Why Fungally Dominant Soils Are the Foundation of Plant Immunity

How the fungal-to-bacterial ratio in your soil determines whether your crop fights off pests and diseases on its own, or leans on a spray programme to stay alive.

Walk into an old-growth forest and turn over a handful of soil. You will find a dense, white, cobweb-like mat running through the leaf litter. That is fungal mycelium, and it is the reason the forest does not need a fertiliser truck or a fungicide programme to stay healthy. Now walk onto a conventionally farmed orchard and dig the same hole. The soil will smell sour, look grey, and the mycelium will be gone.

That difference is not cosmetic. It is the single biggest reason your crop is vulnerable to pests, diseases and drought. The ratio of fungi to bacteria in your soil, what soil biologists call the F:B ratio, sets a hard ceiling on how high your plants can climb on the immunity ladder. Below a certain point, no foliar spray, no synthetic fertiliser, and no resistant variety can fully compensate.

What Is a Fungally Dominant Soil?

A fungally dominant soil is one where the biomass of beneficial fungi outweighs the biomass of bacteria. Soil biologists express this as the fungal-to-bacterial ratio, or F:B ratio. When the number is below 1, the soil is bacterial-dominated. When it climbs above 1, the soil moves into fungal dominance. Old-growth forests sit at F:B ratios of 100 to 1 or more. Most commercial South African agricultural soils sit at 0.1 to 0.3, which is the bacterial-dominant end of the spectrum.

Bacteria and fungi do different jobs underground. Bacteria are fast, simple and short-lived. They cycle volatile nutrients quickly, mostly as nitrate, and they thrive in disturbed, tilled, high-nitrogen environments. Fungi are slow, structural and long-lived. They build the physical scaffolding of the soil, mine recalcitrant minerals out of bedrock, and release nitrogen as ammonium, the form that woody perennials and high-value crops actually prefer.

What the F:B Ratio Tells You About Your Soil

Dr Elaine Ingham, who pioneered the soil food web framework at Soil Foodweb Inc., has shown that different plant communities sit at different points on the F:B spectrum. The plant tells you what biology it needs. The biology tells you what plant the soil will support. When the two do not match, the farmer pays the difference in inputs.

Annual weeds and brassicas dominate at F:B ratios well below 1, where bacteria run the show. Vegetables and grains sit around 0.5 to 1. Berries, vines and fruit trees climb toward 2:1 to 5:1. Mature forests run as high as 100:1 or more. The implication for South African macadamia, avocado, citrus and vine producers is uncomfortable: most of you are farming high-value perennials in soil that ecologically resembles a recently disturbed roadside verge.

The result is exactly what we see across the industry. Chronic nutrient deficiencies. Falling Brix. Rising pest pressure. An ever-growing chemical input bill. None of it improves until the underlying soil biology shifts.

The Plant Health Pyramid Explained

This is where the F:B ratio meets plant immunity directly. John Kempf, the founder of Advancing Eco Agriculture, built a framework called the Plant Health Pyramid that ties soil biology to pest and disease resistance. It has four levels, and each level unlocks a specific class of immunity.

Level 1 is photosynthesis. A plant that is photosynthesising properly produces enough simple sugars to resist soil-borne fungal pathogens like Pythium, Fusarium and Rhizoctonia. Most commercial crops never operate above 30 percent of their photosynthetic potential, which is why root rots are so common.

Level 2 is complete protein synthesis. When the plant has enough sugars, plus enough trace minerals and microbial support, it converts soluble nitrate into complete amino acids and proteins. A plant operating at Level 2 stops being attractive to sap-sucking insects, the aphids, whitefly, thrips and stinkbug that feed on free amino acids and free nitrates in the leaf sap. They literally cannot digest a plant whose nitrogen is fully assembled into protein.

Level 3 is lipid and oil synthesis. Surplus sugars beyond what the plant needs for proteins get converted into plant lipids, the building blocks of strong cell walls and waxy leaf cuticles. A plant operating at Level 3 resists airborne fungal diseases, including powdery mildew, downy mildew, rust and botrytis. The cuticle is too tough for the spore to penetrate.

Level 4 is plant secondary metabolites. At the top of the pyramid, the plant produces terpenes, alkaloids, flavonoids and the full library of defensive compounds. A Level 4 plant is unattractive to chewing insects, including caterpillars, beetles and the macadamia nut borer. It also resists viral infection.

Here is the part most agronomists miss. The transition from Level 2 to Level 3, and especially the climb to Level 4, depends on the soil delivering a steady, balanced supply of trace minerals, ammonium nitrogen, and complex carbon compounds. Bacteria cannot deliver this. Only a fungal-dominant soil food web, with its mycorrhizal networks, saprophytic decomposers, and humic substance production, can sustain a crop at the top of the pyramid.

A bacterial-dominated soil traps the plant at Level 1 or Level 2, no matter what you spray on it. That is the agronomic reality the spray programme is hiding from you.

Why Bacterial-Dominant Soils Hold Your Crops Back

Decades of tillage, synthetic nitrogen, glyphosate and broad-spectrum fungicides have pushed nearly every commercial soil in the country toward bacterial dominance. Tillage physically shreds fungal hyphae. Synthetic nitrate fertiliser feeds bacteria preferentially and suppresses mycorrhizal colonisation. Fungicides obviously kill fungi, including the beneficial ones.

