Unit 3: Agricultural Microbiology

1. General Account of Microorganisms in Biogeochemical Cycles

Biogeochemical cycles are the pathways by which chemical elements move through the Earth's biotic (living) and abiotic (non-living) components. Microorganisms are the primary drivers of these cycles, transforming elements from one form to another.

Nitrogen Cycle

Nitrogen is essential for proteins and nucleic acids. Although the atmosphere is 78% N2 gas, most organisms cannot use it in this form. Microbes are essential for converting it.

• 1. Nitrogen Fixation: The conversion of atmospheric N2 gas into ammonia (NH3). This is exclusively a microbial process.
  • Symbiotic: Rhizobium (in legume root nodules).
  • Free-living (Asymbiotic): Azotobacter (aerobic), Clostridium (anaerobic).
• 2. Ammonification: The decomposition of organic nitrogen (from dead plants/animals) into ammonia (NH3). Done by a wide range of bacteria and fungi.
• 3. Nitrification: A two-step process of oxidizing ammonia to nitrate (NO3-), the form most readily absorbed by plants.
  • Step A: Ammonia (NH3) → Nitrite (NO2-). Done by Nitrosomonas.
  • Step B: Nitrite (NO2-) → Nitrate (NO3-). Done by Nitrobacter.
• 4. Denitrification: The reduction of nitrate (NO3-) back to N2 gas, which returns to the atmosphere. This is an anaerobic process, often detrimental to agriculture as it removes nitrogen from the soil. Done by bacteria like Pseudomonas.

Carbon Cycle

This cycle involves the movement of carbon between the atmosphere, oceans, and living organisms.

• Carbon Fixation (Photosynthesis): Autotrophs (plants, algae, cyanobacteria) convert atmospheric CO2 into organic compounds (sugars).
• Respiration & Decomposition: Heterotrophs (animals, fungi) and autotrophs respire, releasing CO2. Microorganisms (bacteria, fungi) are the primary decomposers that break down dead organic matter, returning CO2 to the atmosphere.
• Methanogenesis: Under anaerobic conditions, methanogens (Archaea) convert CO2 or organic acids into methane (CH4).
• Methanotrophy: Methanotrophs (bacteria) use methane (CH4) as their carbon source, oxidizing it back to CO2.

Sulphur Cycle

Sulphur is vital for certain amino acids (cysteine, methionine).

• Decomposition: Microbes decompose organic sulphur compounds into hydrogen sulfide (H2S), which has a "rotten egg" smell.
• Sulphur Oxidation: In aerobic conditions, chemosynthetic bacteria (e.g., Thiobacillus) oxidize H2S and elemental sulphur (S) into sulfate (SO4 2-), which plants can absorb.
• Sulphate Reduction: In anaerobic conditions (like waterlogged soil), sulphate-reducing bacteria (e.g., Desulfovibrio) use sulphate as an electron acceptor, reducing it back to H2S.

2. Plant Growth Promoting Bacteria (PGPR)

Definition: PGPRs are a group of free-living soil bacteria that, when applied to seeds or crops, colonize the roots (rhizosphere) and enhance plant growth.

PGPRs work through two main mechanisms:

1. Direct Mechanisms (Biofertilizers):
   • Nitrogen Fixation: Providing fixed nitrogen to the plant (e.g., Azotobacter, Azospirillum).
   • Phosphate Solubilization: Secreting acids that dissolve mineral-bound phosphate (e.g., phosphate rock) into a form the plant can absorb (e.g., Pseudomonas, Bacillus).
   • Phytohormone Production: Producing plant hormones like auxins (IAA), gibberellins, and cytokinins that stimulate root growth and development.
2. Indirect Mechanisms (Biocontrol):
   • Antibiosis: Producing antibiotics or enzymes (like chitinase) that suppress or kill plant pathogens (e.g., fungi).
   • Siderophore Production: Producing siderophores, which are compounds that strongly bind iron. This "steals" the iron from plant pathogens, inhibiting their growth.
   • Induced Systemic Resistance (ISR): The presence of the PGPR "primes" the plant's own immune system, making it more resistant to a broad range of future infections.

3. Rhizosphere and Phyllosphere

Rhizosphere

• Definition: The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
• The Rhizosphere Effect: The root surface (rhizoplane) and the surrounding soil (rhizosphere) have a much higher concentration and activity of microbes than the bulk soil.
• Reason: Plant roots excrete substances called root exudates (sugars, amino acids, vitamins), which serve as a rich food source for microorganisms.
• Significance: This is the "hotspot" for PGPR activity, nitrogen fixation, and nutrient cycling.

