Soil microorganisms (bacteria, actinomycetes, fungi, algae), soil fauna (earthworms, nematodes, protozoa), and their roles in agriculture
A paddy farmer in Kerala notices that his fields receiving no nitrogen fertilizer still produce reasonable yields year after year. The secret? Blue-green algae (BGA) thriving in the waterlogged rice soil fix atmospheric nitrogen, adding an estimated 20-30 kg N/ha per crop season -- free of cost. Beneath every productive field is a hidden army of billions of organisms that decompose organic matter, fix nitrogen, cycle nutrients, and build soil structure. Understanding soil biology is essential for sustainable farming.
What is Soil Biology?
Soil biology studies microbial and faunal activity and ecology in soil. A single teaspoon of healthy soil can contain billions of microorganisms. These organisms include bacteria, actinomycetes, fungi, algae, earthworms, nematodes, and protozoa. The Father of Soil Microbiology is S.N. Winogradsky, who pioneered the study of nitrifying bacteria and chemolithotrophy.
Rod-shaped (~1 um wide, 3 um long) or spherical (~2 um diameter)
Abundance
Most abundant group in soil
Population
10⁸ - 10⁹ per gram of soil
Biomass
450-4500 kg/ha
Optimum pH
6.0-8.0
Optimum temperature
25-30 degree C
Classification of Bacteria
By food preparation:
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Mind Map: Soil Biology
A paddy farmer in Kerala notices that his fields receiving no nitrogen fertilizer still produce reasonable yields year after year. The secret? Blue-green algae (BGA) thriving in the waterlogged rice soil fix atmospheric nitrogen, adding an estimated 20-30 kg N/ha per crop season -- free of cost. Beneath every productive field is a hidden army of billions of organisms that decompose organic matter, fix nitrogen, cycle nutrients, and build soil structure. Understanding soil biology is essential for sustainable farming.
What is Soil Biology?
Soil biology studies microbial and faunal activity and ecology in soil. A single teaspoon of healthy soil can contain billions of microorganisms. These organisms include bacteria, actinomycetes, fungi, algae, earthworms, nematodes, and protozoa. The Father of Soil Microbiology is S.N. Winogradsky, who pioneered the study of nitrifying bacteria and chemolithotrophy.
Rod-shaped (~1 um wide, 3 um long) or spherical (~2 um diameter)
Abundance
Most abundant group in soil
Population
10⁸ - 10⁹ per gram of soil
Biomass
450-4500 kg/ha
Optimum pH
6.0-8.0
Optimum temperature
25-30 degree C
Classification of Bacteria
By food preparation:
Type
Description
Examples
Autotroph
Produce own food from inorganic sources
Nitrifiers, S-oxidizers
Heterotroph
Depend on organic matter for food
Symbiotic N-fixers, decomposers
Chemoautotroph
Derive energy from chemical reactions of inorganic substances
See below
Key chemoautotrophic bacteria:
Bacterium
Substrate
Reaction
Nitrosomonas
Ammonia
NH₄⁺ → NO₂⁻ (Step 1 of nitrification)
Nitrobacter
Nitrite
NO₂⁻ → NO₃⁻ (Step 2 of nitrification)
Thiobacillus
Sulphur compounds
S → SO₄²⁻
Ferrobacillus
Ferrous iron
Fe²⁺ → Fe³⁺
By symbiotic relationship:
Type
Association
Examples
Function
Symbiotic N-fixers
Associated with host plant
Rhizobium in legume root nodules
Fix atmospheric N₂; both partners benefit
Non-symbiotic N-fixers
Free-living (no plant association)
Azotobacter (aerobic), Clostridium (anaerobic)
Fix atmospheric N₂ independently
Classification summary: Symbiotic, non-symbiotic, and cellulose decomposers are heterotrophs. Nitrifiers, denitrifiers, and sulphur oxidizers are autotrophs.
Role of Bacteria
Function
Agricultural Example
Decomposition of organic matter and humus synthesis
Breaking down FYM and crop residues
Enzymatic transformations
Converting unavailable nutrients to available forms
N-fixation
Rhizobium in chickpea, soybean, groundnut nodules
Nitrification
NH₄⁺ → NO₃⁻ (making N plant-available)
Sulphur oxidation
Converting elemental S to plant-available SO₄²⁻
Growth conditions: Optimal at pH 6.0-8.0; exchangeable Ca is more important than pH for bacterial populations.
2. Actinomycetes -- The Filamentous Bacteria
Feature
Detail
Cell type
Unicellular like bacteria, same size
Structure
Filamentous and profusely branched
Mycelial threads
Smaller than those of fungi
Nuclear membrane
Absent (like bacteria)
Alternative name
Filamentous bacteria
Optimum
Temperature 25-30 degree C; pH 6.5-8.0
Metabolism
Heterotrophic
Key Facts about Actinomycetes
Fact
Detail
Sensitive to
Acid soils
Potato scab disease
Caused by Streptomyces scabies; controlled by lowering soil pH using sulphur
Earthy smell
The aroma of freshly ploughed land is due to geosmin produced by actinomycetes
Population
Second only to bacteria; proportion increases with soil depth
Functions
Decompose chitin, phospholipids, and other complex organic compounds
Farm example: Potato scab is a major disease in alkaline soils. Farmers apply elemental sulphur to lower pH below 5.5, which suppresses Streptomyces scabies.