The downstream consequences are predictable. Soil structure collapses because the glomalin produced by mycorrhizal fungi, the glue that binds soil aggregates, disappears. Wright and Upadhyaya (1996), publishing in Plant and Soil, first quantified just how much soil carbon is held up by glomalin alone. Water holding capacity falls. Mineral availability narrows to whatever the bacteria can cycle, which is mainly nitrate and a handful of soluble nutrients. Recalcitrant minerals like phosphorus, calcium, silicon and the trace elements stay locked in the soil because the fungi that mine them are gone.

The plant responds by drawing harder on whatever is in the leaf sap, which means rising free nitrate and rising free amino acid concentrations. That is the chemical signature sap-sucking insects use to find their next meal. The plant has effectively turned itself into a beacon for pest pressure, not because it is weak in any genetic sense, but because the soil biology can no longer support its full metabolic chain.

How to Increase Fungi in Your Soil

The good news is that the F:B ratio is not fixed. Soil biology responds to management within a season, and dramatic shifts are visible within twelve to twenty-four months when the right inputs are stacked correctly.

Stop the Bleeding First

Reduce or eliminate the practices that destroy fungi. Park the disc and the rotavator. Cut synthetic nitrate to a minimum, or replace it with foliar urea and biological inputs. Stop the calendar fungicide programme and move to a curative-only model based on monitoring. Every pass of a fungicide is a setback of months for fungal recovery.

Stop Bare Soil

Fungal hyphae need a continuous food source, which comes from living plant roots. Bare soil means dead fungi within weeks. Cover crops, living mulches, inter-row vegetation and orchard understorey plantings keep the fungal network fed year-round. Diverse cover crop mixes, including grasses, legumes and brassicas, support different fungal guilds.

Build Solid Carbon on the Surface

Fungi feed on complex, lignin-rich materials that bacteria cannot easily digest. Wood chips, bark mulch, sugarcane bagasse and crop residues all favour fungal growth. In a macadamia orchard, leaving the husks and shell on the ground is one of the cheapest fungal-promotion strategies available. The carbon-to-nitrogen ratio of your surface mulch matters: aim for 30:1 or higher to favour fungi.

Inoculate with High-Quality Fungal Compost

A Johnson-Su bioreactor produces an exceptionally fungal-dominant compost. Dr David Johnson's published work in AIMS Agriculture and Food (2017) shows F:B ratios above 10:1 in mature Johnson-Su compost, which is orders of magnitude higher than anything you can buy at a garden centre. A small volume of this material, applied at planting or as a slurry, seeds the orchard with the right biology.

Brew and Apply Liquid IMO (LIMO)

This is where Korean Natural Farming becomes a serious commercial tool. A properly engineered Liquid IMO extract, brewed from solid IMO 3 compost on a substrate of sugarcane bagasse and maize bran, delivers a fungal-dominant biology in a form that fits modern fertigation and foliar spraying. The key is what you feed the brew. Simple sugars like molasses produce a bacterial bloom. Complex foods like fish hydrolysate, humic acid and oat flour drive fungal dominance.

Apply LIMO at 1:500 to 1:1000 dilution as a soil drench, at a target rate of 935 litres per hectare. For foliar application, dilute at 1:200 to 1:500 and target 234 litres per hectare. Always apply in the late afternoon or on overcast days to protect the microbes from UV.

Feed the Fungi with Marine Lipids

Cold-processed fish hydrolysate is the single most effective fungal-promotion input available to commercial agriculture. The complex marine lipids and intact long-chain proteins are exactly what mycorrhizal and saprophytic fungi need to build their cell walls and synthesise ergosterol, the primary structural component of fungal membranes. Bacteria lack the lipase enzymes to compete for these foods in an aerated water column, which means fish hydrolysate acts as a selective biological pressure that favours the fungi you want.

This is not a small detail. The difference between a fish emulsion, which is heat-rendered and stripped of lipids, and a true cold-processed fish hydrolysate, which is enzymatically digested with the full lipid profile preserved, is the difference between feeding bacteria and feeding fungi. If you are buying fish input for your orchard, this is the spec line that actually matters. Read more on the science of LAB fermentation and cold biological processing here.

The Bottom Line

Plant immunity is not a spray decision. It is a soil biology decision, made years before the pest arrives. Crops trapped at Level 1 or Level 2 of the Plant Health Pyramid, in bacterial-dominated soils, will need a chemical crutch every season. Crops operating at Level 3 and Level 4, in fungal-dominant soils, defend themselves.

The F:B ratio is the simplest single number that tells you which side of that line your farm sits on. If your soil is below 1, you are farming against ecological succession, and the cost of that fight shows up on every line of your input bill. If you can lift it above 1, and ideally toward 2 or 3 for tree crops, the soil starts doing the work that you have been paying spray contractors to do.

Shifting the ratio is a multi-year project, but it is not complicated. Stop tilling. Keep living roots in the ground year-round. Build solid carbon on the surface. Inoculate with fungal-dominant compost. Feed the system with marine lipids and complex carbon, not sugar and synthetic nitrate. Within two seasons, the soil structure will change, the spray bill will start dropping, and the crop will begin climbing the Plant Health Pyramid on its own.

That is what regenerative agriculture actually delivers, when it is executed with the right biology.