Phyllosphere

• Definition: The habitat provided by the above-ground surfaces of plants, primarily the leaves.
• Environment: This is a much harsher environment than the rhizosphere, subject to fluctuating temperature, UV radiation, and low water/nutrient availability.
• Inhabitants: Microbes (bacteria, yeasts, fungi) that can tolerate these conditions. Some can fix nitrogen, others can protect the plant from pathogens, and some (like *Erwinia*) can be plant pathogens.

4. Positive and Negative Interactions of Microorganisms

In any environment, microbes constantly interact with each other.

5. Microorganisms and Their Role in Agriculture and Horticulture

Microbes are fundamental to sustainable agriculture and horticulture.

• Biofertilizers: Preparations containing live microbes that enhance soil fertility and plant growth.
  • Nitrogen-fixers: Rhizobium, Azotobacter.
  • Phosphate-solubilizers: Pseudomonas, Bacillus.
  • Mycorrhizal fungi (VAM): Help in P and water uptake.
• Biopesticides (Biocontrol Agents): Using microbes to control pests and diseases, reducing reliance on chemical pesticides.
  • Bacillus thuringiensis (Bt): Produces a toxin that kills specific insect pests (caterpillars).
  • Trichoderma (fungus): A biocontrol agent that parasitizes pathogenic fungi (like *Pythium*).
• Decomposition & Composting: Microbes (bacteria, fungi, actinomycetes) are essential for breaking down crop residues and organic waste (manure, leaves) into compost, a stable, nutrient-rich soil amendment.
• Soil Structure: Fungal hyphae and bacterial secretions (polysaccharides) help bind soil particles together into aggregates, improving soil structure, aeration, and water-holding capacity.

6. Mechanism of Biological Nitrogen Fixation

This is the conversion of N2 gas to ammonia (NH3), a highly energy-intensive process.

The Equation: N2 + 8H+ + 8e- + 16 ATP → 2NH3 + H2 + 16 ADP + 16 Pi

• The Enzyme: The reaction is catalyzed by the nitrogenase enzyme complex.
• Oxygen Sensitivity: Nitrogenase is extremely sensitive to oxygen and is irreversibly inactivated by it. Therefore, nitrogen fixation must occur in an anaerobic (or microaerophilic) environment.
• Mechanism in Rhizobium (Symbiotic):
  1. Recognition & Infection: The legume root releases flavonoids, which attract *Rhizobium*. The bacteria attach to the root hair and form an "infection thread," traveling into the root cortex.
  2. Nodule Formation: The bacteria and plant cells multiply, forming a root nodule. The bacteria are released into plant cells and become "bacteroids."
  3. Protecting Nitrogenase: The nodule creates the necessary low-oxygen environment. The plant produces a special protein called leghemoglobin (le-gume-hemoglobin). This protein, which is red (similar to blood hemoglobin), binds to oxygen and "buffers" its concentration, delivering just enough for the bacteria to respire but not enough to damage the nitrogenase enzyme.
  4. Fixation: Inside the nodule, the bacteroids use the nitrogenase enzyme to fix N2 gas, using energy (ATP) supplied by the plant. The resulting ammonia is then given to the plant to make amino acids.

7. VAM Fungi and Their Importance

• What is VAM? Vesicular-Arbuscular Mycorrhizae (now more commonly called Arbuscular Mycorrhizal Fungi or AMF) are a type of fungus that forms a mutualistic symbiosis with the roots of most plants (over 80%).
• Nature of Symbiosis: The fungus is an obligate biotroph; it cannot survive without the host plant. The plant provides the fungus with sugars (carbon).
• Structures:
  • The fungus grows its hyphae into the soil, acting as a vast extension of the plant's root system.
  • It also grows *into* the root cortex, forming two key structures:
  • Arbuscules: Highly branched, tree-like structures *inside* the plant cells. This is the primary site of nutrient exchange (fungus gives minerals, plant gives sugar).
  • Vesicles: Swollen, sac-like structures, often used for energy storage (lipids).
• Importance (Benefits to Plant):
  • Phosphate (P) Uptake: This is the most important benefit. Phosphate is often "locked" in the soil and immobile. The fungal hyphae are much finer than plant roots and can explore a larger soil volume, scavenging for phosphate and delivering it to the plant.
  • Water Uptake: The extended hyphal network also helps in absorbing water, increasing the plant's drought tolerance.
  • Nutrient Uptake: They also help in the uptake of other immobile nutrients like zinc (Zn) and copper (Cu).
  • Pathogen Resistance: The presence of the VAM fungus can make the plant more resistant to root pathogens.