Soil Biology and Mycorrhizae on Organic Farms: Practical Guide

A teaspoon of healthy soil contains 100 million to 1 billion bacteria, 100,000 to 1 million fungi, and thousands of nematodes, protozoa, and other organisms — and these organisms, not synthetic fertiliser, are what make organic farming work. The soil food web is the farm’s biological infrastructure: bacteria fix nitrogen and release phosphorus; fungi extend plant root reach by 100–1,000×; earthworms create drainage channels and nutrient-rich castings; protozoa release nutrients by consuming bacteria. When this system functions well, the farm needs far fewer external inputs — nature is doing the work. When it is damaged by tillage, synthetic chemicals, or bare soil, the farmer must substitute external inputs for what biology would have provided for free.

What Is the Soil Food Web and Why Does It Matter?

The nutrient cycling chain:

1. Plants release 20–40% of their photosynthesised carbon through roots as exudates (sugars, amino acids) — deliberately feeding soil microbes
2. Bacteria and fungi consume these exudates; multiply; consume each other and soil organic matter
3. Protozoa and nematodes eat bacteria; release nutrients in plant-available forms (ammonium, phosphate)
4. Plant roots absorb the released nutrients; produce more exudates; feed more microbes
5. The cycle is self-reinforcing — a healthy soil biology feeds itself and the plant simultaneously

What mycorrhizal fungi specifically do:

• Arbuscular Mycorrhizal Fungi (AMF) are the most important: they colonise roots of 80%+ of land plants and extend fine hyphae (fungal threads) far into soil spaces that root hairs cannot reach
• Through these hyphae, the plant can access phosphorus, zinc, copper, and water from a much larger soil volume — typically 3–5 litres of soil per plant vs 0.3–0.5 litres without fungi
• In exchange, the plant feeds the fungi with carbon
• Net result: mycorrhizal plants can grow in lower-fertility soil and access water more efficiently — critical for organic farms and drought-prone areas

What Damages Soil Biology?

How Do You Inoculate Crops with Mycorrhizal Fungi?

Commercial mycorrhizal inoculant (available in India):

• Products containing Rhizophagus irregularis (formerly Glomus intraradices) and other AMF species are available from companies like T.Stanes, Agri Diagnostics, and others
• Cost: ₹200–500 per kg; apply 2–5 grams per transplant hole or mix into nursery media
• Application: Place a small amount of dry inoculant directly in the transplant hole, in contact with the roots

Jeevamrutha as biological inoculant:

• Fresh Jeevamrutha contains a broad diversity of soil microbes including beneficial bacteria and some fungal species
• Not a concentrated mycorrhizal inoculant (it is primarily bacterial), but regular application maintains and introduces diverse microbial communities
• The Jeevamrutha system over years creates conditions where native soil mycorrhizal populations naturally build up

Farm-made fungal inoculant (from forest soil):

• Collect 500g of leaf litter and soil from the base of a healthy tree in a natural forest (not disturbed land)
• This forest soil is rich in native mycorrhizal spores
• Mix into transplant holes at 1–2 tablespoons per plant
• Costs nothing; introduces native species adapted to local conditions
• Traditional ZBNF and permaculture practice

How Do You Know If Your Soil Biology Is Healthy?

Field indicators of good soil biology:

• Earthworms: find 5+ earthworms in a cubic foot of soil = healthy
• Smell: good soil smells rich and earthy (petrichor) — the smell is produced by actinomycetes bacteria
• Structure: soil crumbles easily into small aggregates; does not form a hard cap after rain; does not compact under foot
• Decomposition rate: a teabag test — bury an unbleached cotton teabag 15 cm deep; dig up after 3 months; a healthy soil will have decomposed most of the cotton fibre

Lab indicators:

• Soil Biological Activity test (basal respiration): measures CO₂ produced by soil microbes; higher = more active biology
• PLFA (Phospholipid Fatty Acid) analysis: measures microbial community diversity and biomass; available at UAS and ICAR labs

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Last updated: March 2026