3. Fungi -- Dominant in Acid Soils
Feature
Detail
Structure
Mycelium of individual hyphae (5-20 um diameter, several cm long)
Metabolism
Most are heterotrophic
Oxygen
Strictly aerobic
pH preference
Dominant in acid soils (can tolerate up to pH 9.0)
Farm example: In acid forest soils of the Western Ghats, fungi are the primary decomposers because bacteria cannot thrive at low pH.
Yeasts
Feature
Detail
Structure
Unicellular fungi
Reproduction
By fission or budding
Soil occurrence
Not common in soils
Use
Food supplement; production of alcoholic beverages
Mushrooms
Feature
Detail
Habitat
Forests and grasslands with ample moisture and organic residues
Edibility
Some species are edible
Soil occurrence
Not common in cultivated soils
Structure
Visible part is the fruiting body (above ground); main body is underground mycelium network
4. Algae -- The Photosynthetic Soil Organisms
Feature
Detail
Structure
Filamentous, ~10 um diameter
Population
1-10 billion/m²
Biomass
50-600 kg/ha of furrow slice
Nutrition
Photo-autotrophs (produce own food using sunlight)
Groups
Blue-green, Green, Yellow-green, Diatoms
Blue-Green Algae (BGA) in Agriculture
Fact
Detail
Most numerous in
Rice (paddy) soils
N-fixation
20-30 kg N/ha per crop season
Azolla association
BGA (Anabaena) growing within leaves of aquatic fern Azolla fix atmospheric N₂
TIP
Key N-fixation associations to remember:
Rhizobium = symbiotic N-fixer in legumes
Azotobacter = free-living aerobic N-fixer
Clostridium = free-living anaerobic N-fixer
BGA/Azolla = N-fixers in rice paddies
Farm example: Paddy farmers in Tamil Nadu use Azolla as a green manure in rice fields. The Azolla-Anabaena association fixes atmospheric nitrogen, reducing the need for urea by 20-30 kg N/ha.
Soil Fauna
1. Earthworms -- "Nature's Plough" (Macro Fauna)
Feature
Detail
Known species
~1800 species worldwide
Common Indian species
Pheretima posthuma, P. elongata, Lampita mauritii
Population
1,25,000 to 10,00,000/ha
Biomass
110-1100 kg/ha
Preferred temperature
21 degree C
Preferred conditions
Warm, well-aerated soils with organic matter
Active season
Monsoon
C:N ratio of casts
Low (nutrient-rich)
Benefits of Earthworms
Benefit
Mechanism
Nutrient-rich castings
Casts are richer in N, P, K, and Ca than surrounding soil (enzymatic processing during digestion)
Aeration and drainage
Create extensive burrows that increase soil porosity
Aggregate stability
Increase size and stability of soil aggregates
Soil mixing
Ingest and eject soil, mixing organic matter into deeper layers
Farm example: Vermicompost produced by earthworms is widely used in organic farming across India. The castings have a low C:N ratio, making nutrients readily available to plants.
2. Ants and Termites
Feature
Detail
Effect
Local but significant soil turnover
Ants
Some break down woody materials; produce mounds or underground nests
Termites
Can move enormous quantities of soil; create characteristic mounds
Both
Modify soil structure and effectively till the soil
Farm example: Termite mounds in tropical soils of Chhattisgarh and Jharkhand significantly alter soil profiles, bringing subsoil minerals to the surface.
3. Nematodes (Thread Worms / Eelworms)
Feature
Detail
Size
Microscopic
Feeding
Most are saprophytes; some feed on bacteria, algae, protozoa, and other nematodes
Vegetable crops -- severe root galling and yield loss
Farm example: Root-knot nematodes (Meloidogyne) cause severe damage in tomato, brinjal, and okra fields, forming characteristic galls on roots that block water and nutrient uptake.
4. Protozoa (Micro Fauna)
Feature
Detail
Cell type
Single-celled, larger and more complex than bacteria
Types
Amoeba, Ciliates, Flagellates
Species in soil
More than 250
Biomass
15-175 kg/ha
Habitat
Moist, well-drained soils
Key role
Grazing on bacteria releases nutrients back into soil solution (microbial loop)
5. Rotifers
Feature
Detail
Species
~100 species studied
Habitat
Peat bogs and wet areas of mineral soils
Plant Roots as Soil Organisms
Plant roots are themselves important contributors to soil biology:
Contribution
Detail
Food and energy
Roots supply food for microflora and fauna as they grow and die
Soil modification
Push through cracks, create new openings
Aggregation
Moisture removal creates physical stress that stimulates aggregate formation
Root exudates
Chemicals that stabilize soil structure
Humus synthesis
Decaying roots supply material for humus formation
Proportion
Roots = 15-40% of above-ground crop biomass
Mycorrhizae
This topic will be covered in the manures lesson.
Exam Tips and Mnemonics
Most abundant soil organisms: Bacteria (10⁸-10⁹/g)
Dominant in acid soils: Fungi (not bacteria)
Earthy smell of ploughed land: Actinomycetes (geosmin)
Potato scab: Streptomyces scabies -- controlled by lowering pH with sulphur
