 5 days, the final DO level is measured. 4. BOD = (Initial DO) - (Final DO).
• Significance: A high BOD means there is a lot of organic pollution, which will lead to oxygen depletion and kill fish. (Clean water: BOD < 5 mg/L; Raw sewage: BOD > 200 mg/L).

COD (Chemical Oxygen Demand)

• Definition: The amount of oxygen required to decompose all oxidizable organic matter (both biodegradable and non-biodegradable) in a water sample using a strong chemical oxidant (like potassium dichromate).
• How it's measured: A sample is chemically digested at high heat. The amount of oxidant used is measured and converted to an oxygen equivalent. This test is much faster (a few hours).
• Significance: COD is always higher than BOD because it measures *everything* that can be chemically oxidized, not just what microbes can eat. It is useful for measuring industrial wastewater that may contain chemicals resistant to biodegradation.

4. Microorganisms as Indicators of Water Quality (Coliforms)

It is impractical to test water for every possible pathogen. Instead, we test for indicator organisms. A good indicator is one that is:

1. Always present when pathogens are present.
2. Absent (or rare) in safe, uncontaminated water.
3. Easy, fast, and cheap to detect.

The standard indicators are coliforms.

• What are they? Coliforms (e.g., Enterobacter, Klebsiella) are Gram-negative, non-spore-forming rods that ferment lactose with gas production at 35°C.
• Fecal Coliforms (e.g., E. coli): These are a subgroup of coliforms that live in the intestines of warm-blooded animals. E. coli is the ideal indicator of fecal contamination.
• Significance: If E. coli is found in water, it means the water has been contaminated with feces and *may* also contain intestinal pathogens like Salmonella or Vibrio cholerae.
• Tests for Coliforms:
  • Most Probable Number (MPN) Test: A statistical test using multiple tubes of lactose broth to estimate the number of coliforms.
  • Membrane Filtration (MF) Test: A water sample is passed through a filter, and the filter is placed on a selective/differential agar (like m-Endo agar). Coliforms grow as distinct colonies that can be counted.

5. Bioremediation of Contaminated Soil

Definition: Bioremediation is the use of living organisms (primarily microbes) to degrade, detoxify, or immobilize environmental pollutants.

This is often used to clean up soil contaminated with organic pollutants like petroleum (oil spills) or pesticides.

• Mechanism: Microbes use the pollutant as a food source (carbon and energy). They have enzymes that can break down complex chemicals into simpler, harmless products (like CO2 and water).
• Strategies:
  • Biostimulation: "Encouraging" the native microbes that are already present. This involves adding nutrients (like nitrogen and phosphorus) and oxygen (e.g., by tilling the soil) to speed up their activity.
  • Bioaugmentation: "Adding" specialized microbes. If the native population is not effective, lab-grown strains of bacteria known to degrade the specific pollutant are added to the soil.
• Example: After an oil spill, soil can be biostimulated with fertilizers. Hydrocarbon-degrading bacteria (like Pseudomonas) will multiply and "eat" the oil.

6. Control of Air-borne Microorganisms

This is crucial in places like hospitals (to prevent infection), food processing plants, and "clean rooms" for research.

• Filtration (HEPA Filters): High-Efficiency Particulate Air (HEPA) filters are the most common method. They are physical filters that can remove >99.97% of all airborne particles larger than 0.3 µm, including bacteria, spores, and viruses. They are used in laminar flow hoods and hospital ventilation systems.
• UV Radiation: UV-C light (254 nm) is germicidal. It damages microbial DNA. UV lamps are often placed in air ducts or used to sterilize surfaces in empty rooms (e.g., operating rooms).
• Chemical Vapors: Some disinfectants can be "fogged" or vaporized (e.g., hydrogen peroxide vapor) to decontaminate the air and surfaces in a sealed room.

7. Biogas Production

• What is it? Biogas is a mixture of gases (primarily methane, CH4, and carbon dioxide, CO2) produced from the anaerobic digestion of organic matter (e.g., manure, sewage sludge, food waste).
• Process: This is a complex microbial process involving several groups of bacteria working in sequence inside an "anaerobic digester."
  1. Hydrolysis: Bacteria with extracellular enzymes break down complex polymers (carbs, proteins) into simple sugars and amino acids.
  2. Acidogenesis: Fermentative bacteria convert these simple molecules into organic acids (like acetic acid, propionic acid), H2, and CO2.
  3. Acetogenesis: Bacteria convert the larger organic acids into acetic acid, H2, and CO2.
  4. Methanogenesis: This is the final and most critical step. Methanogens (Archaea) convert the acetic acid, H2, and CO2 into methane (CH4).
• Importance: It is a renewable energy source (methane is natural gas) and a way to manage waste.

8. Microbes in Biodegradation of Xenobiotics

Definition: Xenobiotics are man-made chemicals that are "foreign" to biological systems. They are often toxic and persistent in the environment because microbes have not evolved enzymes to degrade them.

• Examples: Pesticides (DDT, 2,4-D), plastics, synthetic dyes, industrial solvents (PCBs).
• Biodegradation: While difficult, some microbes can degrade xenobiotics.
  • Recalcitrance: The property of a chemical to resist biodegradation.
  • Co-metabolism: A common mechanism. The microbe does not use the xenobiotic as a food source. Instead, an enzyme produced for a *different* substrate accidentally acts on the xenobiotic, breaking it down. The microbe gets no energy from this.
• Application: This is a key part of bioremediation. Scientists try to find or engineer microbes (e.g., Pseudomonas) with enzymes that can break down specific, persistent pollutants.

9. Human Diseases (Causes and Preventive Measures)

This section covers several key bacterial diseases.

10. Probiotics

Definition (WHO): "Live microorganisms which, when administered in adequate amounts, confer a health benefit on the host."

• Concept: These are "good" or "friendly" bacteria that are part of a healthy gut microbiome.
• Common Genera:
  • Lactobacillus
  • Bifidobacterium
• Sources: Found in fermented foods like yogurt, kefir, kimchi, and available as dietary supplements (capsules, powders).
• Benefits:
  • Digestive Health: Can help manage diarrhea (especially after antibiotic use), irritable bowel syndrome (IBS).
  • Immune Support: The gut microbiome plays a huge role in training the immune system.
  • Competitive Exclusion: They "crowd out" or compete with pathogenic bacteria in the gut, making it harder for them to cause infection.